From e80032969bb7266c2726468a96837c1de9a9191b Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Fri, 30 Jun 2023 02:27:03 -0500
Subject: [PATCH 001/350] Fix errors in docs (#4064)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 docs/container.md | 4 ++--
 docs/executor.md  | 6 ++++++
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/docs/container.md b/docs/container.md
index da44cf565a..5f43db1a31 100644
--- a/docs/container.md
+++ b/docs/container.md
@@ -66,7 +66,7 @@ Unlike Docker, Nextflow does not automatically mount host paths in the container
 When a process input is a *symbolic link* file, make sure the linked file is stored in a host folder that is accessible from a bind path defined in your Apptainer installation. Otherwise the process execution will fail because the launched container won't be able to access the linked file.
 :::
 
-:::{versionchanged} 22.07.0-edge
+:::{versionchanged} 23.07.0-edge
 Nextflow no longer mounts the home directory when launching an Apptainer container. To re-enable the old behavior, set the environment variable `NXF_APPTAINER_HOME_MOUNT` to `true`.
 :::
 
@@ -579,7 +579,7 @@ Unlike Docker, Nextflow does not automatically mount host paths in the container
 When a process input is a *symbolic link* file, make sure the linked file is stored in a host folder that is accessible from a bind path defined in your Singularity installation. Otherwise the process execution will fail because the launched container won't be able to access the linked file.
 :::
 
-:::{versionchanged} 22.07.0-edge
+:::{versionchanged} 23.07.0-edge
 Nextflow no longer mounts the home directory when launching a Singularity container. To re-enable the old behavior, set the environment variable `NXF_SINGULARITY_HOME_MOUNT` to `true`.
 :::
 
diff --git a/docs/executor.md b/docs/executor.md
index 431a1bb5aa..4adc9c0d92 100644
--- a/docs/executor.md
+++ b/docs/executor.md
@@ -158,7 +158,13 @@ Make sure the TES backend can access the Nextflow work directory when data is ex
 ### Known Limitations
 
 - Automatic deployment of workflow scripts in the `bin` folder is not supported.
+
+  :::{versionchanged} 23.07.0-edge
+  Automatic upload of the `bin` directory is now supported.
+  :::
+
 - Process output directories are not supported. For details see [#76](https://github.com/ga4gh/task-execution-schemas/issues/76).
+
 - Glob patterns in process output declarations are not supported. For details see [#77](https://github.com/ga4gh/task-execution-schemas/issues/77).
 
 (google-batch-executor)=

From 761fd3b0962e353682aa03ebe7df860d563f831f Mon Sep 17 00:00:00 2001
From: Duncan Parkes <duncan.parkes@gmail.com>
Date: Mon, 3 Jul 2023 15:39:47 +0100
Subject: [PATCH 002/350] Fix docs typo (#4073)

Signed-off-by: Duncan Parkes <duncan.parkes@gmail.com>
---
 docs/script.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/script.md b/docs/script.md
index 3778126c3f..c5b63012b0 100644
--- a/docs/script.md
+++ b/docs/script.md
@@ -1134,7 +1134,7 @@ for( def file : file('any/path').list() ) {
 }
 ```
 
-Additionally, the `eachFile()` method allows you to iterate through the first-level elements only (just like `listFiles()`). As with other `each*()` methods, `eachFiles()` takes a closure as a parameter:
+Additionally, the `eachFile()` method allows you to iterate through the first-level elements only (just like `listFiles()`). As with other `each*()` methods, `eachFile()` takes a closure as a parameter:
 
 ```groovy
 myDir.eachFile { item ->

From 31b696e5e2b056eddaa3dee39222e4cee0d825ca Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Tue, 4 Jul 2023 18:34:33 +0200
Subject: [PATCH 003/350] Netlify: No deployment (previews) unless 'docs/'
 files change (#4067)

Signed-off-by: Phil Ewels <phil.ewels@seqera.io>
---
 docs/netlify.toml | 10 ++++++++++
 1 file changed, 10 insertions(+)
 create mode 100644 docs/netlify.toml

diff --git a/docs/netlify.toml b/docs/netlify.toml
new file mode 100644
index 0000000000..419673f57f
--- /dev/null
+++ b/docs/netlify.toml
@@ -0,0 +1,10 @@
+# No deployment previews unless the docs are edited
+[build]
+  ignore = "git diff --quiet $CACHED_COMMIT_REF $COMMIT_REF ."
+
+# Tell Google not to spider the Netlify staging site
+[[headers]]
+for = "/*"
+
+[headers.values]
+    X-Robots-Tag = "noindex"

From e0d91bf7df176d5f17589484d1a3ef2209a8d2d0 Mon Sep 17 00:00:00 2001
From: Sabrina Krakau <sabrinakrakau@gmail.com>
Date: Wed, 5 Jul 2023 10:57:23 +0200
Subject: [PATCH 004/350] Add CPU model name to trace files and traceRecord
 (#3946)

This commit add the `cpu_model` in the Nextflow trace record.

Note: the field is not included in the default trace file, but it can be added by adding
in the nextflow config the setting

```
trace.fields = '..,cpu_model'
```


Signed-off-by: Sabrina Krakau <sabrinakrakau@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/tracing.md                                            | 5 +++++
 .../src/main/groovy/nextflow/trace/TraceRecord.groovy      | 7 ++++++-
 .../src/main/resources/nextflow/executor/command-trace.txt | 4 ++++
 .../nextflow/executor/test-bash-wrapper-with-trace.txt     | 4 ++++
 4 files changed, 19 insertions(+), 1 deletion(-)

diff --git a/docs/tracing.md b/docs/tracing.md
index b53cbf19b4..98cdb167b4 100644
--- a/docs/tracing.md
+++ b/docs/tracing.md
@@ -307,6 +307,11 @@ The following table shows the fields that can be included in the execution repor
   :::
 : The host on which the task was executed. Supported only for the Kubernetes executor yet. Activate with `k8s.fetchNodeName = true` in the Nextflow config file.
 
+`cpu_model`
+: :::{versionadded} 22.07.0-edge
+  :::
+: The name of the CPU model used to execute the task. This data is read from file `/proc/cpuinfo`.
+
 :::{note}
 These metrics provide an estimation of the resources used by running tasks. They are not an alternative to low-level performance analysis tools, and they may not be completely accurate, especially for very short-lived tasks (running for less than a few seconds).
 :::
diff --git a/modules/nextflow/src/main/groovy/nextflow/trace/TraceRecord.groovy b/modules/nextflow/src/main/groovy/nextflow/trace/TraceRecord.groovy
index 96e0f372c7..0662c8fb20 100644
--- a/modules/nextflow/src/main/groovy/nextflow/trace/TraceRecord.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/trace/TraceRecord.groovy
@@ -100,7 +100,8 @@ class TraceRecord implements Serializable {
             error_action:'str',
             vol_ctxt: 'num',
             inv_ctxt: 'num',
-            hostname: 'str'
+            hostname: 'str',
+            cpu_model:  'str'
     ]
 
     static public Map<String,Closure<String>> FORMATTER = [
@@ -448,6 +449,10 @@ class TraceRecord implements Serializable {
                     this.put(name, val)
                     break
 
+                case 'cpu_model':
+                    this.put(name, value)
+                    break
+
                 default:
                     def val = parseLong(value, file, name)
                     this.put(name, val)
diff --git a/modules/nextflow/src/main/resources/nextflow/executor/command-trace.txt b/modules/nextflow/src/main/resources/nextflow/executor/command-trace.txt
index 9cf1292962..62da5a46ce 100644
--- a/modules/nextflow/src/main/resources/nextflow/executor/command-trace.txt
+++ b/modules/nextflow/src/main/resources/nextflow/executor/command-trace.txt
@@ -127,6 +127,7 @@ nxf_write_trace() {
     echo "nextflow.trace/v2"           > $trace_file
     echo "realtime=$wall_time"         >> $trace_file
     echo "%cpu=$ucpu"                  >> $trace_file
+    echo "cpu_model=$cpu_model"        >> $trace_file
     echo "rchar=${io_stat1[0]}"        >> $trace_file
     echo "wchar=${io_stat1[1]}"        >> $trace_file
     echo "syscr=${io_stat1[2]}"        >> $trace_file
@@ -144,6 +145,7 @@ nxf_trace_mac() {
     local end_millis=$(nxf_date)
     local wall_time=$((end_millis-start_millis))
     local ucpu=''
+    local cpu_model=''
     local io_stat1=('' '' '' '' '' '')
     nxf_write_trace
 }
@@ -163,6 +165,7 @@ nxf_trace_linux() {
     ##  https://stackoverflow.com/questions/27508531/calculate-cpu-per-process/27514562##27514562
     ##  https://stackoverflow.com/questions/16726779/how-do-i-get-the-total-cpu-usage-of-an-application-from-proc-pid-stat
     local num_cpus=$(< /proc/cpuinfo grep '^processor' -c)
+    local cpu_model=$(< /proc/cpuinfo grep '^model name' | head -n 1 | awk 'BEGIN{FS="\t: "} { print $2 }')
     local tot_time0=$(grep '^cpu ' /proc/stat | awk '{sum=$2+$3+$4+$5+$6+$7+$8+$9; printf "%.0f",sum}')
     local cpu_time0=$(2> /dev/null < /proc/$pid/stat awk '{printf "%.0f", ($16+$17)*10 }' || echo -n 'X')
     local io_stat0=($(2> /dev/null < /proc/$pid/io sed 's/^.*:\s*//' | head -n 6 | tr '\n' ' ' || echo -n '0 0 0 0 0 0'))
@@ -199,6 +202,7 @@ nxf_trace_linux() {
     echo "nextflow.trace/v2"           > $trace_file
     echo "realtime=$wall_time"         >> $trace_file
     echo "%cpu=$ucpu"                  >> $trace_file
+    echo "cpu_model=$cpu_model"        >> $trace_file
     echo "rchar=${io_stat1[0]}"        >> $trace_file
     echo "wchar=${io_stat1[1]}"        >> $trace_file
     echo "syscr=${io_stat1[2]}"        >> $trace_file
diff --git a/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper-with-trace.txt b/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper-with-trace.txt
index f97c04e61b..49ea12e675 100644
--- a/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper-with-trace.txt
+++ b/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper-with-trace.txt
@@ -109,6 +109,7 @@ nxf_write_trace() {
     echo "nextflow.trace/v2"           > $trace_file
     echo "realtime=$wall_time"         >> $trace_file
     echo "%cpu=$ucpu"                  >> $trace_file
+    echo "cpu_model=$cpu_model"        >> $trace_file
     echo "rchar=${io_stat1[0]}"        >> $trace_file
     echo "wchar=${io_stat1[1]}"        >> $trace_file
     echo "syscr=${io_stat1[2]}"        >> $trace_file
@@ -125,6 +126,7 @@ nxf_trace_mac() {
     local end_millis=$(nxf_date)
     local wall_time=$((end_millis-start_millis))
     local ucpu=''
+    local cpu_model=''
     local io_stat1=('' '' '' '' '' '')
     nxf_write_trace
 }
@@ -139,6 +141,7 @@ nxf_trace_linux() {
     local pid=$$
     command -v ps &>/dev/null || { >&2 echo "Command 'ps' required by nextflow to collect task metrics cannot be found"; exit 1; }
     local num_cpus=$(< /proc/cpuinfo grep '^processor' -c)
+    local cpu_model=$(< /proc/cpuinfo grep '^model name' | head -n 1 | awk 'BEGIN{FS="\t: "} { print $2 }')
     local tot_time0=$(grep '^cpu ' /proc/stat | awk '{sum=$2+$3+$4+$5+$6+$7+$8+$9; printf "%.0f",sum}')
     local cpu_time0=$(2> /dev/null < /proc/$pid/stat awk '{printf "%.0f", ($16+$17)*10 }' || echo -n 'X')
     local io_stat0=($(2> /dev/null < /proc/$pid/io sed 's/^.*:\s*//' | head -n 6 | tr '\n' ' ' || echo -n '0 0 0 0 0 0'))
@@ -171,6 +174,7 @@ nxf_trace_linux() {
     echo "nextflow.trace/v2"           > $trace_file
     echo "realtime=$wall_time"         >> $trace_file
     echo "%cpu=$ucpu"                  >> $trace_file
+    echo "cpu_model=$cpu_model"        >> $trace_file
     echo "rchar=${io_stat1[0]}"        >> $trace_file
     echo "wchar=${io_stat1[1]}"        >> $trace_file
     echo "syscr=${io_stat1[2]}"        >> $trace_file

From 53e33cde9e679e0d339b7855f2d2ed6ccd3879eb Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Wed, 5 Jul 2023 04:05:16 -0500
Subject: [PATCH 005/350] Add support for AWS SSO credentials provider (#4045)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/aws.md                                   | 37 ++++++----
 plugins/nf-amazon/build.gradle                |  2 +
 .../cloud/aws/AwsClientFactory.groovy         |  6 +-
 .../aws/util/SsoCredentialsProviderV1.groovy  | 68 +++++++++++++++++++
 4 files changed, 98 insertions(+), 15 deletions(-)
 create mode 100644 plugins/nf-amazon/src/main/nextflow/cloud/aws/util/SsoCredentialsProviderV1.groovy

diff --git a/docs/aws.md b/docs/aws.md
index edc1853595..c2f0b69724 100644
--- a/docs/aws.md
+++ b/docs/aws.md
@@ -6,21 +6,30 @@
 
 Nextflow uses the [AWS security credentials](https://docs.aws.amazon.com/general/latest/gr/aws-sec-cred-types.html) to make programmatic calls to AWS services.
 
-You can provide your AWS access keys using the standard AWS variables shown below:
+The AWS credentials are selected from the following sources, in order of descending priority:
 
-- `AWS_ACCESS_KEY_ID`
-- `AWS_SECRET_ACCESS_KEY`
-- `AWS_DEFAULT_REGION`
+1. Nextflow configuration file - `aws.accessKey` and `aws.secretKey`. See {ref}`AWS configuration<config-aws>` for more details.
 
-If `AWS_ACCESS_KEY_ID` and `AWS_SECRET_ACCESS_KEY` are not defined in the environment, Nextflow will attempt to
-retrieve credentials from your `~/.aws/credentials` and `~/.aws/config` files. The `default` profile can be
-overridden via the environmental variable `AWS_PROFILE` (or `AWS_DEFAULT_PROFILE`).
+2. A custom profile in `$HOME/.aws/credentials` and/or `$HOME/.aws/config`. The profile can be supplied from the `aws.profile` config option, or the `AWS_PROFILE` or `AWS_DEFAULT_PROFILE` environmental variables.
 
-Alternatively AWS credentials and profile can be specified in the Nextflow configuration file. See {ref}`AWS configuration<config-aws>` for more details.
+3. Environment variables - `AWS_ACCESS_KEY_ID` and `AWS_SECRET_ACCESS_KEY`.
 
-:::{note}
-Credentials can also be provided by using an IAM Instance Role. The benefit of this approach is that it spares you from managing/distributing AWS keys explicitly. Read the [IAM Roles](http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/iam-roles-for-amazon-ec2.html) documentation and [this blog post](https://aws.amazon.com/blogs/security/granting-permission-to-launch-ec2-instances-with-iam-roles-passrole-permission/) for more details.
-:::
+4. The `default` profile in `~/.aws/credentials` and/or `~/.aws/config`.
+
+5. Single Sign-On (SSO) credentials. See the [AWS documentation](https://docs.aws.amazon.com/cli/latest/userguide/sso-configure-profile-token.html) for more details.
+
+   :::{versionadded} 23.07.0-edge
+   :::
+
+6. EC2 instance profile credentials. See the [AWS documentation](http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/iam-roles-for-amazon-ec2.html) and [this blog post](https://aws.amazon.com/blogs/security/granting-permission-to-launch-ec2-instances-with-iam-roles-passrole-permission/) for more details.
+
+The AWS region is selected from the following sources, in order of descending priority:
+
+1. Nextflow configuration file - `aws.region`
+2. Environment variables - `AWS_REGION` or `AWS_DEFAULT_REGION`
+3. EC2 instance metadata (if Nextflow is running in an EC2 instance)
+
+SSO credentials and instance profile credentials are the most recommended because they don't require you to manage and distribute AWS keys explicitly. SSO credentials are ideal for launching pipelines from outside of AWS (e.g. your laptop), while instance profile credentials are ideal for launching pipelines within AWS (e.g. an EC2 instance).
 
 ## AWS IAM policies
 
@@ -30,7 +39,7 @@ Minimal permissions policies to be attached to the AWS account used by Nextflow
 
 - To use AWS Batch:
 
-  ```
+  ```json
   "batch:DescribeJobQueues"
   "batch:CancelJob"
   "batch:SubmitJob"
@@ -44,7 +53,7 @@ Minimal permissions policies to be attached to the AWS account used by Nextflow
 
 - To view [EC2](https://aws.amazon.com/ec2/) instances:
 
-  ```
+  ```json
   "ecs:DescribeTasks"
   "ec2:DescribeInstances"
   "ec2:DescribeInstanceTypes"
@@ -55,7 +64,7 @@ Minimal permissions policies to be attached to the AWS account used by Nextflow
 
 - To pull container images from [ECR](https://aws.amazon.com/ecr/) repositories:
 
-  ```
+  ```json
   "ecr:GetAuthorizationToken"
   "ecr:BatchCheckLayerAvailability"
   "ecr:GetDownloadUrlForLayer"
diff --git a/plugins/nf-amazon/build.gradle b/plugins/nf-amazon/build.gradle
index c310d0c309..8499e56160 100644
--- a/plugins/nf-amazon/build.gradle
+++ b/plugins/nf-amazon/build.gradle
@@ -47,6 +47,8 @@ dependencies {
     api ('com.amazonaws:aws-java-sdk-codecommit:1.12.429')
     api ('com.amazonaws:aws-java-sdk-sts:1.12.429')
     api ('com.amazonaws:aws-java-sdk-ses:1.12.429')
+    api ('software.amazon.awssdk:sso:2.20.89')
+    api ('software.amazon.awssdk:ssooidc:2.20.89')
 
     constraints {
         api 'com.fasterxml.jackson.core:jackson-databind:2.12.7.1'
diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/AwsClientFactory.groovy b/plugins/nf-amazon/src/main/nextflow/cloud/aws/AwsClientFactory.groovy
index 52de386018..2c49df323c 100644
--- a/plugins/nf-amazon/src/main/nextflow/cloud/aws/AwsClientFactory.groovy
+++ b/plugins/nf-amazon/src/main/nextflow/cloud/aws/AwsClientFactory.groovy
@@ -54,6 +54,7 @@ import nextflow.SysEnv
 import nextflow.cloud.aws.config.AwsConfig
 import nextflow.cloud.aws.util.ConfigParser
 import nextflow.cloud.aws.util.S3CredentialsProvider
+import nextflow.cloud.aws.util.SsoCredentialsProviderV1
 import nextflow.exception.AbortOperationException
 /**
  * Implement a factory class for AWS client objects
@@ -272,7 +273,9 @@ class AwsClientFactory {
         }
 
         if( profile ) {
-            return new ProfileCredentialsProvider(configFile(), profile)
+            return new AWSCredentialsProviderChain(List.of(
+                    new ProfileCredentialsProvider(configFile(), profile),
+                    new SsoCredentialsProviderV1(profile)))
         }
 
         return new AWSCredentialsProviderChain(List.of(
@@ -280,6 +283,7 @@ class AwsClientFactory {
                 new SystemPropertiesCredentialsProvider(),
                 WebIdentityTokenCredentialsProvider.create(),
                 new ProfileCredentialsProvider(configFile(), null),
+                new SsoCredentialsProviderV1(),
                 new EC2ContainerCredentialsProviderWrapper()))
     }
 
diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/util/SsoCredentialsProviderV1.groovy b/plugins/nf-amazon/src/main/nextflow/cloud/aws/util/SsoCredentialsProviderV1.groovy
new file mode 100644
index 0000000000..db3e0517c2
--- /dev/null
+++ b/plugins/nf-amazon/src/main/nextflow/cloud/aws/util/SsoCredentialsProviderV1.groovy
@@ -0,0 +1,68 @@
+/*
+ * Copyright 2013-2023, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package nextflow.cloud.aws.util
+
+import com.amazonaws.auth.AWSCredentials
+import com.amazonaws.auth.AWSCredentialsProvider
+import com.amazonaws.auth.BasicAWSCredentials
+import com.amazonaws.auth.BasicSessionCredentials
+import groovy.transform.CompileStatic
+import groovy.util.logging.Slf4j
+import software.amazon.awssdk.auth.credentials.AwsSessionCredentials
+import software.amazon.awssdk.auth.credentials.ProfileCredentialsProvider
+
+/**
+ * Adapter for the SSO credentials provider from the SDK v2.
+ *
+ * @author Ben Sherman <bentshermann@gmail.com>
+ */
+@Slf4j
+@CompileStatic
+class SsoCredentialsProviderV1 implements AWSCredentialsProvider {
+
+    private ProfileCredentialsProvider delegate
+
+    SsoCredentialsProviderV1() {
+        this.delegate = ProfileCredentialsProvider.create()
+    }
+
+    SsoCredentialsProviderV1(String profile) {
+        this.delegate = ProfileCredentialsProvider.create(profile)
+    }
+
+    @Override
+    AWSCredentials getCredentials() {
+        final credentials = delegate.resolveCredentials()
+
+        if( credentials instanceof AwsSessionCredentials )
+            new BasicSessionCredentials(
+                    credentials.accessKeyId(),
+                    credentials.secretAccessKey(),
+                    credentials.sessionToken())
+
+        else
+            new BasicAWSCredentials(
+                    credentials.accessKeyId(),
+                    credentials.secretAccessKey())
+    }
+
+    @Override
+    void refresh() {
+        throw new UnsupportedOperationException()
+    }
+}

From 0f4d886776831a187c2a78cafff10a0c1b0c51c8 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Wed, 5 Jul 2023 12:06:32 +0200
Subject: [PATCH 006/350] Fix Improve error message for invalid Azure URI

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../cloud/azure/file/AzPathFactory.groovy     |  3 +++
 .../cloud/azure/file/AzPathFactoryTest.groovy | 19 +++++++++++++++++++
 2 files changed, 22 insertions(+)

diff --git a/plugins/nf-azure/src/main/nextflow/cloud/azure/file/AzPathFactory.groovy b/plugins/nf-azure/src/main/nextflow/cloud/azure/file/AzPathFactory.groovy
index 116857f3bf..d81f37a52a 100644
--- a/plugins/nf-azure/src/main/nextflow/cloud/azure/file/AzPathFactory.groovy
+++ b/plugins/nf-azure/src/main/nextflow/cloud/azure/file/AzPathFactory.groovy
@@ -45,6 +45,9 @@ class AzPathFactory extends FileSystemPathFactory {
         if( !uri.startsWith('az://') )
             return null
 
+        if( uri.startsWith('az:///') )
+            throw new IllegalArgumentException("Invalid Azure path URI - make sure the schema prefix does not container more than two slash characters - offending value: $uri")
+
         final storageConfigEnv = AzConfig.getConfig().storage().getEnv()
 
         final activeDirectoryConfigEnv = AzConfig.getConfig().activeDirectory().getEnv()
diff --git a/plugins/nf-azure/src/test/nextflow/cloud/azure/file/AzPathFactoryTest.groovy b/plugins/nf-azure/src/test/nextflow/cloud/azure/file/AzPathFactoryTest.groovy
index 53bcd8942d..a5fb0f4eca 100644
--- a/plugins/nf-azure/src/test/nextflow/cloud/azure/file/AzPathFactoryTest.groovy
+++ b/plugins/nf-azure/src/test/nextflow/cloud/azure/file/AzPathFactoryTest.groovy
@@ -45,4 +45,23 @@ class AzPathFactoryTest extends Specification {
         'az://my-data/data/*{1,2}.fq.gz'| 'my-data'     | 'data/*{1,2}.fq.gz'
     }
 
+
+
+    def 'should throw illegal path' () {
+        given:
+        def CONFIG = [azure: [
+                storage: [
+                        accountKey: System.getenv('AZURE_STORAGE_ACCOUNT_KEY'),
+                        accountName: System.getenv('AZURE_STORAGE_ACCOUNT_NAME'),
+                ]
+        ]]
+        Global.session = Mock(Session) { getConfig() >> CONFIG }
+        and:
+
+        when:
+        AzPathFactory.parse('az:///fooo')
+        then:
+        def e = thrown(IllegalArgumentException)
+        e.message == 'Invalid Azure path URI - make sure the schema prefix does not container more than two slash characters - offending value: az:///fooo'
+    }
 }

From 96c04e3b3b1bf4dc40d84b388b2a78a2b485c586 Mon Sep 17 00:00:00 2001
From: Fritjof Lammers <25619971+mobilegenome@users.noreply.github.com>
Date: Thu, 6 Jul 2023 09:37:03 +0200
Subject: [PATCH 007/350] Allow SLURM executor option `--mem-per-cpu` (#4023)
 [ci fast]

Signed-off-by: Fritjof Lammers <25619971+mobilegenome@users.noreply.github.com>
Signed-off-by: Fritjof Lammers <fritjof.lammers@vogelwarte.ch>
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Co-authored-by: Ben Sherman <bentshermann@gmail.com>
---
 docs/config.md                                |  6 ++++++
 docs/executor.md                              |  6 +++++-
 .../nextflow/executor/SlurmExecutor.groovy    | 14 +++++++++++++-
 .../executor/SlurmExecutorTest.groovy         | 19 ++++++++++++++++++-
 4 files changed, 42 insertions(+), 3 deletions(-)

diff --git a/docs/config.md b/docs/config.md
index 5f43dd876f..1332c4faa4 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -608,6 +608,12 @@ The following settings are available:
 `executor.name`
 : The name of the executor to be used (default: `local`).
 
+`executor.perCpuMemAllocation`
+: :::{versionadded} 23.07.0-edge
+  :::
+: *Used only by the {ref}`slurm-executor` executor.*
+: When `true`, specifies memory allocations for SLURM jobs as `--mem-per-cpu <task.memory / task.cpus>` instead of `--mem <task.memory>`.
+
 `executor.perJobMemLimit`
 : Specifies Platform LSF *per-job* memory limit mode. See {ref}`lsf-executor`.
 
diff --git a/docs/executor.md b/docs/executor.md
index 4adc9c0d92..1cce5ecd1d 100644
--- a/docs/executor.md
+++ b/docs/executor.md
@@ -513,6 +513,10 @@ Resource requests and other job characteristics can be controlled via the follow
 SLURM partitions can be specified with the `queue` directive.
 :::
 
-:::{tip}
+:::{note}
 Nextflow does not provide direct support for SLURM multi-clusters. If you need to submit workflow executions to a cluster other than the current one, specify it with the `SLURM_CLUSTERS` variable in the launch environment.
 :::
+
+:::{versionadded} 23.07.0-edge
+Some SLURM clusters require memory allocations to be specified with `--mem-per-cpu` instead of `--mem`. You can specify `executor.perCpuMemAllocation = true` in the Nextflow configuration to enable this behavior. Nextflow will automatically compute the memory per CPU for each task (by default 1 CPU is used).
+:::
diff --git a/modules/nextflow/src/main/groovy/nextflow/executor/SlurmExecutor.groovy b/modules/nextflow/src/main/groovy/nextflow/executor/SlurmExecutor.groovy
index 70d4ace298..f195e280e6 100644
--- a/modules/nextflow/src/main/groovy/nextflow/executor/SlurmExecutor.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/executor/SlurmExecutor.groovy
@@ -37,6 +37,8 @@ class SlurmExecutor extends AbstractGridExecutor {
 
     static private Pattern SUBMIT_REGEX = ~/Submitted batch job (\d+)/
 
+    private boolean perCpuMemAllocation
+
     private boolean hasSignalOpt(Map config) {
         def opts = config.clusterOptions?.toString()
         return opts ? opts.contains('--signal ') || opts.contains('--signal=') : false
@@ -76,7 +78,11 @@ class SlurmExecutor extends AbstractGridExecutor {
             // be stored, just collected). In both cases memory use is based upon the job's
             // Resident Set Size (RSS). A task may exceed the memory limit until the next periodic
             // accounting sample. -- https://slurm.schedmd.com/sbatch.html
-            result << '--mem' << task.config.getMemory().toMega().toString() + 'M'
+            final mem = task.config.getMemory().toMega()
+            if( perCpuMemAllocation )
+                result << '--mem-per-cpu' << mem.intdiv(task.config.getCpus()).toString() + 'M'
+            else
+                result << '--mem' << mem.toString() + 'M'
         }
 
         // the requested partition (a.k.a queue) name
@@ -190,6 +196,12 @@ class SlurmExecutor extends AbstractGridExecutor {
         return result
     }
 
+    @Override
+    void register() {
+        super.register()
+        perCpuMemAllocation = session.getExecConfigProp(name, 'perCpuMemAllocation', false)
+    }
+
     @Override
     protected boolean pipeLauncherScript() {
         return isFusionEnabled()
diff --git a/modules/nextflow/src/test/groovy/nextflow/executor/SlurmExecutorTest.groovy b/modules/nextflow/src/test/groovy/nextflow/executor/SlurmExecutorTest.groovy
index 3027f19e37..89059b56bc 100644
--- a/modules/nextflow/src/test/groovy/nextflow/executor/SlurmExecutorTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/executor/SlurmExecutorTest.groovy
@@ -80,7 +80,7 @@ class SlurmExecutorTest extends Specification {
     def testGetHeaders() {
 
         setup:
-        // LSF executor
+        // SLURM executor
         def executor = [:] as SlurmExecutor
 
         // mock process
@@ -186,6 +186,23 @@ class SlurmExecutorTest extends Specification {
                 #SBATCH -x 3
                 '''
                 .stripIndent().leftTrim()
+
+        // test perCpuMemAllocation
+        when:
+        executor.@perCpuMemAllocation = true
+        task.config = new TaskConfig()
+        task.config.cpus = 8
+        task.config.memory = '24 GB'
+        then:
+        executor.getHeaders(task) == '''
+                #SBATCH -J nf-the_task_name
+                #SBATCH -o /work/path/.command.log
+                #SBATCH --no-requeue
+                #SBATCH --signal B:USR2@30
+                #SBATCH -c 8
+                #SBATCH --mem-per-cpu 3072M
+                '''
+                .stripIndent().leftTrim()
     }
 
     def testWorkDirWithBlanks() {

From 60a5f1a7e97c30f149e6b7ab5ae123eb3c4e1f6c Mon Sep 17 00:00:00 2001
From: George Hartzell <hartzell@alerce.com>
Date: Thu, 6 Jul 2023 23:15:23 -0600
Subject: [PATCH 008/350] Wait for all child processes in nxf_parallel (#4050)

nxf_parallel runs a number of processes in parallel, distributing them
across a limited number of workers.

Prior to PR #1884, errors were not being checked.  PR#1884 was
intended to remedy this but effectively only checked the _last_
command to exit (which was, unfortunately the case that was tested
for).

Processes that exit while there is still work going on were not being
"waited" on, so their exit status was not being checked, and failures
were escaping unnoticed.

This commit:

- updates the loop that's tracking the work so that it waits on
  processes that have exited; and
- updates the test cases so that the failing command is _not_ the
  last in the list and ensures that the templated text is as expected.


Signed-off-by: George Hartzell <hartzell@alerce.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../nextflow/executor/BashFunLib.groovy       |  4 +++-
 .../nextflow/executor/BashFunLibTest.groovy   |  6 +++--
 .../batch/AwsBatchFileCopyStrategyTest.groovy |  8 +++++--
 .../batch/AwsBatchScriptLauncherTest.groovy   | 16 +++++++++----
 .../cloud/aws/util/S3BashLibTest.groovy       | 24 ++++++++++++++-----
 .../BashWrapperBuilderWithS3Test.groovy       |  4 +++-
 .../azure/batch/AzFileCopyStrategyTest.groovy | 12 +++++++---
 .../cloud/azure/file/AzBashLibTest.groovy     |  8 +++++--
 .../google/lifesciences/bash-wrapper-gcp.txt  |  4 +++-
 .../cloud/google/util/GsBashLibTest.groovy    |  8 +++++--
 10 files changed, 70 insertions(+), 24 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/executor/BashFunLib.groovy b/modules/nextflow/src/main/groovy/nextflow/executor/BashFunLib.groovy
index 012ad55d06..d506b3931a 100644
--- a/modules/nextflow/src/main/groovy/nextflow/executor/BashFunLib.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/executor/BashFunLib.groovy
@@ -95,7 +95,9 @@ class BashFunLib<V extends BashFunLib> {
             while ((i<\${#cmd[@]})); do
                 local copy=()
                 for x in "\${pid[@]}"; do
-                  [[ -e /proc/\$x ]] && copy+=(\$x)
+                  # if the process exist, keep in the 'copy' array, otherwise wait on it to capture the exit code
+                  # see https://github.com/nextflow-io/nextflow/pull/4050
+                  [[ -e /proc/\$x ]] && copy+=(\$x) || wait \$x
                 done
                 pid=("\${copy[@]}")
                 
diff --git a/modules/nextflow/src/test/groovy/nextflow/executor/BashFunLibTest.groovy b/modules/nextflow/src/test/groovy/nextflow/executor/BashFunLibTest.groovy
index 03462d5828..9efd714d6b 100644
--- a/modules/nextflow/src/test/groovy/nextflow/executor/BashFunLibTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/executor/BashFunLibTest.groovy
@@ -52,7 +52,9 @@ class BashFunLibTest extends Specification {
                 while ((i<${#cmd[@]})); do
                     local copy=()
                     for x in "${pid[@]}"; do
-                      [[ -e /proc/$x ]] && copy+=($x)
+                      # if the process exist, keep in the 'copy' array, otherwise wait on it to capture the exit code
+                      # see https://github.com/nextflow-io/nextflow/pull/4050
+                      [[ -e /proc/$x ]] && copy+=($x) || wait $x
                     done
                     pid=("${copy[@]}")
             
@@ -88,8 +90,8 @@ class BashFunLibTest extends Specification {
 
         """
         cmds=()
-        cmds+=("true")
         cmds+=("false")
+        cmds+=("true")
         nxf_parallel "\${cmds[@]}"
         """.stripIndent()
 
diff --git a/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchFileCopyStrategyTest.groovy b/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchFileCopyStrategyTest.groovy
index 156a5945b9..780d71b647 100644
--- a/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchFileCopyStrategyTest.groovy
+++ b/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchFileCopyStrategyTest.groovy
@@ -164,7 +164,9 @@ class AwsBatchFileCopyStrategyTest extends Specification {
                         while ((i<${#cmd[@]})); do
                             local copy=()
                             for x in "${pid[@]}"; do
-                              [[ -e /proc/$x ]] && copy+=($x)
+                              # if the process exist, keep in the 'copy' array, otherwise wait on it to capture the exit code
+                              # see https://github.com/nextflow-io/nextflow/pull/4050
+                              [[ -e /proc/$x ]] && copy+=($x) || wait $x
                             done
                             pid=("${copy[@]}")
                     
@@ -253,7 +255,9 @@ class AwsBatchFileCopyStrategyTest extends Specification {
                     while ((i<${#cmd[@]})); do
                         local copy=()
                         for x in "${pid[@]}"; do
-                          [[ -e /proc/$x ]] && copy+=($x)
+                          # if the process exist, keep in the 'copy' array, otherwise wait on it to capture the exit code
+                          # see https://github.com/nextflow-io/nextflow/pull/4050
+                          [[ -e /proc/$x ]] && copy+=($x) || wait $x
                         done
                         pid=("${copy[@]}")
                 
diff --git a/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchScriptLauncherTest.groovy b/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchScriptLauncherTest.groovy
index 250c69e0eb..1e36120d09 100644
--- a/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchScriptLauncherTest.groovy
+++ b/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchScriptLauncherTest.groovy
@@ -94,7 +94,9 @@ class AwsBatchScriptLauncherTest extends Specification {
                     while ((i<${#cmd[@]})); do
                         local copy=()
                         for x in "${pid[@]}"; do
-                          [[ -e /proc/$x ]] && copy+=($x)
+                          # if the process exist, keep in the 'copy' array, otherwise wait on it to capture the exit code
+                          # see https://github.com/nextflow-io/nextflow/pull/4050
+                          [[ -e /proc/$x ]] && copy+=($x) || wait $x
                         done
                         pid=("${copy[@]}")
                 
@@ -271,7 +273,9 @@ class AwsBatchScriptLauncherTest extends Specification {
                         while ((i<${#cmd[@]})); do
                             local copy=()
                             for x in "${pid[@]}"; do
-                              [[ -e /proc/$x ]] && copy+=($x)
+                              # if the process exist, keep in the 'copy' array, otherwise wait on it to capture the exit code
+                              # see https://github.com/nextflow-io/nextflow/pull/4050
+                              [[ -e /proc/$x ]] && copy+=($x) || wait $x
                             done
                             pid=("${copy[@]}")
                     
@@ -441,7 +445,9 @@ class AwsBatchScriptLauncherTest extends Specification {
                         while ((i<${#cmd[@]})); do
                             local copy=()
                             for x in "${pid[@]}"; do
-                              [[ -e /proc/$x ]] && copy+=($x)
+                              # if the process exist, keep in the 'copy' array, otherwise wait on it to capture the exit code
+                              # see https://github.com/nextflow-io/nextflow/pull/4050
+                              [[ -e /proc/$x ]] && copy+=($x) || wait $x
                             done
                             pid=("${copy[@]}")
                     
@@ -552,7 +558,9 @@ class AwsBatchScriptLauncherTest extends Specification {
                         while ((i<${#cmd[@]})); do
                             local copy=()
                             for x in "${pid[@]}"; do
-                              [[ -e /proc/$x ]] && copy+=($x)
+                              # if the process exist, keep in the 'copy' array, otherwise wait on it to capture the exit code
+                              # see https://github.com/nextflow-io/nextflow/pull/4050
+                              [[ -e /proc/$x ]] && copy+=($x) || wait $x
                             done
                             pid=("${copy[@]}")
                     
diff --git a/plugins/nf-amazon/src/test/nextflow/cloud/aws/util/S3BashLibTest.groovy b/plugins/nf-amazon/src/test/nextflow/cloud/aws/util/S3BashLibTest.groovy
index 4e5d3a0cb9..f3c3608a18 100644
--- a/plugins/nf-amazon/src/test/nextflow/cloud/aws/util/S3BashLibTest.groovy
+++ b/plugins/nf-amazon/src/test/nextflow/cloud/aws/util/S3BashLibTest.groovy
@@ -63,7 +63,9 @@ class S3BashLibTest extends Specification {
                         while ((i<${#cmd[@]})); do
                             local copy=()
                             for x in "${pid[@]}"; do
-                              [[ -e /proc/$x ]] && copy+=($x)
+                              # if the process exist, keep in the 'copy' array, otherwise wait on it to capture the exit code
+                              # see https://github.com/nextflow-io/nextflow/pull/4050
+                              [[ -e /proc/$x ]] && copy+=($x) || wait $x
                             done
                             pid=("${copy[@]}")
                     
@@ -160,7 +162,9 @@ class S3BashLibTest extends Specification {
                         while ((i<${#cmd[@]})); do
                             local copy=()
                             for x in "${pid[@]}"; do
-                              [[ -e /proc/$x ]] && copy+=($x)
+                              # if the process exist, keep in the 'copy' array, otherwise wait on it to capture the exit code
+                              # see https://github.com/nextflow-io/nextflow/pull/4050
+                              [[ -e /proc/$x ]] && copy+=($x) || wait $x
                             done
                             pid=("${copy[@]}")
                     
@@ -405,7 +409,9 @@ class S3BashLibTest extends Specification {
                 while ((i<${#cmd[@]})); do
                     local copy=()
                     for x in "${pid[@]}"; do
-                      [[ -e /proc/$x ]] && copy+=($x)
+                      # if the process exist, keep in the 'copy' array, otherwise wait on it to capture the exit code
+                      # see https://github.com/nextflow-io/nextflow/pull/4050
+                      [[ -e /proc/$x ]] && copy+=($x) || wait $x
                     done
                     pid=("${copy[@]}")
             
@@ -494,7 +500,9 @@ class S3BashLibTest extends Specification {
                 while ((i<${#cmd[@]})); do
                     local copy=()
                     for x in "${pid[@]}"; do
-                      [[ -e /proc/$x ]] && copy+=($x)
+                      # if the process exist, keep in the 'copy' array, otherwise wait on it to capture the exit code
+                      # see https://github.com/nextflow-io/nextflow/pull/4050
+                      [[ -e /proc/$x ]] && copy+=($x) || wait $x
                     done
                     pid=("${copy[@]}")
             
@@ -586,7 +594,9 @@ class S3BashLibTest extends Specification {
                 while ((i<${#cmd[@]})); do
                     local copy=()
                     for x in "${pid[@]}"; do
-                      [[ -e /proc/$x ]] && copy+=($x)
+                      # if the process exist, keep in the 'copy' array, otherwise wait on it to capture the exit code
+                      # see https://github.com/nextflow-io/nextflow/pull/4050
+                      [[ -e /proc/$x ]] && copy+=($x) || wait $x
                     done
                     pid=("${copy[@]}")
             
@@ -682,7 +692,9 @@ class S3BashLibTest extends Specification {
                 while ((i<${#cmd[@]})); do
                     local copy=()
                     for x in "${pid[@]}"; do
-                      [[ -e /proc/$x ]] && copy+=($x)
+                      # if the process exist, keep in the 'copy' array, otherwise wait on it to capture the exit code
+                      # see https://github.com/nextflow-io/nextflow/pull/4050
+                      [[ -e /proc/$x ]] && copy+=($x) || wait $x
                     done
                     pid=("${copy[@]}")
             
diff --git a/plugins/nf-amazon/src/test/nextflow/executor/BashWrapperBuilderWithS3Test.groovy b/plugins/nf-amazon/src/test/nextflow/executor/BashWrapperBuilderWithS3Test.groovy
index f31153917d..26ab4eb176 100644
--- a/plugins/nf-amazon/src/test/nextflow/executor/BashWrapperBuilderWithS3Test.groovy
+++ b/plugins/nf-amazon/src/test/nextflow/executor/BashWrapperBuilderWithS3Test.groovy
@@ -166,7 +166,9 @@ class BashWrapperBuilderWithS3Test extends Specification {
                 while ((i<${#cmd[@]})); do
                     local copy=()
                     for x in "${pid[@]}"; do
-                      [[ -e /proc/$x ]] && copy+=($x)
+                      # if the process exist, keep in the 'copy' array, otherwise wait on it to capture the exit code
+                      # see https://github.com/nextflow-io/nextflow/pull/4050
+                      [[ -e /proc/$x ]] && copy+=($x) || wait $x
                     done
                     pid=("${copy[@]}")
             
diff --git a/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzFileCopyStrategyTest.groovy b/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzFileCopyStrategyTest.groovy
index c50aac74c6..60eaf1ffb6 100644
--- a/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzFileCopyStrategyTest.groovy
+++ b/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzFileCopyStrategyTest.groovy
@@ -132,7 +132,9 @@ class AzFileCopyStrategyTest extends Specification {
                     while ((i<${#cmd[@]})); do
                         local copy=()
                         for x in "${pid[@]}"; do
-                          [[ -e /proc/$x ]] && copy+=($x)
+                          # if the process exist, keep in the 'copy' array, otherwise wait on it to capture the exit code
+                          # see https://github.com/nextflow-io/nextflow/pull/4050
+                          [[ -e /proc/$x ]] && copy+=($x) || wait $x
                         done
                         pid=("${copy[@]}")
                 
@@ -267,7 +269,9 @@ class AzFileCopyStrategyTest extends Specification {
                     while ((i<${#cmd[@]})); do
                         local copy=()
                         for x in "${pid[@]}"; do
-                          [[ -e /proc/$x ]] && copy+=($x)
+                          # if the process exist, keep in the 'copy' array, otherwise wait on it to capture the exit code
+                          # see https://github.com/nextflow-io/nextflow/pull/4050
+                          [[ -e /proc/$x ]] && copy+=($x) || wait $x
                         done
                         pid=("${copy[@]}")
                 
@@ -426,7 +430,9 @@ class AzFileCopyStrategyTest extends Specification {
                         while ((i<${#cmd[@]})); do
                             local copy=()
                             for x in "${pid[@]}"; do
-                              [[ -e /proc/$x ]] && copy+=($x)
+                              # if the process exist, keep in the 'copy' array, otherwise wait on it to capture the exit code
+                              # see https://github.com/nextflow-io/nextflow/pull/4050
+                              [[ -e /proc/$x ]] && copy+=($x) || wait $x
                             done
                             pid=("${copy[@]}")
 
diff --git a/plugins/nf-azure/src/test/nextflow/cloud/azure/file/AzBashLibTest.groovy b/plugins/nf-azure/src/test/nextflow/cloud/azure/file/AzBashLibTest.groovy
index 58140d2383..b300da8f5e 100644
--- a/plugins/nf-azure/src/test/nextflow/cloud/azure/file/AzBashLibTest.groovy
+++ b/plugins/nf-azure/src/test/nextflow/cloud/azure/file/AzBashLibTest.groovy
@@ -94,7 +94,9 @@ class AzBashLibTest extends Specification {
                 while ((i<${#cmd[@]})); do
                     local copy=()
                     for x in "${pid[@]}"; do
-                      [[ -e /proc/$x ]] && copy+=($x)
+                      # if the process exist, keep in the 'copy' array, otherwise wait on it to capture the exit code
+                      # see https://github.com/nextflow-io/nextflow/pull/4050
+                      [[ -e /proc/$x ]] && copy+=($x) || wait $x
                     done
                     pid=("${copy[@]}")
             
@@ -194,7 +196,9 @@ class AzBashLibTest extends Specification {
                 while ((i<${#cmd[@]})); do
                     local copy=()
                     for x in "${pid[@]}"; do
-                      [[ -e /proc/$x ]] && copy+=($x)
+                      # if the process exist, keep in the 'copy' array, otherwise wait on it to capture the exit code
+                      # see https://github.com/nextflow-io/nextflow/pull/4050
+                      [[ -e /proc/$x ]] && copy+=($x) || wait $x
                     done
                     pid=("${copy[@]}")
             
diff --git a/plugins/nf-google/src/test/nextflow/cloud/google/lifesciences/bash-wrapper-gcp.txt b/plugins/nf-google/src/test/nextflow/cloud/google/lifesciences/bash-wrapper-gcp.txt
index d123b024e1..ff58667ae8 100644
--- a/plugins/nf-google/src/test/nextflow/cloud/google/lifesciences/bash-wrapper-gcp.txt
+++ b/plugins/nf-google/src/test/nextflow/cloud/google/lifesciences/bash-wrapper-gcp.txt
@@ -41,7 +41,9 @@ nxf_parallel() {
     while ((i<${#cmd[@]})); do
         local copy=()
         for x in "${pid[@]}"; do
-          [[ -e /proc/$x ]] && copy+=($x)
+          # if the process exist, keep in the 'copy' array, otherwise wait on it to capture the exit code
+          # see https://github.com/nextflow-io/nextflow/pull/4050
+          [[ -e /proc/$x ]] && copy+=($x) || wait $x
         done
         pid=("${copy[@]}")
 
diff --git a/plugins/nf-google/src/test/nextflow/cloud/google/util/GsBashLibTest.groovy b/plugins/nf-google/src/test/nextflow/cloud/google/util/GsBashLibTest.groovy
index 372cbe7b68..18cd512dae 100644
--- a/plugins/nf-google/src/test/nextflow/cloud/google/util/GsBashLibTest.groovy
+++ b/plugins/nf-google/src/test/nextflow/cloud/google/util/GsBashLibTest.groovy
@@ -151,7 +151,9 @@ class GsBashLibTest extends Specification {
                 while ((i<${#cmd[@]})); do
                     local copy=()
                     for x in "${pid[@]}"; do
-                      [[ -e /proc/$x ]] && copy+=($x)
+                      # if the process exist, keep in the 'copy' array, otherwise wait on it to capture the exit code
+                      # see https://github.com/nextflow-io/nextflow/pull/4050
+                      [[ -e /proc/$x ]] && copy+=($x) || wait $x
                     done
                     pid=("${copy[@]}")
             
@@ -256,7 +258,9 @@ class GsBashLibTest extends Specification {
                 while ((i<${#cmd[@]})); do
                     local copy=()
                     for x in "${pid[@]}"; do
-                      [[ -e /proc/$x ]] && copy+=($x)
+                      # if the process exist, keep in the 'copy' array, otherwise wait on it to capture the exit code
+                      # see https://github.com/nextflow-io/nextflow/pull/4050
+                      [[ -e /proc/$x ]] && copy+=($x) || wait $x
                     done
                     pid=("${copy[@]}")
             

From 9a52f8480342f2ad5682f9036d965f8e604abbcd Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Fri, 7 Jul 2023 07:55:05 +0200
Subject: [PATCH 009/350] Fix failing test

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../nextflow/executor/BashWrapperBuilderWithAzTest.groovy     | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/plugins/nf-azure/src/test/nextflow/executor/BashWrapperBuilderWithAzTest.groovy b/plugins/nf-azure/src/test/nextflow/executor/BashWrapperBuilderWithAzTest.groovy
index 5b94fe15a3..eb72d25163 100644
--- a/plugins/nf-azure/src/test/nextflow/executor/BashWrapperBuilderWithAzTest.groovy
+++ b/plugins/nf-azure/src/test/nextflow/executor/BashWrapperBuilderWithAzTest.groovy
@@ -171,7 +171,9 @@ class BashWrapperBuilderWithAzTest extends Specification {
                 while ((i<${#cmd[@]})); do
                     local copy=()
                     for x in "${pid[@]}"; do
-                      [[ -e /proc/$x ]] && copy+=($x)
+                      # if the process exist, keep in the 'copy' array, otherwise wait on it to capture the exit code
+                      # see https://github.com/nextflow-io/nextflow/pull/4050
+                      [[ -e /proc/$x ]] && copy+=($x) || wait $x
                     done
                     pid=("${copy[@]}")
             

From 84f7a61a1f5c763c86cd09fa8f9c4d1a3eb0db99 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Tue, 11 Jul 2023 11:11:58 +0200
Subject: [PATCH 010/350] Improve handling Wave server errors

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../src/main/io/seqera/wave/plugin/WaveClient.groovy  | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
index a1aa642878..8f88e82f99 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
@@ -607,7 +607,16 @@ class WaveClient {
         return Failsafe.with(policy).get(action)
     }
 
+    static private List<Integer> SERVER_ERRORS = [502,503,504]
+
     protected HttpResponse<String> httpSend(HttpRequest req)  {
-        return safeApply(() -> httpClient.send(req, HttpResponse.BodyHandlers.ofString()))
+        return safeApply(() -> {
+            final resp=httpClient.send(req, HttpResponse.BodyHandlers.ofString())
+            if( resp.statusCode() in SERVER_ERRORS) {
+                // throws an IOException so that the condition is handled by the retry policy
+                throw new IOException("Unexpected server response code ${resp.statusCode()} - message: ${resp.body()}")
+            }
+            return resp
+        })
     }
 }

From 099e5039d8929040e0f439792e88e820c0c9a0b7 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Sat, 15 Jul 2023 12:08:23 -0500
Subject: [PATCH 011/350] Remove logging of report JSON data (#4098) [ci fast]

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 .../src/main/groovy/nextflow/trace/ReportObserver.groovy      | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/trace/ReportObserver.groovy b/modules/nextflow/src/main/groovy/nextflow/trace/ReportObserver.groovy
index c4633fc56f..978e248983 100644
--- a/modules/nextflow/src/main/groovy/nextflow/trace/ReportObserver.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/trace/ReportObserver.groovy
@@ -237,9 +237,7 @@ class ReportObserver implements TraceObserver {
     }
 
     protected String renderSummaryJson() {
-        final result = aggregator.renderSummaryJson()
-        log.debug "Execution report summary data:\n  ${result}"
-        return result
+        aggregator.renderSummaryJson()
     }
 
     protected String renderPayloadJson() {

From 6307f9b50f73b86a79831e7f51528082fc488cd0 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sun, 16 Jul 2023 11:58:40 +0200
Subject: [PATCH 012/350] Bump micromamba 1.4.9

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../src/main/io/seqera/wave/config/CondaOpts.java      |  2 +-
 .../test/io/seqera/wave/plugin/WaveClientTest.groovy   |  4 ++--
 .../io/seqera/wave/plugin/config/WaveConfigTest.groovy |  2 +-
 .../test/io/seqera/wave/util/DockerHelperTest.groovy   | 10 +++++-----
 4 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/plugins/nf-wave/src/main/io/seqera/wave/config/CondaOpts.java b/plugins/nf-wave/src/main/io/seqera/wave/config/CondaOpts.java
index 9d4fe2c952..fe36f8aa8c 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/config/CondaOpts.java
+++ b/plugins/nf-wave/src/main/io/seqera/wave/config/CondaOpts.java
@@ -26,7 +26,7 @@
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
  */
 public class CondaOpts {
-    final public static String DEFAULT_MAMBA_IMAGE = "mambaorg/micromamba:1.4.2";
+    final public static String DEFAULT_MAMBA_IMAGE = "mambaorg/micromamba:1.4.9";
 
     final public String mambaImage;
     final public List<String> commands;
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
index 90eb9f8d83..c7e17e1c47 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
@@ -448,7 +448,7 @@ class WaveClientTest extends Specification {
         def assets = client.resolveAssets(task, null)
         then:
         assets.dockerFileContent == '''\
-                FROM mambaorg/micromamba:1.4.2
+                FROM mambaorg/micromamba:1.4.9
                 RUN \\
                     micromamba install -y -n base -c conda-forge -c defaults \\
                     salmon=1.2.3 \\
@@ -517,7 +517,7 @@ class WaveClientTest extends Specification {
         def assets = client.resolveAssets(task, null)
         then:
         assets.dockerFileContent == '''\
-                FROM mambaorg/micromamba:1.4.2
+                FROM mambaorg/micromamba:1.4.9
                 COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml
                 RUN micromamba install -y -n base -f /tmp/conda.yml \\
                     && micromamba clean -a -y
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy
index a2971d6786..1e141e8a3b 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy
@@ -86,7 +86,7 @@ class WaveConfigTest extends Specification {
         when:
         def opts = new WaveConfig([:])
         then:
-        opts.condaOpts().mambaImage == 'mambaorg/micromamba:1.4.2'
+        opts.condaOpts().mambaImage == 'mambaorg/micromamba:1.4.9'
         opts.condaOpts().commands == null
 
         when:
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/util/DockerHelperTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/util/DockerHelperTest.groovy
index c98b1cdd1b..566838978a 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/util/DockerHelperTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/util/DockerHelperTest.groovy
@@ -36,7 +36,7 @@ class DockerHelperTest extends Specification {
 
         expect:
         DockerHelper.condaFileToDockerFile(CONDA_OPTS)== '''\
-                FROM mambaorg/micromamba:1.4.2
+                FROM mambaorg/micromamba:1.4.9
                 COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml
                 RUN micromamba install -y -n base -f /tmp/conda.yml \\
                     && micromamba install -y -n base conda-forge::procps-ng \\
@@ -48,7 +48,7 @@ class DockerHelperTest extends Specification {
 
         expect:
         DockerHelper.condaFileToDockerFile(new CondaOpts([:]))== '''\
-                FROM mambaorg/micromamba:1.4.2
+                FROM mambaorg/micromamba:1.4.9
                 COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml
                 RUN micromamba install -y -n base -f /tmp/conda.yml \\
                     && micromamba clean -a -y
@@ -62,7 +62,7 @@ class DockerHelperTest extends Specification {
         def CHANNELS = ['conda-forge', 'defaults']
         expect:
         DockerHelper.condaPackagesToDockerFile(PACKAGES, CHANNELS, new CondaOpts([:])) == '''\
-                FROM mambaorg/micromamba:1.4.2
+                FROM mambaorg/micromamba:1.4.9
                 RUN \\
                     micromamba install -y -n base -c conda-forge -c defaults \\
                     bwa=0.7.15 salmon=1.1.1 \\
@@ -78,7 +78,7 @@ class DockerHelperTest extends Specification {
 
         expect:
         DockerHelper.condaPackagesToDockerFile(PACKAGES, CHANNELS, CONDA_OPTS) == '''\
-                FROM mambaorg/micromamba:1.4.2
+                FROM mambaorg/micromamba:1.4.9
                 RUN \\
                     micromamba install -y -n base -c conda-forge -c defaults \\
                     bwa=0.7.15 salmon=1.1.1 \\
@@ -94,7 +94,7 @@ class DockerHelperTest extends Specification {
 
         expect:
         DockerHelper.condaPackagesToDockerFile(PACKAGES, CHANNELS, new CondaOpts([:])) == '''\
-                FROM mambaorg/micromamba:1.4.2
+                FROM mambaorg/micromamba:1.4.9
                 RUN \\
                     micromamba install -y -n base -c foo -c bar \\
                     bwa=0.7.15 salmon=1.1.1 \\

From 9a5903e6ddba41a41952c30059360dbb7e20f8be Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Tue, 18 Jul 2023 09:04:43 +0200
Subject: [PATCH 013/350] Add support for Wave container freeze

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../plugin/SubmitContainerTokenRequest.groovy |   5 +
 .../SubmitContainerTokenResponse.groovy       |  11 ++
 .../io/seqera/wave/plugin/WaveClient.groovy   |  99 ++++------
 .../io/seqera/wave/plugin/WaveObserver.groovy |   5 +-
 .../wave/plugin/config/WaveConfig.groovy      |   4 +
 .../seqera/wave/plugin/WaveClientTest.groovy  | 169 +++---------------
 6 files changed, 80 insertions(+), 213 deletions(-)

diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/SubmitContainerTokenRequest.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/SubmitContainerTokenRequest.groovy
index 2787724bfc..08a5369917 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/SubmitContainerTokenRequest.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/SubmitContainerTokenRequest.groovy
@@ -106,4 +106,9 @@ class SubmitContainerTokenRequest {
      */
     String fingerprint
 
+    /**
+     * Enable freeze container mode
+     */
+    boolean freeze
+
 }
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/SubmitContainerTokenResponse.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/SubmitContainerTokenResponse.groovy
index 2f6184edad..707e8d9f41 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/SubmitContainerTokenResponse.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/SubmitContainerTokenResponse.groovy
@@ -39,4 +39,15 @@ class SubmitContainerTokenResponse {
      * The fully qualified wave container name to be used
      */
     String targetImage
+
+    /**
+     * The source container image that originated this request
+     */
+    String containerImage
+
+    /**
+     * The ID of the build associated with this request or null of the image already exists
+     */
+    String buildId
+
 }
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
index 8f88e82f99..b39735492f 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
@@ -23,7 +23,7 @@ import java.net.http.HttpClient
 import java.net.http.HttpRequest
 import java.net.http.HttpResponse
 import java.nio.file.Path
-import java.time.Instant
+import java.time.Duration
 import java.time.OffsetDateTime
 import java.time.temporal.ChronoUnit
 import java.util.concurrent.Callable
@@ -35,7 +35,6 @@ import com.google.common.cache.Cache
 import com.google.common.cache.CacheBuilder
 import com.google.common.util.concurrent.UncheckedExecutionException
 import com.google.gson.Gson
-import com.google.gson.GsonBuilder
 import com.google.gson.reflect.TypeToken
 import dev.failsafe.Failsafe
 import dev.failsafe.RetryPolicy
@@ -45,7 +44,6 @@ import dev.failsafe.function.CheckedSupplier
 import groovy.json.JsonOutput
 import groovy.transform.CompileStatic
 import groovy.transform.Memoized
-import io.seqera.wave.plugin.adapter.InstantAdapter
 import io.seqera.wave.plugin.config.TowerConfig
 import io.seqera.wave.plugin.config.WaveConfig
 import io.seqera.wave.plugin.exception.BadResponseException
@@ -167,7 +165,8 @@ class WaveClient {
                 buildRepository: config().buildRepository(),
                 cacheRepository: config.cacheRepository(),
                 timestamp: OffsetDateTime.now().toString(),
-                fingerprint: assets.fingerprint()
+                fingerprint: assets.fingerprint(),
+                freeze: config.freezeMode()
         )
     }
 
@@ -189,7 +188,9 @@ class WaveClient {
                 towerAccessToken: tower.accessToken,
                 towerWorkspaceId: tower.workspaceId,
                 towerEndpoint: tower.endpoint,
-                workflowId: tower.workflowId)
+                workflowId: tower.workflowId,
+                freeze: config.freezeMode()
+        )
         return sendRequest(request)
     }
 
@@ -456,6 +457,13 @@ class WaveClient {
             final key = assets.fingerprint()
             // get from cache or submit a new request
             final response = cache.get(key, { sendRequest(assets) } as Callable )
+            if( config.freezeMode() )  {
+                if( response.buildId ) {
+                    // await the image to be available when a new image is being built
+                    awaitImage(response.targetImage)
+                }
+                return new ContainerInfo(assets.containerImage, response.containerImage, key)
+            }
             // assemble the container info response
             return new ContainerInfo(assets.containerImage, response.targetImage, key)
         }
@@ -464,7 +472,30 @@ class WaveClient {
         }
     }
 
+    protected URI imageToManifestUri(String image) {
+        final p = image.indexOf('/')
+        if( p==-1 ) throw new IllegalArgumentException("Invalid container name: $image")
+        final result = 'https://' + image.substring(0,p) + '/v2' + image.substring(p).replace(':','/manifests/')
+        return new URI(result)
+    }
 
+    protected void awaitImage(String image) {
+        final manifest = imageToManifestUri(image)
+        final req = HttpRequest.newBuilder()
+                .uri(manifest)
+                .headers('Content-Type','application/json')
+                .timeout(Duration.ofSeconds(15 * 60 + 10))
+                .GET()
+                .build()
+        final begin = System.currentTimeMillis()
+        final resp = httpClient.send(req, HttpResponse.BodyHandlers.ofString())
+        final code = resp.statusCode()
+        if( code>=200 && code<400 ) {
+            log.debug "Wave container available in ${nextflow.util.Duration.of(System.currentTimeMillis()-begin)}: [$code] ${resp.body()}"
+        }
+        else
+            throw new BadResponseException("Unexpected response for \'$manifest\': [${resp.statusCode()}] ${resp.body()}")
+    }
 
     static protected boolean isCondaLocalFile(String value) {
         if( value.contains('\n') )
@@ -526,64 +557,6 @@ class WaveClient {
         return null
     }
 
-    String resolveSourceContainer(String container) {
-        final token = getWaveToken(container)
-        if( !token )
-            return container
-        final resp = fetchContainerInfo(token)
-        final describe = jsonToDescribeContainerResponse(resp)
-        return describe.source.digest==describe.wave.digest
-                ? digestImage(describe.source)      // when the digest are equals, return the source because it's a stable name
-                : digestImage(describe.wave)        // otherwise returns the wave container name
-    }
-
-    protected String digestImage(DescribeContainerResponse.ContainerInfo info) {
-        if( !info.digest )
-            return info.image
-        final p = info.image.lastIndexOf(':')
-        return p!=-1
-            ? info.image.substring(0,p) + '@' + info.digest
-            : info.image + '@' + info.digest
-    }
-
-    protected String getWaveToken(String name) {
-        if( !name )
-            return null
-        final matcher = CONTAINER_PATH.matcher(name)
-        if( !matcher.find() )
-            return null
-        return matcher.group(1)==waveRegistry
-                ? matcher.group(2)
-                : null
-    }
-
-    @Memoized
-    protected String fetchContainerInfo(String token) {
-        final uri = new URI("$endpoint/container-token/$token")
-        log.trace "Wave request container info: $uri"
-        final req = HttpRequest.newBuilder()
-                .uri(uri)
-                .headers('Content-Type','application/json')
-                .GET()
-                .build()
-
-        final resp = httpClient.send(req, HttpResponse.BodyHandlers.ofString())
-        final code = resp.statusCode()
-        if( code>=200 && code<400 ) {
-            log.debug "Wave container config info: [$code] ${resp.body()}"
-            return resp.body()
-        }
-        throw new BadResponseException("Unexpected response for \'$uri\': [${resp.statusCode()}] ${resp.body()}")
-    }
-
-    protected DescribeContainerResponse jsonToDescribeContainerResponse(String json) {
-        final gson = new GsonBuilder()
-                .registerTypeAdapter(Instant.class, new InstantAdapter())
-                .create();
-        final type = new TypeToken<DescribeContainerResponse>(){}.getType()
-        return gson.fromJson(json, type)
-    }
-
     protected <T> RetryPolicy<T> retryPolicy(Predicate<? extends Throwable> cond) {
         final cfg = config.retryOpts()
         final listener = new EventListener<ExecutionAttemptedEvent<T>>() {
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveObserver.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveObserver.groovy
index 0dbdf863bf..1032c873d0 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveObserver.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveObserver.groovy
@@ -43,10 +43,7 @@ class WaveObserver implements TraceObserver {
 
     protected void apply(TaskHandler handler) {
         final process = handler.task.getProcessor().getName()
-        containers.computeIfAbsent(process, (String it) -> {
-            final container = handler.task.getContainer()
-            return client.resolveSourceContainer(container)
-        })
+        containers.computeIfAbsent(process, (String it) -> handler.task.getContainer())
     }
 
     void onProcessComplete(TaskHandler handler, TraceRecord trace){
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/WaveConfig.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/WaveConfig.groovy
index aa8414e572..03c3926574 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/WaveConfig.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/WaveConfig.groovy
@@ -47,10 +47,12 @@ class WaveConfig {
     final private ReportOpts reportOpts
     final private RetryOpts retryOpts
     final private HttpOpts httpClientOpts
+    final private Boolean freezeMode
 
     WaveConfig(Map opts, Map<String,String> env=System.getenv()) {
         this.enabled = opts.enabled
         this.endpoint = (opts.endpoint?.toString() ?: env.get('WAVE_API_ENDPOINT') ?: DEF_ENDPOINT)?.stripEnd('/')
+        this.freezeMode = opts.freeze as Boolean
         this.containerConfigUrl = parseConfig(opts, env)
         this.tokensCacheMaxDuration = opts.navigate('tokens.cache.maxDuration', '30m') as Duration
         this.condaOpts = opts.navigate('build.conda', Collections.emptyMap()) as CondaOpts
@@ -80,6 +82,8 @@ class WaveConfig {
 
     List<String> strategy() { this.strategy }
 
+    boolean freezeMode() { return this.freezeMode }
+
     boolean bundleProjectResources() { bundleProjectResources }
 
     String buildRepository() { buildRepository }
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
index c7e17e1c47..4005b1c0b8 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
@@ -165,6 +165,29 @@ class WaveClientTest extends Specification {
         !req.condaFile
         !req.spackFile
         !req.containerConfig.layers
+        !req.freeze
+        and:
+        req.fingerprint == 'bd2cb4b32df41f2d290ce2366609f2ad'
+        req.timestamp instanceof String
+    }
+
+    def 'should create request object with freeze mode' () {
+        given:
+        def session = Mock(Session) { getConfig() >> [wave:[freeze:true]]}
+        def IMAGE =  'foo:latest'
+        def wave = new WaveClient(session)
+
+        when:
+        def req = wave.makeRequest(WaveAssets.fromImage(IMAGE))
+        then:
+        req.containerImage == IMAGE
+        !req.containerPlatform
+        !req.containerFile
+        !req.condaFile
+        !req.spackFile
+        !req.containerConfig.layers
+        and:
+        req.freeze
         and:
         req.fingerprint == 'bd2cb4b32df41f2d290ce2366609f2ad'
         req.timestamp instanceof String
@@ -850,150 +873,4 @@ class WaveClientTest extends Specification {
         'http://foo.com'    | false
     }
 
-    @Unroll
-    def 'should find wave token' () {
-        given:
-        def sess = Mock(Session) {getConfig() >> [wave:[endpoint: 'http://foo.com']] }
-        and:
-        def wave = Spy(new WaveClient(sess))
-
-        expect:
-        wave.getWaveToken(CONTAINER) == EXPECTED
-
-        where:
-        EXPECTED            | CONTAINER
-        null                | null
-        null                | 'ubunutu:latest'
-        null                | 'xyz.com/wt/3aec54700cff/wave-build-repo:rnaseq-nf_v1.0'
-        and:
-        '3aec54700cff'      | 'foo.com/wt/3aec54700cff/wave-build-repo:rnaseq-nf_v1.0'
-    }
-
-    def 'should convert json to describe container response'() {
-        given:
-        def JSON = '''
-            {
-              "token": "3aec54700cff",
-              "expiration": "2023-03-02T18:07:50.488226285Z",
-              "request": {
-                "user": {
-                  "id": 8083,
-                  "userName": "pditommaso",
-                  "email": "pditommaso@me.com"
-                },
-                "workspaceId": 88265370860066,
-                "containerImage": "1234567890.dkr.ecr.us-west-2.amazonaws.com/wave-build-repo:rnaseq-nf_v1.0",
-                "containerConfig": {
-                  "entrypoint": [
-                    "/opt/fusion/entrypoint.sh"
-                  ],
-                  "layers": [
-                    {
-                      "location": "data:DATA+OMITTED",
-                      "gzipDigest": "sha256:dc8dd4ebf839869abb81d35fe3f265de9f3ac7b9b285e274c6b92072b02a84ec",
-                      "gzipSize": 202,
-                      "tarDigest": "sha256:dc4d652cd223da5bca40d08890686c4198769fb7bfc09de2ed3c3c77dead4bf9"
-                    },
-                    {
-                      "location": "https://fusionfs.seqera.io/releases/pkg/0/6/4/fusionfs-amd64.tar.gz",
-                      "gzipDigest": "sha256:c55640ae3284715e5c7a1c1f6c6ec2de77a881a08f5a9c46f077ecd0379e8477",
-                      "gzipSize": 6191418,
-                      "tarDigest": "sha256:e24642d65d5b21987666cf1ce4ba007ecadedbcefae9601669ab43a566682aa6"
-                    }
-                  ]
-                },
-                "towerEndpoint": "https://api.tower.nf",
-                "fingerprint": "779855a0ffc582ef3170f7dab8829465",
-                "timestamp": "2023-03-01T20:07:49.933811174Z",
-                "zoneId": "Z",
-                "ipAddress": "54.190.237.226"
-              },
-              "build": {
-                "buildRepository": "1234567890.dkr.ecr.us-west-2.amazonaws.com/wave-build-repo",
-                "cacheRepository": "1234567890.dkr.ecr.us-west-2.amazonaws.com/wave-cache-repo"
-              },
-              "source": {
-                "image": "1234567890.dkr.ecr.us-west-2.amazonaws.com/wave-build-repo:rnaseq-nf_v1.0",
-                "digest": "sha256:d6f56ed0eae171fabd324bf582dd5c49c6462662c80a7e69632c57043b6af143"
-              },
-              "wave": {
-                "image": "wave.seqera.io/wt/3aec54700cff/wave-build-repo:rnaseq-nf_v1.0",
-                "digest": "sha256:d8f4f9aa77b4d1941b50a050ed71473a0e04720f38a12d497557c39a25398830"
-              }
-            }
-            '''
-        and:
-        def sess = Mock(Session) {getConfig() >> [:] }
-        def wave = Spy(new WaveClient(sess))
-
-        when:
-        def resp = wave.jsonToDescribeContainerResponse(JSON)
-        then:
-        resp.token == '3aec54700cff'
-        and:
-        resp.wave.image == 'wave.seqera.io/wt/3aec54700cff/wave-build-repo:rnaseq-nf_v1.0'
-        resp.wave.digest == 'sha256:d8f4f9aa77b4d1941b50a050ed71473a0e04720f38a12d497557c39a25398830'
-        and:
-        resp.request.user.id == 8083
-        resp.request.user.userName == 'pditommaso'
-
-    }
-
-    def 'should resolve wave container' () {
-        given:
-        def RESP1 = '''
-            {
-              "token": "3aec54700cff",
-              "source": {
-                "image": "docker.io/library/ubuntu:latest",
-                "digest": "sha256:d6f56ed0eae171fabd324bf582dd5c49c6462662c80a7e69632c57043b6af143"
-              },
-              "wave": {
-                "image": "wave.seqera.io/wt/3aec54700cff/library/ubuntu:latest",
-                "digest": "sha256:d8f4f9aa77b4d1941b50a050ed71473a0e04720f38a12d497557c39a25398830"
-              }
-            }
-        '''
-        and:
-        def sess = Mock(Session) {getConfig() >> [:] }
-        def wave = Spy(new WaveClient(sess))
-        
-        when:
-        def result = wave.resolveSourceContainer('ubuntu')
-        then:
-        0 * wave.fetchContainerInfo(_) >> null
-        result == 'ubuntu'
-
-        when:
-        result = wave.resolveSourceContainer('wave.seqera.io/wt/3aec54700cff/library/ubuntu:latest')
-        then:
-        1 * wave.fetchContainerInfo('3aec54700cff') >> RESP1
-        result == 'wave.seqera.io/wt/3aec54700cff/library/ubuntu@sha256:d8f4f9aa77b4d1941b50a050ed71473a0e04720f38a12d497557c39a25398830'
-    }
-
-    def 'should return source container' () {
-        given:
-        def RESP = '''
-            {
-              "token": "3aec54700cff",
-              "source": {
-                "image": "docker.io/library/ubuntu:latest",
-                "digest": "sha256:d6f56ed0eae171fabd324bf582dd5c49c6462662c80a7e69632c57043b6af143"
-              },
-              "wave": {
-                "image": "wave.seqera.io/wt/3aec54700cff/library/ubuntu:latest",
-                "digest": "sha256:d6f56ed0eae171fabd324bf582dd5c49c6462662c80a7e69632c57043b6af143"
-              }
-            }
-        '''
-        and:
-        def sess = Mock(Session) {getConfig() >> [:] }
-        def wave = Spy(new WaveClient(sess))
-
-        when:
-        def result = wave.resolveSourceContainer('wave.seqera.io/wt/3aec54700cff/library/ubuntu:latest')
-        then:
-        1 * wave.fetchContainerInfo('3aec54700cff') >> RESP
-        result == 'docker.io/library/ubuntu@sha256:d6f56ed0eae171fabd324bf582dd5c49c6462662c80a7e69632c57043b6af143'
-    }
 }

From 9180d63377809040bae74f9f1d6a1415ea7f17d3 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Tue, 18 Jul 2023 11:46:24 +0200
Subject: [PATCH 014/350] Allow disabling the Wave requirement when Fusion is
 enabled

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/config.md                                |  5 +++
 .../io/seqera/wave/plugin/WaveFactory.groovy  | 15 ++++++---
 .../seqera/wave/plugin/WaveFactoryTest.groovy | 33 +++++++++++++++++++
 3 files changed, 49 insertions(+), 4 deletions(-)

diff --git a/docs/config.md b/docs/config.md
index 1332c4faa4..8048ee1cf5 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -1546,6 +1546,11 @@ The following environment variables control the configuration of the Nextflow ru
   :::
 : Disables the cancellation of child jobs on workflow execution termination.
 
+`NXF_DISABLE_WAVE_REQUIREMENT`
+: :::{versionadded} 23.07.0-edge
+:::
+: Disables the requirement for Wave service when enabling the Fusion file system.
+
 `NXF_ENABLE_SECRETS`
 : :::{versionadded} 21.09.0-edge
   :::
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveFactory.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveFactory.groovy
index 7be24ca2f0..ec091cdc9e 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveFactory.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveFactory.groovy
@@ -20,6 +20,7 @@ package io.seqera.wave.plugin
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import nextflow.Session
+import nextflow.SysEnv
 import nextflow.exception.AbortOperationException
 import nextflow.trace.TraceObserver
 import nextflow.trace.TraceObserverFactory
@@ -38,10 +39,16 @@ class WaveFactory implements TraceObserverFactory {
         final wave = (Map)config.wave
         final fusion = (Map)config.fusion
         if( fusion?.enabled ) {
-            if( !wave?.enabled ) throw new AbortOperationException("Fusion feature requires enabling Wave service")
-            log.debug "Detected Fusion enabled -- Enabling bundle project resources -- Disabling upload of remote bin directory"
-            wave.bundleProjectResources = true
-            session.disableRemoteBinDir = true
+            if( !wave?.enabled ) {
+                if( SysEnv.get('NXF_DISABLE_WAVE_REQUIREMENT') )
+                    return
+                throw new AbortOperationException("Fusion feature requires enabling Wave service")
+            }
+            else {
+                log.debug "Detected Fusion enabled -- Enabling bundle project resources -- Disabling upload of remote bin directory"
+                wave.bundleProjectResources = true
+                session.disableRemoteBinDir = true
+            }
         }
 
         final observer = new WaveObserver(session)
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveFactoryTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveFactoryTest.groovy
index 0eb6754557..b06392952b 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveFactoryTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveFactoryTest.groovy
@@ -18,6 +18,8 @@
 package io.seqera.wave.plugin
 
 import nextflow.Session
+import nextflow.SysEnv
+import nextflow.exception.AbortOperationException
 import spock.lang.Specification
 import spock.lang.Unroll
 
@@ -47,4 +49,35 @@ class WaveFactoryTest extends Specification {
         [wave:[enabled:true], fusion:[enabled:true]]     | [wave:[enabled:true,bundleProjectResources:true], fusion:[enabled:true]] | 1
     }
 
+    def 'should fail when wave is disabled' () {
+        given:
+        def CONFIG = [wave:[:], fusion:[enabled:true]]
+        def session = Mock(Session) { getConfig() >> CONFIG }
+        def factory = new WaveFactory()
+
+        when:
+        factory.create(session)
+        then:
+        def e = thrown(AbortOperationException)
+        e.message == 'Fusion feature requires enabling Wave service'
+    }
+
+    def 'should not fail when wave is disabled' () {
+        given:
+        SysEnv.push(NXF_DISABLE_WAVE_REQUIREMENT: 'true')
+        def CONFIG = [wave:[:], fusion:[enabled:true]]
+        def session = Mock(Session) { getConfig() >> CONFIG }
+        def factory = new WaveFactory()
+
+        when:
+        factory.create(session)
+        then:
+        noExceptionThrown()
+        and:
+        0 * session.setDisableRemoteBinDir(true) >> null
+        and:
+        CONFIG == [wave:[:], fusion:[enabled:true]]
+    }
+
+
 }

From 9a1c584d9c75c11e2ba2e3b33184d6fe0b6e1289 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Tue, 18 Jul 2023 12:07:18 +0200
Subject: [PATCH 015/350] Add ability to disable CLI params type detection

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/config.md                                     |  5 +++++
 .../src/main/groovy/nextflow/cli/CmdRun.groovy     |  5 ++++-
 .../src/test/groovy/nextflow/cli/CmdRunTest.groovy | 14 ++++++++++++++
 3 files changed, 23 insertions(+), 1 deletion(-)

diff --git a/docs/config.md b/docs/config.md
index 8048ee1cf5..f4e740f71d 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -1546,6 +1546,11 @@ The following environment variables control the configuration of the Nextflow ru
   :::
 : Disables the cancellation of child jobs on workflow execution termination.
 
+`NXF_DISABLE_PARAMS_TYPE_DETECTION`
+: :::{versionadded} 23.07.0-edge
+:::
+: Disables the automatic type detection of command line parameters.
+
 `NXF_DISABLE_WAVE_REQUIREMENT`
 : :::{versionadded} 23.07.0-edge
 :::
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
index 71a32c0e4f..d1bb17fe20 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
@@ -32,6 +32,7 @@ import groovyx.gpars.GParsConfig
 import nextflow.Const
 import nextflow.NF
 import nextflow.NextflowMeta
+import nextflow.SysEnv
 import nextflow.config.ConfigBuilder
 import nextflow.config.ConfigMap
 import nextflow.exception.AbortOperationException
@@ -619,7 +620,9 @@ class CmdRun extends CmdBase implements HubOptions {
     }
 
 
-    static protected parseParamValue(String str ) {
+    static protected parseParamValue(String str) {
+        if ( SysEnv.get('NXF_DISABLE_PARAMS_TYPE_DETECTION') )
+            return str
 
         if ( str == null ) return null
 
diff --git a/modules/nextflow/src/test/groovy/nextflow/cli/CmdRunTest.groovy b/modules/nextflow/src/test/groovy/nextflow/cli/CmdRunTest.groovy
index bdb29effdb..86917bba53 100644
--- a/modules/nextflow/src/test/groovy/nextflow/cli/CmdRunTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/cli/CmdRunTest.groovy
@@ -19,6 +19,7 @@ package nextflow.cli
 
 import java.nio.file.Files
 
+import nextflow.SysEnv
 import nextflow.config.ConfigMap
 import nextflow.exception.AbortOperationException
 import org.junit.Rule
@@ -60,6 +61,19 @@ class CmdRunTest extends Specification {
         '..20'      | '..20'
     }
 
+    def 'should not detect params type' () {
+        given:
+        SysEnv.push(NXF_DISABLE_PARAMS_TYPE_DETECTION: 'true')
+
+        expect:
+        CmdRun.parseParamValue('true')  == 'true'
+        CmdRun.parseParamValue('1000')  == '1000'
+        CmdRun.parseParamValue('hola')  == 'hola'
+
+        cleanup:
+        SysEnv.pop()
+    }
+
     def 'should parse nested params' () {
         when:
         CmdRun.addParam(PARAMS, KEY, VALUE)

From f9f2c338f9fdfdc637c238fab6ffdeeb7e15f17e Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Tue, 18 Jul 2023 19:41:31 +0200
Subject: [PATCH 016/350] Implement Weblog feature as an external plugin

This commit remove the weblog as a core feature and move
it into a plugin maintained separately. See the link below

https://github.com/nextflow-io/nf-weblog

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/config.md                                |  14 -
 docs/tracing.md                               | 202 -------------
 .../nextflow/config/ConfigBuilder.groovy      |   3 +-
 .../trace/DefaultObserverFactory.groovy       |  15 -
 .../nextflow/trace/WebLogObserver.groovy      | 268 ------------------
 .../nextflow/config/ConfigBuilderTest.groovy  |   3 +-
 .../nextflow/trace/WebLogObserverTest.groovy  | 120 --------
 .../main/nextflow/plugin/PluginsFacade.groovy |   3 +
 8 files changed, 5 insertions(+), 623 deletions(-)
 delete mode 100644 modules/nextflow/src/main/groovy/nextflow/trace/WebLogObserver.groovy
 delete mode 100644 modules/nextflow/src/test/groovy/nextflow/trace/WebLogObserverTest.groovy

diff --git a/docs/config.md b/docs/config.md
index f4e740f71d..19f68d5418 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -1410,20 +1410,6 @@ trace {
 
 Read the {ref}`trace-report` page to learn more about the execution report that can be generated by Nextflow.
 
-(config-weblog)=
-
-### Scope `weblog`
-
-The `weblog` scope allows you to send detailed {ref}`trace <trace-fields>` information as HTTP POST requests to a webserver, shipped as a JSON object.
-
-Detailed information about the JSON fields can be found in the {ref}`weblog description<weblog-service>`.
-
-`weblog.enabled`
-: If `true` it will send HTTP POST requests to a given url.
-
-`weblog.url`
-: The url where to send HTTP POST requests (default: `http:localhost`).
-
 (config-miscellaneous)=
 
 ### Miscellaneous
diff --git a/docs/tracing.md b/docs/tracing.md
index 98cdb167b4..686e3173cc 100644
--- a/docs/tracing.md
+++ b/docs/tracing.md
@@ -426,205 +426,3 @@ And the final image produced with the [Mermaid Live Editor](https://mermaid-js.g
 
 ```{image} images/dag-mermaid.png
 ```
-
-(weblog-service)=
-
-## Weblog via HTTP
-
-Nextflow can send detailed workflow execution metadata and runtime statistics to a HTTP endpoint. To enable this feature, use the `-with-weblog` as shown below:
-
-```bash
-nextflow run <pipeline name> -with-weblog [url]
-```
-
-Workflow events are sent as HTTP POST requests to the given URL. The message consists of the following JSON structure:
-
-```json
-{
-  "runName": "<run name>",
-  "runId": "<uuid>",
-  "event": "<started|process_submitted|process_started|process_completed|error|completed>",
-  "utcTime": "<UTC timestamp>",
-  "trace": {  },
-  "metadata": {  }
-}
-```
-
-The JSON object contains the following attributes:
-
-`runName`
-: The workflow execution run name.
-
-`runId`
-: The workflow execution unique ID.
-
-`event`
-: The workflow execution event. One of `started`, `process_submitted`, `process_started`, `process_completed`, `error`, `completed`.
-
-`utcTime`
-: The UTC timestamp in ISO 8601 format.
-
-`trace`
-: *Included only for the following events: `process_submitted`, `process_started`, `process_completed`, `error`*
-: The task runtime information as described in the {ref}`trace fields<trace-fields>` section.
-: The set of included fields is determined by the `trace.fields` setting in the Nextflow configuration file. See the {ref}`Trace configuration<config-trace>` and [Trace report](#trace-report) sections to learn more.
-
-`metadata`
-: *Included only for the following events: `started`, `completed`*
-: The workflow metadata including the {ref}`config manifest<config-manifest>`. For a list of all fields, have a look at the bottom message examples.
-
-### Example `started` event
-
-When a workflow execution is started, a message like the following is posted to the specified end-point. Be aware that the properties in the parameter scope will look different for your workflow. Here is an example output from the `nf-core/hlatyping` pipeline with the weblog feature enabled:
-
-```json
-{
-  "runName": "friendly_pesquet",
-  "runId": "170aa09c-105f-49d0-99b4-8eb6a146e4a7",
-  "event": "started",
-  "utcTime": "2018-10-07T11:42:08Z",
-  "metadata": {
-    "params": {
-      "container": "nfcore/hlatyping:1.1.4",
-      "help": false,
-      "outdir": "results",
-      "bam": true,
-      "singleEnd": false,
-      "single-end": false,
-      "reads": "data/test*{1,2}.fq.gz",
-      "seqtype": "dna",
-      "solver": "glpk",
-      "igenomes_base": "./iGenomes",
-      "multiqc_config": "/Users/sven1103/.nextflow/assets/nf-core/hlatyping/conf/multiqc_config.yaml",
-      "clusterOptions": false,
-      "cluster-options": false,
-      "enumerations": 1,
-      "beta": 0.009,
-      "prefix": "hla_run",
-      "base_index": "/Users/sven1103/.nextflow/assets/nf-core/hlatyping/data/indices/yara/hla_reference_",
-      "index": "/Users/sven1103/.nextflow/assets/nf-core/hlatyping/data/indices/yara/hla_reference_dna",
-      "custom_config_version": "master",
-      "custom_config_base": "https://raw.githubusercontent.com/nf-core/configs/master"
-    },
-    "workflow": {
-      "start": "2019-03-25T12:09:52Z",
-      "projectDir": "/Users/sven1103/.nextflow/assets/nf-core/hlatyping",
-      "manifest": {
-        "nextflowVersion": ">=18.10.1",
-        "defaultBranch": "master",
-        "version": "1.1.4",
-        "homePage": "https://github.com/nf-core/hlatyping",
-        "gitmodules": null,
-        "description": "Precision HLA typing from next-generation sequencing data.",
-        "name": "nf-core/hlatyping",
-        "mainScript": "main.nf",
-        "author": null
-      },
-      "complete": null,
-      "profile": "docker,test",
-      "homeDir": "/Users/sven1103",
-      "workDir": "/Users/sven1103/git/nextflow/work",
-      "container": "nfcore/hlatyping:1.1.4",
-      "commitId": "4bcced898ee23600bd8c249ff085f8f88db90e7c",
-      "errorMessage": null,
-      "repository": "https://github.com/nf-core/hlatyping.git",
-      "containerEngine": "docker",
-      "scriptFile": "/Users/sven1103/.nextflow/assets/nf-core/hlatyping/main.nf",
-      "userName": "sven1103",
-      "launchDir": "/Users/sven1103/git/nextflow",
-      "runName": "shrivelled_cantor",
-      "configFiles": [
-        "/Users/sven1103/.nextflow/assets/nf-core/hlatyping/nextflow.config"
-      ],
-      "sessionId": "7f344978-999c-480d-8439-741bc7520f6a",
-      "errorReport": null,
-      "scriptId": "2902f5aa7f297f2dccd6baebac7730a2",
-      "revision": "master",
-      "exitStatus": null,
-      "commandLine": "./launch.sh run nf-core/hlatyping -profile docker,test -with-weblog 'http://localhost:4567'",
-      "nextflow": {
-        "version": "19.03.0-edge",
-        "build": 5137,
-        "timestamp": "2019-03-28T14:46:55Z"
-      },
-    },
-    "stats": {
-      "computeTimeFmt": "(a few seconds)",
-      "cachedCount": 0,
-      "cachedDuration": 0,
-      "failedDuration": 0,
-      "succeedDuration": 0,
-      "failedCount": 0,
-      "cachedPct": 0.0,
-      "cachedCountFmt": "0",
-      "succeedCountFmt": "0",
-      "failedPct": 0.0,
-      "failedCountFmt": "0",
-      "ignoredCountFmt": "0",
-      "ignoredCount": 0,
-      "succeedPct": 0.0,
-      "succeedCount": 0,
-      "ignoredPct": 0.0
-    },
-    "resume": false,
-    "success": false,
-    "scriptName": "main.nf",
-    "duration": null
-  }
-}
-```
-
-### Example `completed` event
-
-When a task is completed, a message like the following is posted to the specified end-point:
-
-```json
-{
-  "runName": "friendly_pesquet",
-  "runId": "170aa09c-105f-49d0-99b4-8eb6a146e4a7",
-  "event": "process_completed",
-  "utcTime": "2018-10-07T11:45:30Z",
-  "trace": {
-    "task_id": 2,
-    "status": "COMPLETED",
-    "hash": "a1/0024fd",
-    "name": "make_ot_config",
-    "exit": 0,
-    "submit": 1538912529498,
-    "start": 1538912529629,
-    "process": "make_ot_config",
-    "tag": null,
-    "module": [
-
-    ],
-    "container": "nfcore/hlatyping:1.1.1",
-    "attempt": 1,
-    "script": "\n    configbuilder --max-cpus 2 --solver glpk > config.ini\n    ",
-    "scratch": null,
-    "workdir": "/home/sven1103/git/hlatyping-workflow/work/a1/0024fd028375e2b601aaed44d112e3",
-    "queue": null,
-    "cpus": 1,
-    "memory": 7516192768,
-    "disk": null,
-    "time": 7200000,
-    "env": "PATH=/home/sven1103/git/hlatyping-workflow/bin:$PATH\n",
-    "error_action": null,
-    "complete": 1538912730599,
-    "duration": 201101,
-    "realtime": 69,
-    "%cpu": 0.0,
-    "%mem": 0.1,
-    "vmem": 54259712,
-    "rss": 10469376,
-    "peak_vmem": 20185088,
-    "peak_rss": 574972928,
-    "rchar": 7597,
-    "wchar": 162,
-    "syscr": 16,
-    "syscw": 4083712,
-    "read_bytes": 4096,
-    "write_bytes": 0,
-    "native_id": 27185
-  }
-}
-```
diff --git a/modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy
index 0ed8d4c6b2..bb963d1684 100644
--- a/modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy
@@ -39,7 +39,6 @@ import nextflow.trace.GraphObserver
 import nextflow.trace.ReportObserver
 import nextflow.trace.TimelineObserver
 import nextflow.trace.TraceFileObserver
-import nextflow.trace.WebLogObserver
 import nextflow.util.HistoryFile
 import nextflow.util.SecretHelper
 /**
@@ -678,7 +677,7 @@ class ConfigBuilder {
             if( cmdRun.withWebLog != '-' )
                 config.weblog.url = cmdRun.withWebLog
             else if( !config.weblog.url )
-                config.weblog.url = WebLogObserver.DEF_URL
+                config.weblog.url = 'http://localhost'
         }
 
         // -- sets tower options
diff --git a/modules/nextflow/src/main/groovy/nextflow/trace/DefaultObserverFactory.groovy b/modules/nextflow/src/main/groovy/nextflow/trace/DefaultObserverFactory.groovy
index 42325c723a..6c391625c9 100644
--- a/modules/nextflow/src/main/groovy/nextflow/trace/DefaultObserverFactory.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/trace/DefaultObserverFactory.groovy
@@ -24,7 +24,6 @@ class DefaultObserverFactory implements TraceObserverFactory {
         createReportObserver(result)
         createTimelineObserver(result)
         createDagObserver(result)
-        createWebLogObserver(result)
         createAnsiLogObserver(result)
         return result
     }
@@ -36,20 +35,6 @@ class DefaultObserverFactory implements TraceObserverFactory {
         }
     }
 
-    /**
-     * Create workflow message observer
-     * @param result
-     */
-    protected void createWebLogObserver(Collection<TraceObserver> result) {
-        Boolean isEnabled = config.navigate('weblog.enabled') as Boolean
-        String url = config.navigate('weblog.url') as String
-        if ( isEnabled ) {
-            if ( !url ) url = WebLogObserver.DEF_URL
-            def observer = new WebLogObserver(url)
-            result << observer
-        }
-    }
-
     /**
      * Create workflow report file observer
      */
diff --git a/modules/nextflow/src/main/groovy/nextflow/trace/WebLogObserver.groovy b/modules/nextflow/src/main/groovy/nextflow/trace/WebLogObserver.groovy
deleted file mode 100644
index ae7bab3c69..0000000000
--- a/modules/nextflow/src/main/groovy/nextflow/trace/WebLogObserver.groovy
+++ /dev/null
@@ -1,268 +0,0 @@
-/*
- * Copyright 2013-2023, Seqera Labs
- * Copyright 2018, University of Tübingen, Quantitative Biology Center (QBiC)
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package nextflow.trace
-
-import groovy.json.JsonGenerator
-import groovy.transform.CompileStatic
-import groovy.util.logging.Slf4j
-import groovyx.gpars.agent.Agent
-import nextflow.Const
-import nextflow.NextflowMeta
-import nextflow.Session
-import nextflow.processor.TaskHandler
-import nextflow.script.ScriptBinding.ParamsMap
-import nextflow.script.WorkflowMetadata
-import nextflow.util.Duration
-import nextflow.util.SimpleHttpClient
-
-import java.nio.file.Path
-
-/**
- * Send out messages via HTTP to a configured URL on different workflow
- * execution events.
- *
- * @author Sven Fillinger <sven.fillinger@qbic.uni-tuebingen.de>
- * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
- */
-@Slf4j
-@CompileStatic
-class WebLogObserver implements TraceObserver{
-
-    private Session session
-
-    private static final TimeZone UTC = TimeZone.getTimeZone("UTC")
-
-    /**
-     * Workflow identifier, will be taken from the Session() object later
-     */
-    private String runName
-
-    /**
-     * Store the sessions unique ID for downstream reference purposes
-     */
-    private String runId
-
-    /**
-     * The default url is localhost
-     */
-    static public String DEF_URL = 'http://localhost'
-
-    /**
-     * Simple http client object that will send out messages
-     */
-    private SimpleHttpClient httpClient = new SimpleHttpClient()
-
-    /**
-     * An agent for the http request in an own thread
-     */
-    private Agent<WebLogObserver> webLogAgent
-
-    /**
-     * Json generator for weblog payloads
-     */
-    private JsonGenerator generator
-
-    private String endpoint
-
-    /**
-     * Constructor that consumes a URL and creates
-     * a basic HTTP client.
-     * @param url The target address for sending messages to
-     */
-    WebLogObserver(String url) {
-        this.endpoint = checkUrl(url)
-        this.webLogAgent = new Agent<>(this)
-        this.generator = createJsonGeneratorForPayloads()
-    }
-
-    /**
-     * only for testing purpose -- do not use
-     */
-    protected WebLogObserver() {
-
-    }
-
-    /**
-     * Check the URL and create an HttpPost() object. If a invalid i.e. protocol is used,
-     * the constructor will raise an exception.
-     *
-     * The RegEx was taken and adapted from http://urlregex.com
-     *
-     * @param url String with target URL
-     * @return The requested url or the default url, if invalid
-     */
-    protected String checkUrl(String url){
-        if( url =~ "^(https|http)://[-a-zA-Z0-9+&@#/%?=~_|!:,.;]*[-a-zA-Z0-9+&@#/%=~_|]" ) {
-            return url
-        }
-        throw new IllegalArgumentException("Only http and https are supported -- The given URL was: ${url}")
-    }
-
-    /**
-     * On workflow start, submit a message with some basic
-     * information, like Id, activity and an ISO 8601 formatted
-     * timestamp.
-     * @param session The current Nextflow session object
-     */
-    @Override
-    void onFlowCreate(Session session) {
-        this.session = session
-        runName = session.getRunName()
-        runId = session.getUniqueId()
-
-        asyncHttpMessage("started", createFlowPayloadFromSession(session))
-    }
-
-    /**
-     * Send an HTTP message when the workflow is completed.
-     */
-    @Override
-    void onFlowComplete() {
-        asyncHttpMessage("completed", createFlowPayloadFromSession(this.session))
-        webLogAgent.await()
-    }
-
-    /**
-     * Send an HTTP message when a process has been submitted
-     *
-     * @param handler A {@link TaskHandler} object representing the task submitted
-     * @param trace A {@link TraceRecord} object holding the task metadata and runtime info
-     */
-    @Override
-    void onProcessSubmit(TaskHandler handler, TraceRecord trace) {
-        asyncHttpMessage("process_submitted", trace)
-    }
-
-    /**
-     * Send an HTTP message, when a process has started
-     *
-     * @param handler A {@link TaskHandler} object representing the task started
-     * @param trace A {@link TraceRecord} object holding the task metadata and runtime info
-     */
-    @Override
-    void onProcessStart(TaskHandler handler, TraceRecord trace) {
-        asyncHttpMessage("process_started", trace)
-    }
-
-    /**
-     * Send an HTTP message, when a process completed
-     *
-     * @param handler A {@link TaskHandler} object representing the task completed
-     * @param trace A {@link TraceRecord} object holding the task metadata and runtime info
-     */
-    @Override
-    void onProcessComplete(TaskHandler handler, TraceRecord trace) {
-        asyncHttpMessage("process_completed", trace)
-    }
-
-    /**
-     * Send an HTTP message, when a workflow has failed
-     *
-     * @param handler A {@link TaskHandler} object representing the task that caused the workflow execution to fail (it may be null)
-     * @param trace A {@link TraceRecord} object holding the task metadata and runtime info (it may be null)
-     */
-    @Override
-    void onFlowError(TaskHandler handler, TraceRecord trace) {
-        asyncHttpMessage("error", trace)
-    }
-
-    /**
-     * Little helper method that sends a HTTP POST message as JSON with
-     * the current run status, ISO 8601 UTC timestamp, run name and the TraceRecord
-     * object, if present.
-     * @param event The current run status. One of {'started', 'process_submit', 'process_start',
-     * 'process_complete', 'error', 'completed'}
-     * @param payload An additional object to send. Must be of type TraceRecord or Manifest
-     */
-    protected void sendHttpMessage(String event, Object payload = null){
-
-        // Set the message info
-        final time = new Date().format(Const.ISO_8601_DATETIME_FORMAT, UTC)
-
-        final message = new HashMap(4)
-        message.runName = runName
-        message.runId = runId
-        message.event = event
-        message.utcTime = time
-
-        if (payload instanceof TraceRecord)
-                message.trace = (payload as TraceRecord).store
-        else if (payload instanceof FlowPayload)
-                message.metadata = payload
-        else if (payload != null)
-            throw new IllegalArgumentException("Only TraceRecord and Manifest class types are supported: [${payload.getClass().getName()}] $payload")
-
-        // The actual HTTP request
-        httpClient.sendHttpMessage(endpoint, generator.toJson(message))
-        logHttpResponse()
-    }
-
-    protected static FlowPayload createFlowPayloadFromSession(Session session) {
-        def params = session.binding.getProperty('params') as ParamsMap
-        def workflow = session.getWorkflowMetadata()
-        new FlowPayload(params, workflow)
-    }
-
-    /**
-     * Asynchronous HTTP POST request wrapper.
-     * @param event The workflow run status
-     * @param payload An additional object to send. Must be of type TraceRecord or Manifest
-     */
-    protected void asyncHttpMessage(String event, Object payload = null){
-        webLogAgent.send{sendHttpMessage(event, payload)}
-    }
-
-    /**
-     * Little helper function that can be called for logging upon an incoming HTTP response
-     */
-    protected void logHttpResponse(){
-        def statusCode = httpClient.getResponseCode()
-        if (statusCode >= 200 && statusCode < 300) {
-            log.debug "Successfully sent message to ${endpoint} -- received status code ${statusCode}."
-        } else {
-            def msg = """\
-                Unexpected HTTP response.
-                Failed to send message to ${endpoint} -- received 
-                - status code : $statusCode    
-                - response msg: ${httpClient.getResponse()}  
-                """.stripIndent(true)
-            log.debug msg
-        }
-    }
-
-    private static JsonGenerator createJsonGeneratorForPayloads() {
-        new JsonGenerator.Options()
-                .addConverter(Path) { Path p, String key -> p.toUriString() }
-                .addConverter(Duration) { Duration d, String key -> d.durationInMillis }
-                .addConverter(NextflowMeta) { meta, key -> meta.toJsonMap() }
-                .dateFormat(Const.ISO_8601_DATETIME_FORMAT).timezone("UTC")
-                .build()
-    }
-
-    private static class FlowPayload {
-
-        final ParamsMap parameters
-
-        final WorkflowMetadata workflow
-
-        FlowPayload(ParamsMap params, WorkflowMetadata workflow ) {
-            this.parameters = params
-            this.workflow = workflow
-        }
-    }
-}
diff --git a/modules/nextflow/src/test/groovy/nextflow/config/ConfigBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/config/ConfigBuilderTest.groovy
index 048fb1a3e4..c5d9b5d6bc 100644
--- a/modules/nextflow/src/test/groovy/nextflow/config/ConfigBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/config/ConfigBuilderTest.groovy
@@ -27,7 +27,6 @@ import nextflow.cli.Launcher
 import nextflow.exception.AbortOperationException
 import nextflow.exception.ConfigParseException
 import nextflow.trace.TraceHelper
-import nextflow.trace.WebLogObserver
 import nextflow.util.ConfigHelper
 import spock.lang.Ignore
 import spock.lang.Specification
@@ -1000,7 +999,7 @@ class ConfigBuilderTest extends Specification {
         then:
         config.weblog instanceof Map
         config.weblog.enabled
-        config.weblog.url == WebLogObserver.DEF_URL
+        config.weblog.url == 'http://localhost'
 
     }
 
diff --git a/modules/nextflow/src/test/groovy/nextflow/trace/WebLogObserverTest.groovy b/modules/nextflow/src/test/groovy/nextflow/trace/WebLogObserverTest.groovy
deleted file mode 100644
index 56e4dffa83..0000000000
--- a/modules/nextflow/src/test/groovy/nextflow/trace/WebLogObserverTest.groovy
+++ /dev/null
@@ -1,120 +0,0 @@
-/*
- * Copyright 2013-2023, Seqera Labs
- * Copyright 2018, University of Tübingen, Quantitative Biology Center (QBiC)
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package nextflow.trace
-
-import spock.lang.Specification
-
-import groovy.json.JsonGenerator
-import groovy.json.JsonSlurper
-import nextflow.Session
-import nextflow.processor.TaskHandler
-import nextflow.script.ScriptBinding
-import nextflow.script.WorkflowMetadata
-import nextflow.util.SimpleHttpClient
-
-class WebLogObserverTest extends Specification {
-
-    def 'do not send messages on wrong formatted url'() {
-
-        when:
-        new WebLogObserver("localhost")
-
-        then:
-        thrown(IllegalArgumentException)
-    }
-
-    def 'send message on different workflow events' () {
-
-        given:
-        WebLogObserver httpPostObserver0 = Spy(WebLogObserver, constructorArgs: ["http://localhost"])
-        WorkflowMetadata workflowMeta = Mock(WorkflowMetadata)
-
-        def bindingStub = Mock(ScriptBinding){
-            getProperty('params') >> new ScriptBinding.ParamsMap()
-        }
-        def sessionStub = Mock(Session){
-            getRunName() >> "testRun"
-            getUniqueId() >> UUID.randomUUID()
-            getBinding() >> bindingStub
-            getWorkflowMetadata() >> workflowMeta
-        }
-        def traceStub = Mock(TraceRecord)
-        def handlerStub = Mock(TaskHandler)
-
-        when:
-        def payload = WebLogObserver.createFlowPayloadFromSession(sessionStub)
-        httpPostObserver0.onFlowCreate(sessionStub)
-        httpPostObserver0.onProcessSubmit(handlerStub, traceStub)
-        httpPostObserver0.onProcessStart(handlerStub, traceStub)
-        httpPostObserver0.onProcessComplete(handlerStub, traceStub)
-        httpPostObserver0.onFlowError(handlerStub, traceStub)
-        httpPostObserver0.onFlowComplete()
-
-        then:
-        assert payload.workflow instanceof WorkflowMetadata
-        6 * httpPostObserver0.asyncHttpMessage(!null, !null) >> null
-
-    }
-
-    def 'should create a json message' () {
-
-        given:
-        def observer = Spy(WebLogObserver)
-        def CLIENT = Mock(SimpleHttpClient)
-        observer.@endpoint = 'http://foo.com'
-        observer.@httpClient = CLIENT
-        observer.@runName = 'foo'
-        observer.@runId = 'xyz'
-        observer.@generator = new JsonGenerator.Options().build()
-        def TRACE = new TraceRecord([hash: '4a4a4a', process: 'bar'])
-
-        when:
-        observer.sendHttpMessage('started', TRACE)
-
-        then:
-        1 * observer.logHttpResponse() >> null
-        1 * CLIENT.sendHttpMessage( 'http://foo.com', _ as String ) >> { it ->
-            def message = (Map)new JsonSlurper().parseText((String)it[1])
-            assert message.runName == 'foo'
-            assert message.runId == 'xyz'
-            assert message.event == 'started'
-            assert message.trace.hash == '4a4a4a'
-            assert message.trace.process == 'bar'
-            return null
-        }
-
-    }
-
-    def 'should validate URL' () {
-        given:
-        def observer = new WebLogObserver()
-        
-        expect:
-        observer.checkUrl('http://localhost') == 'http://localhost'
-        observer.checkUrl('http://google.com') == 'http://google.com'
-        observer.checkUrl('https://google.com') == 'https://google.com'
-        observer.checkUrl('http://google.com:8080') == 'http://google.com:8080'
-        observer.checkUrl('http://google.com:8080/foo/bar') == 'http://google.com:8080/foo/bar'
-
-        when:
-        observer.checkUrl('ftp://localhost')
-        then:
-        def e = thrown(IllegalArgumentException)
-        e.message == 'Only http and https are supported -- The given URL was: ftp://localhost'
-    }
-}
diff --git a/modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy b/modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy
index db68dbe6a7..bc5049d305 100644
--- a/modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy
+++ b/modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy
@@ -401,6 +401,9 @@ class PluginsFacade implements PluginStateListener {
         if( executor == 'azurebatch' || workDir?.startsWith('az://') || bucketDir?.startsWith('az://') )
             plugins << defaultPlugins.getPlugin('nf-azure')
 
+        if( Bolts.navigate(config, 'weblog.enabled'))
+            plugins << new PluginSpec('nf-weblog')
+            
         return plugins
     }
 

From d39866e6ff4a5b5abed948dac3e14207e463b372 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Wed, 19 Jul 2023 10:03:22 +0200
Subject: [PATCH 017/350] Add missing header to wave container await [ci fast]

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../src/main/io/seqera/wave/plugin/WaveClient.groovy | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
index b39735492f..e512f90fe2 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
@@ -29,7 +29,6 @@ import java.time.temporal.ChronoUnit
 import java.util.concurrent.Callable
 import java.util.concurrent.TimeUnit
 import java.util.function.Predicate
-import java.util.regex.Pattern
 
 import com.google.common.cache.Cache
 import com.google.common.cache.CacheBuilder
@@ -69,7 +68,14 @@ class WaveClient {
 
     private static Logger log = LoggerFactory.getLogger(WaveClient)
 
-    private static final Pattern CONTAINER_PATH = ~/(\S+)\/wt\/([a-z0-9]+)\/\S+/
+    final static private String[] REQUEST_HEADERS =  new String[]{
+                        'Content-Type','application/json',
+                        'Accept','application/json',
+                        'Accept','application/vnd.oci.image.index.v1+json',
+                        'Accept','application/vnd.oci.image.manifest.v1+json',
+                        'Accept','application/vnd.docker.distribution.manifest.v1+prettyjws',
+                        'Accept','application/vnd.docker.distribution.manifest.v2+json',
+                        'Accept','application/vnd.docker.distribution.manifest.list.v2+json' }
 
     private static final List<String> DEFAULT_CONDA_CHANNELS = ['conda-forge','defaults']
 
@@ -483,7 +489,7 @@ class WaveClient {
         final manifest = imageToManifestUri(image)
         final req = HttpRequest.newBuilder()
                 .uri(manifest)
-                .headers('Content-Type','application/json')
+                .headers(REQUEST_HEADERS)
                 .timeout(Duration.ofSeconds(15 * 60 + 10))
                 .GET()
                 .build()

From 0933f47e67a6e5f271c5990a371512388aa70d7f Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Wed, 19 Jul 2023 03:56:39 -0500
Subject: [PATCH 018/350] Fix stage script in Fusion script launcher (#4109)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 .../main/groovy/nextflow/fusion/FusionScriptLauncher.groovy  | 5 +++++
 .../groovy/nextflow/executor/BashWrapperBuilderTest.groovy   | 1 +
 2 files changed, 6 insertions(+)

diff --git a/modules/nextflow/src/main/groovy/nextflow/fusion/FusionScriptLauncher.groovy b/modules/nextflow/src/main/groovy/nextflow/fusion/FusionScriptLauncher.groovy
index ed070a28dd..274ecc8861 100644
--- a/modules/nextflow/src/main/groovy/nextflow/fusion/FusionScriptLauncher.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/fusion/FusionScriptLauncher.groovy
@@ -110,6 +110,11 @@ class FusionScriptLauncher extends BashWrapperBuilder {
         return remoteWorkDir.resolve(TaskRun.CMD_INFILE)
     }
 
+    @Override
+    protected Path targetStageFile() {
+        return remoteWorkDir.resolve(TaskRun.CMD_STAGE)
+    }
+
     List<String> fusionSubmitCli(TaskRun task) {
         final runFile = toContainerMount(task.workDir.resolve(TaskRun.CMD_RUN), scheme)
         return List.of(FUSION_PATH, 'bash', runFile.toString())
diff --git a/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
index 5694435e22..cda97f5bc6 100644
--- a/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
@@ -165,6 +165,7 @@ class BashWrapperBuilderTest extends Specification {
         builder.targetInputFile() == folder.resolve('.command.in')
         builder.targetScriptFile() == folder.resolve('.command.sh')
         builder.targetWrapperFile() == folder.resolve('.command.run')
+        builder.targetStageFile() == folder.resolve('.command.stage')
         and:
         Files.exists(folder.resolve('.command.sh'))
         Files.exists(folder.resolve('.command.run'))

From bda4756730509f5b76416bb8b0c8d924edcea4fd Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Wed, 19 Jul 2023 10:16:53 -0500
Subject: [PATCH 019/350] Document `NXF_WRAPPER_STAGE_FILE_THRESHOLD`
 environment variable (#4113) [ci skip]

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 docs/config.md | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/docs/config.md b/docs/config.md
index 19f68d5418..a186e13c62 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -1555,6 +1555,12 @@ The following environment variables control the configuration of the Nextflow ru
 `NXF_EXECUTOR`
 : Defines the default process executor e.g. `sge`
 
+`NXF_FILE_ROOT`
+: :::{versionadded} 23.05.0-edge
+  :::
+: The file storage path against which relative file paths are resolved.
+: For example, with `NXF_FILE_ROOT=/some/root/path`, the use of `file('foo')` will be resolved to the absolute path `/some/root/path/foo`. A remote root path can be specified using the usual protocol prefix, e.g. `NXF_FILE_ROOT=s3://my-bucket/data`. Files defined using an absolute path are not affected by this setting.
+
 `NXF_HOME`
 : Nextflow home directory (default: `$HOME/.nextflow`).
 
@@ -1613,11 +1619,11 @@ The following environment variables control the configuration of the Nextflow ru
 `NXF_WORK`
 : Directory where working files are stored (usually your *scratch* directory)
 
-`NXF_FILE_ROOT`
+`NXF_WRAPPER_STAGE_FILE_THRESHOLD`
 : :::{versionadded} 23.05.0-edge
   :::
-: The file storage path against which relative file paths are resolved.
-: For example, with `NXF_FILE_ROOT=/some/root/path`, the use of `file('foo')` will be resolved to the absolute path `/some/root/path/foo`. A remote root path can be specified using the usual protocol prefix, e.g. `NXF_FILE_ROOT=s3://my-bucket/data`. Files defined using an absolute path are not affected by this setting.
+: Defines the minimum size of the `.command.run` staging script for it to be written to a separate `.command.stage` file (default: `'1 MB'`).
+: This setting is useful for executors that impose a size limit on job scripts.
 
 `JAVA_HOME`
 : Defines the path location of the Java VM installation used to run Nextflow.

From ac90cc26877328a96f5fadc914270aba248f7d35 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Thu, 20 Jul 2023 02:47:00 -0500
Subject: [PATCH 020/350] Add cloudcache plugin (#4097)

The nf-cloudcache plugin allows persisting the nextflow cache metadata
into a cloud object storage instead of using the embedded  leveldb engine

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/config.md                                |   5 +
 docs/plugins.md                               |   1 +
 .../nextflow/cache/DefaultCacheFactory.groovy |   2 +
 plugins/nf-cloudcache/build.gradle            |  41 ++++
 .../src/main/nextflow/CloudCachePlugin.groovy |  31 +++
 .../nextflow/cache/CloudCacheFactory.groovy   |  46 +++++
 .../nextflow/cache/CloudCacheStore.groovy     | 193 ++++++++++++++++++
 .../src/resources/META-INF/MANIFEST.MF        |   6 +
 .../src/resources/META-INF/extensions.idx     |  17 ++
 settings.gradle                               |   1 +
 validation/awsbatch.sh                        |  15 +-
 validation/azure.sh                           |  23 ++-
 validation/google.sh                          |  20 +-
 13 files changed, 391 insertions(+), 10 deletions(-)
 create mode 100644 plugins/nf-cloudcache/build.gradle
 create mode 100644 plugins/nf-cloudcache/src/main/nextflow/CloudCachePlugin.groovy
 create mode 100644 plugins/nf-cloudcache/src/main/nextflow/cache/CloudCacheFactory.groovy
 create mode 100644 plugins/nf-cloudcache/src/main/nextflow/cache/CloudCacheStore.groovy
 create mode 100644 plugins/nf-cloudcache/src/resources/META-INF/MANIFEST.MF
 create mode 100644 plugins/nf-cloudcache/src/resources/META-INF/extensions.idx

diff --git a/docs/config.md b/docs/config.md
index a186e13c62..cf68380b31 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -1502,6 +1502,11 @@ The following environment variables control the configuration of the Nextflow ru
 `NXF_ASSETS`
 : Defines the directory where downloaded pipeline repositories are stored (default: `$NXF_HOME/assets`)
 
+`NXF_CLOUDCACHE_PATH`
+: :::{versionadded} 23.07.0-edge
+  :::
+: Defines the base cache path when using the cloud cache store.
+
 `NXF_CHARLIECLOUD_CACHEDIR`
 : Directory where remote Charliecloud images are stored. When using a computing cluster it must be a shared folder accessible from all compute nodes.
 
diff --git a/docs/plugins.md b/docs/plugins.md
index 5f68cc26ac..eb46489260 100644
--- a/docs/plugins.md
+++ b/docs/plugins.md
@@ -13,6 +13,7 @@ Currently the following functionalities are implemented as plugin components and
 - `nf-console`: Implement Nextflow [REPL console](https://www.nextflow.io/blog/2015/introducing-nextflow-console.html).
 - `nf-ga4gh`: Support [GA4GH APIs](https://www.ga4gh.org/).
 - `nf-google`: Support for Google cloud.
+- `nf-cloudcache`: Support for Nextflow cache in object storage.
 - `nf-tower`: Support for [Nextflow Tower](https://tower.nf) platform.
 
 ## Configuration
diff --git a/modules/nextflow/src/main/groovy/nextflow/cache/DefaultCacheFactory.groovy b/modules/nextflow/src/main/groovy/nextflow/cache/DefaultCacheFactory.groovy
index 183c02fbba..2b4c0387e6 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cache/DefaultCacheFactory.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cache/DefaultCacheFactory.groovy
@@ -21,6 +21,7 @@ import java.nio.file.Path
 
 import groovy.transform.CompileStatic
 import nextflow.exception.AbortOperationException
+import nextflow.plugin.Priority
 
 /**
  * Implements the default cache factory
@@ -30,6 +31,7 @@ import nextflow.exception.AbortOperationException
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
  */
 @CompileStatic
+@Priority(0)
 class DefaultCacheFactory extends CacheFactory {
 
     @Override
diff --git a/plugins/nf-cloudcache/build.gradle b/plugins/nf-cloudcache/build.gradle
new file mode 100644
index 0000000000..977c686c08
--- /dev/null
+++ b/plugins/nf-cloudcache/build.gradle
@@ -0,0 +1,41 @@
+/*
+ * Copyright 2013-2023, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+apply plugin: 'groovy'
+
+sourceSets {
+    main.java.srcDirs = []
+    main.groovy.srcDirs = ['src/main']
+    main.resources.srcDirs = ['src/resources']
+    test.groovy.srcDirs = ['src/test']
+    test.java.srcDirs = []
+    test.resources.srcDirs = []
+}
+
+configurations {
+    // see https://docs.gradle.org/4.1/userguide/dependency_management.html#sub:exclude_transitive_dependencies
+    runtimeClasspath.exclude group: 'org.slf4j', module: 'slf4j-api'
+}
+
+dependencies {
+    compileOnly project(':nextflow')
+    compileOnly 'org.slf4j:slf4j-api:2.0.7'
+    compileOnly 'org.pf4j:pf4j:3.4.1'
+
+    testImplementation(testFixtures(project(":nextflow")))
+    testImplementation "org.codehaus.groovy:groovy:3.0.18"
+    testImplementation "org.codehaus.groovy:groovy-nio:3.0.18"
+}
+
diff --git a/plugins/nf-cloudcache/src/main/nextflow/CloudCachePlugin.groovy b/plugins/nf-cloudcache/src/main/nextflow/CloudCachePlugin.groovy
new file mode 100644
index 0000000000..fba6dff438
--- /dev/null
+++ b/plugins/nf-cloudcache/src/main/nextflow/CloudCachePlugin.groovy
@@ -0,0 +1,31 @@
+/*
+ * Copyright 2013-2023, Seqera Labs
+ *
+ * This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ *
+ * This Source Code Form is "Incompatible With Secondary Licenses", as
+ * defined by the Mozilla Public License, v. 2.0.
+ */
+
+package nextflow
+
+import groovy.transform.CompileStatic
+import groovy.util.logging.Slf4j
+import nextflow.plugin.BasePlugin
+import org.pf4j.PluginWrapper
+/**
+ * Nextflow cloud cache plugin
+ *
+ * @author Ben Sherman <bentshermann@gmail.com>
+ */
+@Slf4j
+@CompileStatic
+class CloudCachePlugin extends BasePlugin {
+
+    CloudCachePlugin(PluginWrapper wrapper) {
+        super(wrapper)
+    }
+
+}
diff --git a/plugins/nf-cloudcache/src/main/nextflow/cache/CloudCacheFactory.groovy b/plugins/nf-cloudcache/src/main/nextflow/cache/CloudCacheFactory.groovy
new file mode 100644
index 0000000000..41f00b98fb
--- /dev/null
+++ b/plugins/nf-cloudcache/src/main/nextflow/cache/CloudCacheFactory.groovy
@@ -0,0 +1,46 @@
+/*
+ * Copyright 2013-2023, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package nextflow.cache
+
+import java.nio.file.Path
+
+import groovy.transform.CompileStatic
+import nextflow.cache.CacheDB
+import nextflow.cache.CacheFactory
+import nextflow.exception.AbortOperationException
+import nextflow.plugin.Priority
+/**
+ * Implements the cloud cache factory
+ *
+ * @see CloudCacheStore
+ *
+ * @author Ben Sherman <bentshermann@gmail.com>
+ */
+@CompileStatic
+@Priority(-10)
+class CloudCacheFactory extends CacheFactory {
+
+    @Override
+    protected CacheDB newInstance(UUID uniqueId, String runName, Path home) {
+        if( !uniqueId ) throw new AbortOperationException("Missing cache `uuid`")
+        if( !runName ) throw new AbortOperationException("Missing cache `runName`")
+        final store = new CloudCacheStore(uniqueId, runName, home)
+        return new CacheDB(store)
+    }
+
+}
diff --git a/plugins/nf-cloudcache/src/main/nextflow/cache/CloudCacheStore.groovy b/plugins/nf-cloudcache/src/main/nextflow/cache/CloudCacheStore.groovy
new file mode 100644
index 0000000000..3ebcb40f0b
--- /dev/null
+++ b/plugins/nf-cloudcache/src/main/nextflow/cache/CloudCacheStore.groovy
@@ -0,0 +1,193 @@
+/*
+ * Copyright 2013-2023, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package nextflow.cache
+
+import java.nio.file.Files
+import java.nio.file.NoSuchFileException
+import java.nio.file.Path
+
+import com.google.common.hash.HashCode
+import groovy.transform.CompileStatic
+import nextflow.SysEnv
+import nextflow.exception.AbortOperationException
+import nextflow.extension.FilesEx
+import nextflow.util.CacheHelper
+/**
+ * Implements the cloud cache store
+ *
+ * @author Ben Sherman <bentshermann@gmail.com>
+ */
+@CompileStatic
+class CloudCacheStore implements CacheStore {
+
+    private final String LOCK_NAME = 'LOCK'
+
+    private final int KEY_SIZE
+
+    /** The session UUID */
+    private UUID uniqueId
+
+    /** The unique run name associated with this cache instance */
+    private String runName
+
+    /** The base path for the entire cache */
+    private Path basePath
+
+    /** The base path for this cache instance */
+    private Path dataPath
+
+    /** The lock file for this cache instance */
+    private Path lock
+
+    /** The path to the index file */
+    private Path indexPath
+
+    /** Index file input stream */
+    private InputStream indexReader
+
+    /** Index file output stream */
+    private OutputStream indexWriter
+
+    CloudCacheStore(UUID uniqueId, String runName, Path basePath=null) {
+        this.KEY_SIZE = CacheHelper.hasher('x').hash().asBytes().size()
+        this.uniqueId = uniqueId
+        this.runName = runName
+        this.basePath = basePath ?: defaultBasePath()
+        this.dataPath = this.basePath.resolve("$uniqueId")
+        this.lock = dataPath.resolve(LOCK_NAME)
+        this.indexPath = dataPath.resolve("index.$runName")
+    }
+
+    private Path defaultBasePath() {
+        final basePath = SysEnv.get('NXF_CLOUDCACHE_PATH')
+        if( !basePath )
+            throw new IllegalArgumentException("NXF_CLOUDCACHE_PATH must be defined when using the path-based cache store")
+
+        return basePath as Path
+    }
+
+    @Override
+    CloudCacheStore open() {
+        acquireLock()
+        indexWriter = new BufferedOutputStream(Files.newOutputStream(indexPath))
+        return this
+    }
+
+    @Override
+    CloudCacheStore openForRead() {
+        if( !dataPath.exists() )
+            throw new AbortOperationException("Missing cache directory: $dataPath")
+        acquireLock()
+        indexReader = Files.newInputStream(indexPath)
+        return this
+    }
+
+    private void acquireLock() {
+        if( lock.exists() ) {
+            final msg = """
+                Unable to acquire lock for session with ID ${uniqueId}
+
+                Common reasons for this error are:
+                - You are trying to resume the execution of an already running pipeline
+                - A previous execution was abruptly interrupted, leaving the session open
+
+                You can see the name of the conflicting run by inspecting the contents of the following path: ${lock}
+                """
+            throw new IOException(msg)
+        }
+
+        lock.text = runName
+    }
+
+    @Override
+    void drop() {
+        dataPath.deleteDir()
+    }
+
+    @Override
+    void close() {
+        FilesEx.closeQuietly(indexWriter)
+        lock.delete()
+    }
+
+    @Override
+    void writeIndex(HashCode key, boolean cached) {
+        indexWriter.write(key.asBytes())
+        indexWriter.write(cached ? 1 : 0)
+    }
+
+    @Override
+    void deleteIndex() {
+        indexPath.delete()
+    }
+
+    @Override
+    Iterator<Index> iterateIndex() {
+        return new Iterator<Index>() {
+            private Index next
+
+            {
+                next = fetch()
+            }
+
+            @Override
+            boolean hasNext() {
+                return next != null
+            }
+
+            @Override
+            Index next() {
+                final result = next
+                next = fetch()
+                return result
+            }
+
+            private Index fetch() {
+                byte[] key = new byte[KEY_SIZE]
+                if( indexReader.read(key) == -1 )
+                    return null
+                final cached = indexReader.read() == 1
+                return new Index(HashCode.fromBytes(key), cached)
+            }
+        }
+    }
+
+    @Override
+    byte[] getEntry(HashCode key) {
+        try {
+            return getCachePath(key).bytes
+        }
+        catch( NoSuchFileException e ) {
+            return null
+        }
+    }
+
+    @Override
+    void putEntry(HashCode key, byte[] value) {
+        getCachePath(key).bytes = value
+    }
+
+    @Override
+    void deleteEntry(HashCode key) {
+        getCachePath(key).delete()
+    }
+
+    private Path getCachePath(HashCode key) {
+        dataPath.resolve(key.toString())
+    }
+}
diff --git a/plugins/nf-cloudcache/src/resources/META-INF/MANIFEST.MF b/plugins/nf-cloudcache/src/resources/META-INF/MANIFEST.MF
new file mode 100644
index 0000000000..f000ea6e0a
--- /dev/null
+++ b/plugins/nf-cloudcache/src/resources/META-INF/MANIFEST.MF
@@ -0,0 +1,6 @@
+Manifest-Version: 1.0
+Plugin-Class: nextflow.CloudCachePlugin
+Plugin-Id: nf-cloudcache
+Plugin-Version: 0.1.0
+Plugin-Provider: Seqera Labs
+Plugin-Requires: >=23.04.0
diff --git a/plugins/nf-cloudcache/src/resources/META-INF/extensions.idx b/plugins/nf-cloudcache/src/resources/META-INF/extensions.idx
new file mode 100644
index 0000000000..ca38f10d03
--- /dev/null
+++ b/plugins/nf-cloudcache/src/resources/META-INF/extensions.idx
@@ -0,0 +1,17 @@
+#
+# Copyright 2013-2023, Seqera Labs
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+nextflow.cache.CloudCacheFactory
diff --git a/settings.gradle b/settings.gradle
index b73e95f132..ca6ae0164a 100644
--- a/settings.gradle
+++ b/settings.gradle
@@ -33,3 +33,4 @@ include 'plugins:nf-console'
 include 'plugins:nf-azure'
 include 'plugins:nf-codecommit'
 include 'plugins:nf-wave'
+include 'plugins:nf-cloudcache'
diff --git a/validation/awsbatch.sh b/validation/awsbatch.sh
index 27f5508de9..504e0a8b63 100644
--- a/validation/awsbatch.sh
+++ b/validation/awsbatch.sh
@@ -36,7 +36,20 @@ $NXF_CMD run test-complexpaths.nf -resume -c awsbatch.config
 
 $NXF_CMD run test-subdirs.nf -c awsbatch.config
 
+NXF_CLOUDCACHE_PATH=s3://nextflow-ci/cache \
 $NXF_CMD run nextflow-io/rnaseq-nf \
     -profile batch \
     -with-report \
-    -with-trace
+    -with-trace \
+    -plugins nf-cloudcache
+[[ `grep -c 'Using Nextflow cache factory: nextflow.cache.CloudCacheFactory' .nextflow.log` == 1 ]] || false
+
+NXF_CLOUDCACHE_PATH=s3://nextflow-ci/cache \
+$NXF_CMD run nextflow-io/rnaseq-nf \
+    -profile batch \
+    -with-report \
+    -with-trace \
+    -plugins nf-cloudcache \
+    -resume
+[[ `grep -c 'Using Nextflow cache factory: nextflow.cache.CloudCacheFactory' .nextflow.log` == 1 ]] || false
+[[ `grep -c 'Cached process > ' .nextflow.log` == 4 ]] || false
diff --git a/validation/azure.sh b/validation/azure.sh
index 3aa67848d0..856931fb0d 100644
--- a/validation/azure.sh
+++ b/validation/azure.sh
@@ -9,11 +9,6 @@ export NXF_CMD=${NXF_CMD:-$(get_abs_filename ../launch.sh)}
 
 [[ $TOWER_ACCESS_TOKEN ]] && OPTS='-with-tower' || OPTS=''
 set -x
-$NXF_CMD -C ./azure.config \
-    run nextflow-io/rnaseq-nf \
-    -with-report \
-    -with-trace $OPTS
-
 $NXF_CMD -C ./azure.config \
     run ./test-readspair.nf \
     -with-report \
@@ -50,3 +45,21 @@ $NXF_CMD -C ./azure.config run ./test-complexpaths.nf -resume
 
 ## run test-subdirs inputs/outputs
 $NXF_CMD -C ./azure.config run ./test-subdirs.nf
+
+NXF_CLOUDCACHE_PATH=az://my-data/cache \
+$NXF_CMD -C ./azure.config \
+    run nextflow-io/rnaseq-nf \
+    -with-report \
+    -with-trace $OPTS \
+    -plugins nf-cloudcache
+[[ `grep -c 'Using Nextflow cache factory: nextflow.cache.CloudCacheFactory' .nextflow.log` == 1 ]] || false
+
+NXF_CLOUDCACHE_PATH=az://my-data/cache \
+$NXF_CMD -C ./azure.config \
+    run nextflow-io/rnaseq-nf \
+    -with-report \
+    -with-trace $OPTS \
+    -plugins nf-cloudcache \
+    -resume
+[[ `grep -c 'Using Nextflow cache factory: nextflow.cache.CloudCacheFactory' .nextflow.log` == 1 ]] || false
+[[ `grep -c 'Cached process > ' .nextflow.log` == 4 ]] || false
diff --git a/validation/google.sh b/validation/google.sh
index c45c1c5a13..e0f7792870 100644
--- a/validation/google.sh
+++ b/validation/google.sh
@@ -20,10 +20,6 @@ export GOOGLE_APPLICATION_CREDENTIALS=$PWD/google_credentials.json
 
 [[ $TOWER_ACCESS_TOKEN ]] && OPTS='-with-tower' || OPTS=''
 set -x
-$NXF_CMD -C ./google.config \
-    run nextflow-io/rnaseq-nf \
-    -with-report \
-    -with-trace $OPTS
 
 $NXF_CMD -C ./google.config \
     run ./test-readspair.nf \
@@ -68,4 +64,20 @@ $NXF_CMD -C ./gls.config run ./test-overwrite.nf
 ## re-executing should overwrite the published file
 [ `$NXF_CMD -C ./gls.config run ./test-overwrite.nf -resume | { grep 'Failed to publish file' -c || true; }` == 0 ] && echo OK || { echo 'Failed to publish file' && false; }
 
+NXF_CLOUDCACHE_PATH=gs://rnaseq-nf/cache \
+$NXF_CMD -C ./google.config \
+    run nextflow-io/rnaseq-nf \
+    -with-report \
+    -with-trace $OPTS \
+    -plugins nf-cloudcache
+[[ `grep -c 'Using Nextflow cache factory: nextflow.cache.CloudCacheFactory' .nextflow.log` == 1 ]] || false
 
+NXF_CLOUDCACHE_PATH=gs://rnaseq-nf/cache \
+$NXF_CMD -C ./google.config \
+    run nextflow-io/rnaseq-nf \
+    -with-report \
+    -with-trace $OPTS \
+    -plugins nf-cloudcache \
+    -resume
+[[ `grep -c 'Using Nextflow cache factory: nextflow.cache.CloudCacheFactory' .nextflow.log` == 1 ]] || false
+[[ `grep -c 'Cached process > ' .nextflow.log` == 4 ]] || false

From 97fd33586d3f67d211809f109b54797071a21a53 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Thu, 20 Jul 2023 15:41:31 -0500
Subject: [PATCH 021/350] Fix Treat HTTP headers as case insensitive (#4116)
 [ci fast]

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../main/nextflow/util/InsensitiveMap.groovy  | 50 ++++++++++++++++
 .../nextflow/util/InsensitiveMapTest.groovy   | 60 +++++++++++++++++++
 .../file/http/XFileSystemProvider.groovy      | 10 ++--
 .../file/http/XFileSystemProviderTest.groovy  |  4 +-
 4 files changed, 118 insertions(+), 6 deletions(-)
 create mode 100644 modules/nf-commons/src/main/nextflow/util/InsensitiveMap.groovy
 create mode 100644 modules/nf-commons/src/test/nextflow/util/InsensitiveMapTest.groovy

diff --git a/modules/nf-commons/src/main/nextflow/util/InsensitiveMap.groovy b/modules/nf-commons/src/main/nextflow/util/InsensitiveMap.groovy
new file mode 100644
index 0000000000..0be4ef9059
--- /dev/null
+++ b/modules/nf-commons/src/main/nextflow/util/InsensitiveMap.groovy
@@ -0,0 +1,50 @@
+/*
+ * Copyright 2013-2023, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package nextflow.util
+
+import groovy.transform.CompileStatic
+
+/**
+ * A {@link Map} that handles keys in a case insensitive manner
+ * 
+ * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
+ */
+@CompileStatic
+class InsensitiveMap<K,V> implements Map<K,V> {
+
+    @Delegate
+    private Map<K,V> target
+
+    private InsensitiveMap(Map<K,V> map) {
+        this.target = map
+    }
+
+    @Override
+    boolean containsKey(Object key) {
+        target.any( it -> key?.toString()?.toLowerCase() == it.key?.toString()?.toLowerCase())
+    }
+
+    @Override
+    V get(Object key) {
+        target.find(it -> key?.toString()?.toLowerCase() == it.key?.toString()?.toLowerCase())?.value
+    }
+
+    static <K,V> Map<K,V> of(Map<K,V> target) {
+        new InsensitiveMap(target)
+    }
+}
diff --git a/modules/nf-commons/src/test/nextflow/util/InsensitiveMapTest.groovy b/modules/nf-commons/src/test/nextflow/util/InsensitiveMapTest.groovy
new file mode 100644
index 0000000000..99a3bb394c
--- /dev/null
+++ b/modules/nf-commons/src/test/nextflow/util/InsensitiveMapTest.groovy
@@ -0,0 +1,60 @@
+/*
+ * Copyright 2013-2023, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package nextflow.util
+
+import spock.lang.Specification
+
+/**
+ *
+ * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
+ */
+class InsensitiveMapTest extends Specification {
+
+    def 'should get value by case insensitive keys' () {
+        given:
+        def map = InsensitiveMap.of([alpha: 1, BETA: 2])
+
+        expect:
+        map.alpha == 1
+        map.ALPHA == 1
+        map.Alpha == 1
+        and:
+        map.get('alpha') == 1
+        map.get('ALPHA') == 1
+        map.get('Alpha') == 1
+        and:
+        map.beta == 2
+        map.BETA == 2
+        map.Beta == 2
+        and:
+        map.get('beta') == 2
+        map.get('BETA') == 2
+        map.get('Beta') == 2
+        and:
+        map.foo == null
+        and:
+        map.containsKey('alpha')
+        map.containsKey('ALPHA')
+        and:
+        map.containsKey('beta')
+        map.containsKey('BETA')
+        and:
+        !map.containsKey('foo')
+    }
+
+}
diff --git a/modules/nf-httpfs/src/main/nextflow/file/http/XFileSystemProvider.groovy b/modules/nf-httpfs/src/main/nextflow/file/http/XFileSystemProvider.groovy
index 67e7f9bde0..1fa43da22f 100644
--- a/modules/nf-httpfs/src/main/nextflow/file/http/XFileSystemProvider.groovy
+++ b/modules/nf-httpfs/src/main/nextflow/file/http/XFileSystemProvider.groovy
@@ -44,6 +44,7 @@ import groovy.transform.PackageScope
 import groovy.util.logging.Slf4j
 import nextflow.SysEnv
 import nextflow.extension.FilesEx
+import nextflow.util.InsensitiveMap
 import sun.net.www.protocol.ftp.FtpURLConnection
 
 import static XFileSystemConfig.*
@@ -191,7 +192,7 @@ abstract class XFileSystemProvider extends FileSystemProvider {
             XAuthRegistry.instance.authorize(conn)
         }
         if ( conn instanceof HttpURLConnection && conn.getResponseCode() in [307, 308] && attempt < MAX_REDIRECT_HOPS ) {
-            def header = conn.getHeaderFields()
+            final header = InsensitiveMap.of(conn.getHeaderFields())
             String location = header.get("Location")?.get(0)
             URL newPath = new URI(location).toURL()
             log.debug "Remote redirect URL: $newPath"
@@ -454,15 +455,16 @@ abstract class XFileSystemProvider extends FileSystemProvider {
             return new XFileAttributes(null,-1)
         }
         if ( conn instanceof HttpURLConnection && conn.getResponseCode() in [200, 301, 302, 307, 308]) {
-            def header = conn.getHeaderFields()
+            final header = conn.getHeaderFields()
             return readHttpAttributes(header)
         }
         return null
     }
 
     protected XFileAttributes readHttpAttributes(Map<String,List<String>> header) {
-        def lastMod = header.get("Last-Modified")?.get(0)
-        long contentLen = header.get("Content-Length")?.get(0)?.toLong() ?: -1
+        final header0 = InsensitiveMap.<String,List<String>>of(header)
+        def lastMod = header0.get("Last-Modified")?.get(0)
+        long contentLen = header0.get("Content-Length")?.get(0)?.toLong() ?: -1
         def dateFormat = new SimpleDateFormat('E, dd MMM yyyy HH:mm:ss Z', Locale.ENGLISH) // <-- make sure date parse is not language dependent (for the week day)
         def modTime = lastMod ? FileTime.from(dateFormat.parse(lastMod).time, TimeUnit.MILLISECONDS) : (FileTime)null
         new XFileAttributes(modTime, contentLen)
diff --git a/modules/nf-httpfs/src/test/nextflow/file/http/XFileSystemProviderTest.groovy b/modules/nf-httpfs/src/test/nextflow/file/http/XFileSystemProviderTest.groovy
index 85c4c9479c..9bbabfa06e 100644
--- a/modules/nf-httpfs/src/test/nextflow/file/http/XFileSystemProviderTest.groovy
+++ b/modules/nf-httpfs/src/test/nextflow/file/http/XFileSystemProviderTest.groovy
@@ -63,7 +63,7 @@ class XFileSystemProviderTest extends Specification {
     def "should read file attributes from map"() {
         given:
         def fs = new HttpFileSystemProvider()
-        def attrMap = ['Last-Modified': ['Fri, 04 Nov 2016 21:50:34 GMT'], 'Content-Length': ['21729']]
+        def attrMap = ['last-modified': ['Fri, 04 Nov 2016 21:50:34 GMT'], 'content-length': ['21729']]
 
         when:
         def attrs = fs.readHttpAttributes(attrMap)
@@ -85,7 +85,7 @@ class XFileSystemProviderTest extends Specification {
         def GERMAN = new Locale.Builder().setLanguage("de").setRegion("DE").build()
         Locale.setDefault(Locale.Category.FORMAT, GERMAN)
         def fs = new HttpFileSystemProvider()
-        def attrMap = ['Last-Modified': ['Fri, 04 Nov 2016 21:50:34 GMT'], 'Content-Length': ['21729']]
+        def attrMap = ['last-modified': ['Fri, 04 Nov 2016 21:50:34 GMT'], 'content-length': ['21729']]
 
         when:
         def attrs = fs.readHttpAttributes(attrMap)

From 903e4d906b9e7d3c51797e6db4a777e1913b7424 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Fri, 21 Jul 2023 12:56:33 +0200
Subject: [PATCH 022/350] Increase wave timeout to 60 mins

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../src/main/io/seqera/wave/plugin/config/HttpOpts.groovy   | 2 +-
 .../test/io/seqera/wave/plugin/config/HttpOptsTest.groovy   | 6 +++---
 .../test/io/seqera/wave/plugin/config/WaveConfigTest.groovy | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/HttpOpts.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/HttpOpts.groovy
index 8d70ec60f8..20d72ca9d9 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/HttpOpts.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/HttpOpts.groovy
@@ -32,7 +32,7 @@ class HttpOpts {
     final private Duration connectTimeout
 
     HttpOpts(Map opts) {
-        connectTimeout = opts.connectTimeout as Duration ?: Duration.of('30s')
+        connectTimeout = opts.connectTimeout as Duration ?: Duration.of('60s')
     }
 
     java.time.Duration connectTimeout() {
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/HttpOptsTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/HttpOptsTest.groovy
index 8f17add048..53908327cd 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/HttpOptsTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/HttpOptsTest.groovy
@@ -30,12 +30,12 @@ class HttpOptsTest extends Specification {
         when:
         def opts = new HttpOpts([:])
         then:
-        opts.connectTimeout() == Duration.ofSeconds(30)
+        opts.connectTimeout() == Duration.ofSeconds(60)
 
         when:
-        opts = new HttpOpts([connectTimeout:'50s'])
+        opts = new HttpOpts([connectTimeout:'120s'])
         then:
-        opts.connectTimeout() == Duration.ofSeconds(50)
+        opts.connectTimeout() == Duration.ofSeconds(120)
 
     }
 }
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy
index 1e141e8a3b..8b7353f472 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy
@@ -186,7 +186,7 @@ class WaveConfigTest extends Specification {
         when:
         def opts = new WaveConfig([:])
         then:
-        opts.httpOpts().connectTimeout() == java.time.Duration.ofSeconds(30)
+        opts.httpOpts().connectTimeout() == java.time.Duration.ofSeconds(60)
 
         when:
         opts = new WaveConfig([httpClient: [connectTimeout: '90s']])

From 9fc1d3bd951b1d9d75ba8e64a5aa497cc087f62c Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Fri, 21 Jul 2023 13:01:11 +0200
Subject: [PATCH 023/350] Add retry logic to wave image await [ci fast]

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy  | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
index e512f90fe2..339283f9d5 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
@@ -490,11 +490,11 @@ class WaveClient {
         final req = HttpRequest.newBuilder()
                 .uri(manifest)
                 .headers(REQUEST_HEADERS)
-                .timeout(Duration.ofSeconds(15 * 60 + 10))
+                .timeout(Duration.ofMinutes(5))
                 .GET()
                 .build()
         final begin = System.currentTimeMillis()
-        final resp = httpClient.send(req, HttpResponse.BodyHandlers.ofString())
+        final resp = httpSend(req)
         final code = resp.statusCode()
         if( code>=200 && code<400 ) {
             log.debug "Wave container available in ${nextflow.util.Duration.of(System.currentTimeMillis()-begin)}: [$code] ${resp.body()}"

From ef9d3cf02c63da09a04df31452e8dc37ffc421df Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Sat, 22 Jul 2023 09:28:20 -0500
Subject: [PATCH 024/350] Improve "Unexpected input: '{'" error message (#4122)
 [ci fast]

---
 .../src/main/groovy/nextflow/script/ScriptParser.groovy        | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/modules/nextflow/src/main/groovy/nextflow/script/ScriptParser.groovy b/modules/nextflow/src/main/groovy/nextflow/script/ScriptParser.groovy
index 88046d723e..4feb2446c9 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/ScriptParser.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/ScriptParser.groovy
@@ -184,6 +184,9 @@ class ScriptParser {
             msg = msg != 'startup failed' ? msg : header
             msg = msg.replaceAll(/startup failed:\n/,'')
             msg = msg.replaceAll(~/$clazzName(: \d+:\b*)?/, header+'\n- cause:')
+            if( msg.contains "Unexpected input: '{'" ) {
+                msg += "\nNOTE: If this is the beginning of a process or workflow, there may be a syntax error in the body, such as a missing or extra comma, for which a more specific error message could not be produced."
+            }
             throw new ScriptCompilationException(msg, e)
         }
     }

From 8975734d1219efc9eb068055cfa53d8189e0bf82 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Sat, 22 Jul 2023 09:29:12 -0500
Subject: [PATCH 025/350] Improve description of channels and channel types
 (#4120)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 docs/channel.md | 12 +++++-------
 1 file changed, 5 insertions(+), 7 deletions(-)

diff --git a/docs/channel.md b/docs/channel.md
index fcab491dca..754d48c4ad 100644
--- a/docs/channel.md
+++ b/docs/channel.md
@@ -2,12 +2,12 @@
 
 # Channels
 
-Nextflow is based on the Dataflow programming model in which processes communicate through channels.
+Nextflow is based on the dataflow programming model in which processes communicate through channels.
 
 A channel has two major properties:
 
-1. Sending a message is an *asynchronous* operation which completes immediately, without having to wait for the receiving process.
-2. Receiving data is a blocking operation which stops the receiving process until the message has arrived.
+1. Sending a message is an *asynchronous* (i.e. non-blocking) operation, which means the sender doesn't have to wait for the receiving process.
+2. Receiving a message is a *synchronous* (i.e. blocking) operation, which means the receiving process must wait until a message has arrived.
 
 (channel-types)=
 
@@ -27,12 +27,10 @@ A queue channel can be created by factory methods ([of](#of), [fromPath](#frompa
 
 ### Value channel
 
-A *value channel* a.k.a. *singleton channel* is bound to a single value and can be read any number of times without being consumed.
+A *value channel* contains a single value and can be consumed any number of times by a process or operator.
 
 A value channel can be created with the [value](#value) factory method or by any operator that produces a single value ({ref}`operator-first`, {ref}`operator-collect`, {ref}`operator-reduce`, etc). Additionally, a process will emit value channels if it is invoked with all value channels, including simple values which are implicitly wrapped in a value channel.
 
-A value channel is implicitly created by a process when it is invoked with a simple value. Furthermore, a value channel is also implicitly created as output for a process whose inputs are all value channels.
-
 For example:
 
 ```groovy
@@ -54,7 +52,7 @@ workflow {
 }
 ```
 
-In the above example, since the `foo` process is invoked with a simple value instead of a channel, the input is implicitly converted to a value channel, and the output is also emitted as a value channel.
+In the above example, since the `foo` process is invoked with a simple value instead of a channel, the input is implicitly wrapped in a value channel, and the output is also emitted as a value channel.
 
 See also: {ref}`process-multiple-input-channels`.
 

From 9bcb0fc53e877868dd99703b374be5154f0c0fa6 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 22 Jul 2023 16:43:13 +0200
Subject: [PATCH 026/350] Revert "Increase wave timeout to 60 mins"

This reverts commit 903e4d906b9e7d3c51797e6db4a777e1913b7424.
---
 .../src/main/io/seqera/wave/plugin/config/HttpOpts.groovy   | 2 +-
 .../test/io/seqera/wave/plugin/config/HttpOptsTest.groovy   | 6 +++---
 .../test/io/seqera/wave/plugin/config/WaveConfigTest.groovy | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/HttpOpts.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/HttpOpts.groovy
index 20d72ca9d9..8d70ec60f8 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/HttpOpts.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/HttpOpts.groovy
@@ -32,7 +32,7 @@ class HttpOpts {
     final private Duration connectTimeout
 
     HttpOpts(Map opts) {
-        connectTimeout = opts.connectTimeout as Duration ?: Duration.of('60s')
+        connectTimeout = opts.connectTimeout as Duration ?: Duration.of('30s')
     }
 
     java.time.Duration connectTimeout() {
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/HttpOptsTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/HttpOptsTest.groovy
index 53908327cd..8f17add048 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/HttpOptsTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/HttpOptsTest.groovy
@@ -30,12 +30,12 @@ class HttpOptsTest extends Specification {
         when:
         def opts = new HttpOpts([:])
         then:
-        opts.connectTimeout() == Duration.ofSeconds(60)
+        opts.connectTimeout() == Duration.ofSeconds(30)
 
         when:
-        opts = new HttpOpts([connectTimeout:'120s'])
+        opts = new HttpOpts([connectTimeout:'50s'])
         then:
-        opts.connectTimeout() == Duration.ofSeconds(120)
+        opts.connectTimeout() == Duration.ofSeconds(50)
 
     }
 }
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy
index 8b7353f472..1e141e8a3b 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy
@@ -186,7 +186,7 @@ class WaveConfigTest extends Specification {
         when:
         def opts = new WaveConfig([:])
         then:
-        opts.httpOpts().connectTimeout() == java.time.Duration.ofSeconds(60)
+        opts.httpOpts().connectTimeout() == java.time.Duration.ofSeconds(30)
 
         when:
         opts = new WaveConfig([httpClient: [connectTimeout: '90s']])

From 9be64c17bf1e02f3c6d294c8765f93ab8b626eaf Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 22 Jul 2023 16:47:39 +0200
Subject: [PATCH 027/350] Fix comment

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../io/seqera/wave/plugin/SubmitContainerTokenRequest.groovy    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/SubmitContainerTokenRequest.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/SubmitContainerTokenRequest.groovy
index 08a5369917..875cdfe338 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/SubmitContainerTokenRequest.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/SubmitContainerTokenRequest.groovy
@@ -52,7 +52,7 @@ class SubmitContainerTokenRequest {
     String towerEndpoint
 
     /**
-     * The ID of the executed container
+     * The ID of the workflow that submitted this container request
      */
     String workflowId
 

From cb6242c4ce6e6c80d7e1b6fe3f896d01208c8dd4 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 22 Jul 2023 17:17:06 +0200
Subject: [PATCH 028/350] Bump nf-cloudcache@0.1.0

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-cloudcache/changelog.txt | 4 ++++
 1 file changed, 4 insertions(+)
 create mode 100644 plugins/nf-cloudcache/changelog.txt

diff --git a/plugins/nf-cloudcache/changelog.txt b/plugins/nf-cloudcache/changelog.txt
new file mode 100644
index 0000000000..0906ab5bb8
--- /dev/null
+++ b/plugins/nf-cloudcache/changelog.txt
@@ -0,0 +1,4 @@
+nf-cloudcache changelog
+=======================
+0.1.0 - 22 Jul 2023
+- Initial version

From 57464746b6b0320dd5bbd99d7f313a79c01508f8 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 22 Jul 2023 17:19:11 +0200
Subject: [PATCH 029/350] Bump nf-amazon@2.1.0

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-amazon/changelog.txt                      | 6 ++++++
 plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/plugins/nf-amazon/changelog.txt b/plugins/nf-amazon/changelog.txt
index bbd5bfe8a5..4472d2b1cb 100644
--- a/plugins/nf-amazon/changelog.txt
+++ b/plugins/nf-amazon/changelog.txt
@@ -1,5 +1,11 @@
 nf-amazon changelog
 ===================
+2.1.0 - 22 Jul 2023
+- Add support for AWS SSO credentials provider (#4045) [53e33cde]
+- Wait for all child processes in nxf_parallel (#4050) [60a5f1a7]
+- Ignore accelerator type for AWS Batch (#4043) [263ecca8]
+- Bump Groovy 3.0.18 [207eb535]
+
 2.0.1 - 14 Jun 2023
 - Add support for AWS SES as mail sending provider [df85d443]
 - Fix access to public S3 bucket when no creds are provided (#3992) [cf8ba466]
diff --git a/plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF b/plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF
index 862abca814..6c9c9e82fd 100644
--- a/plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: nextflow.cloud.aws.AmazonPlugin
 Plugin-Id: nf-amazon
-Plugin-Version: 2.0.1
+Plugin-Version: 2.1.0
 Plugin-Provider: Seqera Labs
 Plugin-Requires: >=23.05.0-edge

From 1895efc4ee28cd30b6b2b0accbd8eeff33a33844 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 22 Jul 2023 17:19:24 +0200
Subject: [PATCH 030/350] Bump nf-azure@1.1.4

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-azure/changelog.txt                      | 7 +++++++
 plugins/nf-azure/src/resources/META-INF/MANIFEST.MF | 2 +-
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/plugins/nf-azure/changelog.txt b/plugins/nf-azure/changelog.txt
index 121c4d7392..bcfce7cfe9 100644
--- a/plugins/nf-azure/changelog.txt
+++ b/plugins/nf-azure/changelog.txt
@@ -1,5 +1,12 @@
 nf-azure changelog
 ===================
+1.1.4 - 22 Jul 2023
+- Fix failing test [9a52f848]
+- Fix Improve error message for invalid Azure URI [0f4d8867]
+- Fix invalid detection of hierarchical namespace stub blobs as files (#4046) [ce06c877]
+- Wait for all child processes in nxf_parallel (#4050) [60a5f1a7]
+- Bump Groovy 3.0.18 [207eb535]
+
 1.1.3 - 19 Jum 2023
 - Increase Azure min retry delay to 250ms [2e77e5e4]
 - Fix AzFileSystem retry policy (2) [c2f3cc96]
diff --git a/plugins/nf-azure/src/resources/META-INF/MANIFEST.MF b/plugins/nf-azure/src/resources/META-INF/MANIFEST.MF
index 1f0f5822e4..72c440d1a9 100644
--- a/plugins/nf-azure/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-azure/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: nextflow.cloud.azure.AzurePlugin
 Plugin-Id: nf-azure
-Plugin-Version: 1.1.3
+Plugin-Version: 1.1.4
 Plugin-Provider: Seqera Labs
 Plugin-Requires: >=23.01.0-edge

From f98feb7797f4427df79f5bf2f5e289a28b1e9696 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 22 Jul 2023 17:19:39 +0200
Subject: [PATCH 031/350] Bump nf-ga4gh@1.1.0

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-ga4gh/src/resources/META-INF/MANIFEST.MF | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/plugins/nf-ga4gh/src/resources/META-INF/MANIFEST.MF b/plugins/nf-ga4gh/src/resources/META-INF/MANIFEST.MF
index a5c9623cda..2835d79c84 100644
--- a/plugins/nf-ga4gh/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-ga4gh/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: nextflow.ga4gh.Ga4ghPlugin
 Plugin-Id: nf-ga4gh
-Plugin-Version: 1.0.6
+Plugin-Version: 1.1.0
 Plugin-Provider: Seqera Labs
 Plugin-Requires: >=23.05.0-edge

From 6aede7c0d10c7ccc6801364167f065f664f2a012 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 22 Jul 2023 17:19:55 +0200
Subject: [PATCH 032/350] Bump nf-google@1.8.1

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-google/changelog.txt                      | 4 ++++
 plugins/nf-google/src/resources/META-INF/MANIFEST.MF | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/plugins/nf-google/changelog.txt b/plugins/nf-google/changelog.txt
index 0b6a190eff..ff439bc729 100644
--- a/plugins/nf-google/changelog.txt
+++ b/plugins/nf-google/changelog.txt
@@ -1,5 +1,9 @@
 nf-google changelog
 ===================
+1.8.1 - 22 Jul 2023
+- Wait for all child processes in nxf_parallel (#4050) [60a5f1a7]
+- Bump Groovy 3.0.18 [207eb535]
+
 1.8.0 - 14 Jun 2023
 - Add httpConnectTimeout and httpReadTimeout to Google options (#3974) [49fa15f7]
 - Add disk resource with type option for Google Batch (#3861) [166b3638]
diff --git a/plugins/nf-google/src/resources/META-INF/MANIFEST.MF b/plugins/nf-google/src/resources/META-INF/MANIFEST.MF
index bdd904e78e..92e475ff8d 100644
--- a/plugins/nf-google/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-google/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: nextflow.cloud.google.GoogleCloudPlugin
 Plugin-Id: nf-google
-Plugin-Version: 1.8.0
+Plugin-Version: 1.8.1
 Plugin-Provider: Seqera Labs
 Plugin-Requires: >=23.02.0-edge

From 3278d798bece82431d37aa1ca9c0613c162430de Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 22 Jul 2023 17:20:16 +0200
Subject: [PATCH 033/350] Bump nf-tower@1.5.15

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-tower/changelog.txt                      | 3 +++
 plugins/nf-tower/src/resources/META-INF/MANIFEST.MF | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/plugins/nf-tower/changelog.txt b/plugins/nf-tower/changelog.txt
index 3fc20448ba..dd3e42551a 100644
--- a/plugins/nf-tower/changelog.txt
+++ b/plugins/nf-tower/changelog.txt
@@ -1,5 +1,8 @@
 nf-tower changelog
 ===================
+1.5.15 - 22 Jul 2023
+- Bump Groovy 3.0.18 [207eb535]
+
 1.5.14 - 14 Jun 2023
 - Update workflow.revision max length to match the one in Tower (#4010) [1433a903]
 
diff --git a/plugins/nf-tower/src/resources/META-INF/MANIFEST.MF b/plugins/nf-tower/src/resources/META-INF/MANIFEST.MF
index 096e8fa201..6fc78a5d49 100644
--- a/plugins/nf-tower/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-tower/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: io.seqera.tower.plugin.TowerPlugin
 Plugin-Id: nf-tower
-Plugin-Version: 1.5.14
+Plugin-Version: 1.5.15
 Plugin-Provider: Seqera Labs
 Plugin-Requires: >=23.05.0-edge

From 2998db5d576f3db7154e95fe1055e225e66740d6 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 22 Jul 2023 17:20:33 +0200
Subject: [PATCH 034/350] Bump nf-wave@0.11.0

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-wave/changelog.txt                      | 11 +++++++++++
 plugins/nf-wave/src/resources/META-INF/MANIFEST.MF |  2 +-
 2 files changed, 12 insertions(+), 1 deletion(-)

diff --git a/plugins/nf-wave/changelog.txt b/plugins/nf-wave/changelog.txt
index bc30e545af..e0b6743fe7 100644
--- a/plugins/nf-wave/changelog.txt
+++ b/plugins/nf-wave/changelog.txt
@@ -1,5 +1,16 @@
 nf-wave changelog
 ==================
+0.11.0 - 22 Jul 2023
+- Add support legacy wave retry [ci fast] [73a1e7d4]
+- Add support for Wave container freeze [9a5903e6]
+- Add retry logic to wave image await [ci fast] [9fc1d3bd]
+- Add missing header to wave container await [ci fast] [d39866e6]
+- Allow disabling the Wave requirement when Fusion is enabled [9180d633]
+- Improve handling Wave server errors [84f7a61a]
+- Bump micromamba 1.4.9 [6307f9b5]
+- Remove default arch from wave request [ci fast] [f0e5c0c1]
+- Bump Groovy 3.0.18 [207eb535]
+
 0.10.0 - 14 Jun 2023
 - Add retry policy to Wave http client [1daebeef]
 - Add support for arch auto-detection to Wave [7b5fdaf0]
diff --git a/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF b/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF
index ece0b6c6e2..d30a66bedb 100644
--- a/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: io.seqera.wave.plugin.WavePlugin
 Plugin-Id: nf-wave
-Plugin-Version: 0.10.0
+Plugin-Version: 0.11.0
 Plugin-Provider: Seqera Labs
 Plugin-Requires: >=23.05.0-edge

From 5754bf8265c54def527e0aa8a5c4d8cfbaea99a3 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 22 Jul 2023 17:38:37 +0200
Subject: [PATCH 035/350] Update changelog

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 changelog.txt | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/changelog.txt b/changelog.txt
index 2518538584..62d965f729 100644
--- a/changelog.txt
+++ b/changelog.txt
@@ -26,6 +26,8 @@ NEXTFLOW CHANGE-LOG
 - Fix packing all including Wave [735b8d9c]
 - Fix static compiler errors [f48a473c]
 - Improve documentation on Nextflow scripts (#3953) [80050c03]
+- Improve description of channels and channel types (#4120) [8975734d]
+- Improve "Unexpected input: '{'" error message (#4122) [ci fast] [ef9d3cf0]
 - Minor change in Wave config [4da0442a]
 - Prevent null exit code when Google batch is unable to acces exit status [f68a39ec]
 - Refactor Conda and Spack support for Wave to Java [36b9e226]
@@ -33,11 +35,13 @@ NEXTFLOW CHANGE-LOG
 - Update workflow.revision max length to match the one in Tower (#4010) [1433a903]
 - Bump amazocorretto:17.0.7 [c8aa1214]
 - Bump azure-storage-blob:12.22.1 [2a36fa77]
-- Bump nf-wave@0.10.0 [0872fba5]
-- Bump nf-tower@1.5.14 [64bf3115]
-- Bump nf-google@1.8.0 [7ca7d808]
-- Bump nf-azure@1.1.1 [afd368c4]
-- Bump nf-amazon@2.0.1 [58c332a1]
+- Bump nf-wave@0.11.0 [2998db5d]
+- Bump nf-tower@1.5.15 [3278d798]
+- Bump nf-google@1.8.1 [6aede7c0]
+- Bump nf-ga4gh@1.1.0 [f98feb77]
+- Bump nf-azure@1.1.4 [1895efc4]
+- Bump nf-amazon@2.1.0 [57464746]
+- Bump nf-cloudcache@0.1.0 [cb6242c4]
 
 23.05.0-edge - 15 May 2023
 - Add support for custom custom root directory to resolve relative paths (#3942) [f06bb1f7]

From fd4ff04f827ebca0f25efd3b079a68f390a82079 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 22 Jul 2023 17:46:29 +0200
Subject: [PATCH 036/350] [release 23.07.0-edge] Update timestamp and build
 number [ci fast]

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 VERSION                                             |  2 +-
 docs/conf.py                                        |  4 ++--
 .../src/main/resources/META-INF/plugins-info.txt    | 13 +++++++------
 modules/nf-commons/src/main/nextflow/Const.groovy   |  6 +++---
 nextflow                                            |  2 +-
 nextflow.md5                                        |  2 +-
 nextflow.sha1                                       |  2 +-
 nextflow.sha256                                     |  2 +-
 8 files changed, 17 insertions(+), 16 deletions(-)

diff --git a/VERSION b/VERSION
index 28d5238c54..59200001a7 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-23.06.0-edge
\ No newline at end of file
+23.07.0-edge
\ No newline at end of file
diff --git a/docs/conf.py b/docs/conf.py
index 1104ea6aac..be318c7325 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -58,9 +58,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '23.06'
+version = '23.07'
 # The full version, including alpha/beta/rc tags.
-release = '23.06.0-edge'
+release = '23.07.0-edge'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
diff --git a/modules/nextflow/src/main/resources/META-INF/plugins-info.txt b/modules/nextflow/src/main/resources/META-INF/plugins-info.txt
index 12241cd1e6..604d402fab 100644
--- a/modules/nextflow/src/main/resources/META-INF/plugins-info.txt
+++ b/modules/nextflow/src/main/resources/META-INF/plugins-info.txt
@@ -1,8 +1,9 @@
-nf-amazon@2.0.1
-nf-azure@1.1.3
+nf-amazon@2.1.0
+nf-azure@1.1.4
+nf-cloudcache@0.1.0
 nf-codecommit@0.1.5
 nf-console@1.0.6
-nf-ga4gh@1.0.6
-nf-google@1.8.0
-nf-tower@1.5.14
-nf-wave@0.10.0
\ No newline at end of file
+nf-ga4gh@1.1.0
+nf-google@1.8.1
+nf-tower@1.5.15
+nf-wave@0.11.0
\ No newline at end of file
diff --git a/modules/nf-commons/src/main/nextflow/Const.groovy b/modules/nf-commons/src/main/nextflow/Const.groovy
index ce4af4bc56..f2652b923b 100644
--- a/modules/nf-commons/src/main/nextflow/Const.groovy
+++ b/modules/nf-commons/src/main/nextflow/Const.groovy
@@ -52,17 +52,17 @@ class Const {
     /**
      * The application version
      */
-    static public final String APP_VER = "23.06.0-edge"
+    static public final String APP_VER = "23.07.0-edge"
 
     /**
      * The app build time as linux/unix timestamp
      */
-    static public final long APP_TIMESTAMP = 1686776566745
+    static public final long APP_TIMESTAMP = 1690040653541
 
     /**
      * The app build number
      */
-    static public final int APP_BUILDNUM = 5864
+    static public final int APP_BUILDNUM = 5870
 
     /**
      * The app build time string relative to UTC timezone
diff --git a/nextflow b/nextflow
index 07f27a1a36..61160e818f 100755
--- a/nextflow
+++ b/nextflow
@@ -15,7 +15,7 @@
 #  limitations under the License.
 
 [[ "$NXF_DEBUG" == 'x' ]] && set -x
-NXF_VER=${NXF_VER:-'23.06.0-edge'}
+NXF_VER=${NXF_VER:-'23.07.0-edge'}
 NXF_ORG=${NXF_ORG:-'nextflow-io'}
 NXF_HOME=${NXF_HOME:-$HOME/.nextflow}
 NXF_PROT=${NXF_PROT:-'https'}
diff --git a/nextflow.md5 b/nextflow.md5
index d5f6e0ece0..6bfd0cfe97 100644
--- a/nextflow.md5
+++ b/nextflow.md5
@@ -1 +1 @@
-424fe74b9ce5d22dc33024cc11e2f3e2
+d7cff3459c0394236a4f1781843f4655
diff --git a/nextflow.sha1 b/nextflow.sha1
index 1e93fd2666..c056fda67a 100644
--- a/nextflow.sha1
+++ b/nextflow.sha1
@@ -1 +1 @@
-8efb680493dbf8ecff34d3915fc80b1597b952b0
+a45925a853a3e516e5343b46ae291d66e93a047b
diff --git a/nextflow.sha256 b/nextflow.sha256
index 06db20c470..7e2e60eb3a 100644
--- a/nextflow.sha256
+++ b/nextflow.sha256
@@ -1 +1 @@
-e40f11caadbe721fac44e6db4b58ff2c151d95c3a88cb5d7362bb379c0d7dbbf
+185b41f6b7cdf8061f1fb93621fd5a9e648d6eb152ce66044a9ff6c98506b608

From 00eb145cc758db038bcbe11bc53315877cdf3514 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 22 Jul 2023 18:24:29 +0200
Subject: [PATCH 037/350] Bump amazoncorretto:17.0.8

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docker/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docker/Dockerfile b/docker/Dockerfile
index 26e49b8ed5..5fbe9209ed 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -1,4 +1,4 @@
-FROM amazoncorretto:17.0.7
+FROM amazoncorretto:17.0.8
 RUN yum install -y procps-ng shadow-utils
 
 ENV NXF_HOME=/.nextflow

From 547fad62749111d14085bd504b66862a32792ce7 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Mon, 24 Jul 2023 10:21:32 +0200
Subject: [PATCH 038/350] Improve wave config logging

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
index 339283f9d5..c7b3554590 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
@@ -116,7 +116,7 @@ class WaveClient {
         this.tower = new TowerConfig(session.config.tower as Map ?: Collections.emptyMap(), SysEnv.get())
         this.endpoint = config.endpoint()
         this.condaChannels = session.getCondaConfig()?.getChannels() ?: DEFAULT_CONDA_CHANNELS
-        log.debug "Wave server endpoint: ${endpoint}"
+        log.debug "Wave endpoint: ${endpoint}; config: $config"
         this.packer = new Packer()
         this.waveRegistry = new URI(endpoint).getAuthority()
         // create cache

From 9a33e93651b4b628f9fba70f0d595e8b286efbcb Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Mon, 24 Jul 2023 12:37:04 +0200
Subject: [PATCH 039/350] Fix missing changelog for version 23.07.0-edge [ci
 fast]

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 changelog.txt | 44 +++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 43 insertions(+), 1 deletion(-)

diff --git a/changelog.txt b/changelog.txt
index 62d965f729..ecd6880229 100644
--- a/changelog.txt
+++ b/changelog.txt
@@ -1,5 +1,47 @@
 NEXTFLOW CHANGE-LOG
 ===================
+23.07.0-edge - 23 Jul 2023
+- Add CPU model name to trace files and traceRecord (#3946) [e0d91bf7]
+- Add ability to disable CLI params type detection [9a1c584d]
+- Add cloudcache plugin (#4097) [ac90cc26]
+- Add missing header to Wave container await [d39866e6]
+- Add remote bin support for TES in a workdir (#3990) [8a22168a]
+- Add retry logic to wave image await [9fc1d3bd]
+- Add rule to build Nextflow docker image for ARM (#4020) [705d55f5]
+- Add support for AWS SSO credentials provider (#4045) [53e33cde]
+- Add support for Wave container freeze [9a5903e6]
+- Add support legacy Wave retry [73a1e7d4]
+- Allow SLURM executor option `--mem-per-cpu` (#4023) [96c04e3b]
+- Allow disabling the Wave requirement when Fusion is enabled [9180d633]
+- Disable Singularity and Apptainer home mount by default (#4056) [a0ee4657]
+- Document `NXF_WRAPPER_STAGE_FILE_THRESHOLD` environment variable (#4113) [ci skip] [bda47567]
+- Fix AzFileSystem retry policy [ba9b6d18] [c2f3cc96]
+- Fix Improve error message for invalid Azure URI [0f4d8867]
+- Fix Treat HTTP headers as case insensitive (#4116) [97fd3358]
+- Fix invalid detection of hierarchical namespace stub blobs as files (#4046) [ce06c877]
+- Fix stage script in Fusion script launcher (#4109) [0933f47e]
+- Ignore accelerator type for AWS Batch (#4043) [263ecca8]
+- Implement Weblog feature as an external plugin [f9f2c338]
+- Improve "Unexpected input: '{'" error message (#4122) [ef9d3cf0]
+- Improve Azure retry logging [de58697a]
+- Improve description of channels and channel types (#4120) [8975734d]
+- Improve handling Wave server errors [84f7a61a]
+- Increase Azure min retry delay to 250ms [2e77e5e4]
+- Remove default arch from wave request [f0e5c0c1]
+- Remove logging of report JSON data (#4098) [099e5039]
+- Wait for all child processes in nxf_parallel (#4050) [60a5f1a7]
+- Bump Groovy 3.0.18 [207eb535]
+- Bump micromamba 1.4.9 [6307f9b5]
+- Bump nf-amazon@2.1.0 [57464746]
+- Bump nf-azure@1.1.2 [e1512f6a]
+- Bump nf-azure@1.1.3 [27e7f663]
+- Bump nf-azure@1.1.4 [1895efc4]
+- Bump nf-cloudcache@0.1.0 [cb6242c4]
+- Bump nf-ga4gh@1.1.0 [f98feb77]
+- Bump nf-google@1.8.1 [6aede7c0]
+- Bump nf-tower@1.5.15 [3278d798]
+- Bump nf-wave@0.11.0 [2998db5d]
+
 23.06.0-edge - 14 Jun 2023
 - Add AWS Kms integration test [19449bf4]
 - Add Wave containers reports (preview) [9d9e2758]
@@ -27,7 +69,7 @@ NEXTFLOW CHANGE-LOG
 - Fix static compiler errors [f48a473c]
 - Improve documentation on Nextflow scripts (#3953) [80050c03]
 - Improve description of channels and channel types (#4120) [8975734d]
-- Improve "Unexpected input: '{'" error message (#4122) [ci fast] [ef9d3cf0]
+- Improve "Unexpected input: '{'" error message (#4122) [ef9d3cf0]
 - Minor change in Wave config [4da0442a]
 - Prevent null exit code when Google batch is unable to acces exit status [f68a39ec]
 - Refactor Conda and Spack support for Wave to Java [36b9e226]

From 22638d460ae61d308103bf7291f22c9586d10f87 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Tue, 25 Jul 2023 03:15:39 -0500
Subject: [PATCH 040/350] Improve plugin docs (#3957)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Phil Ewels <phil.ewels@seqera.io>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Phil Ewels <phil.ewels@seqera.io>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/cli.md     |  22 +++
 docs/config.md  |   5 +
 docs/plugins.md | 358 +++++++++++++++++++++++++++++++++++++++++-------
 docs/sharing.md |   4 +
 4 files changed, 342 insertions(+), 47 deletions(-)

diff --git a/docs/cli.md b/docs/cli.md
index 164ca94a04..9e707d294f 100644
--- a/docs/cli.md
+++ b/docs/cli.md
@@ -469,6 +469,8 @@ profiles {
 }
 ```
 
+(cli-console)=
+
 ### console
 
 Launch the Nextflow interactive console.
@@ -886,6 +888,26 @@ $ nextflow log tiny_leavitt -F 'process =~ /splitLetters/'
 work/1f/f1ea9158fb23b53d5083953121d6b6
 ```
 
+(cli-plugin)=
+
+### plugin
+
+Manage plugins and run plugin-specific commands.
+
+```console
+$ nextflow plugin <subcommand> [options]
+```
+
+The `plugin` command provides several subcommands for managing and using plugins:
+
+`install <plugin[@version],..>`
+
+: Install a plugin. Multiple plugins can be specified as a comma-separated list. Each plugin id consists of a name and optional version separated by a `@`.
+
+`<plugin>:<subcommand> [options]`
+
+: Execute a plugin-specific command.
+
 ### pull
 
 Download or update a project.
diff --git a/docs/config.md b/docs/config.md
index cf68380b31..f28cf22659 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -1594,6 +1594,11 @@ The following environment variables control the configuration of the Nextflow ru
 `NXF_PID_FILE`
 : Name of the file where the process PID is saved when Nextflow is launched in background.
 
+`NXF_PLUGINS_TEST_REPOSITORY`
+: :::{versionadded} 23.04.0
+  :::
+: Defines a custom plugin registry or plugin release URL for testing plugins outside of the main registry. See {ref}`testing-plugins` for more information.
+
 `NXF_SCM_FILE`
 : :::{versionadded} 20.10.0
   :::
diff --git a/docs/plugins.md b/docs/plugins.md
index eb46489260..f7f1c22d69 100644
--- a/docs/plugins.md
+++ b/docs/plugins.md
@@ -2,89 +2,205 @@
 
 # Plugins
 
-## Main concepts
+Nextflow has a plugin system that allows the use of extensible components that are downloaded and installed at runtime.
 
-Nextflow is based on a plugins system that allows extending core functionalities via pluggable components that are download and installed at runtime.
+## Core plugins
 
-Currently the following functionalities are implemented as plugin components and they make part of the Nextflow *default* plugins:
+The following functionalities are provided via plugin components, and they make part of the Nextflow *core* plugins:
 
 - `nf-amazon`: Support for Amazon cloud.
 - `nf-azure`: Support for Azure cloud.
 - `nf-console`: Implement Nextflow [REPL console](https://www.nextflow.io/blog/2015/introducing-nextflow-console.html).
 - `nf-ga4gh`: Support [GA4GH APIs](https://www.ga4gh.org/).
 - `nf-google`: Support for Google cloud.
-- `nf-cloudcache`: Support for Nextflow cache in object storage.
-- `nf-tower`: Support for [Nextflow Tower](https://tower.nf) platform.
+- `nf-tower`: Support for [Tower](https://tower.nf) cloud platform.
+- `nf-wave`: Support for [Wave containers](https://seqera.io/wave/) service.
 
-## Configuration
 
-Nextflow *default* plugins do not require any configuration. They are automatically installed when the corresponding feature is requested by a Nextflow pipeline.
+## Using plugins
 
-To use **non-default** plugins in your pipeline execution, you must declare them in the Nextflow configuration file, listing each plugin as shown below:
+The core plugins do not require any configuration. They are automatically installed when the corresponding feature is requested by a Nextflow pipeline. You can still specify them as described below, e.g. if you want to pin the version of a plugin, however if you try to use a plugin version that isn't compatible with your Nextflow version, Nextflow will fail.
+
+You can enable a plugin by declaring it in your Nextflow configuration:
 
 ```groovy
 plugins {
-  id 'nf-hello@0.1.0'
+    id 'nf-hello@0.1.0'
 }
 ```
 
-The plugin identifier consists of the plugin name and plugin version separated by a `@`.
-
-Alternatively, plugins can be required using the `-plugins` command line option:
+Or you can use the `-plugins` command line option:
 
 ```bash
-nextflow run <PIPELINE NAME> -plugins nf-hello@0.1.0
+nextflow run <pipeline> -plugins nf-hello@0.1.0
 ```
 
-Multiple plugins can be specified by separating them with a comma. When specifying plugins via the command line, any plugin declarations in the Nextflow config file are ignored.
+The plugin identifier consists of the plugin name and plugin version separated by a `@`. Multiple plugins can be specified 
+in the configuration with multiple `id` declarations, or on the command line as a comma-separated list. When specifying 
+plugins via the command line, any plugin declarations in the configuration file are ignored.
 
-## Index
+The default plugins are documented in this documentation. For all other plugins, please refer to the plugin's code repository 
+for documentation and support.
 
-Nextflow resolves plugins download location through the [Plugins index](https://github.com/nextflow-io/plugins/). The index stores for each plugin the available version, the creation date, checksum and the link from where the plugin file is downloaded.
+## Writing plugins
 
-To add a new plugin to the Index, create a pull request including the request plugin metadata. The [nf-hello](https://github.com/nextflow-io/nf-hello) repository provides a minimal code example for the implementation of a Nextflow plugin.
+To get started with your own plugin, refer to the [nf-hello](https://github.com/nextflow-io/nf-hello) repository, 
+which provides a minimal plugin implementation with several examples of different extension points, as well as instructions 
+for building, testing, and publishing.
 
-## Import operators from plugin
+Nextflow's plugin system exposes a variety of extension points for plugins. The following sections describe how to use 
+these extension points when writing a plugin, as well as how they are used in a pipeline.
 
-:::{versionadded} 22.04.0
+:::{note}
+If you would like to implement something in a plugin that isn't covered by any of the following sections, feel free to 
+create an issue on GitHub and describe your use case. In general, any class in the Nextflow codebase that implements 
+`ExtensionPoint` can be extended by a plugin, and existing plugins are a great source of examples when writing new plugins.
 :::
 
-Nextflow supports the inclusion of custom operators from Nextflow plugins.
+:::{note}
+Plugin extension points must be added to `extensions.idx` in the plugin repository to make them discoverable. 
+See the `nf-hello` plugin for an example.
+:::
 
-For example:
+### Commands
+
+Plugins can define custom CLI commands that can be executed with the `nextflow plugin` command.
+
+To implement a plugin-specific command, implement the `PluginExecAware` interface in your plugin entrypoint 
+(the class that extends `BasePlugin`). Alternatively, you can implement the `PluginAbstractExec` trait, which 
+provides an abstract implementation with some boilerplate code. This trait requires you to implement two methods, 
+`getCommands()` and `exec()`:
 
 ```groovy
-include { sqlInsert; fromQuery as selectFromTable } from 'plugin/nf-sqldb'
+import nextflow.cli.PluginAbstractExec
+import nextflow.plugin.BasePlugin
+
+class MyPlugin extends BasePlugin implements PluginAbstractExec {
+    @Override
+    List<String> getCommands() {
+        [ 'hello' ]
+    }
+
+    @Override
+    int exec(String cmd, List<String> args) {
+        if( cmd == 'hello' ) {
+            println "Hello! You gave me these arguments: ${args.join(' ')}"
+            return 0
+        }
+        else {
+            System.err.println "Invalid command: ${cmd}"
+            return 1
+        }
+    }
+}
+```
 
-def sql = "select * from FOO"
-channel
-    .selectFromTable(sql, db: "test", emitColumns:true)
-    .sqlInsert(into:"BAR", columns:'id', db:"test")
+You can then execute this command using the `nextflow plugin` command:
+
+```bash
+nextflow plugin my-plugin:hello --foo --bar
 ```
 
-The above snippet includes the operators `sqlInsert` and `fromQuery` from the [nf-sqldb](https://github.com/nextflow-io/nf-sqldb) plugin. The latter will be accessible using the `selectFromTable` alias in the script.
+See the {ref}`cli-plugin` CLI command for usage information.
 
-:::{note}
-The prefix `plugin/` must precede the plugin name in the include `from` statement.
+### Configuration
+
+Plugins can access the resolved Nextflow configuration through the session object using `session.config.navigate()`. 
+Several extension points provide the session object for this reason. This method allows you to query any configuration 
+option in a safe manner -- if the option isn't defined, it will return `null`. A common practice is to define any 
+configuration for your plugin in a custom config scope.
+
+Here is an example of querying a config option in a trace observer hook:
+
+```groovy
+import nextflow.Session
+import nextflow.trace.TraceObserver
+
+class MyObserver implements TraceObserver {
+
+    @Override
+    void onFlowCreate(Session session) {
+        final message = session.config.navigate('myplugin.create.message')
+        println message
+    }
+}
+```
+
+You can then set this option in your config file:
+
+```groovy
+// dot syntax
+myplugin.create.message = "I'm alive!"
+
+// closure syntax
+myplugin {
+    create {
+        message = "I'm alive!"
+    }
+}
+```
+
+### Executors
+
+Plugins can define custom executors that can then be used with the `executor` process directive.
+
+To implement an executor, create a class in your plugin that extends the [`Executor`](https://github.com/nextflow-io/nextflow/blob/master/modules/nextflow/src/main/groovy/nextflow/executor/Executor.groovy) class and implements the `ExtensionPoint` interface. Add the `@ServiceName` annotation to your class with the name of your executor:
+
+```groovy
+import nextflow.executor.Executor
+import nextflow.util.ServiceName
+import org.pf4j.ExtensionPoint
+
+@ServiceName('my-executor')
+class MyExecutor extends Executor implements ExtensionPoint {
+
+    // ...
+
+}
+```
+
+You can then use this executor in your pipeline:
+
+```groovy
+process foo {
+    executor 'my-executor'
+}
+```
+
+:::{tip}
+Refer to the source code of Nextflow's built-in executors to see how to implement the various components of an executor. 
+You might be able to implement most of your executor by simply reusing existing code.
 :::
 
-## Import custom functions from plugin
+### Functions
 
 :::{versionadded} 22.09.0-edge
 :::
 
-Nextflow supports the inclusion of custom functions from Nextflow plugins.
+Plugins can define custom Groovy functions, which can then be included into Nextflow pipelines.
 
-For example, a plugin can export a util function to reverse a String:
+To implement a custom function, create a class in your plugin that extends the `PluginExtensionPoint` class, and implement 
+your function with the `Function` annotation:
 
 ```groovy
-@nextflow.plugin.extension.Function
-String reverseString( String origin ){
-     origin.reverse()
+import nextflow.Session
+import nextflow.plugin.extension.Function
+import nextflow.plugin.extension.PluginExtensionPoint
+
+class MyExtension implements PluginExtensionPoint {
+
+    @Override
+    void init(Session session) {}
+
+    @Function
+    String reverseString(String origin) {
+        origin.reverse()
+    }
+
 }
 ```
 
-And this function can be used by the pipeline:
+You can then use this function in your pipeline:
 
 ```groovy
 include { reverseString } from 'plugin/my-plugin'
@@ -92,29 +208,177 @@ include { reverseString } from 'plugin/my-plugin'
 channel.of( reverseString('hi') )
 ```
 
-The above snippet includes a function from the plugin and allows the channel to call it directly.
-
-In the same way as operators, functions can be aliased:
+You can also use an alias:
 
 ```groovy
 include { reverseString as anotherReverseMethod } from 'plugin/my-plugin'
 ```
 
-## Testing custom plugins
+### Operators
 
-To make a plugin available to Nextflow, it needs to be included in the [plugins repository index](https://github.com/nextflow-io/plugins).
+:::{versionadded} 22.04.0
+:::
+
+Plugins can define custom channel factories and operators, which can then be included into Nextflow pipelines.
+
+To implement a custom factory or operator, create a class in your plugin that extends the `PluginExtensionPoint` class, 
+and implement your function with the `Factory` or `Operator` annotation:
+
+```groovy
+import groovyx.gpars.dataflow.DataflowReadChannel
+import groovyx.gpars.dataflow.DataflowWriteChannel
+import nextflow.Session
+import nextflow.plugin.extension.Factory
+import nextflow.plugin.extension.Operator
+import nextflow.plugin.extension.PluginExtensionPoint
+
+class MyExtension implements PluginExtensionPoint {
+
+    @Override
+    void init(Session session) {}
 
-However, in order to validate a plugin before it's published in the repository index, it is possible to use the environment
-variable `NXF_PLUGINS_TEST_REPOSITORY` to specify the URI of a custom index JSON file or the plugin JSON meta file.
+    @Factory
+    DataflowWriteChannel fromQuery(Map opts, String query) {
+        // ...
+    }
+
+    @Operator
+    DataflowWriteChannel sqlInsert(DataflowReadChannel source, Map opts) {
+        // ...
+    }
+
+}
+```
+
+You can then use them in your pipeline:
+
+```groovy
+include { sqlInsert; fromQuery as fromTable } from 'plugin/nf-sqldb'
+
+def sql = 'select * from FOO'
+channel
+    .fromTable(sql, db: 'test', emitColumns: true)
+    .sqlInsert(into: 'BAR', columns: 'id', db: 'test')
+```
+
+The above snippet is based on the [nf-sqldb](https://github.com/nextflow-io/nf-sqldb) plugin. The `fromQuery` factory 
+is included under the alias `fromTable`.
+
+### Trace observers
+
+A *trace observer* in Nextflow is an entity that can listen and react to workflow events, such as when a workflow starts, 
+a task completes, a file is published, etc. Several components in Nextflow, such as the execution report and DAG visualization, 
+are implemented as trace observers.
+
+Plugins can define custom trace observers that react to workflow events with custom behavior. To implement a trace observer, 
+create a class that implements the `TraceObserver` trait and another class that implements the `TraceObserverFactory` interface. 
+Implement any of the hooks defined in `TraceObserver`, and implement the `create()` method in your observer factory:
+
+```groovy
+// MyObserverFactory.groovy
+import nextflow.Session
+import nextflow.trace.TraceObserver
+import nextflow.trace.TraceObserverFactory
+
+class MyObserverFactory implements TraceObserverFactory {
+
+    @Override
+    Collection<TraceObserver> create(Session session) {
+        final enabled = session.config.navigate('myplugin.enabled')
+        return enabled ? [ new MyObserver() ] : []
+    }
+}
+
+// MyObserver.groovy
+import java.nio.file.Path
+
+import nextflow.processor.TaskHandler
+import nextflow.trace.TraceObserver
+import nextflow.trace.TraceRecord
+
+class MyObserver implements TraceObserver {
+    
+    @Override
+    void onFlowBegin() {
+        println "Okay, let's begin!"
+    }
+
+    @Override
+    void onProcessComplete(TaskHandler handler, TraceRecord trace) {
+        println "I completed a task! It's name is '${handler.task.name}'"
+    }
+
+    @Override
+    void onProcessCached(TaskHandler handler, TraceRecord trace) {
+        println "I found a task in the cache! It's name is '${handler.task.name}'"
+    }
+
+    @Override
+    void onFilePublish(Path destination, Path source) {
+        println "I published a file! It's located at ${path.toUriString()}"
+    }
+    
+    @Override
+    void onFlowError(TaskHandler handler, TraceRecord trace) {
+        println "Uh oh, something went wrong..."
+    }
+
+    @Override
+    void onFlowComplete() {
+        println 'All done!'
+    }
+}
+```
+
+You can then use your trace observer by simply enabling the plugin in your pipeline. In the above example, the observer 
+must also be enabled with a config option:
+
+```groovy
+myplugin.enabled = true
+```
+
+Refer to the `TraceObserver` [source code](https://github.com/nextflow-io/nextflow/blob/master/modules/nextflow/src/main/groovy/nextflow/trace/TraceObserver.groovy) for descriptions of the available workflow events.
+
+## Plugin registry
+
+Nextflow resolves plugins through a plugin registry, which stores metadata for each plugin version, including the publishing date, 
+checksum, and download URL for the plugin binary. The default registry is located on GitHub at [nextflow-io/plugins](https://github.com/nextflow-io/plugins/).
+
+To publish a plugin release to the main registry, simply create a pull request with the requested plugin metadata.
+
+(testing-plugins)=
+
+### Testing plugins
+
+:::{versionadded} 23.04.0
+:::
+
+You can also use a different plugin registry with the `NXF_PLUGINS_TEST_REPOSITORY` environment variable. This setting 
+is useful for testing a plugin release before publishing it to the main registry. It can refer to the JSON file for a 
+custom registry or a plugin release.
 
 For example:
 
 ```bash
+# custom registry at https://github.com/my-org/plugins
+export NXF_PLUGINS_TEST_REPOSITORY="https://raw.githubusercontent.com/my-org/plugins/main/plugins.json"
+
+# custom plugin release
 export NXF_PLUGINS_TEST_REPOSITORY="https://github.com/nextflow-io/nf-hello/releases/download/0.3.0/nf-hello-0.3.0-meta.json"
+
+nextflow run <pipeline> -plugins nf-hello
 ```
 
-Then run Nextflow with the expected plugin:
+## Offline usage
 
-```bash
-nextflow rub <your script> -plugins nf-hello
-```
+To use Nextflow plugins in an offline environment:
+
+1. Download the {ref}`"all" release <getstarted-install>` of Nextflow, which comes with the following default plugins: `nf-amazon`, `nf-google`, `nf-tower`.
+
+2. Download any additional plugins by running `nextflow plugin install <pluginId,..>`. Alternatively, simply run your pipeline once and Nextflow will download all of the plugins that it needs.
+
+3. Copy the `nextflow` binary and `$HOME/.nextflow` folder to your offline environment.
+
+4. In your Nextflow configuration file, specify each plugin that you downloaded, both name and version, including default plugins. This will prevent Nextflow from trying to download newer versions of plugins.
+
+Nextflow caches the plugins that it downloads, so as long as you keep using the same Nextflow version and pin your plugin versions in your config file, Nextflow will use the locally installed plugins and won't try to download them from the Internet.
diff --git a/docs/sharing.md b/docs/sharing.md
index aac7341d37..f1291381cc 100644
--- a/docs/sharing.md
+++ b/docs/sharing.md
@@ -195,6 +195,8 @@ The following configuration properties are supported for each provider configura
 : *Required only for private SCM servers*
 : SCM API `endpoint` URL e.g. `https://api.github.com` (default: the same as `providers.<provider>.server`).
 
+## SCM providers
+
 ### BitBucket credentials
 
 Create a `bitbucket` entry in the [SCM configuration file](#scm-configuration-file) specifying your user name and app password, as shown below:
@@ -307,6 +309,8 @@ providers {
 The Personal access token can be generated in the repository `Clone Repository` dialog.
 :::
 
+(aws-codecommit)=
+
 ### AWS CodeCommit credentials
 
 :::{versionadded} 22.06.0-edge

From b14674dc6fb2e228a71976f93660354d68555359 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 25 Jul 2023 09:20:16 +0100
Subject: [PATCH 041/350] Add deleteTasksOnCompletion to Azure Batch
 configuration (#4114)

Deleting Azure Tasks was checking the configuration object
deleteJobsOnCompletion which was incorrect since a task belongs to a
job. This adds the equivalent configuration for tasks which is checked
before deleting the tasks.



Signed-off-by: Adam Talbot <adam.talbot@seqera.io>
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Co-authored-by: Ben Sherman <bentshermann@gmail.com>
---
 docs/config.md                                | 21 +++++++++---
 .../cloud/azure/batch/AzBatchService.groovy   | 32 ++++++++-----------
 .../azure/batch/AzBatchTaskHandler.groovy     |  4 +--
 .../cloud/azure/config/AzBatchOpts.groovy     |  4 ++-
 .../azure/batch/AzBatchServiceTest.groovy     | 24 ++++++++++----
 .../cloud/azure/config/AzureConfigTest.groovy | 11 +++++--
 6 files changed, 61 insertions(+), 35 deletions(-)

diff --git a/docs/config.md b/docs/config.md
index f28cf22659..ed1c11cb4f 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -330,14 +330,20 @@ The following settings are available:
 `azure.batch.copyToolInstallMode`
 : Specify where the `azcopy` tool used by Nextflow. When `node` is specified it's copied once during the pool creation. When `task` is provider, it's installed for each task execution (default: `node`).
 
-`azure.batch.terminateJobsOnCompletion`
-: Enables the Batch Job to automatically terminate a job once all tasks have completed (default: `true`).
-
 `azure.batch.deleteJobsOnCompletion`
-: Enable the automatic deletion of jobs created by the pipeline execution (default: `true`).
+: Delete all jobs when the workflow completes (default: `false`).
+: :::{versionchanged} 23.08.0-edge
+  Default value was changed from `true` to `false`.
+  :::
 
 `azure.batch.deletePoolsOnCompletion`
-: Enable the automatic deletion of compute node pools upon pipeline completion (default: `false`).
+: Delete all compute node pools when the workflow completes (default: `false`).
+
+`azure.batch.deleteTasksOnCompletion`
+: :::{versionadded} 23.08.0-edge
+  :::
+: Delete each task when it completes (default: `true`).
+: Although this setting is enabled by default, failed tasks will not be deleted unless it is explicitly enabled. This way, the default behavior is that successful tasks are deleted while failed tasks are preserved for debugging purposes.
 
 `azure.batch.endpoint`
 : The batch service endpoint e.g. `https://nfbatch1.westeurope.batch.azure.com`.
@@ -345,6 +351,11 @@ The following settings are available:
 `azure.batch.location`
 : The name of the batch service region, e.g. `westeurope` or `eastus2`. This is not needed when the endpoint is specified.
 
+`azure.batch.terminateJobsOnCompletion`
+: :::{versionadded} 23.05.0-edge
+  :::
+: When the workflow completes, set all jobs to terminate on task completion. (default: `true`).
+
 `azure.batch.pools.<name>.autoScale`
 : Enable autoscaling feature for the pool identified with `<name>`.
 
diff --git a/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchService.groovy b/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchService.groovy
index 38d10b0c06..bff0b013d1 100644
--- a/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchService.groovy
+++ b/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchService.groovy
@@ -785,17 +785,13 @@ class AzBatchService implements Closeable {
         apply(() -> client.taskOperations().deleteTask(key.jobId, key.taskId))
     }
 
+    /**
+     * Set all jobs to terminate on completion.
+     */
     protected void terminateJobs() {
-        /* 
-        We set the job to terminate when all tasks are complete rather than directly terminating, this allows Azure Batch to handle the termination for us.
-        */
-
-        for( Map.Entry<TaskProcessor,String> entry : allJobIds ) {
-            final proc = entry.key
-            final jobId = entry.value
-
+        for( String jobId : allJobIds.values() ) {
             try {
-                log.trace "Terminating Azure job ${jobId}"
+                log.trace "Setting Azure job ${jobId} to terminate on completion"
 
                 CloudJob job = apply(() -> client.jobOperations().getJob(jobId))
                 final poolInfo = job.poolInfo()
@@ -813,10 +809,7 @@ class AzBatchService implements Closeable {
     }
 
     protected void cleanupJobs() {
-        for( Map.Entry<TaskProcessor,String> entry : allJobIds ) {
-            final proc = entry.key
-            final jobId = entry.value
-
+        for( String jobId : allJobIds.values() ) {
             try {
                 log.trace "Deleting Azure job ${jobId}"
                 apply(() -> client.jobOperations().deleteJob(jobId))
@@ -828,7 +821,7 @@ class AzBatchService implements Closeable {
     }
 
     protected void cleanupPools() {
-        for( String poolId : allPools.keySet()) {
+        for( String poolId : allPools.keySet() ) {
             try {
                 apply(() -> client.poolOperations().deletePool(poolId))
             }
@@ -849,17 +842,20 @@ class AzBatchService implements Closeable {
         }
         return identity
     }
+
     @Override
     void close() {
-        // Terminate existing jobs to prevent them occupying quota
-        if( config.batch().terminateJobsOnCompletion!=Boolean.FALSE ) {
+        // terminate all jobs to prevent them from occupying quota
+        if( config.batch().terminateJobsOnCompletion ) {
             terminateJobs()
         }
 
-        // cleanup app successful jobs
-        if( config.batch().deleteJobsOnCompletion!=Boolean.FALSE ) {
+        // delete all jobs
+        if( config.batch().deleteJobsOnCompletion ) {
             cleanupJobs()
         }
+
+        // delete all autopools
         if( config.batch().canCreatePool() && config.batch().deletePoolsOnCompletion ) {
             cleanupPools()
         }
diff --git a/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchTaskHandler.groovy b/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchTaskHandler.groovy
index 0559958870..5326c34598 100644
--- a/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchTaskHandler.groovy
+++ b/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchTaskHandler.groovy
@@ -130,7 +130,7 @@ class AzBatchTaskHandler extends TaskHandler implements FusionAwareTask {
     }
 
     private Boolean shouldDelete() {
-        executor.config.batch().deleteJobsOnCompletion
+        executor.config.batch().deleteTasksOnCompletion
     }
 
     protected void deleteTask(AzTaskKey taskKey, TaskRun task) {
@@ -138,7 +138,7 @@ class AzBatchTaskHandler extends TaskHandler implements FusionAwareTask {
             return
 
         if( !task.isSuccess() && shouldDelete()==null ) {
-            // do not delete successfully executed pods for debugging purpose
+            // preserve failed tasks for debugging purposes, unless deletion is explicitly enabled
             return
         }
 
diff --git a/plugins/nf-azure/src/main/nextflow/cloud/azure/config/AzBatchOpts.groovy b/plugins/nf-azure/src/main/nextflow/cloud/azure/config/AzBatchOpts.groovy
index bd6f38d517..7bafefbfe7 100644
--- a/plugins/nf-azure/src/main/nextflow/cloud/azure/config/AzBatchOpts.groovy
+++ b/plugins/nf-azure/src/main/nextflow/cloud/azure/config/AzBatchOpts.groovy
@@ -50,6 +50,7 @@ class AzBatchOpts implements CloudTransferOptions {
     Boolean terminateJobsOnCompletion
     Boolean deleteJobsOnCompletion
     Boolean deletePoolsOnCompletion
+    Boolean deleteTasksOnCompletion
     CopyToolInstallMode copyToolInstallMode
 
     Map<String,AzPoolOpts> pools
@@ -63,9 +64,10 @@ class AzBatchOpts implements CloudTransferOptions {
         location = config.location
         autoPoolMode = config.autoPoolMode
         allowPoolCreation = config.allowPoolCreation
-        terminateJobsOnCompletion = config.terminateJobsOnCompletion
+        terminateJobsOnCompletion = config.terminateJobsOnCompletion != Boolean.FALSE
         deleteJobsOnCompletion = config.deleteJobsOnCompletion
         deletePoolsOnCompletion = config.deletePoolsOnCompletion
+        deleteTasksOnCompletion = config.deleteTasksOnCompletion
         pools = parsePools(config.pools instanceof Map ? config.pools as Map<String,Map> : Collections.<String,Map>emptyMap())
         maxParallelTransfers = config.maxParallelTransfers ? config.maxParallelTransfers as int : MAX_TRANSFER
         maxTransferAttempts = config.maxTransferAttempts ? config.maxTransferAttempts as int : MAX_TRANSFER_ATTEMPTS
diff --git a/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchServiceTest.groovy b/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchServiceTest.groovy
index c7566abcc8..055a795b27 100644
--- a/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchServiceTest.groovy
+++ b/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchServiceTest.groovy
@@ -350,8 +350,7 @@ class AzBatchServiceTest extends Specification {
 
     }
 
-
-    def 'should cleanup jobs by default' () {
+    def 'should set jobs to automatically terminate by default' () {
         given:
         def CONFIG = [:]
         def exec = Mock(AzBatchExecutor) {getConfig() >> new AzConfig(CONFIG) }
@@ -359,12 +358,12 @@ class AzBatchServiceTest extends Specification {
         when:
         svc.close()
         then:
-        1 * svc.cleanupJobs() >> null
+        1 * svc.terminateJobs() >> null
     }
 
-    def 'should cleanup jobs no cleanup jobs' () {
+    def 'should not cleanup jobs by default' () {
         given:
-        def CONFIG = [batch:[deleteJobsOnCompletion: false]]
+        def CONFIG = [:]
         def exec = Mock(AzBatchExecutor) {getConfig() >> new AzConfig(CONFIG) }
         AzBatchService svc = Spy(AzBatchService, constructorArgs:[exec])
         when:
@@ -373,7 +372,18 @@ class AzBatchServiceTest extends Specification {
         0 * svc.cleanupJobs() >> null
     }
 
-    def 'should cleanup not cleanup pools by default' () {
+    def 'should cleanup jobs if specified' () {
+        given:
+        def CONFIG = [batch:[deleteJobsOnCompletion: true]]
+        def exec = Mock(AzBatchExecutor) {getConfig() >> new AzConfig(CONFIG) }
+        AzBatchService svc = Spy(AzBatchService, constructorArgs:[exec])
+        when:
+        svc.close()
+        then:
+        1 * svc.cleanupJobs() >> null
+    }
+
+    def 'should not cleanup pools by default' () {
         given:
         def CONFIG = [:]
         def exec = Mock(AzBatchExecutor) {getConfig() >> new AzConfig(CONFIG) }
@@ -395,7 +405,7 @@ class AzBatchServiceTest extends Specification {
         1 * svc.cleanupPools() >> null
     }
 
-    def 'should cleanup cleanup pools with allowPoolCreation' () {
+    def 'should cleanup pools with allowPoolCreation' () {
         given:
         def CONFIG = [batch:[allowPoolCreation: true, deletePoolsOnCompletion: true]]
         def exec = Mock(AzBatchExecutor) {getConfig() >> new AzConfig(CONFIG) }
diff --git a/plugins/nf-azure/src/test/nextflow/cloud/azure/config/AzureConfigTest.groovy b/plugins/nf-azure/src/test/nextflow/cloud/azure/config/AzureConfigTest.groovy
index 4ba18c1a8d..71cd83dc5e 100644
--- a/plugins/nf-azure/src/test/nextflow/cloud/azure/config/AzureConfigTest.groovy
+++ b/plugins/nf-azure/src/test/nextflow/cloud/azure/config/AzureConfigTest.groovy
@@ -70,8 +70,10 @@ class AzureConfigTest extends Specification {
 
         and:
         cfg.batch().endpoint == null
+        cfg.batch().terminateJobsOnCompletion == true
         cfg.batch().deleteJobsOnCompletion == null
         cfg.batch().deletePoolsOnCompletion == null
+        cfg.batch().deleteTasksOnCompletion == null
         cfg.batch().location == null
         cfg.batch().autoPoolMode == null
         cfg.batch().allowPoolCreation == null
@@ -99,8 +101,11 @@ class AzureConfigTest extends Specification {
                                              endpoint: ENDPOINT,
                                              location: LOCATION,
                                              autoPoolMode: true,
-                                             allowPoolCreation: true,                                            deleteJobsOnCompletion: false,
+                                             allowPoolCreation: true,
+                                             terminateJobsOnCompletion: false,
+                                             deleteJobsOnCompletion: true,
                                              deletePoolsOnCompletion: true,
+                                             deleteTasksOnCompletion: false,
                                              pools: [ myPool: [
                                                      vmType: 'Foo_A1',
                                                      autoScale: true,
@@ -124,8 +129,10 @@ class AzureConfigTest extends Specification {
         cfg.batch().location == LOCATION
         cfg.batch().autoPoolMode == true
         cfg.batch().allowPoolCreation == true
-        cfg.batch().deleteJobsOnCompletion == false
+        cfg.batch().terminateJobsOnCompletion == false
+        cfg.batch().deleteJobsOnCompletion == true
         cfg.batch().deletePoolsOnCompletion == true
+        cfg.batch().deleteTasksOnCompletion == false
         cfg.batch().canCreatePool()
         and:
         cfg.batch().pool('myPool').vmType == 'Foo_A1'

From 46e828e189b32146d1151f8a35f21e45dd4100e2 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Tue, 25 Jul 2023 04:20:11 -0500
Subject: [PATCH 042/350] Disable cache backup/restore if cloudcache is used
 (#4125)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../seqera/tower/plugin/CacheCommand.groovy   |  4 +++-
 .../seqera/tower/plugin/CacheManager.groovy   | 11 ++++++---
 .../tower/plugin/CacheManagerTest.groovy      | 24 +++++++++++++++++++
 3 files changed, 35 insertions(+), 4 deletions(-)

diff --git a/plugins/nf-tower/src/main/io/seqera/tower/plugin/CacheCommand.groovy b/plugins/nf-tower/src/main/io/seqera/tower/plugin/CacheCommand.groovy
index 7c009ec3b6..4c19948769 100644
--- a/plugins/nf-tower/src/main/io/seqera/tower/plugin/CacheCommand.groovy
+++ b/plugins/nf-tower/src/main/io/seqera/tower/plugin/CacheCommand.groovy
@@ -46,7 +46,9 @@ class CacheCommand implements PluginAbstractExec {
 
     protected void cacheBackup() {
         log.debug "Running Nextflow cache backup"
-        new CacheManager(System.getenv()).saveCacheFiles()
+        final manager = new CacheManager(System.getenv())
+        manager.saveCacheFiles()
+        manager.saveMiscFiles()
     }
 
     protected void archiveLogs(Session sess) {
diff --git a/plugins/nf-tower/src/main/io/seqera/tower/plugin/CacheManager.groovy b/plugins/nf-tower/src/main/io/seqera/tower/plugin/CacheManager.groovy
index 5c890f7752..f273ee3ad9 100644
--- a/plugins/nf-tower/src/main/io/seqera/tower/plugin/CacheManager.groovy
+++ b/plugins/nf-tower/src/main/io/seqera/tower/plugin/CacheManager.groovy
@@ -65,7 +65,10 @@ class CacheManager {
         if( !sessionUuid )
             throw new AbortOperationException("Missing target uuid - cache sync cannot be performed")
 
-        this.localCachePath = Paths.get(".nextflow/cache/${sessionUuid}")
+        // ignore the `localCachePath` when the `NXF_CLOUDCACHE_PATH` variable is set because
+        // the nextflow cache metadata is going to be managed (and stored) via the nf-cloudcache plugin
+        if( !env.containsKey('NXF_CLOUDCACHE_PATH') )
+            this.localCachePath = Paths.get(".nextflow/cache/${sessionUuid}")
 
         if( env.NXF_OUT_FILE )
             localOutFile = Paths.get(env.NXF_OUT_FILE)
@@ -80,7 +83,7 @@ class CacheManager {
     }
 
     protected void restoreCacheFiles() {
-        if( !remoteWorkDir || !sessionUuid )
+        if( !remoteWorkDir || !sessionUuid || !localCachePath )
             return
 
         if(!Files.exists(remoteCachePath)) {
@@ -100,7 +103,7 @@ class CacheManager {
     }
 
     protected void saveCacheFiles() {
-        if( !remoteWorkDir || !sessionUuid )
+        if( !remoteWorkDir || !sessionUuid || !localCachePath )
             return
 
         if( !Files.exists(localCachePath) ) {
@@ -118,7 +121,9 @@ class CacheManager {
         catch (Throwable e) {
             log.warn "Failed to backup resume metadata to remote store path: ${remoteCachePath.toUriString()} — cause: ${e}", e
         }
+    }
 
+    protected void saveMiscFiles() {
         // — upload out file
         try {
             if( localOutFile?.exists() )
diff --git a/plugins/nf-tower/src/test/io/seqera/tower/plugin/CacheManagerTest.groovy b/plugins/nf-tower/src/test/io/seqera/tower/plugin/CacheManagerTest.groovy
index 70e4579a19..67ce4d7d75 100644
--- a/plugins/nf-tower/src/test/io/seqera/tower/plugin/CacheManagerTest.groovy
+++ b/plugins/nf-tower/src/test/io/seqera/tower/plugin/CacheManagerTest.groovy
@@ -78,6 +78,7 @@ class CacheManagerTest extends Specification {
         tower.localCachePath.resolve('db/yyy').text = 'data yyy'
         and:
         tower.saveCacheFiles()
+        tower.saveMiscFiles()
         then:
         tower.remoteCachePath.resolve('index-foo').text == 'index foo'
         tower.remoteCachePath.resolve('db/xxx').text == 'data xxx'
@@ -99,6 +100,7 @@ class CacheManagerTest extends Specification {
         tower.localCachePath.resolve('db/delta').text = 'data delta'
         and:
         tower.saveCacheFiles()
+        tower.saveMiscFiles()
         then:
         tower.remoteCachePath.resolve('index-bar').text == 'index bar'
         tower.remoteCachePath.resolve('db/alpha').text == 'data alpha'
@@ -154,4 +156,26 @@ class CacheManagerTest extends Specification {
         cleanup:
         folder?.deleteDir()
     }
+
+    def 'should not backup/restore cache if cloudcache is enabled' () {
+        given:
+        def ENV = [
+                NXF_UUID: 'uuid',
+                NXF_WORK: '/work',
+                NXF_CLOUDCACHE_PATH: 's3://my-bucket/cache'
+        ]
+        and:
+        def tower = new CacheManager(ENV)
+
+        when:
+        tower.saveCacheFiles()
+        then:
+        0 * tower.getRemoteCachePath()
+
+        when:
+        tower.restoreCacheFiles()
+        then:
+        0 * tower.getRemoteCachePath()
+
+    }
 }

From 8b7e3d4892e27735c4c3f80bf71a726c9f88c1bd Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Wed, 26 Jul 2023 04:26:53 -0500
Subject: [PATCH 043/350] Document behavior of withName selector with included
 aliases (#4129)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 docs/config.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/docs/config.md b/docs/config.md
index ed1c11cb4f..76d5fa2b99 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -1173,6 +1173,10 @@ process {
 }
 ```
 
+:::{note}
+The `withName` selector applies to a process even when it is included from a module under an alias. For example, `withName: hello` will apply to any process originally defined as `hello`, regardless of whether it is included under an alias. Similarly, it will not apply to any process not originally defined as `hello`, even if it is included under the alias `hello`.
+:::
+
 :::{tip}
 Label and process names do not need to be enclosed with quotes, provided the name does not include special characters (`-`, `!`, etc) and is not a keyword or a built-in type identifier. When in doubt, you can enclose the label name or process name with single or double quotes.
 :::

From 077ed5dd04240f86e1aff8178938891d7d70adf8 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Wed, 26 Jul 2023 21:23:00 +0200
Subject: [PATCH 044/350] Logging improvements

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../groovy/nextflow/processor/TaskPollingMonitor.groovy  | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskPollingMonitor.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskPollingMonitor.groovy
index 173579de39..17c2694c46 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskPollingMonitor.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskPollingMonitor.groovy
@@ -271,7 +271,7 @@ class TaskPollingMonitor implements TaskMonitor {
      */
     @Override
     TaskMonitor start() {
-        log.trace ">>> barrier register (monitor: ${this.name})"
+        log.debug ">>> barrier register (monitor: ${this.name})"
         session.barrier.register(this)
 
         this.taskCompleteLock = new ReentrantLock()
@@ -292,8 +292,11 @@ class TaskPollingMonitor implements TaskMonitor {
             try {
                 pollLoop()
             }
+            catch (Throwable e) {
+                log.debug "Unexpected error in tasks monitor pool loop", e
+            }
             finally {
-                log.trace "<<< barrier arrives (monitor: ${this.name})"
+                log.debug "<<< barrier arrives (monitor: ${this.name}) - terminating tasks monitor poll loop"
                 session.barrier.arrive(this)
             }
         }
@@ -434,7 +437,7 @@ class TaskPollingMonitor implements TaskMonitor {
         try {
             def pending = runningQueue.size()
             if( !pending ) {
-                log.debug "No more task to compute -- ${session.dumpNetworkStatus() ?: 'Execution may be stalled'}"
+                log.debug "!! executor $name > No more task to compute -- ${session.dumpNetworkStatus() ?: 'Execution may be stalled'}"
                 return
             }
 

From dd32f80aef1479750e2a001828473f2116538905 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Wed, 26 Jul 2023 21:45:13 +0200
Subject: [PATCH 045/350] Allow use virtual threads in Wave client

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../main/io/seqera/wave/plugin/WaveClient.groovy   | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
index c7b3554590..bf91dcc053 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
@@ -27,6 +27,7 @@ import java.time.Duration
 import java.time.OffsetDateTime
 import java.time.temporal.ChronoUnit
 import java.util.concurrent.Callable
+import java.util.concurrent.Executors
 import java.util.concurrent.TimeUnit
 import java.util.function.Predicate
 
@@ -56,6 +57,7 @@ import nextflow.processor.Architecture
 import nextflow.processor.TaskRun
 import nextflow.script.bundle.ResourcesBundle
 import nextflow.util.SysHelper
+import nextflow.util.Threads
 import org.slf4j.Logger
 import org.slf4j.LoggerFactory
 /**
@@ -127,12 +129,20 @@ class WaveClient {
         // the cookie manager
         cookieManager = new CookieManager()
         // create http client
-        this.httpClient = HttpClient.newBuilder()
+        this.httpClient = newHttpClient()
+    }
+
+    protected HttpClient newHttpClient() {
+        final builder = HttpClient.newBuilder()
                 .version(HttpClient.Version.HTTP_1_1)
                 .followRedirects(HttpClient.Redirect.NEVER)
                 .cookieHandler(cookieManager)
                 .connectTimeout(config.httpOpts().connectTimeout())
-                .build()
+        // use virtual threads executor if enabled
+        if( Threads.useVirtual() )
+            builder.executor(Executors.newVirtualThreadPerTaskExecutor())
+        // build and return the new client
+        return builder.build()
     }
 
     WaveConfig config() { return config }

From fcdeec02e4ade47683dfd39724c49e5fe6ad6937 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 29 Jul 2023 11:22:51 +0200
Subject: [PATCH 046/350] Fix Redirection http redirection across different
 hosts

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../file/http/XFileSystemProvider.groovy      | 38 +++++++++++----
 .../nextflow/file/http/HttpFilesTests.groovy  |  2 +-
 .../file/http/XFileSystemProviderTest.groovy  | 48 ++++++++++++-------
 3 files changed, 60 insertions(+), 28 deletions(-)

diff --git a/modules/nf-httpfs/src/main/nextflow/file/http/XFileSystemProvider.groovy b/modules/nf-httpfs/src/main/nextflow/file/http/XFileSystemProvider.groovy
index 1fa43da22f..2f00717c2c 100644
--- a/modules/nf-httpfs/src/main/nextflow/file/http/XFileSystemProvider.groovy
+++ b/modules/nf-httpfs/src/main/nextflow/file/http/XFileSystemProvider.groovy
@@ -16,6 +16,8 @@
 
 package nextflow.file.http
 
+import static nextflow.file.http.XFileSystemConfig.*
+
 import java.nio.ByteBuffer
 import java.nio.channels.SeekableByteChannel
 import java.nio.file.AccessDeniedException
@@ -44,13 +46,9 @@ import groovy.transform.PackageScope
 import groovy.util.logging.Slf4j
 import nextflow.SysEnv
 import nextflow.extension.FilesEx
+import nextflow.file.FileHelper
 import nextflow.util.InsensitiveMap
 import sun.net.www.protocol.ftp.FtpURLConnection
-
-import static XFileSystemConfig.*
-
-import static nextflow.file.http.XFileSystemConfig.config
-
 /**
  * Implements a read-only JSR-203 compliant file system provider for http/ftp protocols
  *
@@ -64,6 +62,7 @@ abstract class XFileSystemProvider extends FileSystemProvider {
 
     private Map<URI, FileSystem> fileSystemMap = new LinkedHashMap<>(20)
 
+    private static final int[] REDIRECT_CODES = [301, 302, 307, 308]
 
     protected static String config(String name, def defValue) {
         return SysEnv.containsKey(name) ? SysEnv.get(name) : defValue.toString()
@@ -185,18 +184,25 @@ abstract class XFileSystemProvider extends FileSystemProvider {
     protected URLConnection toConnection0(URL url, int attempt) {
         final conn = url.openConnection()
         conn.setRequestProperty("User-Agent", 'Nextflow/httpfs')
+        if( conn instanceof HttpURLConnection ) {
+            // by default HttpURLConnection does redirect only within the same host
+            // disable the built-in to implement custom redirection logic (see below)
+            conn.setInstanceFollowRedirects(false)
+        }
         if( url.userInfo ) {
             conn.setRequestProperty("Authorization", auth(url.userInfo));
         }
         else {
             XAuthRegistry.instance.authorize(conn)
         }
-        if ( conn instanceof HttpURLConnection && conn.getResponseCode() in [307, 308] && attempt < MAX_REDIRECT_HOPS ) {
+        if ( conn instanceof HttpURLConnection && conn.getResponseCode() in REDIRECT_CODES && attempt < MAX_REDIRECT_HOPS ) {
             final header = InsensitiveMap.of(conn.getHeaderFields())
-            String location = header.get("Location")?.get(0)
-            URL newPath = new URI(location).toURL()
-            log.debug "Remote redirect URL: $newPath"
-            return toConnection0(newPath, attempt+1)
+            final location = header.get("Location")?.get(0)
+            log.debug "Remote redirect location: $location"
+            final newUrl = new URI(absLocation(location,url)).toURL()
+            if( url.protocol=='https' && newUrl.protocol=='http' )
+                throw new IOException("Refuse to follow redirection from HTTPS to HTTP (unsafe) URL - origin: $url - target: $newUrl")
+            return toConnection0(newUrl, attempt+1)
         }
         else if( conn instanceof HttpURLConnection && conn.getResponseCode() in config().retryCodes() && attempt < config().maxAttempts() ) {
             final delay = (Math.pow(config().backOffBase(), attempt) as long) * config().backOffDelay()
@@ -212,6 +218,18 @@ abstract class XFileSystemProvider extends FileSystemProvider {
         return conn
     }
 
+    protected String absLocation(String location, URL target) {
+        assert location, "Missing location argument"
+        assert target, "Missing target URL argument"
+
+        final base = FileHelper.baseUrl(location)
+        if( base )
+            return location
+        if( !location.startsWith('/') )
+            location = '/' + location
+        return "${target.protocol}://${target.authority}$location"
+    }
+
     @Override
     SeekableByteChannel newByteChannel(Path path, Set<? extends OpenOption> options, FileAttribute<?>... attrs) throws IOException {
 
diff --git a/modules/nf-httpfs/src/test/nextflow/file/http/HttpFilesTests.groovy b/modules/nf-httpfs/src/test/nextflow/file/http/HttpFilesTests.groovy
index 3090144fc5..041f1f2f3e 100644
--- a/modules/nf-httpfs/src/test/nextflow/file/http/HttpFilesTests.groovy
+++ b/modules/nf-httpfs/src/test/nextflow/file/http/HttpFilesTests.groovy
@@ -112,7 +112,7 @@ class HttpFilesTests extends Specification {
         def lines = Files.readAllLines(path, Charset.forName('UTF-8'))
         then:
         lines.size()>0
-        lines[0] == '<html>'
+        lines[0] == '<!DOCTYPE html>'
 
     }
 
diff --git a/modules/nf-httpfs/src/test/nextflow/file/http/XFileSystemProviderTest.groovy b/modules/nf-httpfs/src/test/nextflow/file/http/XFileSystemProviderTest.groovy
index 9bbabfa06e..8d6e93463c 100644
--- a/modules/nf-httpfs/src/test/nextflow/file/http/XFileSystemProviderTest.groovy
+++ b/modules/nf-httpfs/src/test/nextflow/file/http/XFileSystemProviderTest.groovy
@@ -21,7 +21,6 @@ import java.nio.file.Path
 
 import com.github.tomakehurst.wiremock.junit.WireMockRule
 import com.github.tomjankes.wiremock.WireMockGroovy
-import nextflow.SysEnv
 import org.junit.Rule
 import spock.lang.Specification
 import spock.lang.Unroll
@@ -106,7 +105,7 @@ class XFileSystemProviderTest extends Specification {
         when:
         def attrs = fsp.readHttpAttributes(path)
         then:
-        attrs.lastModifiedTime() == null
+        attrs.lastModifiedTime()
         attrs.size() > 0
     }
 
@@ -157,6 +156,7 @@ class XFileSystemProviderTest extends Specification {
     @Rule
     WireMockRule wireMockRule = new WireMockRule(18080)
 
+    @Unroll
     def 'should follow a redirect when read a http file '() {
         given:
         def wireMock = new WireMockGroovy(18080)
@@ -180,14 +180,14 @@ class XFileSystemProviderTest extends Specification {
             response {
                 status HTTP_CODE
                 headers {
-                    "Location" "http://localhost:18080/redirected.html"
+                    "Location" "http://localhost:18080/target.html"
                 }
             }
         }
         wireMock.stub {
             request {
                 method "GET"
-                url "/redirected.html"
+                url "/target.html"
             }
             response {
                 status 200
@@ -212,22 +212,36 @@ class XFileSystemProviderTest extends Specification {
         Files.size(path) == EXPECTED
 
         where:
-        HTTP_CODE | REDIRECT_TO        | EXPECTED
-        300       | "/redirected.html" | 10
-        300       | "/index2.html"     | 10
-
-        301       | "/redirected.html" | 10
-        301       | "/index2.html"     | 10
+        HTTP_CODE | REDIRECT_TO         | EXPECTED
+        301       | "/target.html"      | 10
+        301       | "/index2.html"      | 10
 
-        302       | "/redirected.html" | 10
-        302       | "/index2.html"     | 10
+        302       | "/target.html"      | 10
+        302       | "/index2.html"      | 10
 
-        307       | "/redirected.html" | 10
-        307       | "/index2.html"     | 10
+        307       | "/target.html"      | 10
+        307       | "/index2.html"      | 10
 
-        308       | "/redirected.html" | 10
-        308       | "/index2.html"     | 10
+        308       | "/target.html"      | 10
+        308       | "/index2.html"      | 10
         //infinite redirect to himself
-        308       | "/index.html"      | -1
+        308       | "/index.html"       | -1
+    }
+
+    def 'should normalize location' () {
+        given:
+        def provider = Spy(XFileSystemProvider)
+
+        expect:
+        provider.absLocation(LOCATION, new URL(TARGET)) == EXPECTED
+
+        where:
+        LOCATION                | TARGET                    | EXPECTED
+        'https://this/that'     | 'http://foo.com:123'      | 'https://this/that'
+        '/'                     | 'http://foo.com:123'      | 'http://foo.com:123/'
+        '/this/that'            | 'http://foo.com:123'      | 'http://foo.com:123/this/that'
+        '/this/that'            | 'http://foo.com:123/abc'  | 'http://foo.com:123/this/that'
+        'this/that'             | 'http://foo.com:123/abc'  | 'http://foo.com:123/this/that'
+
     }
 }

From 71dfecc2fba482981fb403643219b9079b046699 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 29 Jul 2023 17:15:51 +0200
Subject: [PATCH 047/350] Add tower logs checkpoint (#4132)

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../seqera/tower/plugin/CacheCommand.groovy   |  22 +--
 .../seqera/tower/plugin/LogsCheckpoint.groovy |  90 +++++++++
 ...CacheManager.groovy => LogsHandler.groovy} |  76 ++------
 .../seqera/tower/plugin/TowerFactory.groovy   |  24 ++-
 .../tower/plugin/CacheManagerTest.groovy      | 181 ------------------
 .../tower/plugin/LogsCheckpointTest.groovy    |  84 ++++++++
 .../tower/plugin/LogsHandlerTest.groovy       |  84 ++++++++
 tests/cache-bak.nf                            |   8 -
 tests/checks/cache-bak.nf/.checks             |  42 ----
 9 files changed, 291 insertions(+), 320 deletions(-)
 create mode 100644 plugins/nf-tower/src/main/io/seqera/tower/plugin/LogsCheckpoint.groovy
 rename plugins/nf-tower/src/main/io/seqera/tower/plugin/{CacheManager.groovy => LogsHandler.groovy} (59%)
 delete mode 100644 plugins/nf-tower/src/test/io/seqera/tower/plugin/CacheManagerTest.groovy
 create mode 100644 plugins/nf-tower/src/test/io/seqera/tower/plugin/LogsCheckpointTest.groovy
 create mode 100644 plugins/nf-tower/src/test/io/seqera/tower/plugin/LogsHandlerTest.groovy
 delete mode 100644 tests/cache-bak.nf
 delete mode 100644 tests/checks/cache-bak.nf/.checks

diff --git a/plugins/nf-tower/src/main/io/seqera/tower/plugin/CacheCommand.groovy b/plugins/nf-tower/src/main/io/seqera/tower/plugin/CacheCommand.groovy
index 4c19948769..2abf12e94e 100644
--- a/plugins/nf-tower/src/main/io/seqera/tower/plugin/CacheCommand.groovy
+++ b/plugins/nf-tower/src/main/io/seqera/tower/plugin/CacheCommand.groovy
@@ -19,7 +19,6 @@ package io.seqera.tower.plugin
 
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
-import nextflow.Session
 import nextflow.cli.PluginAbstractExec
 /**
  * Implements nextflow cache and restore commands
@@ -37,7 +36,6 @@ class CacheCommand implements PluginAbstractExec {
 
         if( cmd == 'cache-backup') {
             cacheBackup()
-            archiveLogs(session)
         }
         if( cmd == 'cache-restore' )
             cacheRestore()
@@ -46,26 +44,12 @@ class CacheCommand implements PluginAbstractExec {
 
     protected void cacheBackup() {
         log.debug "Running Nextflow cache backup"
-        final manager = new CacheManager(System.getenv())
-        manager.saveCacheFiles()
-        manager.saveMiscFiles()
-    }
-
-    protected void archiveLogs(Session sess) {
-        // archive logs
-        final archiver = TowerArchiver.create(sess, System.getenv())
-        if( archiver ) try {
-            log.debug "Running Nextflow logs archiver"
-            archiver.archiveLogs()
-        }
-        finally {
-            archiver.shutdown(sess)
-        }
+        new LogsHandler(getSession(), System.getenv()).saveFiles()
     }
 
     protected void cacheRestore() {
-        log.debug "Running Nextflow cache restore"
-        new CacheManager(System.getenv()).restoreCacheFiles()
+        log.debug "Running Nextflow cache restore - DO NOTHING"
+        // this command is only kept for backward compatibility
     }
 
 }
diff --git a/plugins/nf-tower/src/main/io/seqera/tower/plugin/LogsCheckpoint.groovy b/plugins/nf-tower/src/main/io/seqera/tower/plugin/LogsCheckpoint.groovy
new file mode 100644
index 0000000000..2b7da86ec3
--- /dev/null
+++ b/plugins/nf-tower/src/main/io/seqera/tower/plugin/LogsCheckpoint.groovy
@@ -0,0 +1,90 @@
+/*
+ * Copyright 2013-2023, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package io.seqera.tower.plugin
+
+import groovy.transform.CompileStatic
+import groovy.util.logging.Slf4j
+import nextflow.Session
+import nextflow.SysEnv
+import nextflow.trace.TraceObserver
+import nextflow.util.Duration
+import nextflow.util.Threads
+/**
+ * Implements a nextflow observer that periodically checkpoint
+ * log, report and timeline files
+ *
+ * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
+ */
+@Slf4j
+@CompileStatic
+class LogsCheckpoint implements TraceObserver {
+
+    private Session session
+    private Map config
+    private Thread thread
+    private Duration interval
+    private LogsHandler handler
+
+    @Override
+    void onFlowCreate(Session session) {
+        this.session = session
+        this.config = session.config
+        this.handler = new LogsHandler(session, SysEnv.get())
+        this.interval = config.navigate('tower.logs.checkpoint.interval', defaultInterval()) as Duration
+    }
+
+    private String defaultInterval() {
+        SysEnv.get('TOWER_LOGS_CHECKPOINT_INTERVAL','90s')
+    }
+
+    @Override
+    void onFlowBegin() {
+        thread = Threads.start('tower-logs-checkpoint', this.&run)
+    }
+
+    @Override
+    void onFlowComplete() {
+        thread.interrupt()
+        thread.join()
+    }
+
+    protected void run() {
+        log.debug "Starting logs checkpoint thread - interval: ${interval}"
+        try {
+            while( !thread.isInterrupted() ) {
+                // just wait the declared delay
+                await(interval)
+                // checkpoint the logs
+                handler.saveFiles()
+            }
+        }
+        finally {
+            log.debug "Terminating logs checkpoint thread"
+        }
+    }
+
+    protected void await(Duration interval) {
+        try {
+            Thread.sleep(interval.toMillis())
+        }
+        catch (InterruptedException e) {
+            log.trace "Interrupted logs checkpoint thread"
+            Thread.currentThread().interrupt()
+        }
+    }
+}
diff --git a/plugins/nf-tower/src/main/io/seqera/tower/plugin/CacheManager.groovy b/plugins/nf-tower/src/main/io/seqera/tower/plugin/LogsHandler.groovy
similarity index 59%
rename from plugins/nf-tower/src/main/io/seqera/tower/plugin/CacheManager.groovy
rename to plugins/nf-tower/src/main/io/seqera/tower/plugin/LogsHandler.groovy
index f273ee3ad9..4964859efa 100644
--- a/plugins/nf-tower/src/main/io/seqera/tower/plugin/CacheManager.groovy
+++ b/plugins/nf-tower/src/main/io/seqera/tower/plugin/LogsHandler.groovy
@@ -19,28 +19,25 @@ package io.seqera.tower.plugin
 
 import static java.nio.file.StandardCopyOption.*
 
-import java.nio.file.Files
-import java.nio.file.NoSuchFileException
+import java.nio.file.FileSystems
 import java.nio.file.Path
 import java.nio.file.Paths
 
 import groovy.transform.CompileStatic
 import groovy.transform.PackageScope
 import groovy.util.logging.Slf4j
+import nextflow.Session
 import nextflow.exception.AbortOperationException
-import nextflow.extension.FilesEx
 import nextflow.file.FileHelper
 /**
- * Back and restore Nextflow cache
+ * Backup Nextflow logs, timeline and reports files
  *
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
  */
 @Slf4j
 @CompileStatic
-class CacheManager {
+class LogsHandler {
 
-    @PackageScope String sessionUuid
-    @PackageScope Path localCachePath
     @PackageScope Path localOutFile
     @PackageScope Path localLogFile
     @PackageScope Path localTimelineFile
@@ -48,27 +45,18 @@ class CacheManager {
     @PackageScope Path localTowerReports
     @PackageScope Path remoteWorkDir
 
-    @PackageScope Path getRemoteCachePath() { remoteWorkDir.resolve(".nextflow/cache/${sessionUuid}") }
     @PackageScope Path getRemoteOutFile() { remoteWorkDir.resolve(localOutFile.getName()) }
     @PackageScope Path getRemoteLogFile() { remoteWorkDir.resolve(localLogFile.getName()) }
     @PackageScope Path getRemoteTimelineFile() { remoteWorkDir.resolve(localTimelineFile.getName()) }
     @PackageScope Path getRemoteTowerConfig() { remoteWorkDir.resolve(localTowerConfig.getName()) }
     @PackageScope Path getRemoteTowerReports() { remoteWorkDir.resolve(localTowerReports.getName()) }
 
-    CacheManager(Map<String,String> env) {
-        final work = env.get('NXF_WORK') ?: env.get('NXF_TEST_WORK')
-        if( !work )
-            throw new AbortOperationException("Missing target work dir - cache sync cannot be performed")
-        this.remoteWorkDir = FileHelper.asPath(work)
-
-        this.sessionUuid = env.get('NXF_UUID')
-        if( !sessionUuid )
-            throw new AbortOperationException("Missing target uuid - cache sync cannot be performed")
-
-        // ignore the `localCachePath` when the `NXF_CLOUDCACHE_PATH` variable is set because
-        // the nextflow cache metadata is going to be managed (and stored) via the nf-cloudcache plugin
-        if( !env.containsKey('NXF_CLOUDCACHE_PATH') )
-            this.localCachePath = Paths.get(".nextflow/cache/${sessionUuid}")
+    LogsHandler(Session session, Map<String,String> env) {
+        if( !session.workDir )
+            throw new AbortOperationException("Missing workflow work directory")
+        if( session.workDir.fileSystem == FileSystems.default )
+            throw new AbortOperationException("Logs handler is only meant to be used with a remote workflow work directory")
+        this.remoteWorkDir = session.workDir
 
         if( env.NXF_OUT_FILE )
             localOutFile = Paths.get(env.NXF_OUT_FILE)
@@ -82,48 +70,8 @@ class CacheManager {
             localTowerReports = Paths.get(env.TOWER_REPORTS_FILE)
     }
 
-    protected void restoreCacheFiles() {
-        if( !remoteWorkDir || !sessionUuid || !localCachePath )
-            return
-
-        if(!Files.exists(remoteCachePath)) {
-            log.debug "Remote cache path does not exist: $remoteCachePath - skipping cache restore"
-            return
-        }
-
-        try {
-            log.info "Restoring cache: ${remoteCachePath.toUriString()} => ${localCachePath.toUriString()}"
-            localCachePath.deleteDir()
-            localCachePath.parent.mkdirs()
-            FileHelper.copyPath(remoteCachePath, localCachePath, REPLACE_EXISTING)
-        }
-        catch (NoSuchFileException e) {
-            log.info "Remote cache restore ignored — reason: ${e.message ?: e}"
-        }
-    }
-
-    protected void saveCacheFiles() {
-        if( !remoteWorkDir || !sessionUuid || !localCachePath )
-            return
-
-        if( !Files.exists(localCachePath) ) {
-            log.debug "Local cache path does not exist: $localCachePath — skipping cache backup"
-            return
-        }
-
-        // upload nextflow cache metadata
-        try {
-            log.info "Saving cache: ${localCachePath.toUriString()} => ${remoteCachePath.toUriString()}"
-            remoteCachePath.deleteDir()
-            remoteCachePath.parent.mkdirs()
-            FilesEx.copyTo(localCachePath, remoteCachePath)
-        }
-        catch (Throwable e) {
-            log.warn "Failed to backup resume metadata to remote store path: ${remoteCachePath.toUriString()} — cause: ${e}", e
-        }
-    }
-
-    protected void saveMiscFiles() {
+    void saveFiles() {
+        log.trace "Checkpointing logs, timeline and report files"
         // — upload out file
         try {
             if( localOutFile?.exists() )
diff --git a/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerFactory.groovy b/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerFactory.groovy
index 81e9aa0dff..d3e93df3bb 100644
--- a/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerFactory.groovy
+++ b/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerFactory.groovy
@@ -39,13 +39,25 @@ class TowerFactory implements TraceObserverFactory {
     Collection<TraceObserver> create(Session session) {
         final config = session.config
         Boolean isEnabled = config.navigate('tower.enabled') as Boolean || env.get('TOWER_WORKFLOW_ID')
-        String endpoint = config.navigate('tower.endpoint') as String
-        Duration requestInterval = config.navigate('tower.requestInterval') as Duration
-        Duration aliveInterval = config.navigate('tower.aliveInterval') as Duration
 
         if( !isEnabled )
             return Collections.emptyList()
 
+        final result = new ArrayList(1)
+        // create the tower client
+        final tower = createTowerClient(session, config)
+        result.add(tower)
+        // create the logs checkpoint
+        if( env.containsKey('NXF_CLOUDCACHE_PATH') )
+            result.add( new LogsCheckpoint() )
+        return result
+    }
+
+    protected TowerClient createTowerClient(Session session, Map config) {
+        String endpoint = config.navigate('tower.endpoint') as String
+        Duration requestInterval = config.navigate('tower.requestInterval') as Duration
+        Duration aliveInterval = config.navigate('tower.aliveInterval') as Duration
+
         if ( !endpoint || endpoint=='-' )
             endpoint = env.get('TOWER_API_ENDPOINT') ?: TowerClient.DEF_ENDPOINT_URL
 
@@ -64,13 +76,12 @@ class TowerFactory implements TraceObserverFactory {
         tower.workspaceId = env.get('TOWER_WORKFLOW_ID')
                 ? env.get('TOWER_WORKSPACE_ID')
                 : config.navigate('tower.workspaceId', env.get('TOWER_WORKSPACE_ID'))
-        final result = new ArrayList(1)
-        result.add(tower)
+
         // register auth provider
         // note: this is needed to authorize access to resources via XFileSystemProvider used by NF
         // it's not needed by the tower client logic
         XAuthRegistry.instance.register(provider(tower.endpoint, tower.accessToken))
-        return result
+        return tower
     }
 
     protected XAuthProvider provider(String endpoint, String accessToken) {
@@ -79,4 +90,5 @@ class TowerFactory implements TraceObserverFactory {
         final refreshToken = env.get('TOWER_REFRESH_TOKEN')
         return new TowerXAuth(endpoint, accessToken, refreshToken)
     }
+
 }
diff --git a/plugins/nf-tower/src/test/io/seqera/tower/plugin/CacheManagerTest.groovy b/plugins/nf-tower/src/test/io/seqera/tower/plugin/CacheManagerTest.groovy
deleted file mode 100644
index 67ce4d7d75..0000000000
--- a/plugins/nf-tower/src/test/io/seqera/tower/plugin/CacheManagerTest.groovy
+++ /dev/null
@@ -1,181 +0,0 @@
-/*
- * Copyright (c) 2020-2021. Seqera Labs, S.L.
- *
- * All Rights reserved
- *
- */
-
-package io.seqera.tower.plugin
-
-import java.nio.file.Files
-import java.nio.file.Paths
-
-import nextflow.exception.AbortOperationException
-import spock.lang.Specification
-/**
- *
- * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
- */
-class CacheManagerTest extends Specification {
-
-    def 'should init empty files' () {
-        when:
-        new CacheManager([:])
-        then:
-        thrown(AbortOperationException)
-    }
-
-    def 'should upload cache files' () {
-        given:
-        def folder = Files.createTempDirectory('test')
-        def remote = folder.resolve('remote'); remote.mkdir()
-        def local = folder.resolve('local'); local.mkdir()
-        def outFile = local.resolve('nf-out.txt'); outFile.text = 'out file'
-        def logFile = local.resolve('nf-log.txt'); logFile.text = 'log file'
-        def tmlFile = local.resolve('nf-tml.txt'); tmlFile.text = 'tml file'
-        def cfgFile = local.resolve('tw-config.txt'); cfgFile.text = 'config file'
-        def repFile = local.resolve('tw-report.txt'); repFile.text = 'report file'
-        and:
-        def uuid = UUID.randomUUID().toString()
-        and:
-        def ENV = [
-                NXF_UUID:uuid,
-                NXF_WORK: remote.toString(),
-                NXF_OUT_FILE: outFile.toString(),
-                NXF_LOG_FILE: logFile.toString(),
-                NXF_TML_FILE: tmlFile.toString(),
-                TOWER_CONFIG_FILE: cfgFile.toString(),
-                TOWER_REPORTS_FILE: repFile.toString(),
-        ]
-
-        when:
-        def tower = new CacheManager(ENV)
-        then:
-        tower.sessionUuid == uuid
-        tower.localCachePath == Paths.get(".nextflow/cache/$uuid")
-        tower.localOutFile == outFile
-        tower.localLogFile == logFile
-        tower.localTimelineFile == tmlFile
-        tower.localTowerConfig == cfgFile
-        tower.localTowerReports == repFile
-        and:
-        tower.remoteWorkDir == remote
-        and:
-        tower.remoteCachePath == remote.resolve(".nextflow/cache/$uuid")
-        tower.remoteOutFile == remote.resolve( outFile.name )
-        tower.remoteLogFile == remote.resolve( logFile.name )
-        tower.remoteTimelineFile == remote.resolve( tmlFile.name )
-        tower.remoteTowerConfig == remote.resolve( cfgFile.name )
-        tower.remoteTowerReports == remote.resolve( repFile.name )
-
-        when:
-        // create local cache fake data
-        tower.localCachePath = local.resolve(".nextflow/cache/$uuid");
-        tower.localCachePath.mkdirs()
-        tower.localCachePath.resolve('index-foo').text = 'index foo'
-        tower.localCachePath.resolve('db').mkdir()
-        tower.localCachePath.resolve('db/xxx').text = 'data xxx'
-        tower.localCachePath.resolve('db/yyy').text = 'data yyy'
-        and:
-        tower.saveCacheFiles()
-        tower.saveMiscFiles()
-        then:
-        tower.remoteCachePath.resolve('index-foo').text == 'index foo'
-        tower.remoteCachePath.resolve('db/xxx').text == 'data xxx'
-        tower.remoteCachePath.resolve('db/yyy').text == 'data yyy'
-        and:
-        tower.remoteOutFile.text == outFile.text
-        tower.remoteLogFile.text == logFile.text
-        tower.remoteTimelineFile.text == tmlFile.text
-        tower.remoteTowerConfig.text == cfgFile.text
-        tower.remoteTowerReports.text == repFile.text
-
-        // simulate a 2nd run with different data
-        when:
-        tower.localCachePath.deleteDir()
-        tower.localCachePath.mkdirs()
-        tower.localCachePath.resolve('index-bar').text = 'index bar'
-        tower.localCachePath.resolve('db').mkdir()
-        tower.localCachePath.resolve('db/alpha').text = 'data alpha'
-        tower.localCachePath.resolve('db/delta').text = 'data delta'
-        and:
-        tower.saveCacheFiles()
-        tower.saveMiscFiles()
-        then:
-        tower.remoteCachePath.resolve('index-bar').text == 'index bar'
-        tower.remoteCachePath.resolve('db/alpha').text == 'data alpha'
-        tower.remoteCachePath.resolve('db/delta').text == 'data delta'
-        and:
-        !tower.remoteCachePath.resolve('index-foo').exists()
-        !tower.remoteCachePath.resolve('db/xxx').exists()
-        !tower.remoteCachePath.resolve('db/yyy').exists()
-        and:
-        tower.remoteOutFile.text == outFile.text
-        tower.remoteLogFile.text == logFile.text
-        tower.remoteTimelineFile.text == tmlFile.text
-        tower.remoteTowerConfig.text == cfgFile.text
-        tower.remoteTowerReports.text == repFile.text
-
-        cleanup:
-        folder?.deleteDir()
-    }
-
-    def 'should download cache files' () {
-        given:
-        def uuid = UUID.randomUUID().toString()
-        def folder = Files.createTempDirectory('test')
-        def local = folder.resolve('local'); local.mkdir()
-        def outFile = local.resolve('nf-out.txt');
-        def logFile = local.resolve('nf-log.txt')
-        def tmlFile = local.resolve('nf-tml.txt')
-        def cfgFile = local.resolve('tw-config.txt')
-        def repFile = local.resolve('tw-report.txt')
-        and:
-        def remote = folder.resolve('remote'); remote.mkdir()
-        remote.resolve('nf-out.txt').text = 'the out file'
-        remote.resolve('nf-log.txt').text = 'the log file'
-        remote.resolve('nf-tml.txt').text = 'the timeline file'
-        remote.resolve('nf-config.txt').text = 'the config file'
-        remote.resolve('nf-report.txt').text = 'the report file'
-        and:
-        remote.resolve(".nextflow/cache/$uuid").mkdirs()
-        remote.resolve(".nextflow/cache/$uuid").resolve('index-bar').text = 'index bar'
-        remote.resolve(".nextflow/cache/$uuid").resolve('db').mkdirs()
-        remote.resolve(".nextflow/cache/$uuid").resolve('db/alpha').text = 'data alpha'
-        remote.resolve(".nextflow/cache/$uuid").resolve('db/delta').text = 'data delta'
-        and:
-        def tower = new CacheManager([NXF_UUID: uuid, NXF_WORK: remote.toString()])
-
-        when:
-        tower.restoreCacheFiles()
-        then:
-        tower.localCachePath.resolve('index-bar').text == 'index bar'
-        tower.localCachePath.resolve('db/alpha').text == 'data alpha'
-        tower.localCachePath.resolve('db/delta').text == 'data delta'
-
-        cleanup:
-        folder?.deleteDir()
-    }
-
-    def 'should not backup/restore cache if cloudcache is enabled' () {
-        given:
-        def ENV = [
-                NXF_UUID: 'uuid',
-                NXF_WORK: '/work',
-                NXF_CLOUDCACHE_PATH: 's3://my-bucket/cache'
-        ]
-        and:
-        def tower = new CacheManager(ENV)
-
-        when:
-        tower.saveCacheFiles()
-        then:
-        0 * tower.getRemoteCachePath()
-
-        when:
-        tower.restoreCacheFiles()
-        then:
-        0 * tower.getRemoteCachePath()
-
-    }
-}
diff --git a/plugins/nf-tower/src/test/io/seqera/tower/plugin/LogsCheckpointTest.groovy b/plugins/nf-tower/src/test/io/seqera/tower/plugin/LogsCheckpointTest.groovy
new file mode 100644
index 0000000000..1852c1c114
--- /dev/null
+++ b/plugins/nf-tower/src/test/io/seqera/tower/plugin/LogsCheckpointTest.groovy
@@ -0,0 +1,84 @@
+/*
+ * Copyright 2013-2023, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package io.seqera.tower.plugin
+
+import nextflow.Session
+import nextflow.SysEnv
+import nextflow.util.Duration
+import spock.lang.Specification
+import test.TestHelper
+
+/**
+ *
+ * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
+ */
+class LogsCheckpointTest extends Specification {
+
+    def 'should configure default delay' () {
+        given:
+        def session = Mock(Session) {
+            getWorkDir() >> TestHelper.createInMemTempDir()
+            getConfig() >> [:]
+        }
+        and:
+        def checkpoint = new LogsCheckpoint()
+
+        when:
+        checkpoint.onFlowCreate(session)
+        then:
+        checkpoint.@interval == Duration.of('90s')
+    }
+
+    def 'should configure delay via env var' () {
+        given:
+        SysEnv.push(TOWER_LOGS_CHECKPOINT_INTERVAL: '200s')
+        def session = Mock(Session) {
+            getWorkDir() >> TestHelper.createInMemTempDir()
+            getConfig() >> [:]
+        }
+        and:
+        def checkpoint = new LogsCheckpoint()
+
+        when:
+        checkpoint.onFlowCreate(session)
+        then:
+        checkpoint.@interval == Duration.of('200s')
+
+        cleanup:
+        SysEnv.pop()
+    }
+
+    def 'should configure delay via config file' () {
+        given:
+        SysEnv.push(NXF_WORK: '/some/path', TOWER_LOGS_CHECKPOINT_INTERVAL: '200s')
+        def session = Mock(Session) {
+            getConfig()>>[tower:[logs:[checkpoint:[interval: '500s']]]]
+            getWorkDir() >> TestHelper.createInMemTempDir()
+        }
+        and:
+        def checkpoint = new LogsCheckpoint()
+
+        when:
+        checkpoint.onFlowCreate(session)
+        then:
+        checkpoint.@interval == Duration.of('500s')
+
+        cleanup:
+        SysEnv.pop()
+    }
+}
diff --git a/plugins/nf-tower/src/test/io/seqera/tower/plugin/LogsHandlerTest.groovy b/plugins/nf-tower/src/test/io/seqera/tower/plugin/LogsHandlerTest.groovy
new file mode 100644
index 0000000000..5ff927a077
--- /dev/null
+++ b/plugins/nf-tower/src/test/io/seqera/tower/plugin/LogsHandlerTest.groovy
@@ -0,0 +1,84 @@
+/*
+ * Copyright (c) 2020-2021. Seqera Labs, S.L.
+ *
+ * All Rights reserved
+ *
+ */
+
+package io.seqera.tower.plugin
+
+import java.nio.file.Files
+
+import nextflow.Session
+import nextflow.exception.AbortOperationException
+import spock.lang.Specification
+import test.TestHelper
+
+/**
+ *
+ * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
+ */
+class LogsHandlerTest extends Specification {
+
+    def 'should init empty files' () {
+        when:
+        new LogsHandler(Mock(Session), [:])
+        then:
+        thrown(AbortOperationException)
+    }
+
+    def 'should upload cache files' () {
+        given:
+        def folder = Files.createTempDirectory('test')
+        def remote = TestHelper.createInMemTempDir()
+        def local = folder.resolve('local'); local.mkdir()
+        def outFile = local.resolve('nf-out.txt'); outFile.text = 'out file'
+        def logFile = local.resolve('nf-log.txt'); logFile.text = 'log file'
+        def tmlFile = local.resolve('nf-tml.txt'); tmlFile.text = 'tml file'
+        def cfgFile = local.resolve('tw-config.txt'); cfgFile.text = 'config file'
+        def repFile = local.resolve('tw-report.txt'); repFile.text = 'report file'
+        and:
+        def uuid = UUID.randomUUID().toString()
+        and:
+        def session = Mock(Session) {getWorkDir() >> remote }
+        def ENV = [
+                NXF_UUID:uuid,
+                NXF_OUT_FILE: outFile.toString(),
+                NXF_LOG_FILE: logFile.toString(),
+                NXF_TML_FILE: tmlFile.toString(),
+                TOWER_CONFIG_FILE: cfgFile.toString(),
+                TOWER_REPORTS_FILE: repFile.toString(),
+        ]
+
+        when:
+        def tower = new LogsHandler(session, ENV)
+        then:
+        tower.localOutFile == outFile
+        tower.localLogFile == logFile
+        tower.localTimelineFile == tmlFile
+        tower.localTowerConfig == cfgFile
+        tower.localTowerReports == repFile
+        and:
+        tower.remoteWorkDir == remote
+        and:
+        tower.remoteOutFile == remote.resolve( outFile.name )
+        tower.remoteLogFile == remote.resolve( logFile.name )
+        tower.remoteTimelineFile == remote.resolve( tmlFile.name )
+        tower.remoteTowerConfig == remote.resolve( cfgFile.name )
+        tower.remoteTowerReports == remote.resolve( repFile.name )
+
+        when:
+        // create local cache fake data
+        tower.saveFiles()
+        then:
+        tower.remoteOutFile.text == outFile.text
+        tower.remoteLogFile.text == logFile.text
+        tower.remoteTimelineFile.text == tmlFile.text
+        tower.remoteTowerConfig.text == cfgFile.text
+        tower.remoteTowerReports.text == repFile.text
+
+        cleanup:
+        folder?.deleteDir()
+    }
+
+}
diff --git a/tests/cache-bak.nf b/tests/cache-bak.nf
deleted file mode 100644
index 4dee2f21bb..0000000000
--- a/tests/cache-bak.nf
+++ /dev/null
@@ -1,8 +0,0 @@
-workflow {
-  foo()
-}
-
-process foo {
-  debug true
-  /echo Hello world/
-}
diff --git a/tests/checks/cache-bak.nf/.checks b/tests/checks/cache-bak.nf/.checks
deleted file mode 100644
index b1d280b514..0000000000
--- a/tests/checks/cache-bak.nf/.checks
+++ /dev/null
@@ -1,42 +0,0 @@
-set -e
-
-# Skip test if AWS keys are missing
-if [[ ! $AWS_ACCESS_KEY_ID ]]; then
-  echo "Skip cache-bak test since AWS keys are not available"
-  exit 0
-fi
-
-#
-# setup env
-#
-export NXF_IGNORE_RESUME_HISTORY=true
-export NXF_UUID=$(uuidgen | tr [:upper:] [:lower:])
-
-#
-# run normal mode
-#
-$NXF_RUN -name test_1 | tee .stdout
-[[ `grep -c 'Submitted process > foo' .nextflow.log` == 1 ]] || false
-
-#
-# backup cache
-#
-NXF_WORK=s3://nextflow-ci/cache-test  \
-  $NXF_CMD -log .nextflow-backup.log plugin nf-tower:cache-backup
-
-#
-# remove it
-#
-rm -rf .nextflow
-
-#
-# restore cache
-#
-NXF_WORK=s3://nextflow-ci/cache-test  \
-  $NXF_CMD -log .nextflow-restore.log plugin nf-tower:cache-restore
-
-#
-# run resume mode
-#
-$NXF_RUN -name test_2 -resume $NXF_UUID | tee .stdout
-[[ `grep -c 'Cached process > foo' .nextflow.log` == 1 ]] || false

From 51f5c842dd9f4326b6781002155d65c576fd5806 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Sat, 29 Jul 2023 10:56:43 -0500
Subject: [PATCH 048/350] Allow workflow entry from module import (#4128)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../groovy/nextflow/script/BaseScript.groovy  | 12 +--
 .../groovy/nextflow/script/ScriptMeta.groovy  | 24 +++++-
 .../nextflow/script/BaseScriptTest.groovy     | 77 +++++++++++++++++--
 .../nextflow/script/ProcessDefTest.groovy     |  2 +-
 .../nextflow/script/ScriptMetaTest.groovy     |  7 +-
 5 files changed, 103 insertions(+), 19 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/script/BaseScript.groovy b/modules/nextflow/src/main/groovy/nextflow/script/BaseScript.groovy
index ef7e64b42a..5da185edd6 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/BaseScript.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/BaseScript.groovy
@@ -108,15 +108,14 @@ abstract class BaseScript extends Script implements ExecutionContext {
     protected workflow(Closure<BodyDef> workflowBody) {
         // launch the execution
         final workflow = new WorkflowDef(this, workflowBody)
-        if( !binding.entryName )
-            this.entryFlow = workflow
+        // capture the main (unnamed) workflow definition
+        this.entryFlow = workflow
+        // add it to the list of workflow definitions
         meta.addDefinition(workflow)
     }
 
     protected workflow(String name, Closure<BodyDef> workflowDef) {
         final workflow = new WorkflowDef(this,workflowDef,name)
-        if( binding.entryName==name )
-            this.entryFlow = workflow
         meta.addDefinition(workflow)
     }
 
@@ -147,9 +146,10 @@ abstract class BaseScript extends Script implements ExecutionContext {
             return result
         }
 
-        if( binding.entryName && !entryFlow ) {
+        // if an `entryName` was specified via the command line, override the `entryFlow` to be executed
+        if( binding.entryName && !(entryFlow=meta.getWorkflow(binding.entryName) ) ) {
             def msg = "Unknown workflow entry name: ${binding.entryName}"
-            final allNames = meta.getLocalWorkflowNames()
+            final allNames = meta.getWorkflowNames()
             final guess = allNames.closest(binding.entryName)
             if( guess )
                 msg += " -- Did you mean?\n" + guess.collect { "  $it"}.join('\n')
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/ScriptMeta.groovy b/modules/nextflow/src/main/groovy/nextflow/script/ScriptMeta.groovy
index 7b23ae6329..804bcd499f 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/ScriptMeta.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/ScriptMeta.groovy
@@ -237,15 +237,18 @@ class ScriptMeta {
     }
 
     WorkflowDef getWorkflow(String name) {
-        (WorkflowDef)getComponent(name)
+        final result = getComponent(name)
+        return result instanceof WorkflowDef ? result : null
     }
 
     ProcessDef getProcess(String name) {
-        (ProcessDef)getComponent(name)
+        final result = getComponent(name)
+        return result instanceof ProcessDef ? result : null
     }
 
     FunctionDef getFunction(String name) {
-        (FunctionDef)getComponent(name)
+        final result = getComponent(name)
+        return result instanceof FunctionDef ? result : null
     }
 
     Set<String> getAllNames() {
@@ -263,6 +266,21 @@ class ScriptMeta {
         return result
     }
 
+    Set<String> getWorkflowNames() {
+        final result = new HashSet(definitions.size() + imports.size())
+        // local definitions
+        for( def item : definitions.values() ) {
+            if( item instanceof WorkflowDef )
+                result.add(item.name)
+        }
+        // processes from imports
+        for( def item: imports.values() ) {
+            if( item instanceof WorkflowDef )
+                result.add(item.name)
+        }
+        return result
+    }
+
     Set<String> getProcessNames() {
         if( NF.dsl1 )
             return new HashSet<String>(getDsl1ProcessNames())
diff --git a/modules/nextflow/src/test/groovy/nextflow/script/BaseScriptTest.groovy b/modules/nextflow/src/test/groovy/nextflow/script/BaseScriptTest.groovy
index 958656cc8f..fee79ffae9 100644
--- a/modules/nextflow/src/test/groovy/nextflow/script/BaseScriptTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/script/BaseScriptTest.groovy
@@ -21,30 +21,29 @@ import java.nio.file.Paths
 
 import nextflow.NextflowMeta
 import nextflow.Session
-import spock.lang.Specification
+import test.Dsl2Spec
+import test.TestHelper
 /**
  *
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
  */
-class BaseScriptTest extends Specification {
+class BaseScriptTest extends Dsl2Spec {
 
 
     def 'should define implicit variables' () {
 
         given:
         def script = Files.createTempFile('test',null)
-
+        and:
         def WORKFLOW = Mock(WorkflowMetadata)
         def WORK_DIR = Paths.get('/work/dir')
         def PROJECT_DIR = Paths.get('/some/base')
-
         and:
         def session = Mock(Session) {
             getBaseDir() >> PROJECT_DIR
             getWorkDir() >> WORK_DIR
             getWorkflowMetadata() >> WORKFLOW
         }
-
         def binding = new ScriptBinding([:])
         def parser = new ScriptParser(session)
 
@@ -63,9 +62,8 @@ class BaseScriptTest extends Specification {
         parser.setBinding(binding)
         parser.runScript(script)
 
-
         then:
-        binding.result.baseDir ==PROJECT_DIR
+        binding.result.baseDir == PROJECT_DIR
         binding.result.projectDir == PROJECT_DIR
         binding.result.workDir == WORK_DIR
         binding.result.launchDir == Paths.get('.').toRealPath()
@@ -77,5 +75,70 @@ class BaseScriptTest extends Specification {
         script?.delete()
     }
 
+    def 'should use custom entry workflow' () {
+
+        given:
+        def script = Files.createTempFile('test',null)
+        and:
+        def session = Mock(Session)
+        def binding = new ScriptBinding([:])
+        def parser = new ScriptParser(session)
+
+        when:
+        script.text = '''
+                workflow foo {
+                }
+
+                workflow {
+                    error 'you were supposed to run foo!'
+                }
+                '''
+
+        parser.setBinding(binding)
+        parser.setEntryName('foo')
+        parser.runScript(script)
+
+        then:
+        noExceptionThrown()
+
+        cleanup:
+        script?.delete()
+    }
+
+    def 'should use entry workflow from module' () {
+
+        given:
+        def folder = TestHelper.createInMemTempDir()
+        def module = folder.resolve('module.nf')
+        def script = folder.resolve('main.nf')
+        and:
+        def session = Mock(Session)
+        def binding = new ScriptBinding([:])
+        def parser = new ScriptParser(session)
+
+        when:
+        module.text = '''
+                workflow foo {
+                }
+                '''
+
+        script.text = '''
+                include { foo } from './module.nf'
+
+                workflow {
+                    error 'you were supposed to run foo!'
+                }
+                '''
+
+        parser.setBinding(binding)
+        parser.setEntryName('foo')
+        parser.runScript(script)
+
+        then:
+        noExceptionThrown()
+
+        cleanup:
+        folder?.delete()
+    }
 
 }
diff --git a/modules/nextflow/src/test/groovy/nextflow/script/ProcessDefTest.groovy b/modules/nextflow/src/test/groovy/nextflow/script/ProcessDefTest.groovy
index 855a4de864..d008e29491 100644
--- a/modules/nextflow/src/test/groovy/nextflow/script/ProcessDefTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/script/ProcessDefTest.groovy
@@ -44,7 +44,7 @@ class ProcessDefTest extends Specification {
         def script = (BaseScript)new GroovyShell(binding,config).parse(SCRIPT)
 
         then:
-        true
+        ScriptMeta.get(script).getProcessNames() == ['foo','bar'] as Set
 
     }
 
diff --git a/modules/nextflow/src/test/groovy/nextflow/script/ScriptMetaTest.groovy b/modules/nextflow/src/test/groovy/nextflow/script/ScriptMetaTest.groovy
index e3a3b866ed..2e317af7f1 100644
--- a/modules/nextflow/src/test/groovy/nextflow/script/ScriptMetaTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/script/ScriptMetaTest.groovy
@@ -104,12 +104,15 @@ class ScriptMetaTest extends Dsl2Spec {
         meta1.getComponent('xxx') == null
         meta1.getComponent('func3') == null
         meta1.getComponent('proc3') == null
+        and:
         meta1.getComponent('work3') == work3
         meta1.getComponent('my_process') instanceof ProcessDef
         meta1.getComponent('my_process').name == 'my_process'
 
-//        then:
-//        meta1.getProcessNames() == ['proc1','proc2','my_process'] as Set
+        then:
+        meta1.getProcessNames() == ['proc1','proc2','my_process'] as Set
+        and:
+        meta1.getWorkflowNames() == ['work1', 'work2', 'work3'] as Set
     }
 
 

From a59af39f4c8712ebff6d52ab43cde6d5a763be66 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Sat, 29 Jul 2023 11:35:53 -0500
Subject: [PATCH 049/350] Fix incorrect error message on missing comma (#4085)
 [ci fast]

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../nextflow/script/params/BaseParam.groovy   | 28 ++++++++++++++++++-
 .../script/params/ParamsInTest.groovy         | 23 +++++++++++++++
 2 files changed, 50 insertions(+), 1 deletion(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/script/params/BaseParam.groovy b/modules/nextflow/src/main/groovy/nextflow/script/params/BaseParam.groovy
index fcf218ebbf..4a5165f8df 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/params/BaseParam.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/params/BaseParam.groovy
@@ -17,7 +17,8 @@
 package nextflow.script.params
 
 import groovy.util.logging.Slf4j
-
+import nextflow.exception.ScriptRuntimeException
+import nextflow.script.TokenVar
 /**
  * Base class for input/output parameters
  *
@@ -141,4 +142,29 @@ abstract class BaseParam implements Cloneable {
         return mapIndex >= 0
     }
 
+    /**
+     * Report missing method calls as possible syntax errors.
+     */
+    def methodMissing( String name, def args ) {
+        throw new ScriptRuntimeException("Invalid function call `${name}(${argsToString0(args)})` -- possible syntax error")
+    }
+
+    private String argsToString0(args) {
+        if( args instanceof Object[] )
+            args = Arrays.asList(args)
+        if( args instanceof List ) {
+            final result = new ArrayList()
+            for( def it : args )
+                result.add(argsToString1(it))
+            return result.join(',')
+        }
+        return argsToString1(args)
+    }
+
+    private String argsToString1(arg) {
+        if( arg instanceof TokenVar )
+            return arg.name
+        else
+            return String.valueOf((Object)arg)
+    }
 }
diff --git a/modules/nextflow/src/test/groovy/nextflow/script/params/ParamsInTest.groovy b/modules/nextflow/src/test/groovy/nextflow/script/params/ParamsInTest.groovy
index e2ef5258ce..60dba152bc 100644
--- a/modules/nextflow/src/test/groovy/nextflow/script/params/ParamsInTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/script/params/ParamsInTest.groovy
@@ -23,6 +23,7 @@ import java.nio.file.Paths
 import groovyx.gpars.dataflow.DataflowQueue
 import groovyx.gpars.dataflow.DataflowVariable
 import nextflow.Channel
+import nextflow.exception.ScriptRuntimeException
 import nextflow.processor.TaskProcessor
 import spock.lang.Timeout
 import test.Dsl2Spec
@@ -985,4 +986,26 @@ class ParamsInTest extends Dsl2Spec {
         (in1.inner[1] as FileInParam).isNestedParam()
     }
 
+    def 'should throw error on missing comma' () {
+        setup:
+        def text = '''
+            process hola {
+              input:
+              tuple val(x) val(y)
+
+              /command/
+            }
+            
+            workflow {
+              hola(['x', 'y'])
+            }
+            '''
+        when:
+        parseAndReturnProcess(text)
+
+        then:
+        def e = thrown(ScriptRuntimeException)
+        e.message == 'Invalid function call `val(y)` -- possible syntax error'
+    }
+
 }

From a6d08c04a57e522c0d52cc95ea9e223adf399199 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 29 Jul 2023 17:31:46 +0200
Subject: [PATCH 050/350] Remove module all components import

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../groovy/nextflow/script/ScriptMeta.groovy     | 16 ++++++----------
 .../groovy/nextflow/script/ScriptMetaTest.groovy |  4 +++-
 2 files changed, 9 insertions(+), 11 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/script/ScriptMeta.groovy b/modules/nextflow/src/main/groovy/nextflow/script/ScriptMeta.groovy
index 804bcd499f..ffecebc534 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/ScriptMeta.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/ScriptMeta.groovy
@@ -327,16 +327,12 @@ class ScriptMeta {
 
     void addModule(ScriptMeta script, String name, String alias) {
         assert script
-        if( name ) {
-            // include a specific
-            def item = script.getComponent(name)
-            if( !item )
-                throw new MissingModuleComponentException(script, name)
-            addModule0(item, alias)
-        }
-        else for( def item : script.getDefinitions() ) {
-            addModule0(item)
-        }
+        assert name
+        // include a specific
+        def item = script.getComponent(name)
+        if( !item )
+            throw new MissingModuleComponentException(script, name)
+        addModule0(item, alias)
     }
 
     protected void addModule0(ComponentDef component, String alias=null) {
diff --git a/modules/nextflow/src/test/groovy/nextflow/script/ScriptMetaTest.groovy b/modules/nextflow/src/test/groovy/nextflow/script/ScriptMetaTest.groovy
index 2e317af7f1..fac10444f1 100644
--- a/modules/nextflow/src/test/groovy/nextflow/script/ScriptMetaTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/script/ScriptMetaTest.groovy
@@ -83,7 +83,9 @@ class ScriptMetaTest extends Dsl2Spec {
         meta3.addDefinition(proc3, func3, work3)
 
         when:
-        meta1.addModule(meta2, null, null)
+        meta1.addModule(meta2, 'func2', null)
+        meta1.addModule(meta2, 'proc2', null)
+        meta1.addModule(meta2, 'work2', null)
         meta1.addModule(meta3, 'proc3', 'my_process')
         meta1.addModule(meta3, 'work3', null)
 

From f2a2ea353c0a8598c9f7d5eef31e9eca14893e3b Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 29 Jul 2023 19:21:00 +0200
Subject: [PATCH 051/350] Fix Option fixOwnership traverse parent directories

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy | 2 +-
 .../test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy | 2 +-
 .../nextflow/cloud/aws/batch/AwsBatchScriptLauncherTest.groovy  | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
index 218c462048..25b21626ec 100644
--- a/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
@@ -319,7 +319,7 @@ class BashWrapperBuilder {
         binding.after_script = afterScript ? "# 'afterScript' directive\n$afterScript" : null
 
         // patch root ownership problem on files created with docker
-        binding.fix_ownership = fixOwnership() ? "[ \${NXF_OWNER:=''} ] && chown -fR --from root \$NXF_OWNER ${workDir}/{*,.*} || true" : null
+        binding.fix_ownership = fixOwnership() ? "[ \${NXF_OWNER:=''} ] && (shopt -s extglob; GLOBIGNORE='..'; chown -fR --from root \$NXF_OWNER ${workDir}/{*,.*}) || true" : null
 
         binding.trace_script = isTraceRequired() ? getTraceScript(binding) : null
         
diff --git a/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
index cda97f5bc6..20339d9118 100644
--- a/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
@@ -1052,7 +1052,7 @@ class BashWrapperBuilderTest extends Specification {
         def binding = builder.makeBinding()
         then:
         builder.fixOwnership() >> true
-        binding.fix_ownership == '[ ${NXF_OWNER:=\'\'} ] && chown -fR --from root $NXF_OWNER /work/dir/{*,.*} || true'
+        binding.fix_ownership == '[ ${NXF_OWNER:=\'\'} ] && (shopt -s extglob; GLOBIGNORE=\'..\'; chown -fR --from root $NXF_OWNER /work/dir/{*,.*}) || true'
 
 
         when:
diff --git a/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchScriptLauncherTest.groovy b/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchScriptLauncherTest.groovy
index 1e36120d09..d2620c2767 100644
--- a/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchScriptLauncherTest.groovy
+++ b/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchScriptLauncherTest.groovy
@@ -627,7 +627,7 @@ class AwsBatchScriptLauncherTest extends Specification {
         def binding = builder.makeBinding()
         then:
         builder.fixOwnership() >> true
-        binding.fix_ownership == '[ ${NXF_OWNER:=\'\'} ] && chown -fR --from root $NXF_OWNER /work/dir/{*,.*} || true'
+        binding.fix_ownership == '[ ${NXF_OWNER:=\'\'} ] && (shopt -s extglob; GLOBIGNORE=\'..\'; chown -fR --from root $NXF_OWNER /work/dir/{*,.*}) || true'
 
     }
 

From 19a72c402495e72df0140c6af05d299330fa5ba9 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Mon, 31 Jul 2023 14:58:59 +0200
Subject: [PATCH 052/350] Fix glob resolution for remove files

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../nextflow/src/main/groovy/nextflow/Nextflow.groovy |  4 +++-
 .../test/nextflow/file/FilePatternSplitterTest.groovy |  3 ++-
 .../nf-amazon/src/test/nextflow/S3NextflowTest.groovy | 11 +++++++++++
 3 files changed, 16 insertions(+), 2 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/Nextflow.groovy b/modules/nextflow/src/main/groovy/nextflow/Nextflow.groovy
index 24012743ac..dd1b03f8e8 100644
--- a/modules/nextflow/src/main/groovy/nextflow/Nextflow.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/Nextflow.groovy
@@ -18,6 +18,7 @@ package nextflow
 
 import static nextflow.file.FileHelper.*
 
+import java.nio.file.FileSystem
 import java.nio.file.Files
 import java.nio.file.NoSuchFileException
 import java.nio.file.Path
@@ -60,7 +61,8 @@ class Nextflow {
     static private fileNamePattern( FilePatternSplitter splitter, Map opts ) {
 
         final scheme = splitter.scheme
-        final folder = toCanonicalPath(splitter.parent)
+        final target = scheme ? "$scheme://$splitter.parent" : splitter.parent
+        final folder = toCanonicalPath(target)
         final pattern = splitter.fileName
 
         if( opts == null ) opts = [:]
diff --git a/modules/nf-commons/src/test/nextflow/file/FilePatternSplitterTest.groovy b/modules/nf-commons/src/test/nextflow/file/FilePatternSplitterTest.groovy
index 002e517cbf..10173f9804 100644
--- a/modules/nf-commons/src/test/nextflow/file/FilePatternSplitterTest.groovy
+++ b/modules/nf-commons/src/test/nextflow/file/FilePatternSplitterTest.groovy
@@ -112,7 +112,8 @@ class FilePatternSplitterTest extends Specification {
         'test/data/file[a-b]'                   | 'test/data/'      | 'file[a-b]'           | null
         'test/data[a-b]/file'                   | 'test/'           | 'data[a-b]/file'      | null
         '/some/path\\[a-b\\]/data{a,b}/file\\?' | '/some/path[a-b]/'| 'data{a,b}/file\\?'   | null
-
+        's3://foo/bar/*'                        | 'foo/bar/'        | '*'                   | 's3'
+        's3://foo/bar/file.txt'                 | 'foo/bar/'        | 'file.txt'            | 's3'
     }
 
     def 'should strip glob escape chars' () {
diff --git a/plugins/nf-amazon/src/test/nextflow/S3NextflowTest.groovy b/plugins/nf-amazon/src/test/nextflow/S3NextflowTest.groovy
index ce62bd1140..dddfd6be8c 100644
--- a/plugins/nf-amazon/src/test/nextflow/S3NextflowTest.groovy
+++ b/plugins/nf-amazon/src/test/nextflow/S3NextflowTest.groovy
@@ -19,6 +19,8 @@ package nextflow
 
 import java.nio.file.Paths
 
+import spock.lang.IgnoreIf
+import spock.lang.Requires
 import spock.lang.Specification
 /**
  *
@@ -46,4 +48,13 @@ class S3NextflowTest extends Specification {
         SysEnv.pop()
     }
 
+    @IgnoreIf({System.getenv('NXF_SMOKE')})
+    @Requires({System.getenv('AWS_S3FS_ACCESS_KEY') && System.getenv('AWS_S3FS_SECRET_KEY')})
+    def 'should resolve list of files' () {
+        when:
+        def result = Nextflow.files('s3://ngi-igenomes/*')
+        then:
+        result.size() == 3
+    }
+
 }

From d2229bde10e277d0b8d02577c55d8f9633460601 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Thu, 3 Aug 2023 10:01:45 -0500
Subject: [PATCH 053/350] Update Wave and Fusion docs (#4149)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 docs/fusion.md | 11 ++++++-----
 docs/wave.md   | 14 +++++++++-----
 2 files changed, 15 insertions(+), 10 deletions(-)

diff --git a/docs/fusion.md b/docs/fusion.md
index 1aeaeda99d..8b0c1fbca4 100644
--- a/docs/fusion.md
+++ b/docs/fusion.md
@@ -185,8 +185,10 @@ The following configuration options are available:
 : Enable/disable the use of Fusion file system.
 
 `fusion.exportStorageCredentials`
-: When `true` the access credentials required by the underlying object storage are exported the pipeline jobs execution environment
-(requires version `23.05.0-edge` or later).
+: :::{versionadded} 23.05.0-edge
+  This option was previously named `fusion.exportAwsAccessKeys`.
+  :::
+: When `true` the access credentials required by the underlying object storage are exported the pipeline jobs execution environment.
 
 `fusion.containerConfigUrl`
 : The URL from where the container layer provisioning the Fusion client is downloaded. 
@@ -197,9 +199,8 @@ The following configuration options are available:
 `fusion.logOutput`
 : Where the logging output is written. 
 
-`tagsEnabled`
+`fusion.tagsEnabled`
 : Enable/disable the tagging of files created in the underlying object storage via the Fusion client (default: `true`).
 
-`tagsPattern`
+`fusion.tagsPattern`
 : The pattern that determines how tags are applied to files created via the Fusion client (default: `[.command.*|.exitcode|.fusion.*](nextflow.io/metadata=true),[*](nextflow.io/temporary=true)`)
-
diff --git a/docs/wave.md b/docs/wave.md
index a33bb9aa30..8eec01b3d5 100644
--- a/docs/wave.md
+++ b/docs/wave.md
@@ -171,27 +171,31 @@ The following configuration options are available:
 
 `wave.build.spack.basePackages`
 : :::{versionadded} 22.06.0-edge
-:::
+  :::
 : One or more Spack packages to be always added in the resulting container.
 
 `wave.build.spack.commands`
 : :::{versionadded} 22.06.0-edge
-:::
+  :::
 : One or more commands to be added to the Dockerfile used to build a Spack based image.
 
 `wave.httpClient.connectTime`
 : :::{versionadded} 22.06.0-edge
-:::
+  :::
 : Sets the connection timeout duration for the HTTP client connecting to the Wave service (default: `30s`).
 
 `wave.strategy`
 : The strategy to be used when resolving ambiguous Wave container requirements (default: `'container,dockerfile,conda,spack'`).
 
 `wave.report.enabled` (preview)
-: Enable the reporting of the Wave containers used during the pipeline execution (default: `false`, requires version `23.06.0-edge` or later).
+: :::{versionadded} 23.06.0-edge
+  :::
+: Enable the reporting of the Wave containers used during the pipeline execution (default: `false`).
 
 `wave.report.file` (preview)
-: The name of the containers report file (default: `containers-<timestamp>.config` requires version `23.06.0-edge` or later).
+: :::{versionadded} 23.06.0-edge
+  :::
+: The name of the containers report file (default: `'containers-<timestamp>.config'`).
 
 `wave.retryPolicy.delay`
 : :::{versionadded} 22.06.0-edge

From 6b46b507cfe6fcfd0fcd4e1ffd37fd131cb90b31 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Thu, 3 Aug 2023 10:02:12 -0500
Subject: [PATCH 054/350] Fix strict mode docs (#4150)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 docs/config.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/docs/config.md b/docs/config.md
index 76d5fa2b99..b6f662ef90 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -1713,11 +1713,11 @@ Some features can be enabled using the `nextflow.enable` and `nextflow.preview`
 
   - When merging params from a config file with params from the command line, Nextflow will fail if a param is specified from both sources but with different types
 
-  - When using the `join` operator, the `failOnDuplicate` option is `true` by default
+  - When using the `join` operator, the `failOnDuplicate` option is `true` regardless of any user setting
 
-  - When using the `join` operator, the `failOnMismatch` option is `true` by default (unless `remainder` is also `true`)
+  - When using the `join` operator, the `failOnMismatch` option is `true` (unless `remainder` is also `true`) regardless of any user setting
 
-  - When using the `publishDir` process directive, the `failOnError` option is `true` by default
+  - When using the `publishDir` process directive, the `failOnError` option is `true` regardless of any user setting
 
   - In a process definition, Nextflow will fail if an input or output tuple has only one element
 

From 3f4b85574532b3d5d46db0a54710d01a6efdb292 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Thu, 3 Aug 2023 10:03:48 -0500
Subject: [PATCH 055/350] Fix bug with K8s resource labels (#4147) [ci fast]

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 .../src/main/groovy/nextflow/k8s/K8sTaskHandler.groovy    | 2 +-
 .../test/groovy/nextflow/k8s/K8sTaskHandlerTest.groovy    | 8 ++++++--
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/k8s/K8sTaskHandler.groovy b/modules/nextflow/src/main/groovy/nextflow/k8s/K8sTaskHandler.groovy
index 1e3a070dbb..cdbf63411f 100644
--- a/modules/nextflow/src/main/groovy/nextflow/k8s/K8sTaskHandler.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/k8s/K8sTaskHandler.groovy
@@ -278,7 +278,7 @@ class K8sTaskHandler extends TaskHandler implements FusionAwareTask {
         }
         final resLabels = task.config.getResourceLabels()
         if( resLabels )
-            resLabels.putAll(resLabels)
+            result.putAll(resLabels)
         result.'nextflow.io/app' = 'nextflow'
         result.'nextflow.io/runName' = getRunName()
         result.'nextflow.io/taskName' = task.getName()
diff --git a/modules/nextflow/src/test/groovy/nextflow/k8s/K8sTaskHandlerTest.groovy b/modules/nextflow/src/test/groovy/nextflow/k8s/K8sTaskHandlerTest.groovy
index 892e9c3200..ba0ba6404c 100644
--- a/modules/nextflow/src/test/groovy/nextflow/k8s/K8sTaskHandlerTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/k8s/K8sTaskHandlerTest.groovy
@@ -864,7 +864,9 @@ class K8sTaskHandlerTest extends Specification {
         handler.getRunName() >> 'pedantic-joe'
         task.getName() >> 'hello-world-1'
         task.getProcessor() >> proc
-        task.getConfig() >> Mock(TaskConfig)
+        task.getConfig() >> Mock(TaskConfig) {
+            getResourceLabels() >> [mylabel: 'myvalue']
+        }
         proc.getName() >> 'hello-proc'
         exec.getSession() >> sess
         sess.getUniqueId() >> uuid
@@ -873,7 +875,9 @@ class K8sTaskHandlerTest extends Specification {
                 [label: 'app', value: 'nextflow'],
                 [label: 'x', value: 'hello_world']
         ]]
-
+        and:
+        labels.mylabel == 'myvalue'
+        and:
         labels.app == 'nextflow'
         labels.foo == 'bar'
         labels.x == 'hello_world'

From 57e3100b7c4203385ab69a4502bad70534d0a547 Mon Sep 17 00:00:00 2001
From: Aaron Fishman <uk.afishman@gmail.com>
Date: Thu, 3 Aug 2023 18:16:47 +0100
Subject: [PATCH 056/350] Add `-value` option to `config` command (#4142)

Signed-off-by: Aaron Fishman <uk.afishman@gmail.com>
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Co-authored-by: Aaron Fishman <aaron.fishman@achillestx.com>
Co-authored-by: Ben Sherman <bentshermann@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/cli.md                                   | 12 +++++++
 .../main/groovy/nextflow/cli/CmdConfig.groovy | 26 +++++++++++++++
 .../groovy/nextflow/cli/CmdConfigTest.groovy  | 32 +++++++++++++++++--
 3 files changed, 67 insertions(+), 3 deletions(-)

diff --git a/docs/cli.md b/docs/cli.md
index 9e707d294f..b101b568b9 100644
--- a/docs/cli.md
+++ b/docs/cli.md
@@ -411,6 +411,11 @@ The `config` command is used for printing the project's configuration i.e. the `
 `-sort`
 : Sort config attributes.
 
+`-value`
+: :::{versionadded} 23.08.0-edge
+  :::
+: Print the value of a config option, or fail if the option is not defined.
+
 **Examples**
 
 Print out the inferred config using a the default group key-value notation.
@@ -445,6 +450,13 @@ docker.enabled = true
 process.executor = local
 ```
 
+Print out the value of a specific configuration property.
+
+```console
+$ nextflow config -value process.executor
+local
+```
+
 Print out all profiles from the project's configuration.
 
 ```console
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdConfig.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdConfig.groovy
index 4281b15210..f4e17f07ba 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdConfig.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdConfig.groovy
@@ -59,6 +59,8 @@ class CmdConfig extends CmdBase {
     @Parameter(names = '-sort', description = 'Sort config attributes')
     boolean sort
 
+    @Parameter(names = '-value', description = 'Print the value of a config option, or fail if the option is not defined')
+    String printValue
 
     @Override
     String getName() { NAME }
@@ -79,6 +81,12 @@ class CmdConfig extends CmdBase {
         if( printProperties && printFlatten )
             throw new AbortOperationException("Option `-flat` and `-properties` conflicts")
 
+        if ( printValue && printFlatten )
+            throw new AbortOperationException("Option `-value` and `-flat` conflicts")
+
+        if ( printValue && printProperties )
+            throw new AbortOperationException("Option `-value` and `-properties` conflicts")
+
         final builder = new ConfigBuilder()
                 .setShowClosures(true)
                 .showMissingVariables(true)
@@ -94,6 +102,9 @@ class CmdConfig extends CmdBase {
         else if( printFlatten ) {
             printFlatten0(config, stdout)
         }
+        else if( printValue ) {
+            printValue0(config, printValue, stdout)
+        }
         else {
             printCanonical0(config, stdout)
         }
@@ -123,6 +134,21 @@ class CmdConfig extends CmdBase {
         output << ConfigHelper.toPropertiesString(config, sort)
     }
 
+    /**
+     * Prints a property of a {@link ConfigObject}.
+     *
+     * @param config The {@link ConfigObject} representing the parsed workflow configuration
+     * @param name The {@link String} representing the property name using dot notation
+     * @param output The stream where output the formatted configuration notation
+     */
+    @PackageScope void printValue0(ConfigObject config, String name, OutputStream output) {
+        final map = config.flatten()
+        if( !map.containsKey(name) )
+            throw new AbortOperationException("Configuration option '$name' not found")
+
+        output << map.get(name).toString() << '\n'
+    }
+
     /**
      * Prints a {@link ConfigObject} using properties dot notation.
      * String values are enclosed in single quote characters.
diff --git a/modules/nextflow/src/test/groovy/nextflow/cli/CmdConfigTest.groovy b/modules/nextflow/src/test/groovy/nextflow/cli/CmdConfigTest.groovy
index d3295d41d0..6be3ff7d52 100644
--- a/modules/nextflow/src/test/groovy/nextflow/cli/CmdConfigTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/cli/CmdConfigTest.groovy
@@ -16,11 +16,11 @@
 
 package nextflow.cli
 
-import nextflow.plugin.Plugins
-import spock.lang.IgnoreIf
-
 import java.nio.file.Files
 
+import nextflow.exception.AbortOperationException
+import nextflow.plugin.Plugins
+import spock.lang.IgnoreIf
 import spock.lang.Specification
 /**
  *
@@ -166,6 +166,32 @@ class CmdConfigTest extends Specification {
 
     }
 
+    def 'should print the value of a config option' () {
+
+        given:
+        def cmd = new CmdConfig()
+        and:
+        def config = new ConfigObject()
+        config.process.executor = 'slurm'
+        config.process.queue = 'long'
+        config.docker.enabled = true
+        and:
+        def buffer
+
+        when:
+        buffer = new ByteArrayOutputStream()
+        cmd.printValue0(config, 'process.executor', buffer)
+        then:
+        buffer.toString() == 'slurm\n'
+
+        when:
+        buffer = new ByteArrayOutputStream()
+        cmd.printValue0(config, 'does.not.exist', buffer)
+        then:
+        def e = thrown(AbortOperationException)
+        e.message == "Configuration option 'does.not.exist' not found"
+
+    }
 
     def 'should parse config file' () {
         given:

From 8579e7a4739d736851d57ca54d1eebc11f7fe6a3 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Fri, 4 Aug 2023 16:19:59 +0200
Subject: [PATCH 057/350] Fix Wave disable flag

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/config.md                                |  4 ++--
 .../io/seqera/wave/plugin/WaveFactory.groovy  | 19 ++++++++++++-------
 .../seqera/wave/plugin/WaveFactoryTest.groovy |  2 +-
 3 files changed, 15 insertions(+), 10 deletions(-)

diff --git a/docs/config.md b/docs/config.md
index b6f662ef90..4c429499a3 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -1557,8 +1557,8 @@ The following environment variables control the configuration of the Nextflow ru
 :::
 : Disables the automatic type detection of command line parameters.
 
-`NXF_DISABLE_WAVE_REQUIREMENT`
-: :::{versionadded} 23.07.0-edge
+`NXF_DISABLE_WAVE_SERVICE`
+: :::{versionadded} 23.08.0-edge
 :::
 : Disables the requirement for Wave service when enabling the Fusion file system.
 
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveFactory.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveFactory.groovy
index ec091cdc9e..48ae1b974e 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveFactory.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveFactory.groovy
@@ -36,12 +36,17 @@ class WaveFactory implements TraceObserverFactory {
     @Override
     Collection<TraceObserver> create(Session session) {
         final config = session.config
-        final wave = (Map)config.wave
-        final fusion = (Map)config.fusion
-        if( fusion?.enabled ) {
-            if( !wave?.enabled ) {
-                if( SysEnv.get('NXF_DISABLE_WAVE_REQUIREMENT') )
-                    return
+        final wave = (Map)config.wave ?: new HashMap<>(1)
+        final fusion = (Map)config.fusion ?: new HashMap<>(1)
+
+        if( SysEnv.get('NXF_DISABLE_WAVE_SERVICE') ) {
+            log.debug "Detected NXF_DISABLE_WAVE_SERVICE environment variable - Turning off Wave service"
+            wave.enabled = false
+            return List.of()
+        }
+        
+        if( fusion.enabled ) {
+            if( !wave.enabled ) {
                 throw new AbortOperationException("Fusion feature requires enabling Wave service")
             }
             else {
@@ -52,7 +57,7 @@ class WaveFactory implements TraceObserverFactory {
         }
 
         final observer = new WaveObserver(session)
-        return wave?.enabled && observer.reportOpts().enabled()
+        return wave.enabled && observer.reportOpts().enabled()
                 ? List.<TraceObserver>of(observer)
                 : List.<TraceObserver>of()
     }
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveFactoryTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveFactoryTest.groovy
index b06392952b..980c9c9c9d 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveFactoryTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveFactoryTest.groovy
@@ -64,7 +64,7 @@ class WaveFactoryTest extends Specification {
 
     def 'should not fail when wave is disabled' () {
         given:
-        SysEnv.push(NXF_DISABLE_WAVE_REQUIREMENT: 'true')
+        SysEnv.push(NXF_DISABLE_WAVE_SERVICE: 'true')
         def CONFIG = [wave:[:], fusion:[enabled:true]]
         def session = Mock(Session) { getConfig() >> CONFIG }
         def factory = new WaveFactory()

From 6d2690707b510038b7724d24957d8fe4ad8d55f8 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 5 Aug 2023 16:05:13 +0200
Subject: [PATCH 058/350] Restore Tower CacheManager for backward compatibility

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../seqera/tower/plugin/CacheCommand.groovy   |  34 +++-
 .../seqera/tower/plugin/CacheManager.groovy   | 164 ++++++++++++++++++
 .../seqera/tower/plugin/TowerArchiver.groovy  |   1 +
 .../tower/plugin/CacheManagerTest.groovy      | 157 +++++++++++++++++
 tests/cache-bak.nf                            |   8 +
 tests/checks/cache-bak.nf/.checks             |  42 +++++
 6 files changed, 403 insertions(+), 3 deletions(-)
 create mode 100644 plugins/nf-tower/src/main/io/seqera/tower/plugin/CacheManager.groovy
 create mode 100644 plugins/nf-tower/src/test/io/seqera/tower/plugin/CacheManagerTest.groovy
 create mode 100644 tests/cache-bak.nf
 create mode 100644 tests/checks/cache-bak.nf/.checks

diff --git a/plugins/nf-tower/src/main/io/seqera/tower/plugin/CacheCommand.groovy b/plugins/nf-tower/src/main/io/seqera/tower/plugin/CacheCommand.groovy
index 2abf12e94e..846f35f3b9 100644
--- a/plugins/nf-tower/src/main/io/seqera/tower/plugin/CacheCommand.groovy
+++ b/plugins/nf-tower/src/main/io/seqera/tower/plugin/CacheCommand.groovy
@@ -19,6 +19,8 @@ package io.seqera.tower.plugin
 
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
+import nextflow.Session
+import nextflow.SysEnv
 import nextflow.cli.PluginAbstractExec
 /**
  * Implements nextflow cache and restore commands
@@ -36,6 +38,7 @@ class CacheCommand implements PluginAbstractExec {
 
         if( cmd == 'cache-backup') {
             cacheBackup()
+            archiveLogs(session)
         }
         if( cmd == 'cache-restore' )
             cacheRestore()
@@ -44,12 +47,37 @@ class CacheCommand implements PluginAbstractExec {
 
     protected void cacheBackup() {
         log.debug "Running Nextflow cache backup"
-        new LogsHandler(getSession(), System.getenv()).saveFiles()
+        if( !SysEnv.get('NXF_CLOUDCACHE_PATH')) {
+            // legacy cache manager
+            new CacheManager(System.getenv()).saveCacheFiles()
+        }
+        else {
+            new LogsHandler(getSession(), System.getenv()).saveFiles()
+        }
+    }
+
+    protected void archiveLogs(Session sess) {
+        // archive logs
+        final archiver = TowerArchiver.create(sess, System.getenv())
+        if( archiver ) try {
+            log.debug "Running Nextflow logs archiver"
+            archiver.archiveLogs()
+        }
+        finally {
+            archiver.shutdown(sess)
+        }
     }
 
     protected void cacheRestore() {
-        log.debug "Running Nextflow cache restore - DO NOTHING"
-        // this command is only kept for backward compatibility
+        if( !SysEnv.get('NXF_CLOUDCACHE_PATH')) {
+            log.debug "Running Nextflow cache restore"
+            // legacy cache manager
+            new CacheManager(System.getenv()).restoreCacheFiles()
+        }
+        else {
+            // this command is only kept for backward compatibility
+            log.debug "Running Nextflow cache restore - DO NOTHING"
+        }
     }
 
 }
diff --git a/plugins/nf-tower/src/main/io/seqera/tower/plugin/CacheManager.groovy b/plugins/nf-tower/src/main/io/seqera/tower/plugin/CacheManager.groovy
new file mode 100644
index 0000000000..5c890f7752
--- /dev/null
+++ b/plugins/nf-tower/src/main/io/seqera/tower/plugin/CacheManager.groovy
@@ -0,0 +1,164 @@
+/*
+ * Copyright 2013-2023, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package io.seqera.tower.plugin
+
+import static java.nio.file.StandardCopyOption.*
+
+import java.nio.file.Files
+import java.nio.file.NoSuchFileException
+import java.nio.file.Path
+import java.nio.file.Paths
+
+import groovy.transform.CompileStatic
+import groovy.transform.PackageScope
+import groovy.util.logging.Slf4j
+import nextflow.exception.AbortOperationException
+import nextflow.extension.FilesEx
+import nextflow.file.FileHelper
+/**
+ * Back and restore Nextflow cache
+ *
+ * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
+ */
+@Slf4j
+@CompileStatic
+class CacheManager {
+
+    @PackageScope String sessionUuid
+    @PackageScope Path localCachePath
+    @PackageScope Path localOutFile
+    @PackageScope Path localLogFile
+    @PackageScope Path localTimelineFile
+    @PackageScope Path localTowerConfig
+    @PackageScope Path localTowerReports
+    @PackageScope Path remoteWorkDir
+
+    @PackageScope Path getRemoteCachePath() { remoteWorkDir.resolve(".nextflow/cache/${sessionUuid}") }
+    @PackageScope Path getRemoteOutFile() { remoteWorkDir.resolve(localOutFile.getName()) }
+    @PackageScope Path getRemoteLogFile() { remoteWorkDir.resolve(localLogFile.getName()) }
+    @PackageScope Path getRemoteTimelineFile() { remoteWorkDir.resolve(localTimelineFile.getName()) }
+    @PackageScope Path getRemoteTowerConfig() { remoteWorkDir.resolve(localTowerConfig.getName()) }
+    @PackageScope Path getRemoteTowerReports() { remoteWorkDir.resolve(localTowerReports.getName()) }
+
+    CacheManager(Map<String,String> env) {
+        final work = env.get('NXF_WORK') ?: env.get('NXF_TEST_WORK')
+        if( !work )
+            throw new AbortOperationException("Missing target work dir - cache sync cannot be performed")
+        this.remoteWorkDir = FileHelper.asPath(work)
+
+        this.sessionUuid = env.get('NXF_UUID')
+        if( !sessionUuid )
+            throw new AbortOperationException("Missing target uuid - cache sync cannot be performed")
+
+        this.localCachePath = Paths.get(".nextflow/cache/${sessionUuid}")
+
+        if( env.NXF_OUT_FILE )
+            localOutFile = Paths.get(env.NXF_OUT_FILE)
+        if( env.NXF_LOG_FILE )
+            localLogFile = Paths.get(env.NXF_LOG_FILE)
+        if( env.NXF_TML_FILE )
+            localTimelineFile = Paths.get(env.NXF_TML_FILE)
+        if( env.TOWER_CONFIG_FILE )
+            localTowerConfig = Paths.get(env.TOWER_CONFIG_FILE)
+        if( env.TOWER_REPORTS_FILE )
+            localTowerReports = Paths.get(env.TOWER_REPORTS_FILE)
+    }
+
+    protected void restoreCacheFiles() {
+        if( !remoteWorkDir || !sessionUuid )
+            return
+
+        if(!Files.exists(remoteCachePath)) {
+            log.debug "Remote cache path does not exist: $remoteCachePath - skipping cache restore"
+            return
+        }
+
+        try {
+            log.info "Restoring cache: ${remoteCachePath.toUriString()} => ${localCachePath.toUriString()}"
+            localCachePath.deleteDir()
+            localCachePath.parent.mkdirs()
+            FileHelper.copyPath(remoteCachePath, localCachePath, REPLACE_EXISTING)
+        }
+        catch (NoSuchFileException e) {
+            log.info "Remote cache restore ignored — reason: ${e.message ?: e}"
+        }
+    }
+
+    protected void saveCacheFiles() {
+        if( !remoteWorkDir || !sessionUuid )
+            return
+
+        if( !Files.exists(localCachePath) ) {
+            log.debug "Local cache path does not exist: $localCachePath — skipping cache backup"
+            return
+        }
+
+        // upload nextflow cache metadata
+        try {
+            log.info "Saving cache: ${localCachePath.toUriString()} => ${remoteCachePath.toUriString()}"
+            remoteCachePath.deleteDir()
+            remoteCachePath.parent.mkdirs()
+            FilesEx.copyTo(localCachePath, remoteCachePath)
+        }
+        catch (Throwable e) {
+            log.warn "Failed to backup resume metadata to remote store path: ${remoteCachePath.toUriString()} — cause: ${e}", e
+        }
+
+        // — upload out file
+        try {
+            if( localOutFile?.exists() )
+                FileHelper.copyPath(localOutFile, remoteOutFile, REPLACE_EXISTING)
+        }
+        catch (Throwable e) {
+            log.warn "Unable to upload nextflow out file: $localOutFile — reason: ${e.message ?: e}", e
+        }
+        // — upload log file
+        try {
+            if( localLogFile?.exists() )
+                FileHelper.copyPath(localLogFile, remoteLogFile, REPLACE_EXISTING)
+        }
+        catch (Throwable e) {
+            log.warn "Unable to upload nextflow log file: $localLogFile — reason: ${e.message ?: e}", e
+        }
+        // — upload timeline file
+        try {
+            if( localTimelineFile?.exists() )
+                FileHelper.copyPath(localTimelineFile, remoteTimelineFile, REPLACE_EXISTING)
+        }
+        catch (Throwable e) {
+            log.warn "Unable to upload nextflow timeline file: $localTimelineFile — reason: ${e.message ?: e}", e
+        }
+        // — upload tower config file
+        try {
+            if( localTowerConfig?.exists() )
+                FileHelper.copyPath(localTowerConfig, remoteTowerConfig, REPLACE_EXISTING)
+        }
+        catch (Throwable e) {
+            log.warn "Unable to upload tower config file: $localTowerConfig — reason: ${e.message ?: e}", e
+        }
+        // — upload tower reports file
+        try {
+            if( localTowerReports?.exists() )
+                FileHelper.copyPath(localTowerReports, remoteTowerReports, REPLACE_EXISTING)
+        }
+        catch (Throwable e) {
+            log.warn "Unable to upload tower reprts file: $localTowerReports — reason: ${e.message ?: e}", e
+        }
+    }
+
+}
diff --git a/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerArchiver.groovy b/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerArchiver.groovy
index 4aa6afdf90..6f8d270237 100644
--- a/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerArchiver.groovy
+++ b/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerArchiver.groovy
@@ -44,6 +44,7 @@ import nextflow.util.ThreadPoolManager
  */
 @Slf4j
 @CompileStatic
+@Deprecated
 class TowerArchiver {
 
     private static final String RETRY_REASON = 'slowdown|slow down|toomany|too many'
diff --git a/plugins/nf-tower/src/test/io/seqera/tower/plugin/CacheManagerTest.groovy b/plugins/nf-tower/src/test/io/seqera/tower/plugin/CacheManagerTest.groovy
new file mode 100644
index 0000000000..70e4579a19
--- /dev/null
+++ b/plugins/nf-tower/src/test/io/seqera/tower/plugin/CacheManagerTest.groovy
@@ -0,0 +1,157 @@
+/*
+ * Copyright (c) 2020-2021. Seqera Labs, S.L.
+ *
+ * All Rights reserved
+ *
+ */
+
+package io.seqera.tower.plugin
+
+import java.nio.file.Files
+import java.nio.file.Paths
+
+import nextflow.exception.AbortOperationException
+import spock.lang.Specification
+/**
+ *
+ * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
+ */
+class CacheManagerTest extends Specification {
+
+    def 'should init empty files' () {
+        when:
+        new CacheManager([:])
+        then:
+        thrown(AbortOperationException)
+    }
+
+    def 'should upload cache files' () {
+        given:
+        def folder = Files.createTempDirectory('test')
+        def remote = folder.resolve('remote'); remote.mkdir()
+        def local = folder.resolve('local'); local.mkdir()
+        def outFile = local.resolve('nf-out.txt'); outFile.text = 'out file'
+        def logFile = local.resolve('nf-log.txt'); logFile.text = 'log file'
+        def tmlFile = local.resolve('nf-tml.txt'); tmlFile.text = 'tml file'
+        def cfgFile = local.resolve('tw-config.txt'); cfgFile.text = 'config file'
+        def repFile = local.resolve('tw-report.txt'); repFile.text = 'report file'
+        and:
+        def uuid = UUID.randomUUID().toString()
+        and:
+        def ENV = [
+                NXF_UUID:uuid,
+                NXF_WORK: remote.toString(),
+                NXF_OUT_FILE: outFile.toString(),
+                NXF_LOG_FILE: logFile.toString(),
+                NXF_TML_FILE: tmlFile.toString(),
+                TOWER_CONFIG_FILE: cfgFile.toString(),
+                TOWER_REPORTS_FILE: repFile.toString(),
+        ]
+
+        when:
+        def tower = new CacheManager(ENV)
+        then:
+        tower.sessionUuid == uuid
+        tower.localCachePath == Paths.get(".nextflow/cache/$uuid")
+        tower.localOutFile == outFile
+        tower.localLogFile == logFile
+        tower.localTimelineFile == tmlFile
+        tower.localTowerConfig == cfgFile
+        tower.localTowerReports == repFile
+        and:
+        tower.remoteWorkDir == remote
+        and:
+        tower.remoteCachePath == remote.resolve(".nextflow/cache/$uuid")
+        tower.remoteOutFile == remote.resolve( outFile.name )
+        tower.remoteLogFile == remote.resolve( logFile.name )
+        tower.remoteTimelineFile == remote.resolve( tmlFile.name )
+        tower.remoteTowerConfig == remote.resolve( cfgFile.name )
+        tower.remoteTowerReports == remote.resolve( repFile.name )
+
+        when:
+        // create local cache fake data
+        tower.localCachePath = local.resolve(".nextflow/cache/$uuid");
+        tower.localCachePath.mkdirs()
+        tower.localCachePath.resolve('index-foo').text = 'index foo'
+        tower.localCachePath.resolve('db').mkdir()
+        tower.localCachePath.resolve('db/xxx').text = 'data xxx'
+        tower.localCachePath.resolve('db/yyy').text = 'data yyy'
+        and:
+        tower.saveCacheFiles()
+        then:
+        tower.remoteCachePath.resolve('index-foo').text == 'index foo'
+        tower.remoteCachePath.resolve('db/xxx').text == 'data xxx'
+        tower.remoteCachePath.resolve('db/yyy').text == 'data yyy'
+        and:
+        tower.remoteOutFile.text == outFile.text
+        tower.remoteLogFile.text == logFile.text
+        tower.remoteTimelineFile.text == tmlFile.text
+        tower.remoteTowerConfig.text == cfgFile.text
+        tower.remoteTowerReports.text == repFile.text
+
+        // simulate a 2nd run with different data
+        when:
+        tower.localCachePath.deleteDir()
+        tower.localCachePath.mkdirs()
+        tower.localCachePath.resolve('index-bar').text = 'index bar'
+        tower.localCachePath.resolve('db').mkdir()
+        tower.localCachePath.resolve('db/alpha').text = 'data alpha'
+        tower.localCachePath.resolve('db/delta').text = 'data delta'
+        and:
+        tower.saveCacheFiles()
+        then:
+        tower.remoteCachePath.resolve('index-bar').text == 'index bar'
+        tower.remoteCachePath.resolve('db/alpha').text == 'data alpha'
+        tower.remoteCachePath.resolve('db/delta').text == 'data delta'
+        and:
+        !tower.remoteCachePath.resolve('index-foo').exists()
+        !tower.remoteCachePath.resolve('db/xxx').exists()
+        !tower.remoteCachePath.resolve('db/yyy').exists()
+        and:
+        tower.remoteOutFile.text == outFile.text
+        tower.remoteLogFile.text == logFile.text
+        tower.remoteTimelineFile.text == tmlFile.text
+        tower.remoteTowerConfig.text == cfgFile.text
+        tower.remoteTowerReports.text == repFile.text
+
+        cleanup:
+        folder?.deleteDir()
+    }
+
+    def 'should download cache files' () {
+        given:
+        def uuid = UUID.randomUUID().toString()
+        def folder = Files.createTempDirectory('test')
+        def local = folder.resolve('local'); local.mkdir()
+        def outFile = local.resolve('nf-out.txt');
+        def logFile = local.resolve('nf-log.txt')
+        def tmlFile = local.resolve('nf-tml.txt')
+        def cfgFile = local.resolve('tw-config.txt')
+        def repFile = local.resolve('tw-report.txt')
+        and:
+        def remote = folder.resolve('remote'); remote.mkdir()
+        remote.resolve('nf-out.txt').text = 'the out file'
+        remote.resolve('nf-log.txt').text = 'the log file'
+        remote.resolve('nf-tml.txt').text = 'the timeline file'
+        remote.resolve('nf-config.txt').text = 'the config file'
+        remote.resolve('nf-report.txt').text = 'the report file'
+        and:
+        remote.resolve(".nextflow/cache/$uuid").mkdirs()
+        remote.resolve(".nextflow/cache/$uuid").resolve('index-bar').text = 'index bar'
+        remote.resolve(".nextflow/cache/$uuid").resolve('db').mkdirs()
+        remote.resolve(".nextflow/cache/$uuid").resolve('db/alpha').text = 'data alpha'
+        remote.resolve(".nextflow/cache/$uuid").resolve('db/delta').text = 'data delta'
+        and:
+        def tower = new CacheManager([NXF_UUID: uuid, NXF_WORK: remote.toString()])
+
+        when:
+        tower.restoreCacheFiles()
+        then:
+        tower.localCachePath.resolve('index-bar').text == 'index bar'
+        tower.localCachePath.resolve('db/alpha').text == 'data alpha'
+        tower.localCachePath.resolve('db/delta').text == 'data delta'
+
+        cleanup:
+        folder?.deleteDir()
+    }
+}
diff --git a/tests/cache-bak.nf b/tests/cache-bak.nf
new file mode 100644
index 0000000000..728c9b0779
--- /dev/null
+++ b/tests/cache-bak.nf
@@ -0,0 +1,8 @@
+workflow {
+  foo()
+}
+
+process foo {
+  debug true
+  /echo Hello world/
+}
\ No newline at end of file
diff --git a/tests/checks/cache-bak.nf/.checks b/tests/checks/cache-bak.nf/.checks
new file mode 100644
index 0000000000..b1d280b514
--- /dev/null
+++ b/tests/checks/cache-bak.nf/.checks
@@ -0,0 +1,42 @@
+set -e
+
+# Skip test if AWS keys are missing
+if [[ ! $AWS_ACCESS_KEY_ID ]]; then
+  echo "Skip cache-bak test since AWS keys are not available"
+  exit 0
+fi
+
+#
+# setup env
+#
+export NXF_IGNORE_RESUME_HISTORY=true
+export NXF_UUID=$(uuidgen | tr [:upper:] [:lower:])
+
+#
+# run normal mode
+#
+$NXF_RUN -name test_1 | tee .stdout
+[[ `grep -c 'Submitted process > foo' .nextflow.log` == 1 ]] || false
+
+#
+# backup cache
+#
+NXF_WORK=s3://nextflow-ci/cache-test  \
+  $NXF_CMD -log .nextflow-backup.log plugin nf-tower:cache-backup
+
+#
+# remove it
+#
+rm -rf .nextflow
+
+#
+# restore cache
+#
+NXF_WORK=s3://nextflow-ci/cache-test  \
+  $NXF_CMD -log .nextflow-restore.log plugin nf-tower:cache-restore
+
+#
+# run resume mode
+#
+$NXF_RUN -name test_2 -resume $NXF_UUID | tee .stdout
+[[ `grep -c 'Cached process > foo' .nextflow.log` == 1 ]] || false

From fe5dd497c1de8eaf01ce20574399da4779037b5b Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 5 Aug 2023 16:10:44 +0200
Subject: [PATCH 059/350] Increase Wave client max attempts

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../src/main/io/seqera/wave/plugin/config/RetryOpts.groovy    | 4 ++--
 .../test/io/seqera/wave/plugin/config/RetryOptsTest.groovy    | 4 ++--
 .../test/io/seqera/wave/plugin/config/WaveConfigTest.groovy   | 3 ++-
 3 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/RetryOpts.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/RetryOpts.groovy
index 614b2056ef..5b6ceda3ff 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/RetryOpts.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/RetryOpts.groovy
@@ -27,9 +27,9 @@ import nextflow.util.Duration
 @ToString(includeNames = true, includePackage = false)
 @CompileStatic
 class RetryOpts {
-    Duration delay = Duration.of('150ms')
+    Duration delay = Duration.of('450ms')
     Duration maxDelay = Duration.of('90s')
-    int maxAttempts = 5
+    int maxAttempts = 10
     double jitter = 0.25
 
     RetryOpts() {
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/RetryOptsTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/RetryOptsTest.groovy
index 0c53c8cbbb..d2c1342fc0 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/RetryOptsTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/RetryOptsTest.groovy
@@ -29,9 +29,9 @@ class RetryOptsTest extends Specification {
     def 'should create retry config' () {
 
         expect:
-        new RetryOpts().delay == Duration.of('150ms')
+        new RetryOpts().delay == Duration.of('450ms')
         new RetryOpts().maxDelay == Duration.of('90s')
-        new RetryOpts().maxAttempts == 5
+        new RetryOpts().maxAttempts == 10
         new RetryOpts().jitter == 0.25d
 
         and:
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy
index 1e141e8a3b..d7fcc47d2d 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy
@@ -161,7 +161,8 @@ class WaveConfigTest extends Specification {
         when:
         def opts = new WaveConfig([:])
         then:
-        opts.retryOpts().maxAttempts == 5
+        opts.retryOpts().delay == Duration.of('450ms')
+        opts.retryOpts().maxAttempts == 10
         opts.retryOpts().maxDelay == Duration.of('90s')
 
         when:

From 981315add6c7f8441a72214c7a96d72b4b800de3 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 5 Aug 2023 16:31:01 +0200
Subject: [PATCH 060/350] Bump nf-amazon@2.1.1

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-amazon/changelog.txt                      | 4 ++++
 plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/plugins/nf-amazon/changelog.txt b/plugins/nf-amazon/changelog.txt
index 4472d2b1cb..81af4cb0aa 100644
--- a/plugins/nf-amazon/changelog.txt
+++ b/plugins/nf-amazon/changelog.txt
@@ -1,5 +1,9 @@
 nf-amazon changelog
 ===================
+2.1.1 - 5 Aug 2023
+- Fix glob resolution for remove files [19a72c40]
+- Fix Option fixOwnership traverse parent directories [f2a2ea35]
+
 2.1.0 - 22 Jul 2023
 - Add support for AWS SSO credentials provider (#4045) [53e33cde]
 - Wait for all child processes in nxf_parallel (#4050) [60a5f1a7]
diff --git a/plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF b/plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF
index 6c9c9e82fd..d7b0cf833b 100644
--- a/plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: nextflow.cloud.aws.AmazonPlugin
 Plugin-Id: nf-amazon
-Plugin-Version: 2.1.0
+Plugin-Version: 2.1.1
 Plugin-Provider: Seqera Labs
 Plugin-Requires: >=23.05.0-edge

From 5f33ac17ea4e38c06918827e6fe4e7e3b5eba5d4 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 5 Aug 2023 16:32:01 +0200
Subject: [PATCH 061/350] Bump nf-azure@1.2.0

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-azure/changelog.txt                      | 3 +++
 plugins/nf-azure/src/resources/META-INF/MANIFEST.MF | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/plugins/nf-azure/changelog.txt b/plugins/nf-azure/changelog.txt
index bcfce7cfe9..27c932bddc 100644
--- a/plugins/nf-azure/changelog.txt
+++ b/plugins/nf-azure/changelog.txt
@@ -1,5 +1,8 @@
 nf-azure changelog
 ===================
+1.2.0 - 5 Aug 2023
+- Add deleteTasksOnCompletion to Azure Batch configuration (#4114) [b14674dc]
+
 1.1.4 - 22 Jul 2023
 - Fix failing test [9a52f848]
 - Fix Improve error message for invalid Azure URI [0f4d8867]
diff --git a/plugins/nf-azure/src/resources/META-INF/MANIFEST.MF b/plugins/nf-azure/src/resources/META-INF/MANIFEST.MF
index 72c440d1a9..3bf6761375 100644
--- a/plugins/nf-azure/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-azure/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: nextflow.cloud.azure.AzurePlugin
 Plugin-Id: nf-azure
-Plugin-Version: 1.1.4
+Plugin-Version: 1.2.0
 Plugin-Provider: Seqera Labs
 Plugin-Requires: >=23.01.0-edge

From 41c8c1642e6c2992d142d2d2c1afbd722c3e7d6e Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 5 Aug 2023 16:32:28 +0200
Subject: [PATCH 062/350] Bump nf-tower@1.6.0

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-tower/changelog.txt                      | 5 +++++
 plugins/nf-tower/src/resources/META-INF/MANIFEST.MF | 2 +-
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/plugins/nf-tower/changelog.txt b/plugins/nf-tower/changelog.txt
index dd3e42551a..ce9117eb76 100644
--- a/plugins/nf-tower/changelog.txt
+++ b/plugins/nf-tower/changelog.txt
@@ -1,5 +1,10 @@
 nf-tower changelog
 ===================
+1.6.0 - 5 Aug 2023
+- Add Tower logs checkpoint (#4132) [71dfecc2]
+- Restore Tower CacheManager for backward compatibility [6d269070]
+- Disable cache backup/restore if cloudcache is used (#4125) [46e828e1]
+
 1.5.15 - 22 Jul 2023
 - Bump Groovy 3.0.18 [207eb535]
 
diff --git a/plugins/nf-tower/src/resources/META-INF/MANIFEST.MF b/plugins/nf-tower/src/resources/META-INF/MANIFEST.MF
index 6fc78a5d49..d31cd40212 100644
--- a/plugins/nf-tower/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-tower/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: io.seqera.tower.plugin.TowerPlugin
 Plugin-Id: nf-tower
-Plugin-Version: 1.5.15
+Plugin-Version: 1.6.0
 Plugin-Provider: Seqera Labs
 Plugin-Requires: >=23.05.0-edge

From 78e4b278b49d83bc2f5ae1d80c5ec7c207c909ce Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 5 Aug 2023 16:32:47 +0200
Subject: [PATCH 063/350] Bump nf-wave@0.11.1

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-wave/changelog.txt                      | 6 ++++++
 plugins/nf-wave/src/resources/META-INF/MANIFEST.MF | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/plugins/nf-wave/changelog.txt b/plugins/nf-wave/changelog.txt
index e0b6743fe7..d9c4f7fbde 100644
--- a/plugins/nf-wave/changelog.txt
+++ b/plugins/nf-wave/changelog.txt
@@ -1,5 +1,11 @@
 nf-wave changelog
 ==================
+0.11.1 - 5 Aug 2023
+- Improve Wave config logging [547fad62]
+- Increase Wave client max attempts [fe5dd497]
+- Enable use virtual threads in Wave client [dd32f80a]
+- Fix Wave disable flag [8579e7a4]
+
 0.11.0 - 22 Jul 2023
 - Add support legacy wave retry [ci fast] [73a1e7d4]
 - Add support for Wave container freeze [9a5903e6]
diff --git a/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF b/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF
index d30a66bedb..877822c1a2 100644
--- a/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: io.seqera.wave.plugin.WavePlugin
 Plugin-Id: nf-wave
-Plugin-Version: 0.11.0
+Plugin-Version: 0.11.1
 Plugin-Provider: Seqera Labs
 Plugin-Requires: >=23.05.0-edge

From 24db16503cba1cf215b920c186f9552a62e8edf1 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 5 Aug 2023 16:37:07 +0200
Subject: [PATCH 064/350] Update changelog

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 changelog.txt | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/changelog.txt b/changelog.txt
index ecd6880229..6617c767b2 100644
--- a/changelog.txt
+++ b/changelog.txt
@@ -1,5 +1,34 @@
 NEXTFLOW CHANGE-LOG
 ===================
+23.08.0-edge - 5 Aug 2023 
+- Add `-value` option to `config` command (#4142) [57e3100b]
+- Add `deleteTasksOnCompletion` to Azure Batch configuration (#4114) [b14674dc]
+- Add Tower logs checkpoint (#4132) [71dfecc2]
+- Allow use virtual threads in Wave client [dd32f80a]
+- Allow workflow entry from module import (#4128) [51f5c842]
+- Disable cache backup/restore if cloudcache is used (#4125) [46e828e1]
+- Document behavior of withName selector with included aliases (#4129) [8b7e3d48]
+- Fix Option fixOwnership traverse parent directories [f2a2ea35]
+- Fix Redirection http redirection across different hosts [fcdeec02]
+- Fix Wave disable flag [8579e7a4]
+- Fix bug with K8s resource labels (#4147) eu-west-1[3f4b8557]
+- Fix glob resolution for remove files [19a72c40]
+- Fix incorrect error message on missing comma (#4085) eu-west-1[a59af39f]
+- Fix missing changelog for version 23.07.0-edge eu-west-1[9a33e936]
+- Fix strict mode docs (#4150) [6b46b507]
+- Improve plugin docs (#3957) [22638d46]
+- Improve Wave config logging [547fad62]
+- Improve TaskPollingMonitor logging [077ed5dd]
+- Improve Wave and Fusion docs (#4149) [d2229bde]
+- Increase Wave client max attempts [fe5dd497]
+- Remove module all components import [a6d08c04]
+- Restore Tower CacheManager for backward compatibility [6d269070]
+- Bump amazoncorretto:17.0.8 [00eb145c]
+- Bump nf-wave@0.11.1 [78e4b278]
+- Bump nf-tower@1.6.0 [41c8c164]
+- Bump nf-azure@1.2.0 [5f33ac17]
+- Bump nf-amazon@2.1.1 [981315ad]
+
 23.07.0-edge - 23 Jul 2023
 - Add CPU model name to trace files and traceRecord (#3946) [e0d91bf7]
 - Add ability to disable CLI params type detection [9a1c584d]

From ace32d007e545dc3da5924c36c39f628c83b1da8 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 5 Aug 2023 16:37:43 +0200
Subject: [PATCH 065/350] [release 23.08.0-edge] Update timestamp and build
 number [ci fast]

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 VERSION                                                   | 2 +-
 docs/conf.py                                              | 4 ++--
 .../nextflow/src/main/resources/META-INF/plugins-info.txt | 8 ++++----
 modules/nf-commons/src/main/nextflow/Const.groovy         | 6 +++---
 nextflow                                                  | 2 +-
 nextflow.md5                                              | 2 +-
 nextflow.sha1                                             | 2 +-
 nextflow.sha256                                           | 2 +-
 8 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/VERSION b/VERSION
index 59200001a7..867f7aa69d 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-23.07.0-edge
\ No newline at end of file
+23.08.0-edge
\ No newline at end of file
diff --git a/docs/conf.py b/docs/conf.py
index be318c7325..b68f128789 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -58,9 +58,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '23.07'
+version = '23.08'
 # The full version, including alpha/beta/rc tags.
-release = '23.07.0-edge'
+release = '23.08.0-edge'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
diff --git a/modules/nextflow/src/main/resources/META-INF/plugins-info.txt b/modules/nextflow/src/main/resources/META-INF/plugins-info.txt
index 604d402fab..c7fc7ad006 100644
--- a/modules/nextflow/src/main/resources/META-INF/plugins-info.txt
+++ b/modules/nextflow/src/main/resources/META-INF/plugins-info.txt
@@ -1,9 +1,9 @@
-nf-amazon@2.1.0
-nf-azure@1.1.4
+nf-amazon@2.1.1
+nf-azure@1.2.0
 nf-cloudcache@0.1.0
 nf-codecommit@0.1.5
 nf-console@1.0.6
 nf-ga4gh@1.1.0
 nf-google@1.8.1
-nf-tower@1.5.15
-nf-wave@0.11.0
\ No newline at end of file
+nf-tower@1.6.0
+nf-wave@0.11.1
\ No newline at end of file
diff --git a/modules/nf-commons/src/main/nextflow/Const.groovy b/modules/nf-commons/src/main/nextflow/Const.groovy
index f2652b923b..23d624ff1a 100644
--- a/modules/nf-commons/src/main/nextflow/Const.groovy
+++ b/modules/nf-commons/src/main/nextflow/Const.groovy
@@ -52,17 +52,17 @@ class Const {
     /**
      * The application version
      */
-    static public final String APP_VER = "23.07.0-edge"
+    static public final String APP_VER = "23.08.0-edge"
 
     /**
      * The app build time as linux/unix timestamp
      */
-    static public final long APP_TIMESTAMP = 1690040653541
+    static public final long APP_TIMESTAMP = 1691246068029
 
     /**
      * The app build number
      */
-    static public final int APP_BUILDNUM = 5870
+    static public final int APP_BUILDNUM = 5872
 
     /**
      * The app build time string relative to UTC timezone
diff --git a/nextflow b/nextflow
index 61160e818f..75b6424928 100755
--- a/nextflow
+++ b/nextflow
@@ -15,7 +15,7 @@
 #  limitations under the License.
 
 [[ "$NXF_DEBUG" == 'x' ]] && set -x
-NXF_VER=${NXF_VER:-'23.07.0-edge'}
+NXF_VER=${NXF_VER:-'23.08.0-edge'}
 NXF_ORG=${NXF_ORG:-'nextflow-io'}
 NXF_HOME=${NXF_HOME:-$HOME/.nextflow}
 NXF_PROT=${NXF_PROT:-'https'}
diff --git a/nextflow.md5 b/nextflow.md5
index 6bfd0cfe97..14f8bff303 100644
--- a/nextflow.md5
+++ b/nextflow.md5
@@ -1 +1 @@
-d7cff3459c0394236a4f1781843f4655
+e84b9b8b1453bb81540b10e057e126ee
diff --git a/nextflow.sha1 b/nextflow.sha1
index c056fda67a..aa412cac8b 100644
--- a/nextflow.sha1
+++ b/nextflow.sha1
@@ -1 +1 @@
-a45925a853a3e516e5343b46ae291d66e93a047b
+f70facf7083770f11d4d915c6f11502302a3aa4a
diff --git a/nextflow.sha256 b/nextflow.sha256
index 7e2e60eb3a..14fbf058ba 100644
--- a/nextflow.sha256
+++ b/nextflow.sha256
@@ -1 +1 @@
-185b41f6b7cdf8061f1fb93621fd5a9e648d6eb152ce66044a9ff6c98506b608
+1448ebceec2213751c8846f0edc06a6791f2ff0bc996a7553fa7f94bb57c2606

From a66b0e631b1974cae5cc4adeb50999ed79a3b5f5 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Tue, 8 Aug 2023 10:39:09 -0500
Subject: [PATCH 066/350] Enable cloud cache based on environment variable
 (#4160)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 .../src/main/nextflow/plugin/PluginsFacade.groovy          | 5 +++++
 .../src/test/nextflow/plugin/PluginsFacadeTest.groovy      | 7 +++++++
 .../src/main/nextflow/cache/CloudCacheStore.groovy         | 2 +-
 3 files changed, 13 insertions(+), 1 deletion(-)

diff --git a/modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy b/modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy
index bc5049d305..3a2adb200f 100644
--- a/modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy
+++ b/modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy
@@ -371,6 +371,11 @@ class PluginsFacade implements PluginStateListener {
             specs << defaultPlugins.getPlugin('nf-wave')
         }
 
+        // add cloudcache plugin when NXF_CLOUDCACHE_PATH is set
+        if( env.NXF_CLOUDCACHE_PATH ) {
+            specs << defaultPlugins.getPlugin('nf-cloudcache')
+        }
+
         log.debug "Plugins resolved requirement=$specs"
         return specs
     }
diff --git a/modules/nf-commons/src/test/nextflow/plugin/PluginsFacadeTest.groovy b/modules/nf-commons/src/test/nextflow/plugin/PluginsFacadeTest.groovy
index 9c503cb3c8..7dc6f9b3b0 100644
--- a/modules/nf-commons/src/test/nextflow/plugin/PluginsFacadeTest.groovy
+++ b/modules/nf-commons/src/test/nextflow/plugin/PluginsFacadeTest.groovy
@@ -66,6 +66,7 @@ class PluginsFacadeTest extends Specification {
         given:
         def defaults = new DefaultPlugins(plugins: [
                 'nf-amazon': new PluginSpec('nf-amazon', '0.1.0'),
+                'nf-cloudcache': new PluginSpec('nf-cloudcache', '0.1.0'),
                 'nf-google': new PluginSpec('nf-google', '0.1.0'),
                 'nf-tower': new PluginSpec('nf-tower', '0.1.0'),
                 'nf-wave': new PluginSpec('nf-wave', '0.1.0')
@@ -138,6 +139,12 @@ class PluginsFacadeTest extends Specification {
         then:
         result == [ new PluginSpec('nf-google','2.0.0') ]
 
+        when:
+        handler = new PluginsFacade(defaultPlugins: defaults, env: [NXF_CLOUDCACHE_PATH:'xyz'])
+        result = handler.pluginsRequirement([:])
+        then:
+        result == [ new PluginSpec('nf-cloudcache', '0.1.0') ]
+
     }
 
     def 'should return default plugins given config' () {
diff --git a/plugins/nf-cloudcache/src/main/nextflow/cache/CloudCacheStore.groovy b/plugins/nf-cloudcache/src/main/nextflow/cache/CloudCacheStore.groovy
index 3ebcb40f0b..7d8b794739 100644
--- a/plugins/nf-cloudcache/src/main/nextflow/cache/CloudCacheStore.groovy
+++ b/plugins/nf-cloudcache/src/main/nextflow/cache/CloudCacheStore.groovy
@@ -76,7 +76,7 @@ class CloudCacheStore implements CacheStore {
     private Path defaultBasePath() {
         final basePath = SysEnv.get('NXF_CLOUDCACHE_PATH')
         if( !basePath )
-            throw new IllegalArgumentException("NXF_CLOUDCACHE_PATH must be defined when using the path-based cache store")
+            throw new IllegalArgumentException("NXF_CLOUDCACHE_PATH must be defined when using the cloud cache store")
 
         return basePath as Path
     }

From 7e58c94576b28c1bd59e20761a1bfe08fae740e4 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Wed, 9 Aug 2023 18:07:58 +0200
Subject: [PATCH 067/350] Minor changes [ci fast]

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../nf-commons/src/main/nextflow/plugin/PluginUpdater.groovy    | 2 +-
 .../nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-commons/src/main/nextflow/plugin/PluginUpdater.groovy b/modules/nf-commons/src/main/nextflow/plugin/PluginUpdater.groovy
index b2feaebdf2..4e773877af 100644
--- a/modules/nf-commons/src/main/nextflow/plugin/PluginUpdater.groovy
+++ b/modules/nf-commons/src/main/nextflow/plugin/PluginUpdater.groovy
@@ -98,7 +98,7 @@ class PluginUpdater extends UpdateManager {
                         =                                                                           =
                         = ${repos}
                         =                                                                           =
-                        = This is only meant to be used for plugin repos purposes.                  =
+                        = This is only meant to be used for plugin testing purposes.                =
                         =============================================================================
                         """.stripIndent(true)
         log.warn(msg)
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
index bf91dcc053..45e2125cea 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
@@ -596,7 +596,7 @@ class WaveClient {
         return Failsafe.with(policy).get(action)
     }
 
-    static private List<Integer> SERVER_ERRORS = [502,503,504]
+    static private final List<Integer> SERVER_ERRORS = [502,503,504]
 
     protected HttpResponse<String> httpSend(HttpRequest req)  {
         return safeApply(() -> {

From e78bc37eccfa5bb3126c7f69653081138d3ba9e2 Mon Sep 17 00:00:00 2001
From: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
Date: Thu, 10 Aug 2023 05:06:07 -0300
Subject: [PATCH 068/350] Fix typos in source code comments (#4173) [ci fast]

Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 changelog.txt                                 |  2 +-
 .../ast/TaskTemplateVarsXformImpl.groovy      |  2 +-
 .../main/groovy/nextflow/cli/CmdConfig.groovy |  2 +-
 .../groovy/nextflow/conda/CondaConfig.groovy  |  2 +-
 .../nextflow/config/CascadingConfig.groovy    |  2 +-
 .../container/SingularityCache.groovy         |  2 +-
 .../nextflow/executor/ExecutorFactory.groovy  |  2 +-
 .../nextflow/executor/GridTaskHandler.groovy  |  2 +-
 .../nextflow/extension/OperatorImpl.groovy    |  2 +-
 .../nextflow/k8s/model/PodHostMount.groovy    |  2 +-
 .../nextflow/processor/TaskProcessor.groovy   |  2 +-
 .../groovy/nextflow/scm/ProviderPath.groovy   |  2 +-
 .../groovy/nextflow/spack/SpackConfig.groovy  |  2 +-
 .../nextflow/splitter/FastaSplitter.groovy    |  2 +-
 .../nextflow/trace/GraphObserver.groovy       |  2 +-
 .../nextflow/trace/ReportSummary.groovy       | 20 +++++++++----------
 .../nextflow/trace/TraceObserver.groovy       |  8 ++++----
 .../groovy/nextflow/util/LoggerHelper.groovy  |  2 +-
 .../groovy/nextflow/util/NameGenerator.groovy |  4 ++--
 .../src/main/nextflow/extension/Bolts.groovy  |  2 +-
 .../src/main/nextflow/file/FileHelper.groovy  |  2 +-
 .../main/nextflow/plugin/PluginsFacade.groovy |  2 +-
 .../src/main/nextflow/util/CacheHelper.java   |  4 ++--
 .../main/nextflow/util/CharsetHelper.groovy   |  2 +-
 .../nextflow/extension/FilesExTest.groovy     |  2 +-
 .../nextflow/plugin/PluginsFacadeTest.groovy  |  2 +-
 .../plugin/hello/HelloExtension.groovy        |  2 +-
 .../file/http/XFileSystemProvider.groovy      |  2 +-
 plugins/README.md                             |  2 +-
 .../cloud/azure/batch/AzBatchService.groovy   |  4 ++--
 .../io/seqera/tower/plugin/TowerClient.groovy |  2 +-
 31 files changed, 46 insertions(+), 46 deletions(-)

diff --git a/changelog.txt b/changelog.txt
index 6617c767b2..852e84c0bf 100644
--- a/changelog.txt
+++ b/changelog.txt
@@ -1361,7 +1361,7 @@ NEXTFLOW CHANGE-LOG
 - see 20.07.0 and 20.07.0-RC1
 
 20.07.0 - (skipped)
-- Allow unqualified stdin/stdout defintions with DSL2 [bcdcaab6]
+- Allow unqualified stdin/stdout definitions with DSL2 [bcdcaab6]
 
 20.07.0-RC1 - 21 Jul 2020 
 - Add Dsl2 enable flag [08238109]
diff --git a/modules/nextflow/src/main/groovy/nextflow/ast/TaskTemplateVarsXformImpl.groovy b/modules/nextflow/src/main/groovy/nextflow/ast/TaskTemplateVarsXformImpl.groovy
index 4aa32126f7..4be53993bc 100644
--- a/modules/nextflow/src/main/groovy/nextflow/ast/TaskTemplateVarsXformImpl.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/ast/TaskTemplateVarsXformImpl.groovy
@@ -26,7 +26,7 @@ import org.codehaus.groovy.transform.ASTTransformation
 import org.codehaus.groovy.transform.GroovyASTTransformation
 /**
  * Implements a xform that captures variable names declared
- * in task tamplate
+ * in task template
  *
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
  */
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdConfig.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdConfig.groovy
index f4e17f07ba..29b874198b 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdConfig.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdConfig.groovy
@@ -115,7 +115,7 @@ class CmdConfig extends CmdBase {
 
     /**
      * Prints a {@link ConfigObject} using Java {@link Properties} in canonical format
-     * ie. any nested config object is printed withing curly brackets
+     * ie. any nested config object is printed within curly brackets
      *
      * @param config The {@link ConfigObject} representing the parsed workflow configuration
      * @param output The stream where output the formatted configuration notation
diff --git a/modules/nextflow/src/main/groovy/nextflow/conda/CondaConfig.groovy b/modules/nextflow/src/main/groovy/nextflow/conda/CondaConfig.groovy
index e8f7dba54e..a58dc7f562 100644
--- a/modules/nextflow/src/main/groovy/nextflow/conda/CondaConfig.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/conda/CondaConfig.groovy
@@ -55,6 +55,6 @@ class CondaConfig extends LinkedHashMap {
             return value.tokenize(',').collect(it -> it.trim())
         }
 
-        throw new IllegalArgumentException("Unexected conda.channels value: $value")
+        throw new IllegalArgumentException("Unexpected conda.channels value: $value")
     }
 }
diff --git a/modules/nextflow/src/main/groovy/nextflow/config/CascadingConfig.groovy b/modules/nextflow/src/main/groovy/nextflow/config/CascadingConfig.groovy
index 18461cc7c0..f393e224b4 100644
--- a/modules/nextflow/src/main/groovy/nextflow/config/CascadingConfig.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/config/CascadingConfig.groovy
@@ -122,7 +122,7 @@ abstract class CascadingConfig<K,V> {
     /**
      * Convert this object to an equivalent {@link ConfigObject}
      *
-     * @return A {@link ConfigObject} holding teh same data
+     * @return A {@link ConfigObject} holding the same data
      */
     ConfigObject toConfigObject() {
         toConfigObject0(this.config)
diff --git a/modules/nextflow/src/main/groovy/nextflow/container/SingularityCache.groovy b/modules/nextflow/src/main/groovy/nextflow/container/SingularityCache.groovy
index 79203047b3..7e2134aa67 100644
--- a/modules/nextflow/src/main/groovy/nextflow/container/SingularityCache.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/container/SingularityCache.groovy
@@ -224,7 +224,7 @@ class SingularityCache {
             return libraryPath
         }
 
-        // check for the image in teh cache dir
+        // check for the image in the cache dir
         // if the image does not exist in the cache dir, download it
         final localPath = localCachePath(imageUrl)
         if( localPath.exists() ) {
diff --git a/modules/nextflow/src/main/groovy/nextflow/executor/ExecutorFactory.groovy b/modules/nextflow/src/main/groovy/nextflow/executor/ExecutorFactory.groovy
index 6b72deab11..57a1535b6c 100644
--- a/modules/nextflow/src/main/groovy/nextflow/executor/ExecutorFactory.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/executor/ExecutorFactory.groovy
@@ -212,7 +212,7 @@ class ExecutorFactory {
     }
 
     /**
-     * Find out the 'executor' to be used in the process definition or in teh session configuration object
+     * Find out the 'executor' to be used in the process definition or in the session configuration object
      *
      * @param taskConfig
      */
diff --git a/modules/nextflow/src/main/groovy/nextflow/executor/GridTaskHandler.groovy b/modules/nextflow/src/main/groovy/nextflow/executor/GridTaskHandler.groovy
index e0ed5c4bb7..503b679d6a 100644
--- a/modules/nextflow/src/main/groovy/nextflow/executor/GridTaskHandler.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/executor/GridTaskHandler.groovy
@@ -381,7 +381,7 @@ class GridTaskHandler extends TaskHandler implements FusionAwareTask {
         else {
             /*
              * Since working with NFS it may happen that the file exists BUT it is empty due to network latencies,
-             * before retuning an invalid exit code, wait some seconds.
+             * before returning an invalid exit code, wait some seconds.
              *
              * More in detail:
              * 1) the very first time that arrive here initialize the 'exitTimestampMillis' to the current timestamp
diff --git a/modules/nextflow/src/main/groovy/nextflow/extension/OperatorImpl.groovy b/modules/nextflow/src/main/groovy/nextflow/extension/OperatorImpl.groovy
index 12c6abbe28..154dcee0f2 100644
--- a/modules/nextflow/src/main/groovy/nextflow/extension/OperatorImpl.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/extension/OperatorImpl.groovy
@@ -1048,7 +1048,7 @@ class OperatorImpl {
     static private final Map PARAMS_VIEW = [newLine: Boolean]
 
     /**
-     * Print out the channel content retuning a new channel emitting the identical content as the original one
+     * Print out the channel content returning a new channel emitting the identical content as the original one
      *
      * @param source
      * @param closure
diff --git a/modules/nextflow/src/main/groovy/nextflow/k8s/model/PodHostMount.groovy b/modules/nextflow/src/main/groovy/nextflow/k8s/model/PodHostMount.groovy
index 037e6f7fdd..949a10ca06 100644
--- a/modules/nextflow/src/main/groovy/nextflow/k8s/model/PodHostMount.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/k8s/model/PodHostMount.groovy
@@ -21,7 +21,7 @@ import groovy.transform.EqualsAndHashCode
 import groovy.transform.ToString
 
 /**
- * Model a K8s pod host mount defintion
+ * Model a K8s pod host mount definition
  *
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
  */
diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
index 38cac391c9..07fe7a7ef6 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
@@ -379,7 +379,7 @@ class TaskProcessor {
     /**
      * Launch the 'script' define by the code closure as a local bash script
      *
-     * @param code A {@code Closure} retuning a bash script e.g.
+     * @param code A {@code Closure} returning a bash script e.g.
      *          <pre>
      *              {
      *                 """
diff --git a/modules/nextflow/src/main/groovy/nextflow/scm/ProviderPath.groovy b/modules/nextflow/src/main/groovy/nextflow/scm/ProviderPath.groovy
index 01732a89bd..8e4815cf09 100644
--- a/modules/nextflow/src/main/groovy/nextflow/scm/ProviderPath.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/scm/ProviderPath.groovy
@@ -89,7 +89,7 @@ class ProviderPath implements Path {
             return true
         }
         catch (Exception e) {
-            log.trace "Failed to check existance -- cause [${e.class.name}] ${e.message}"
+            log.trace "Failed to check existence -- cause [${e.class.name}] ${e.message}"
             return false
         }
     }
diff --git a/modules/nextflow/src/main/groovy/nextflow/spack/SpackConfig.groovy b/modules/nextflow/src/main/groovy/nextflow/spack/SpackConfig.groovy
index f28e18cca5..6465f87156 100644
--- a/modules/nextflow/src/main/groovy/nextflow/spack/SpackConfig.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/spack/SpackConfig.groovy
@@ -55,6 +55,6 @@ class SpackConfig extends LinkedHashMap {
             return value.tokenize(',').collect(it -> it.trim())
         }
 
-        throw new IllegalArgumentException("Unexected spack.channels value: $value")
+        throw new IllegalArgumentException("Unexpected spack.channels value: $value")
     }
 }
diff --git a/modules/nextflow/src/main/groovy/nextflow/splitter/FastaSplitter.groovy b/modules/nextflow/src/main/groovy/nextflow/splitter/FastaSplitter.groovy
index 2e12cff890..fc492e55a0 100644
--- a/modules/nextflow/src/main/groovy/nextflow/splitter/FastaSplitter.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/splitter/FastaSplitter.groovy
@@ -79,7 +79,7 @@ class FastaSplitter extends AbstractTextSplitter {
     }
 
     /**
-     * Parse a {@code CharSequence} as a FASTA formatted text, retuning a {@code Map} object
+     * Parse a {@code CharSequence} as a FASTA formatted text, returning a {@code Map} object
      * containing the fields as specified by the @{code record} parameter.
      * <p>
      *  For example:
diff --git a/modules/nextflow/src/main/groovy/nextflow/trace/GraphObserver.groovy b/modules/nextflow/src/main/groovy/nextflow/trace/GraphObserver.groovy
index 0a61d43eda..a07f611f16 100644
--- a/modules/nextflow/src/main/groovy/nextflow/trace/GraphObserver.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/trace/GraphObserver.groovy
@@ -67,7 +67,7 @@ class GraphObserver implements TraceObserver {
     @Override
     void onFlowCreate(Session session) {
         this.dag = session.dag
-        // check file existance
+        // check file existence
         final attrs = FileHelper.readAttributes(file)
         if( attrs ) {
             if( overwrite && (attrs.isDirectory() || !file.delete()) )
diff --git a/modules/nextflow/src/main/groovy/nextflow/trace/ReportSummary.groovy b/modules/nextflow/src/main/groovy/nextflow/trace/ReportSummary.groovy
index 427668bb7a..b205e43cdc 100644
--- a/modules/nextflow/src/main/groovy/nextflow/trace/ReportSummary.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/trace/ReportSummary.groovy
@@ -113,11 +113,11 @@ class ReportSummary {
      *      - q3: third quartile
      *      - max: maximum value
      *      - mean: average value
-     *      - minLabel: label fot the task reporting the min value
-     *      - q1Label: label fot the task reporting the q1 value
-     *      - q2Label: label fot the task reporting the q2 value
-     *      - q3Label: label fot the task reporting the q3 value
-     *      - maxLabel: label fot the task reporting the max value
+     *      - minLabel: label for the task reporting the min value
+     *      - q1Label: label for the task reporting the q1 value
+     *      - q2Label: label for the task reporting the q2 value
+     *      - q3Label: label for the task reporting the q3 value
+     *      - maxLabel: label for the task reporting the max value
      */
     Map<String,?> compute(String name) {
         if( !names.contains(name) )
@@ -207,11 +207,11 @@ class ReportSummary {
          *      - q3: third quartile
          *      - max: maximum value
          *      - mean: average value
-         *      - minLabel: label fot the task reporting the min value
-         *      - q1Label: label fot the task reporting the q1 value
-         *      - q2Label: label fot the task reporting the q2 value
-         *      - q3Label: label fot the task reporting the q3 value
-         *      - maxLabel: label fot the task reporting the max value
+         *      - minLabel: label for the task reporting the min value
+         *      - q1Label: label for the task reporting the q1 value
+         *      - q2Label: label for the task reporting the q2 value
+         *      - q3Label: label for the task reporting the q3 value
+         *      - maxLabel: label for the task reporting the max value
          */
         Map<String,?> compute() {
             if( count==0 )
diff --git a/modules/nextflow/src/main/groovy/nextflow/trace/TraceObserver.groovy b/modules/nextflow/src/main/groovy/nextflow/trace/TraceObserver.groovy
index 45e414764e..c5fac42d00 100644
--- a/modules/nextflow/src/main/groovy/nextflow/trace/TraceObserver.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/trace/TraceObserver.groovy
@@ -71,7 +71,7 @@ trait TraceObserver {
      * @param handler
      *      The {@link TaskHandler} instance for the current task.
      * @param trace
-     *      The associated {@link TraceRecord} fot the current task.
+     *      The associated {@link TraceRecord} for the current task.
      */
     void onProcessSubmit(TaskHandler handler, TraceRecord trace){}
 
@@ -81,7 +81,7 @@ trait TraceObserver {
      * @param handler
      *      The {@link TaskHandler} instance for the current task.
      * @param trace
-     *      The associated {@link TraceRecord} fot the current task.
+     *      The associated {@link TraceRecord} for the current task.
      */
     void onProcessStart(TaskHandler handler, TraceRecord trace){}
 
@@ -91,7 +91,7 @@ trait TraceObserver {
      * @param handler
      *      The {@link TaskHandler} instance for the current task.
      * @param trace
-     *      The associated {@link TraceRecord} fot the current task.
+     *      The associated {@link TraceRecord} for the current task.
      */
     void onProcessComplete(TaskHandler handler, TraceRecord trace){}
 
@@ -118,7 +118,7 @@ trait TraceObserver {
      * @param handler
      *      The {@link TaskHandler} instance for the current task.
      * @param trace
-     *      The associated {@link TraceRecord} fot the current task.
+     *      The associated {@link TraceRecord} for the current task.
      */
     void onFlowError(TaskHandler handler, TraceRecord trace){}
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/util/LoggerHelper.groovy b/modules/nextflow/src/main/groovy/nextflow/util/LoggerHelper.groovy
index 3db81305b7..8d995b29b6 100644
--- a/modules/nextflow/src/main/groovy/nextflow/util/LoggerHelper.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/util/LoggerHelper.groovy
@@ -336,7 +336,7 @@ class LoggerHelper {
      *     instead in the file are saved the DEBUG level messages.
      *
      * @param logFileName The file where save the application log
-     * @param quiet When {@code true} only Warning and Error messages are visualized to teh console
+     * @param quiet When {@code true} only Warning and Error messages are visualized to the console
      * @param debugConf The list of packages for which use a Debug logging level
      * @param traceConf The list of packages for which use a Trace logging level
      */
diff --git a/modules/nextflow/src/main/groovy/nextflow/util/NameGenerator.groovy b/modules/nextflow/src/main/groovy/nextflow/util/NameGenerator.groovy
index 3691e50033..9ad2641cb8 100644
--- a/modules/nextflow/src/main/groovy/nextflow/util/NameGenerator.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/util/NameGenerator.groovy
@@ -441,7 +441,7 @@ class NameGenerator {
             // A. P. J. Abdul Kalam - is an Indian scientist aka Missile Man of India for his work on the development of ballistic missile and launch vehicle technology. https://en.wikipedia.org/wiki/A._P._J._Abdul_Kalam
             "kalam",
 
-            // Rudolf E. Kálmán, American engineer and mathematican of Hungarian origin. One of the inventors of the smoother/predictor commonly known as "Kalman Filter". https://en.wikipedia.org/wiki/Rudolf_E._K%C3%A1lm%C3%A1n
+            // Rudolf E. Kálmán, American engineer and mathematician of Hungarian origin. One of the inventors of the smoother/predictor commonly known as "Kalman Filter". https://en.wikipedia.org/wiki/Rudolf_E._K%C3%A1lm%C3%A1n
             "kalman",
 
             // Susan Kare, created the icons and many of the interface elements for the original Apple Macintosh in the 1980s, and was an original employee of NeXT, working as the Creative Director. https://en.wikipedia.org/wiki/Susan_Kare
@@ -654,7 +654,7 @@ class NameGenerator {
             // Max Karl Ernst Ludwig Planck was a German theoretical physicist, best known for the discovery of energy quenta and Planck's constant. https://en.wikipedia.org/wiki/Max_Planck
             "planck",
 
-            // Joseph Plateau - Belgian physisist known for being one of the first persons to demonstrate the illusion of moving image. https://en.wikipedia.org/wiki/Joseph_Plateau
+            // Joseph Plateau - Belgian physicist known for being one of the first persons to demonstrate the illusion of moving image. https://en.wikipedia.org/wiki/Joseph_Plateau
             "plateau",
 
             // Henri Poincaré made fundamental contributions in several fields of mathematics. https://en.wikipedia.org/wiki/Henri_Poincar%C3%A9
diff --git a/modules/nf-commons/src/main/nextflow/extension/Bolts.groovy b/modules/nf-commons/src/main/nextflow/extension/Bolts.groovy
index 0778d810ad..76622474b8 100644
--- a/modules/nf-commons/src/main/nextflow/extension/Bolts.groovy
+++ b/modules/nf-commons/src/main/nextflow/extension/Bolts.groovy
@@ -275,7 +275,7 @@ class Bolts {
     }
 
     /**
-     * Check if a alphabetic characters in a string are lowercase. Non alphabetic characters are ingored
+     * Check if a alphabetic characters in a string are lowercase. Non alphabetic characters are ignored
      * @param self The string to check
      * @return {@true} if the string contains no uppercase characters, {@code false} otherwise
      */
diff --git a/modules/nf-commons/src/main/nextflow/file/FileHelper.groovy b/modules/nf-commons/src/main/nextflow/file/FileHelper.groovy
index a846a86565..b0f0acc85f 100644
--- a/modules/nf-commons/src/main/nextflow/file/FileHelper.groovy
+++ b/modules/nf-commons/src/main/nextflow/file/FileHelper.groovy
@@ -365,7 +365,7 @@ class FileHelper {
                 throw new IllegalArgumentException("Malformed file URI: $uri -- It must start either with a `file:/` or `file:///` prefix")
 
             if( !uri.path )
-                throw new IllegalArgumentException("Malformed file URI: $uri -- Make sure it starts with an absolue path prefix i.e. `file:/`")
+                throw new IllegalArgumentException("Malformed file URI: $uri -- Make sure it starts with an absolute path prefix i.e. `file:/`")
         }
         else if( !uri.path ) {
             throw new IllegalArgumentException("URI path cannot be empty")
diff --git a/modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy b/modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy
index 3a2adb200f..5800582a40 100644
--- a/modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy
+++ b/modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy
@@ -252,7 +252,7 @@ class PluginsFacade implements PluginStateListener {
             return manager.getExtensions(type)
         }
         else {
-            // this should oly be used to load system extensions
+            // this should only be used to load system extensions
             // i.e. included in the app class path not provided by
             // a plugin extension
             log.debug "Using Default plugin manager"
diff --git a/modules/nf-commons/src/main/nextflow/util/CacheHelper.java b/modules/nf-commons/src/main/nextflow/util/CacheHelper.java
index e21a417304..991da6c60a 100644
--- a/modules/nf-commons/src/main/nextflow/util/CacheHelper.java
+++ b/modules/nf-commons/src/main/nextflow/util/CacheHelper.java
@@ -230,7 +230,7 @@ public static Hasher hasher( Hasher hasher, Object value, HashMode mode ) {
      *
      * @param hasher The current {@code Hasher} object
      * @param file The {@code File} object to hash
-     * @param mode When {@code mode} is equals to the string {@code deep} is used teh file content
+     * @param mode When {@code mode} is equals to the string {@code deep} is used the file content
      *   in order to create the hash key for this file, otherwise just the file metadata information
      *   (full name, size and last update timestamp)
      * @return The updated {@code Hasher} object
@@ -244,7 +244,7 @@ static private Hasher hashFile( Hasher hasher, java.io.File file, HashMode mode
      *
      * @param hasher The current {@code Hasher} object
      * @param path The {@code Path} object to hash
-     * @param mode When {@code mode} is equals to the string {@code deep} is used teh file content
+     * @param mode When {@code mode} is equals to the string {@code deep} is used the file content
      *   in order to create the hash key for this file, otherwise just the file metadata information
      *   (full name, size and last update timestamp)
      * @return The updated {@code Hasher} object
diff --git a/modules/nf-commons/src/main/nextflow/util/CharsetHelper.groovy b/modules/nf-commons/src/main/nextflow/util/CharsetHelper.groovy
index 45d3897834..d0af3923cc 100644
--- a/modules/nf-commons/src/main/nextflow/util/CharsetHelper.groovy
+++ b/modules/nf-commons/src/main/nextflow/util/CharsetHelper.groovy
@@ -43,7 +43,7 @@ class CharsetHelper {
             return Charset.forName(object)
 
         if( object != null )
-            log.warn "Invalid charset object: $object -- using defualt: ${Charset.defaultCharset()}"
+            log.warn "Invalid charset object: $object -- using default: ${Charset.defaultCharset()}"
 
         Charset.defaultCharset()
     }
diff --git a/modules/nf-commons/src/test/nextflow/extension/FilesExTest.groovy b/modules/nf-commons/src/test/nextflow/extension/FilesExTest.groovy
index 7b1ecbb7b9..a56b8bbe87 100644
--- a/modules/nf-commons/src/test/nextflow/extension/FilesExTest.groovy
+++ b/modules/nf-commons/src/test/nextflow/extension/FilesExTest.groovy
@@ -1272,7 +1272,7 @@ class FilesExTest extends Specification {
         FilesEx.toPosixFilePermission(0644) == [OWNER_READ, OWNER_WRITE, GROUP_READ, OTHERS_READ] as Set
     }
 
-    def 'should convert permissions to actal' () {
+    def 'should convert permissions to octal' () {
         expect:
         FilesEx.toOctalFileMode([] as Set) == 0
         and:
diff --git a/modules/nf-commons/src/test/nextflow/plugin/PluginsFacadeTest.groovy b/modules/nf-commons/src/test/nextflow/plugin/PluginsFacadeTest.groovy
index 7dc6f9b3b0..d8a58b637e 100644
--- a/modules/nf-commons/src/test/nextflow/plugin/PluginsFacadeTest.groovy
+++ b/modules/nf-commons/src/test/nextflow/plugin/PluginsFacadeTest.groovy
@@ -288,7 +288,7 @@ class PluginsFacadeTest extends Specification {
         plugins.size()==4
         plugins.find { it.id == 'nf-amazon' && it.version=='0.1.0' }    // <-- version from default
         plugins.find { it.id == 'nf-tower' && it.version=='1.0.1' }     // <-- version from the env var
-        plugins.find { it.id == 'nf-foo' && it.version=='2.2.0' }       // <-- version from tne env var
+        plugins.find { it.id == 'nf-foo' && it.version=='2.2.0' }       // <-- version from the env var
         plugins.find { it.id == 'nf-bar' && it.version==null }          // <-- no version 
     }
 
diff --git a/modules/nf-commons/src/testFixtures/groovy/nextflow/plugin/hello/HelloExtension.groovy b/modules/nf-commons/src/testFixtures/groovy/nextflow/plugin/hello/HelloExtension.groovy
index 2c4dc2e7d4..1436a5f790 100644
--- a/modules/nf-commons/src/testFixtures/groovy/nextflow/plugin/hello/HelloExtension.groovy
+++ b/modules/nf-commons/src/testFixtures/groovy/nextflow/plugin/hello/HelloExtension.groovy
@@ -139,7 +139,7 @@ class HelloExtension extends PluginExtensionPoint {
      */
     @Function
     String sayHello(String lang='en'){
-        assert initialized, "PluginExtension was not initilized"
+        assert initialized, "PluginExtension was not initialized"
         // sayHello is the entrypoint where we can write all the logic or delegate to other classes, ...
         return functions.sayHello(lang)
     }
diff --git a/modules/nf-httpfs/src/main/nextflow/file/http/XFileSystemProvider.groovy b/modules/nf-httpfs/src/main/nextflow/file/http/XFileSystemProvider.groovy
index 2f00717c2c..ac3e8cee11 100644
--- a/modules/nf-httpfs/src/main/nextflow/file/http/XFileSystemProvider.groovy
+++ b/modules/nf-httpfs/src/main/nextflow/file/http/XFileSystemProvider.groovy
@@ -389,7 +389,7 @@ abstract class XFileSystemProvider extends FileSystemProvider {
 
     @Override
     DirectoryStream<Path> newDirectoryStream(Path dir, DirectoryStream.Filter<? super Path> filter) throws IOException {
-        throw new UnsupportedOperationException("Direcotry listing unsupported by ${getScheme().toUpperCase()} file system provider")
+        throw new UnsupportedOperationException("Directory listing unsupported by ${getScheme().toUpperCase()} file system provider")
     }
 
     @Override
diff --git a/plugins/README.md b/plugins/README.md
index 5c3569fb13..153eecab26 100644
--- a/plugins/README.md
+++ b/plugins/README.md
@@ -107,7 +107,7 @@ If no plugins are specified in the nextflow.config file, Nextflow default plugin
 The default plugins list is defined in the Nextflow resources file included in the distribution runtime 
 `./modules/nextflow/src/main/resources/META-INF/plugins-info.txt`. 
 
-To disable the use of defualt plugins set the following variable `NXF_PLUGINS_DEFAULT=false`.
+To disable the use of default plugins set the following variable `NXF_PLUGINS_DEFAULT=false`.
 
 ## Gradle Tasks 
 
diff --git a/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchService.groovy b/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchService.groovy
index bff0b013d1..ddd858991f 100644
--- a/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchService.groovy
+++ b/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchService.groovy
@@ -274,7 +274,7 @@ class AzBatchService implements Closeable {
             if (!config.batch().accountName)
                 throw new IllegalArgumentException("Missing Azure Batch account name -- Specify it in the nextflow.config file using the setting 'azure.batch.accountName'")
             if (!config.batch().accountKey)
-                throw new IllegalArgumentException("Missing Azure Batch account key -- Specify it in the nextflow.config file using the setting 'azure.batch.accountKet'")
+                throw new IllegalArgumentException("Missing Azure Batch account key -- Specify it in the nextflow.config file using the setting 'azure.batch.accountKey'")
 
             return new BatchSharedKeyCredentials(config.batch().endpoint, config.batch().accountName, config.batch().accountKey)
 
@@ -872,7 +872,7 @@ class AzBatchService implements Closeable {
         final listener = new EventListener<ExecutionAttemptedEvent<T>>() {
             @Override
             void accept(ExecutionAttemptedEvent<T> event) throws Throwable {
-                log.debug("Azure TooManyRequests reponse error - attempt: ${event.attemptCount}; reason: ${event.lastFailure.message}")
+                log.debug("Azure TooManyRequests response error - attempt: ${event.attemptCount}; reason: ${event.lastFailure.message}")
             }
         }
         return RetryPolicy.<T>builder()
diff --git a/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerClient.groovy b/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerClient.groovy
index 7fa2dac217..b494e8a30b 100644
--- a/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerClient.groovy
+++ b/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerClient.groovy
@@ -652,7 +652,7 @@ class TowerClient implements TraceObserver {
             def map = obj as Map
             return map.collect { k,v -> "$k:$v" }.join(',')
         }
-        throw new IllegalArgumentException("Illegal container attribut type: ${obj.getClass().getName()} = ${obj}" )
+        throw new IllegalArgumentException("Illegal container attribute type: ${obj.getClass().getName()} = ${obj}" )
     }
 
     protected Map makeTaskMap0(TraceRecord trace) {

From 8eb5f30584ef24f02f24c93c4dfc79fe561cdea0 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Thu, 10 Aug 2023 21:51:45 +0200
Subject: [PATCH 069/350] Add 429 http status code to Wave retriable errors

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
index 45e2125cea..d189704e86 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
@@ -596,7 +596,7 @@ class WaveClient {
         return Failsafe.with(policy).get(action)
     }
 
-    static private final List<Integer> SERVER_ERRORS = [502,503,504]
+    static private final List<Integer> SERVER_ERRORS = [429,502,503,504]
 
     protected HttpResponse<String> httpSend(HttpRequest req)  {
         return safeApply(() -> {

From 98f88a502fcbff13c596588d6c912020e013d383 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Fri, 11 Aug 2023 18:41:55 +0000
Subject: [PATCH 070/350] Update changelog

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 changelog.txt | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/changelog.txt b/changelog.txt
index 852e84c0bf..9e2995e8f8 100644
--- a/changelog.txt
+++ b/changelog.txt
@@ -1,5 +1,13 @@
 NEXTFLOW CHANGE-LOG
 ===================
+23.04.3 - 11 Aug 2023
+- Increase Wave client max attempts [8c67610a]
+- Fix log typo [03e19ea2]
+- Add 429 http status code to Wave retriable errors [a8b8c6c5]
+- Improve handling Wave server errors [621c9665]
+- Bump nf-wave@0.8.4 [d7fa3f26]
+- Bump corretto 17.0.8 [7a73a78f]
+
 23.08.0-edge - 5 Aug 2023 
 - Add `-value` option to `config` command (#4142) [57e3100b]
 - Add `deleteTasksOnCompletion` to Azure Batch configuration (#4114) [b14674dc]
@@ -114,6 +122,12 @@ NEXTFLOW CHANGE-LOG
 - Bump nf-amazon@2.1.0 [57464746]
 - Bump nf-cloudcache@0.1.0 [cb6242c4]
 
+23.04.2 - 8 Jun 2023
+- Fix non-deterministic null container engine error [f93221ab]
+- Add retry policy to Wave client [2f1532f6]
+- Fix wave build docs [34a73022]
+- Bump nf-wave@0.8.3 [350201b5]
+
 23.05.0-edge - 15 May 2023
 - Add support for custom custom root directory to resolve relative paths (#3942) [f06bb1f7]
 - Add `arch` directive support for Spack (#3786) [62dfc482]

From 7b19fb03396236f0722b565bdbb017c4c2d5d351 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sun, 13 Aug 2023 10:41:30 +0200
Subject: [PATCH 071/350] Improve Conda build error report [ci fast]

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../nextflow/src/main/groovy/nextflow/conda/CondaCache.groovy | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/conda/CondaCache.groovy b/modules/nextflow/src/main/groovy/nextflow/conda/CondaCache.groovy
index f508c74fdc..451aeecac2 100644
--- a/modules/nextflow/src/main/groovy/nextflow/conda/CondaCache.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/conda/CondaCache.groovy
@@ -315,9 +315,9 @@ class CondaCache {
 
         final max = createTimeout.toMillis()
         final builder = new ProcessBuilder(['bash','-c',cmd])
-        final proc = builder.start()
+        final proc = builder.redirectErrorStream(true).start()
         final err = new StringBuilder()
-        final consumer = proc.consumeProcessErrorStream(err)
+        final consumer = proc.consumeProcessOutputStream(err)
         proc.waitForOrKill(max)
         def status = proc.exitValue()
         if( status != 0 ) {

From d99b34322369c1a2602da26866d5a34302939da2 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sun, 13 Aug 2023 15:55:01 +0200
Subject: [PATCH 072/350] Fix Process hangs when using flatten and finish
 errorStrategy

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../nextflow/extension/OperatorImpl.groovy    | 28 +++++++++++--------
 1 file changed, 16 insertions(+), 12 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/extension/OperatorImpl.groovy b/modules/nextflow/src/main/groovy/nextflow/extension/OperatorImpl.groovy
index 154dcee0f2..16a9b87a45 100644
--- a/modules/nextflow/src/main/groovy/nextflow/extension/OperatorImpl.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/extension/OperatorImpl.groovy
@@ -41,6 +41,7 @@ import nextflow.script.TokenBranchDef
 import nextflow.script.TokenMultiMapDef
 import nextflow.splitter.FastaSplitter
 import nextflow.splitter.FastqSplitter
+import nextflow.splitter.JsonSplitter
 import nextflow.splitter.TextSplitter
 import org.codehaus.groovy.runtime.callsite.BooleanReturningMethodInvoker
 import org.codehaus.groovy.runtime.typehandling.DefaultTypeTransformation
@@ -725,23 +726,26 @@ class OperatorImpl {
 
         final listeners = []
         final target = CH.create()
+        final stopOnFirst = source instanceof DataflowExpression
 
-        if( source instanceof DataflowExpression ) {
-            listeners << new DataflowEventAdapter() {
-                @Override
-                void afterRun(final DataflowProcessor processor, final List<Object> messages) {
-                    processor.bindOutput( Channel.STOP )
+        listeners << new DataflowEventAdapter() {
+            @Override
+            void afterRun(final DataflowProcessor processor, final List<Object> messages) {
+                if( stopOnFirst )
                     processor.terminate()
-                }
+            }
 
-                boolean onException(final DataflowProcessor processor, final Throwable e) {
-                    OperatorImpl.log.error("@unknown", e)
-                    session.abort(e)
-                    return true;
-                }
+            @Override
+            void afterStop(final DataflowProcessor processor) {
+                processor.bindOutput(Channel.STOP)
             }
-        }
 
+            boolean onException(final DataflowProcessor processor, final Throwable e) {
+                OperatorImpl.log.error("@unknown", e)
+                session.abort(e)
+                return true;
+            }
+        }
 
         newOperator(inputs: [source], outputs: [target], listeners: listeners) {  item ->
 

From b238d7e238959edb5300dbebcda67ff4f7929e98 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sun, 13 Aug 2023 16:23:06 +0200
Subject: [PATCH 073/350] Fix Execution should fail if report or timeline file
 already exists

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../src/main/groovy/nextflow/trace/ReportObserver.groovy      | 4 ++++
 .../src/main/groovy/nextflow/trace/TimelineObserver.groovy    | 3 +++
 2 files changed, 7 insertions(+)

diff --git a/modules/nextflow/src/main/groovy/nextflow/trace/ReportObserver.groovy b/modules/nextflow/src/main/groovy/nextflow/trace/ReportObserver.groovy
index 978e248983..b3886ac205 100644
--- a/modules/nextflow/src/main/groovy/nextflow/trace/ReportObserver.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/trace/ReportObserver.groovy
@@ -24,6 +24,7 @@ import groovy.text.GStringTemplateEngine
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import nextflow.Session
+import nextflow.exception.AbortOperationException
 import nextflow.processor.TaskHandler
 import nextflow.processor.TaskId
 import nextflow.processor.TaskProcessor
@@ -127,6 +128,9 @@ class ReportObserver implements TraceObserver {
     void onFlowCreate(Session session) {
         this.session = session
         this.aggregator = new ResourcesAggregator(session)
+        // check if the process exists
+        if( Files.exists(reportFile) && !overwrite )
+            throw new AbortOperationException("Report file already exists: ${reportFile.toUriString()} -- enable the 'report.overwrite' option in your config file to overwrite existing files")
     }
 
     /**
diff --git a/modules/nextflow/src/main/groovy/nextflow/trace/TimelineObserver.groovy b/modules/nextflow/src/main/groovy/nextflow/trace/TimelineObserver.groovy
index e96efab748..8ae3369613 100644
--- a/modules/nextflow/src/main/groovy/nextflow/trace/TimelineObserver.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/trace/TimelineObserver.groovy
@@ -24,6 +24,7 @@ import groovy.text.GStringTemplateEngine
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import nextflow.Session
+import nextflow.exception.AbortOperationException
 import nextflow.processor.TaskHandler
 import nextflow.processor.TaskId
 import nextflow.processor.TaskProcessor
@@ -71,6 +72,8 @@ class TimelineObserver implements TraceObserver {
     @Override
     void onFlowCreate(Session session) {
         beginMillis = startMillis = System.currentTimeMillis()
+        if( Files.exists(reportFile) && !overwrite )
+            throw new AbortOperationException("Timeline file already exists: ${reportFile.toUriString()} -- enable the 'timelime.overwrite' option in your config file to overwrite existing files")
     }
 
     /**

From 8e4d7fedd0b0338ec3752e0d9442c688bc13bbc0 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sun, 13 Aug 2023 17:29:44 +0200
Subject: [PATCH 074/350] Fix env output when changing task workdir

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../nextflow/container/ShifterBuilder.groovy  |  3 ++
 .../executor/BashWrapperBuilder.groovy        |  3 ++
 .../nextflow/executor/command-run.txt         |  1 +
 .../executor/BashWrapperBuilderTest.groovy    | 43 ++++++++++---------
 .../executor/test-bash-wrapper-with-trace.txt |  1 +
 .../nextflow/executor/test-bash-wrapper.txt   |  1 +
 .../google/lifesciences/bash-wrapper-gcp.txt  |  1 +
 7 files changed, 32 insertions(+), 21 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/container/ShifterBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/container/ShifterBuilder.groovy
index d0f757053f..d1cb33bfc1 100644
--- a/modules/nextflow/src/main/groovy/nextflow/container/ShifterBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/container/ShifterBuilder.groovy
@@ -95,6 +95,9 @@ class ShifterBuilder extends ContainerBuilder<ShifterBuilder> {
         else if( env instanceof String && env.contains('=') ) {
             result << env
         }
+        else if( env instanceof String ) {
+            result << "\${$env:+\"$env=\$$env\"}"
+        }
         else if( env ) {
             throw new IllegalArgumentException("Not a valid environment value: $env [${env.class.name}]")
         }
diff --git a/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
index 25b21626ec..835739e5ae 100644
--- a/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
@@ -183,6 +183,7 @@ class BashWrapperBuilder {
         result.append('\n')
         result.append('# capture process environment\n')
         result.append('set +u\n')
+        result.append('cd "$NXF_TASK_WORKDIR"\n')
         for( int i=0; i<names.size(); i++) {
             final key = names[i]
             result.append "echo $key=\${$key[@]} "
@@ -582,6 +583,8 @@ class BashWrapperBuilder {
         if( this.containerCpuset )
             builder.addRunOptions(containerCpuset)
 
+        // export task work directory
+        builder.addEnv('NXF_TASK_WORKDIR')
         // export the nextflow script debug variable
         if( isTraceRequired() )
             builder.addEnv( 'NXF_DEBUG=${NXF_DEBUG:=0}')
diff --git a/modules/nextflow/src/main/resources/nextflow/executor/command-run.txt b/modules/nextflow/src/main/resources/nextflow/executor/command-run.txt
index f98408d195..1c261c937c 100644
--- a/modules/nextflow/src/main/resources/nextflow/executor/command-run.txt
+++ b/modules/nextflow/src/main/resources/nextflow/executor/command-run.txt
@@ -147,6 +147,7 @@ nxf_main() {
     {{task_env}}
     {{secrets_env}}
     [[ $NXF_SCRATCH ]] && cd $NXF_SCRATCH
+    export NXF_TASK_WORKDIR="$PWD"
     {{stage_cmd}}
 
     set +e
diff --git a/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
index 20339d9118..3e2f3a2c93 100644
--- a/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
@@ -216,7 +216,7 @@ class BashWrapperBuilderTest extends Specification {
         def builder = bash.createContainerBuilder(null)
         then:
         builder instanceof SingularityBuilder
-        builder.env == ['FOO','BAR']
+        builder.env == ['NXF_TASK_WORKDIR', 'FOO','BAR']
         builder.workDir == Paths.get('/my/work/dir')
         builder.mounts == [ Paths.get('/my/bin') ]
         
@@ -720,7 +720,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'docker', temp: 'auto', enabled: true] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'docker run -i -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'docker run -i ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
         binding.cleanup_cmd == 'docker rm $NXF_BOXID &>/dev/null || true\n'
         binding.kill_cmd == 'docker stop $NXF_BOXID'
     }
@@ -734,7 +734,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'docker', temp: 'auto', enabled: true] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'docker run -i -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -c "eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
+        binding.launch_cmd == 'docker run -i ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -c "eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
         binding.cleanup_cmd == 'docker rm $NXF_BOXID &>/dev/null || true\n'
         binding.kill_cmd == 'docker stop $NXF_BOXID'
         and:
@@ -755,7 +755,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'docker', temp: 'auto', enabled: true, entrypointOverride: false] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'docker run -i -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'docker run -i ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
         binding.cleanup_cmd == 'docker rm $NXF_BOXID &>/dev/null || true\n'
         binding.kill_cmd == 'docker stop $NXF_BOXID'
     }
@@ -769,7 +769,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'docker', temp: 'auto', enabled: true, entrypointOverride: false] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'docker run -i -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -c "eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
+        binding.launch_cmd == 'docker run -i ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -c "eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
         binding.cleanup_cmd == 'docker rm $NXF_BOXID &>/dev/null || true\n'
         binding.kill_cmd == 'docker stop $NXF_BOXID'
         and:
@@ -790,7 +790,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerEnabled: true  ).makeBinding()
 
         then:
-        binding.launch_cmd == 'sudo docker run -i -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'sudo docker run -i ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
         binding.cleanup_cmd == 'sudo docker rm $NXF_BOXID &>/dev/null || true\n'
         binding.kill_cmd == 'sudo docker stop $NXF_BOXID'
     }
@@ -803,7 +803,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'docker', temp: 'auto', enabled: true, remove:false, kill: false] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'docker run -i -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID ubuntu /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'docker run -i ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID ubuntu /bin/bash -ue /work/dir/.command.sh'
         binding.cleanup_cmd == ""
         binding.kill_cmd == null
         binding.containsKey('kill_cmd')
@@ -817,7 +817,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'docker', enabled: true, remove:false, kill: 'SIGXXX'] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'docker run -i -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID ubuntu /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'docker run -i ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID ubuntu /bin/bash -ue /work/dir/.command.sh'
         binding.cleanup_cmd == ""
         binding.kill_cmd == 'docker kill -s SIGXXX $NXF_BOXID'
         binding.containsKey('kill_cmd')
@@ -832,7 +832,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'docker', enabled: true] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'docker run -i -v /folder\\ with\\ blanks:/folder\\ with\\ blanks -v /work/dir:/work/dir -w "\$PWD" --name \$NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'docker run -i ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} -v /folder\\ with\\ blanks:/folder\\ with\\ blanks -v /work/dir:/work/dir -w "\$PWD" --name \$NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
         binding.cleanup_cmd == 'docker rm $NXF_BOXID &>/dev/null || true\n'
         binding.kill_cmd == 'docker stop $NXF_BOXID'
     }
@@ -847,7 +847,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'docker', sudo: true, enabled: true] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'sudo docker run -i -v /work/dir:/work/dir -v "$PWD":"$PWD" -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'sudo docker run -i ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} -v /work/dir:/work/dir -v "$PWD":"$PWD" -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
         binding.kill_cmd == 'sudo docker stop $NXF_BOXID'
         binding.cleanup_cmd == '''\
                 (sudo -n true && sudo rm -rf "$NXF_SCRATCH" || rm -rf "$NXF_SCRATCH")&>/dev/null || true
@@ -864,7 +864,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'docker', enabled: true] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'docker run -i -v /work/dir:/work/dir -w "$PWD" -v /foo:/bar --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'docker run -i ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} -v /work/dir:/work/dir -w "$PWD" -v /foo:/bar --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
         binding.kill_cmd == 'docker stop $NXF_BOXID'
         binding.cleanup_cmd == 'docker rm $NXF_BOXID &>/dev/null || true\n'
     }
@@ -879,7 +879,7 @@ class BashWrapperBuilderTest extends Specification {
         then:
         binding.launch_cmd == '''\
         sarus pull busybox 1>&2
-        sarus run --mount=type=bind,source=/work/dir,destination=/work/dir -w "$PWD" busybox /bin/bash -ue /work/dir/.command.sh
+        sarus run ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} --mount=type=bind,source=/work/dir,destination=/work/dir -w "$PWD" busybox /bin/bash -ue /work/dir/.command.sh
         '''.stripIndent().rightTrim()
         binding.cleanup_cmd == ""
         binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
@@ -896,7 +896,7 @@ class BashWrapperBuilderTest extends Specification {
         then:
         binding.launch_cmd == '''\
         sarus pull busybox 1>&2
-        sarus run --mount=type=bind,source=/work/dir,destination=/work/dir -w "$PWD" busybox /bin/bash -c "eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"
+        sarus run ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} --mount=type=bind,source=/work/dir,destination=/work/dir -w "$PWD" busybox /bin/bash -c "eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"
         '''.stripIndent().rightTrim()
         binding.cleanup_cmd == ""
         binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
@@ -921,7 +921,7 @@ class BashWrapperBuilderTest extends Specification {
         then:
         binding.launch_cmd == '''\
         sarus pull busybox 1>&2
-        sarus run --mount=type=bind,source=/folder\\ with\\ blanks,destination=/folder\\ with\\ blanks --mount=type=bind,source=/work/dir,destination=/work/dir -w "$PWD" busybox /bin/bash -ue /work/dir/.command.sh
+        sarus run ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} --mount=type=bind,source=/folder\\ with\\ blanks,destination=/folder\\ with\\ blanks --mount=type=bind,source=/work/dir,destination=/work/dir -w "$PWD" busybox /bin/bash -ue /work/dir/.command.sh
         '''.stripIndent().rightTrim()
         binding.cleanup_cmd == ""
         binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
@@ -938,7 +938,7 @@ class BashWrapperBuilderTest extends Specification {
         then:
         binding.launch_cmd == '''\
         sarus pull busybox 1>&2
-        sarus run --mount=type=bind,source=/work/dir,destination=/work/dir -w "$PWD" --mount=type=bind,source=/foo,destination=/bar busybox /bin/bash -ue /work/dir/.command.sh
+        sarus run ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} --mount=type=bind,source=/work/dir,destination=/work/dir -w "$PWD" --mount=type=bind,source=/foo,destination=/bar busybox /bin/bash -ue /work/dir/.command.sh
         '''.stripIndent().rightTrim()
         binding.cleanup_cmd == ""
         binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
@@ -961,7 +961,7 @@ class BashWrapperBuilderTest extends Specification {
             STATUS=$(shifterimg -v pull docker://ubuntu:latest | tail -n2 | head -n1 | awk \'{print $6}\')
             [[ $STATUS == "FAILURE" || -z $STATUS ]] && echo "Shifter failed to pull image \'docker://ubuntu:latest\'" >&2  && exit 1
         done
-        shifter --image docker://ubuntu:latest /bin/bash -c "eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"
+        ${NXF_TASK_WORKDIR:+"NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} shifter --image docker://ubuntu:latest /bin/bash -c "eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"
         '''.stripIndent().rightTrim()
         binding.cleanup_cmd == ""
         binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
@@ -977,7 +977,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [enabled: true, engine: 'singularity'] as ContainerConfig ).makeBinding()
 
         then:
-        binding.launch_cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid docker://ubuntu:latest /bin/bash -c "cd $PWD; eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
+        binding.launch_cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} ${NXF_TASK_WORKDIR:+SINGULARITYENV_NXF_TASK_WORKDIR="$NXF_TASK_WORKDIR"} singularity exec --no-home --pid docker://ubuntu:latest /bin/bash -c "cd $PWD; eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
         binding.cleanup_cmd == ""
         binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
     }
@@ -991,7 +991,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [enabled: true, engine: 'singularity', entrypointOverride: true] as ContainerConfig ).makeBinding()
 
         then:
-        binding.launch_cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid docker://ubuntu:latest /bin/bash -c "cd $PWD; eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
+        binding.launch_cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} ${NXF_TASK_WORKDIR:+SINGULARITYENV_NXF_TASK_WORKDIR="$NXF_TASK_WORKDIR"} singularity exec --no-home --pid docker://ubuntu:latest /bin/bash -c "cd $PWD; eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
         binding.cleanup_cmd == ""
         binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
     }
@@ -1086,6 +1086,7 @@ class BashWrapperBuilderTest extends Specification {
         str == '''
             # capture process environment
             set +u
+            cd "$NXF_TASK_WORKDIR"
             echo FOO=${FOO[@]} > .command.env
             echo BAR=${BAR[@]} >> .command.env
             '''
@@ -1130,7 +1131,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'podman', enabled: true] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'podman run -i -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'podman run -i ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
         binding.cleanup_cmd == 'podman rm $NXF_BOXID &>/dev/null || true\n'
         binding.kill_cmd == 'podman stop $NXF_BOXID'
     }
@@ -1143,7 +1144,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'podman', enabled: true, entrypointOverride: true] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'podman run -i -v /work/dir:/work/dir -w "$PWD" --entrypoint /bin/bash --name $NXF_BOXID busybox -c "/bin/bash -ue /work/dir/.command.sh"'
+        binding.launch_cmd == 'podman run -i ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} -v /work/dir:/work/dir -w "$PWD" --entrypoint /bin/bash --name $NXF_BOXID busybox -c "/bin/bash -ue /work/dir/.command.sh"'
         binding.cleanup_cmd == 'podman rm $NXF_BOXID &>/dev/null || true\n'
         binding.kill_cmd == 'podman stop $NXF_BOXID'
     }
@@ -1157,7 +1158,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'podman', enabled: true] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'podman run -i -v /work/dir:/work/dir -v "$PWD":"$PWD" -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'podman run -i ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} -v /work/dir:/work/dir -v "$PWD":"$PWD" -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
         binding.cleanup_cmd == 'rm -rf $NXF_SCRATCH || true\npodman rm $NXF_BOXID &>/dev/null || true\n'
         binding.kill_cmd == 'podman stop $NXF_BOXID'
     }
diff --git a/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper-with-trace.txt b/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper-with-trace.txt
index 49ea12e675..b0672d36ad 100644
--- a/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper-with-trace.txt
+++ b/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper-with-trace.txt
@@ -305,6 +305,7 @@ nxf_main() {
     set +u
     set -u
     [[ $NXF_SCRATCH ]] && cd $NXF_SCRATCH
+    export NXF_TASK_WORKDIR="$PWD"
     nxf_stage
 
     set +e
diff --git a/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper.txt b/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper.txt
index 2a6a6c0e71..e855aa1a1e 100644
--- a/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper.txt
+++ b/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper.txt
@@ -122,6 +122,7 @@ nxf_main() {
     spack env activate -d /spack/env/path
     set -u
     [[ $NXF_SCRATCH ]] && cd $NXF_SCRATCH
+    export NXF_TASK_WORKDIR="$PWD"
     nxf_stage
 
     set +e
diff --git a/plugins/nf-google/src/test/nextflow/cloud/google/lifesciences/bash-wrapper-gcp.txt b/plugins/nf-google/src/test/nextflow/cloud/google/lifesciences/bash-wrapper-gcp.txt
index ff58667ae8..5cb73b9050 100644
--- a/plugins/nf-google/src/test/nextflow/cloud/google/lifesciences/bash-wrapper-gcp.txt
+++ b/plugins/nf-google/src/test/nextflow/cloud/google/lifesciences/bash-wrapper-gcp.txt
@@ -210,6 +210,7 @@ nxf_main() {
     set +u
     set -u
     [[ $NXF_SCRATCH ]] && cd $NXF_SCRATCH
+    export NXF_TASK_WORKDIR="$PWD"
 
     set +e
     (set -o pipefail; (nxf_launch | tee .command.out) 3>&1 1>&2 2>&3 | tee .command.err) &

From 3051cd13da0298eaca142509ac05c7080a1c4328 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sun, 13 Aug 2023 17:39:11 +0200
Subject: [PATCH 075/350] Improve handling of name-only container env variables

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../container/ContainerBuilder.groovy         |  2 +-
 .../container/ContainerBuilderTest.groovy     |  2 +-
 .../container/DockerBuilderTest.groovy        |  2 +-
 .../container/PodmanBuilderTest.groovy        |  2 +-
 .../executor/BashWrapperBuilderTest.groovy    | 34 +++++++++----------
 5 files changed, 21 insertions(+), 21 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/container/ContainerBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/container/ContainerBuilder.groovy
index 0d02192fb2..9f505f0a29 100644
--- a/modules/nextflow/src/main/groovy/nextflow/container/ContainerBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/container/ContainerBuilder.groovy
@@ -246,7 +246,7 @@ abstract class ContainerBuilder<V extends ContainerBuilder> {
             result << '-e "' << env << '"'
         }
         else if( env instanceof String ) {
-            result << "\${$env:+-e \"$env=\$$env\"}"
+            result << "-e \"$env\""
         }
         else if( env ) {
             throw new IllegalArgumentException("Not a valid environment value: $env [${env.class.name}]")
diff --git a/modules/nextflow/src/test/groovy/nextflow/container/ContainerBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/container/ContainerBuilderTest.groovy
index 45a94927e9..a1c0c4cf8c 100644
--- a/modules/nextflow/src/test/groovy/nextflow/container/ContainerBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/container/ContainerBuilderTest.groovy
@@ -56,7 +56,7 @@ class ContainerBuilderTest extends Specification {
         when:
         result = builder.makeEnv( 'FOO' )
         then:
-        result.toString() == '${FOO:+-e "FOO=$FOO"}'
+        result.toString() == '-e "FOO"'
 
         when:
         builder.makeEnv( 1 )
diff --git a/modules/nextflow/src/test/groovy/nextflow/container/DockerBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/container/DockerBuilderTest.groovy
index 1d0fa6d848..fd94d44262 100644
--- a/modules/nextflow/src/test/groovy/nextflow/container/DockerBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/container/DockerBuilderTest.groovy
@@ -58,7 +58,7 @@ class DockerBuilderTest extends Specification {
         ENV                 | EXPECT
         'X=1'               | '-e "X=1"'
         [VAR_X:1, VAR_Y: 2] | '-e "VAR_X=1" -e "VAR_Y=2"'
-        'BAR'               | '${BAR:+-e "BAR=$BAR"}'
+        'BAR'               | '-e "BAR"'
     }
 
     def 'test docker create command line'() {
diff --git a/modules/nextflow/src/test/groovy/nextflow/container/PodmanBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/container/PodmanBuilderTest.groovy
index 47e6404271..2d57837f84 100644
--- a/modules/nextflow/src/test/groovy/nextflow/container/PodmanBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/container/PodmanBuilderTest.groovy
@@ -62,7 +62,7 @@ class PodmanBuilderTest extends Specification {
         ENV                 | EXPECT
         'X=1'               | '-e "X=1"'
         [VAR_X:1, VAR_Y: 2] | '-e "VAR_X=1" -e "VAR_Y=2"'
-        'BAR'               | '${BAR:+-e "BAR=$BAR"}'
+        'BAR'               | '-e "BAR"'
     }
 
     def 'test podman create command line'() {
diff --git a/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
index 3e2f3a2c93..15c9965a18 100644
--- a/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
@@ -720,7 +720,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'docker', temp: 'auto', enabled: true] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'docker run -i ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'docker run -i -e "NXF_TASK_WORKDIR" -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
         binding.cleanup_cmd == 'docker rm $NXF_BOXID &>/dev/null || true\n'
         binding.kill_cmd == 'docker stop $NXF_BOXID'
     }
@@ -734,7 +734,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'docker', temp: 'auto', enabled: true] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'docker run -i ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -c "eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
+        binding.launch_cmd == 'docker run -i -e "NXF_TASK_WORKDIR" -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -c "eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
         binding.cleanup_cmd == 'docker rm $NXF_BOXID &>/dev/null || true\n'
         binding.kill_cmd == 'docker stop $NXF_BOXID'
         and:
@@ -755,7 +755,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'docker', temp: 'auto', enabled: true, entrypointOverride: false] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'docker run -i ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'docker run -i -e "NXF_TASK_WORKDIR" -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
         binding.cleanup_cmd == 'docker rm $NXF_BOXID &>/dev/null || true\n'
         binding.kill_cmd == 'docker stop $NXF_BOXID'
     }
@@ -769,7 +769,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'docker', temp: 'auto', enabled: true, entrypointOverride: false] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'docker run -i ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -c "eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
+        binding.launch_cmd == 'docker run -i -e "NXF_TASK_WORKDIR" -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -c "eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
         binding.cleanup_cmd == 'docker rm $NXF_BOXID &>/dev/null || true\n'
         binding.kill_cmd == 'docker stop $NXF_BOXID'
         and:
@@ -790,7 +790,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerEnabled: true  ).makeBinding()
 
         then:
-        binding.launch_cmd == 'sudo docker run -i ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'sudo docker run -i -e "NXF_TASK_WORKDIR" -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
         binding.cleanup_cmd == 'sudo docker rm $NXF_BOXID &>/dev/null || true\n'
         binding.kill_cmd == 'sudo docker stop $NXF_BOXID'
     }
@@ -803,7 +803,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'docker', temp: 'auto', enabled: true, remove:false, kill: false] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'docker run -i ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID ubuntu /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'docker run -i -e "NXF_TASK_WORKDIR" -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID ubuntu /bin/bash -ue /work/dir/.command.sh'
         binding.cleanup_cmd == ""
         binding.kill_cmd == null
         binding.containsKey('kill_cmd')
@@ -817,7 +817,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'docker', enabled: true, remove:false, kill: 'SIGXXX'] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'docker run -i ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID ubuntu /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'docker run -i -e "NXF_TASK_WORKDIR" -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID ubuntu /bin/bash -ue /work/dir/.command.sh'
         binding.cleanup_cmd == ""
         binding.kill_cmd == 'docker kill -s SIGXXX $NXF_BOXID'
         binding.containsKey('kill_cmd')
@@ -832,7 +832,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'docker', enabled: true] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'docker run -i ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} -v /folder\\ with\\ blanks:/folder\\ with\\ blanks -v /work/dir:/work/dir -w "\$PWD" --name \$NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'docker run -i -e "NXF_TASK_WORKDIR" -v /folder\\ with\\ blanks:/folder\\ with\\ blanks -v /work/dir:/work/dir -w "\$PWD" --name \$NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
         binding.cleanup_cmd == 'docker rm $NXF_BOXID &>/dev/null || true\n'
         binding.kill_cmd == 'docker stop $NXF_BOXID'
     }
@@ -847,7 +847,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'docker', sudo: true, enabled: true] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'sudo docker run -i ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} -v /work/dir:/work/dir -v "$PWD":"$PWD" -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'sudo docker run -i -e "NXF_TASK_WORKDIR" -v /work/dir:/work/dir -v "$PWD":"$PWD" -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
         binding.kill_cmd == 'sudo docker stop $NXF_BOXID'
         binding.cleanup_cmd == '''\
                 (sudo -n true && sudo rm -rf "$NXF_SCRATCH" || rm -rf "$NXF_SCRATCH")&>/dev/null || true
@@ -864,7 +864,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'docker', enabled: true] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'docker run -i ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} -v /work/dir:/work/dir -w "$PWD" -v /foo:/bar --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'docker run -i -e "NXF_TASK_WORKDIR" -v /work/dir:/work/dir -w "$PWD" -v /foo:/bar --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
         binding.kill_cmd == 'docker stop $NXF_BOXID'
         binding.cleanup_cmd == 'docker rm $NXF_BOXID &>/dev/null || true\n'
     }
@@ -879,7 +879,7 @@ class BashWrapperBuilderTest extends Specification {
         then:
         binding.launch_cmd == '''\
         sarus pull busybox 1>&2
-        sarus run ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} --mount=type=bind,source=/work/dir,destination=/work/dir -w "$PWD" busybox /bin/bash -ue /work/dir/.command.sh
+        sarus run -e "NXF_TASK_WORKDIR" --mount=type=bind,source=/work/dir,destination=/work/dir -w "$PWD" busybox /bin/bash -ue /work/dir/.command.sh
         '''.stripIndent().rightTrim()
         binding.cleanup_cmd == ""
         binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
@@ -896,7 +896,7 @@ class BashWrapperBuilderTest extends Specification {
         then:
         binding.launch_cmd == '''\
         sarus pull busybox 1>&2
-        sarus run ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} --mount=type=bind,source=/work/dir,destination=/work/dir -w "$PWD" busybox /bin/bash -c "eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"
+        sarus run -e "NXF_TASK_WORKDIR" --mount=type=bind,source=/work/dir,destination=/work/dir -w "$PWD" busybox /bin/bash -c "eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"
         '''.stripIndent().rightTrim()
         binding.cleanup_cmd == ""
         binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
@@ -921,7 +921,7 @@ class BashWrapperBuilderTest extends Specification {
         then:
         binding.launch_cmd == '''\
         sarus pull busybox 1>&2
-        sarus run ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} --mount=type=bind,source=/folder\\ with\\ blanks,destination=/folder\\ with\\ blanks --mount=type=bind,source=/work/dir,destination=/work/dir -w "$PWD" busybox /bin/bash -ue /work/dir/.command.sh
+        sarus run -e "NXF_TASK_WORKDIR" --mount=type=bind,source=/folder\\ with\\ blanks,destination=/folder\\ with\\ blanks --mount=type=bind,source=/work/dir,destination=/work/dir -w "$PWD" busybox /bin/bash -ue /work/dir/.command.sh
         '''.stripIndent().rightTrim()
         binding.cleanup_cmd == ""
         binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
@@ -938,7 +938,7 @@ class BashWrapperBuilderTest extends Specification {
         then:
         binding.launch_cmd == '''\
         sarus pull busybox 1>&2
-        sarus run ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} --mount=type=bind,source=/work/dir,destination=/work/dir -w "$PWD" --mount=type=bind,source=/foo,destination=/bar busybox /bin/bash -ue /work/dir/.command.sh
+        sarus run -e "NXF_TASK_WORKDIR" --mount=type=bind,source=/work/dir,destination=/work/dir -w "$PWD" --mount=type=bind,source=/foo,destination=/bar busybox /bin/bash -ue /work/dir/.command.sh
         '''.stripIndent().rightTrim()
         binding.cleanup_cmd == ""
         binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
@@ -1131,7 +1131,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'podman', enabled: true] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'podman run -i ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'podman run -i -e "NXF_TASK_WORKDIR" -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
         binding.cleanup_cmd == 'podman rm $NXF_BOXID &>/dev/null || true\n'
         binding.kill_cmd == 'podman stop $NXF_BOXID'
     }
@@ -1144,7 +1144,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'podman', enabled: true, entrypointOverride: true] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'podman run -i ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} -v /work/dir:/work/dir -w "$PWD" --entrypoint /bin/bash --name $NXF_BOXID busybox -c "/bin/bash -ue /work/dir/.command.sh"'
+        binding.launch_cmd == 'podman run -i -e "NXF_TASK_WORKDIR" -v /work/dir:/work/dir -w "$PWD" --entrypoint /bin/bash --name $NXF_BOXID busybox -c "/bin/bash -ue /work/dir/.command.sh"'
         binding.cleanup_cmd == 'podman rm $NXF_BOXID &>/dev/null || true\n'
         binding.kill_cmd == 'podman stop $NXF_BOXID'
     }
@@ -1158,7 +1158,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'podman', enabled: true] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'podman run -i ${NXF_TASK_WORKDIR:+-e "NXF_TASK_WORKDIR=$NXF_TASK_WORKDIR"} -v /work/dir:/work/dir -v "$PWD":"$PWD" -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'podman run -i -e "NXF_TASK_WORKDIR" -v /work/dir:/work/dir -v "$PWD":"$PWD" -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
         binding.cleanup_cmd == 'rm -rf $NXF_SCRATCH || true\npodman rm $NXF_BOXID &>/dev/null || true\n'
         binding.kill_cmd == 'podman stop $NXF_BOXID'
     }

From 245afa5d5be55ebc46d0d14738c1147a76ceff57 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Sun, 13 Aug 2023 11:13:25 -0500
Subject: [PATCH 076/350] Document error about trailing backslash with space
 (#4180)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 docs/script.md | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/docs/script.md b/docs/script.md
index c5b63012b0..e7bda1c07f 100644
--- a/docs/script.md
+++ b/docs/script.md
@@ -223,6 +223,14 @@ result = myLongCmdline.execute().text
 
 In the preceding example, `blastp` and its `-in`, `-out`, `-db` and `-html` switches and their arguments are effectively a single line.
 
+:::{warning}
+When using backslashes to continue a multi-line command, make sure to not put any spaces after the backslash, otherwise it will be interpreted by the Groovy lexer as an escaped space instead of a backslash, which will make your script incorrect. It will also print this warning:
+
+```
+unknown recognition error type: groovyjarjarantlr4.v4.runtime.LexerNoViableAltException
+```
+:::
+
 (script-regexp)=
 
 ### Regular expressions

From 563bff13eec29095a9e9d86d95033e98377fd2c8 Mon Sep 17 00:00:00 2001
From: Manuele Simi <2822686+manuelesimi@users.noreply.github.com>
Date: Sun, 13 Aug 2023 18:22:55 +0200
Subject: [PATCH 077/350] Update AWS instructions for creating a custom AMI [ci
 skip] (#4174)

Signed-off-by: Manuele Simi <manuele.simi@gmail.com>
---
 docs/aws.md | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

diff --git a/docs/aws.md b/docs/aws.md
index c2f0b69724..4cd2488f1b 100644
--- a/docs/aws.md
+++ b/docs/aws.md
@@ -260,10 +260,11 @@ There are several reasons why you might need to create your own [AMI (Amazon Mac
 
 ### Create your custom AMI
 
-From the EC2 Dashboard, select **Launch Instance**, then select **AWS Marketplace** in the left-hand pane and search for "ECS". In the result list, select **Amazon ECS-Optimized Amazon Linux 2 AMI**, then continue as usual to configure and launch the instance.
+From the EC2 Dashboard, select **Launch Instance**, then select **Browse more AMIs**. In the new page, select 
+**AWS Marketplace AMIs**, and then search for **Amazon ECS-Optimized Amazon Linux 2 (AL2) x86_64 AMI**. Select the AMI and continue as usual to configure and launch the instance.
 
 :::{note}
-The selected instance has a bootstrap volume of 8GB and a second EBS volume of 30GB for scratch storage, which is not enough for real genomic workloads. Make sure to specify an additional volume with enough storage for your pipeline execution.
+The selected instance has a root volume of 30GB. Make sure to increase its size or add a second EBS volume with enough storage for real genomic workloads.
 :::
 
 When the instance is running, SSH into it (or connect with the Session Manager service), install the AWS CLI, and install any other tool that may be required (see following sections).
@@ -303,7 +304,7 @@ Afterwards, verify that the AWS CLI package works correctly:
 
 ```console
 $ ./miniconda/bin/aws --version
-aws-cli/1.19.79 Python/3.8.5 Linux/4.14.231-173.361.amzn2.x86_64 botocore/1.20.79
+aws-cli/1.29.20 Python/3.11.4 Linux/4.14.318-241.531.amzn2.x86_64 botocore/1.31.20
 ```
 
 :::{note}
@@ -328,7 +329,7 @@ The grandparent directory of the `aws` tool will be mounted into the container a
 
 ### Docker installation
 
-Docker is required by Nextflow to execute tasks on AWS Batch. The **Amazon ECS-Optimized Amazon Linux 2** AMI has Docker installed, however, if you create your AMI from a different AMI that does not have Docker installed, you will need to install it manually.
+Docker is required by Nextflow to execute tasks on AWS Batch. The **Amazon ECS-Optimized Amazon Linux 2 (AL2) x86_64 AMI** has Docker installed, however, if you create your AMI from a different AMI that does not have Docker installed, you will need to install it manually.
 
 The following snippet shows how to install Docker on an Amazon EC2 instance:
 
@@ -353,7 +354,7 @@ These steps must be done *before* creating the AMI from the current EC2 instance
 
 The [ECS container agent](https://docs.aws.amazon.com/AmazonECS/latest/developerguide/ECS_agent.html) is a component of Amazon Elastic Container Service (Amazon ECS) and is responsible for managing containers on behalf of ECS. AWS Batch uses ECS to execute containerized jobs, therefore it requires the agent to be installed on EC2 instances within your Compute Environments.
 
-The ECS agent is included in the **Amazon ECS-Optimized Amazon Linux 2** AMI. If you use a different AMI, you can also install the agent on any EC2 instance that supports the Amazon ECS specification.
+The ECS agent is included in the **Amazon ECS-Optimized Amazon Linux 2 (AL2) x86_64 AMI** . If you use a different base AMI, you can also install the agent on any EC2 instance that supports the Amazon ECS specification.
 
 To install the agent, follow these steps:
 
@@ -373,6 +374,10 @@ curl -s http://localhost:51678/v1/metadata | python -mjson.tool (test)
 The `AmazonEC2ContainerServiceforEC2Role` policy must be attached to the instance role in order to be able to connect the EC2 instance created by the Compute Environment to the ECS container.
 :::
 
+:::{note}
+The `AmazonEC2ContainerRegistryReadOnly` policy should be attached to the instance role in order to get read-only access to Amazon EC2 Container Registry repositories.
+:::
+
 ## Jobs & Execution
 
 ### Custom job definition

From 6e6ea579afc203722addb354c7719338cca8e9b2 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Sun, 13 Aug 2023 11:23:21 -0500
Subject: [PATCH 078/350] Remove lock file from cloudcache (#4167)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 .../nextflow/cache/CloudCacheStore.groovy     | 26 -------------------
 1 file changed, 26 deletions(-)

diff --git a/plugins/nf-cloudcache/src/main/nextflow/cache/CloudCacheStore.groovy b/plugins/nf-cloudcache/src/main/nextflow/cache/CloudCacheStore.groovy
index 7d8b794739..c9f98bdef4 100644
--- a/plugins/nf-cloudcache/src/main/nextflow/cache/CloudCacheStore.groovy
+++ b/plugins/nf-cloudcache/src/main/nextflow/cache/CloudCacheStore.groovy
@@ -35,8 +35,6 @@ import nextflow.util.CacheHelper
 @CompileStatic
 class CloudCacheStore implements CacheStore {
 
-    private final String LOCK_NAME = 'LOCK'
-
     private final int KEY_SIZE
 
     /** The session UUID */
@@ -51,9 +49,6 @@ class CloudCacheStore implements CacheStore {
     /** The base path for this cache instance */
     private Path dataPath
 
-    /** The lock file for this cache instance */
-    private Path lock
-
     /** The path to the index file */
     private Path indexPath
 
@@ -69,7 +64,6 @@ class CloudCacheStore implements CacheStore {
         this.runName = runName
         this.basePath = basePath ?: defaultBasePath()
         this.dataPath = this.basePath.resolve("$uniqueId")
-        this.lock = dataPath.resolve(LOCK_NAME)
         this.indexPath = dataPath.resolve("index.$runName")
     }
 
@@ -83,7 +77,6 @@ class CloudCacheStore implements CacheStore {
 
     @Override
     CloudCacheStore open() {
-        acquireLock()
         indexWriter = new BufferedOutputStream(Files.newOutputStream(indexPath))
         return this
     }
@@ -92,28 +85,10 @@ class CloudCacheStore implements CacheStore {
     CloudCacheStore openForRead() {
         if( !dataPath.exists() )
             throw new AbortOperationException("Missing cache directory: $dataPath")
-        acquireLock()
         indexReader = Files.newInputStream(indexPath)
         return this
     }
 
-    private void acquireLock() {
-        if( lock.exists() ) {
-            final msg = """
-                Unable to acquire lock for session with ID ${uniqueId}
-
-                Common reasons for this error are:
-                - You are trying to resume the execution of an already running pipeline
-                - A previous execution was abruptly interrupted, leaving the session open
-
-                You can see the name of the conflicting run by inspecting the contents of the following path: ${lock}
-                """
-            throw new IOException(msg)
-        }
-
-        lock.text = runName
-    }
-
     @Override
     void drop() {
         dataPath.deleteDir()
@@ -122,7 +97,6 @@ class CloudCacheStore implements CacheStore {
     @Override
     void close() {
         FilesEx.closeQuietly(indexWriter)
-        lock.delete()
     }
 
     @Override

From 2b449daa88ac9da0f134da817346c8666f3ba612 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sun, 13 Aug 2023 18:24:20 +0200
Subject: [PATCH 079/350] Fix checkpoint thread termination (#4166)

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../src/main/io/seqera/tower/plugin/LogsCheckpoint.groovy    | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/plugins/nf-tower/src/main/io/seqera/tower/plugin/LogsCheckpoint.groovy b/plugins/nf-tower/src/main/io/seqera/tower/plugin/LogsCheckpoint.groovy
index 2b7da86ec3..3e0edfc9ba 100644
--- a/plugins/nf-tower/src/main/io/seqera/tower/plugin/LogsCheckpoint.groovy
+++ b/plugins/nf-tower/src/main/io/seqera/tower/plugin/LogsCheckpoint.groovy
@@ -39,6 +39,7 @@ class LogsCheckpoint implements TraceObserver {
     private Thread thread
     private Duration interval
     private LogsHandler handler
+    private volatile boolean terminated
 
     @Override
     void onFlowCreate(Session session) {
@@ -59,14 +60,14 @@ class LogsCheckpoint implements TraceObserver {
 
     @Override
     void onFlowComplete() {
-        thread.interrupt()
+        this.terminated = true
         thread.join()
     }
 
     protected void run() {
         log.debug "Starting logs checkpoint thread - interval: ${interval}"
         try {
-            while( !thread.isInterrupted() ) {
+            while( !terminated && !thread.isInterrupted() ) {
                 // just wait the declared delay
                 await(interval)
                 // checkpoint the logs

From 30036dbf3cde48a3aff8d17c7d65b14cb9ef07c4 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Mon, 14 Aug 2023 07:52:10 -0500
Subject: [PATCH 080/350] Update tip about modifying maps (#4153) [ci skip]

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/script.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/script.md b/docs/script.md
index e7bda1c07f..71df9a3487 100644
--- a/docs/script.md
+++ b/docs/script.md
@@ -114,7 +114,7 @@ new_scores = scores + ["Pete": 3, "Cedric": 120]
 When adding two maps, the first map is copied and then appended with the keys from the second map. Any conflicting keys are overwritten by the second map.
 
 :::{tip}
-Appending an "update" map is a safer way to modify maps in Nextflow, specifically when passing maps through channels. This way, any references to the original map elsewhere in the pipeline won't be modified.
+Copying a map with the `+` operator is a safer way to modify maps in Nextflow, specifically when passing maps through channels. This way, a new instance of the map will be created, and any references to the original map won't be affected.
 :::
 
 Learn more about maps:

From 4d91862712ab40686bc69f84c9a312c47229e897 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Mon, 14 Aug 2023 07:53:30 -0500
Subject: [PATCH 081/350] Apply K8s Pod metadata to Job (#4057) [ci fast]

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 .../nextflow/k8s/model/PodSpecBuilder.groovy  |  36 ++---
 .../nextflow/k8s/K8sDriverLauncherTest.groovy |  16 ++-
 .../nextflow/k8s/K8sTaskHandlerTest.groovy    |  33 +++--
 .../k8s/model/PodSpecBuilderTest.groovy       | 126 +++++++-----------
 4 files changed, 87 insertions(+), 124 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/k8s/model/PodSpecBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/k8s/model/PodSpecBuilder.groovy
index 1aea042686..6a36b27e63 100644
--- a/modules/nextflow/src/main/groovy/nextflow/k8s/model/PodSpecBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/k8s/model/PodSpecBuilder.groovy
@@ -564,30 +564,18 @@ class PodSpecBuilder {
     Map buildAsJob() {
         final pod = build()
 
-        // job metadata
-        final metadata = new LinkedHashMap<String,Object>()
-        metadata.name = this.podName    //  just use the podName for simplicity, it may be renamed to just `name` or `resourceName` in the future
-        metadata.namespace = this.namespace ?: 'default'
-
-        // job spec
-        final spec = new LinkedHashMap<String,Object>()
-        spec.backoffLimit = 0
-        spec.template = [spec: pod.spec]
-
-        if( labels )
-            metadata.labels = sanitize(labels, MetaType.LABEL)
-
-        if( annotations )
-            metadata.annotations = sanitize(annotations, MetaType.ANNOTATION)
-
-        final result = [
-                apiVersion: 'batch/v1',
-                kind: 'Job',
-                metadata: metadata,
-                spec: spec ]
-
-        return result
-
+        return [
+            apiVersion: 'batch/v1',
+            kind: 'Job',
+            metadata: pod.metadata,
+            spec: [
+                backoffLimit: 0,
+                template: [
+                    metadata: pod.metadata,
+                    spec: pod.spec
+                ]
+            ]
+        ]
     }
 
     @PackageScope
diff --git a/modules/nextflow/src/test/groovy/nextflow/k8s/K8sDriverLauncherTest.groovy b/modules/nextflow/src/test/groovy/nextflow/k8s/K8sDriverLauncherTest.groovy
index 2c58309ee1..8696f3a41a 100644
--- a/modules/nextflow/src/test/groovy/nextflow/k8s/K8sDriverLauncherTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/k8s/K8sDriverLauncherTest.groovy
@@ -213,6 +213,9 @@ class K8sDriverLauncherTest extends Specification {
         driver.@k8sClient = new K8sClient(new ClientConfig(namespace: 'foo', serviceAccount: 'bar'))
         driver.@k8sConfig = k8s
 
+        and:
+        def metadata = [name: 'foo-boo', namespace: 'foo', labels: [app: 'nextflow', runName: 'foo-boo']]
+
         when:
         def spec = driver.makeLauncherSpec()
         then:
@@ -221,11 +224,12 @@ class K8sDriverLauncherTest extends Specification {
         spec == [
             apiVersion: 'batch/v1', 
             kind: 'Job', 
-            metadata: [name: 'foo-boo', namespace: 'foo', labels: [app: 'nextflow', runName: 'foo-boo']],
+            metadata: metadata,
             spec: [
-               backoffLimit: 0,
-               template: [
-                  spec: [
+                backoffLimit: 0,
+                template: [
+                    metadata: metadata,
+                    spec: [
                         restartPolicy: 'Never',
                         containers: [
                             [
@@ -249,8 +253,8 @@ class K8sDriverLauncherTest extends Specification {
                             [name:'vol-1', persistentVolumeClaim:[claimName:'pvc-1']],
                             [name:'vol-2', configMap:[name:'cfg-2']]
                         ]
-                  ]
-               ]
+                    ]
+                ]
             ]
         ]
     }
diff --git a/modules/nextflow/src/test/groovy/nextflow/k8s/K8sTaskHandlerTest.groovy b/modules/nextflow/src/test/groovy/nextflow/k8s/K8sTaskHandlerTest.groovy
index ba0ba6404c..4d6f06af2f 100644
--- a/modules/nextflow/src/test/groovy/nextflow/k8s/K8sTaskHandlerTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/k8s/K8sTaskHandlerTest.groovy
@@ -605,23 +605,22 @@ class K8sTaskHandlerTest extends Specification {
         1 * task.getConfig() >> config
 
         result == [
-            apiVersion: 'batch/v1', 
-            kind: 'Job', 
-            metadata:[name: 'nf-123', namespace: 'default'], 
-            spec:[
-              backoffLimit: 0,
-              template: [
-                  spec: [
-                     restartPolicy: 'Never',
-                     containers: [
-                       [
-                           name: 'nf-123',
-                           image: 'debian:latest',
-                           command: ['/bin/bash', '-ue','/some/work/dir/.command.run']
-                       ]
-                     ]
-                  ]
-              ]
+            apiVersion: 'batch/v1',
+            kind: 'Job',
+            metadata: [name: 'nf-123', namespace: 'default'],
+            spec: [
+                backoffLimit: 0,
+                template: [
+                    metadata: [name: 'nf-123', namespace: 'default'],
+                    spec: [
+                        restartPolicy: 'Never',
+                        containers: [[
+                            name: 'nf-123',
+                            image: 'debian:latest',
+                            command: ['/bin/bash', '-ue','/some/work/dir/.command.run']
+                        ]]
+                    ]
+                ]
             ]
         ]
     }
diff --git a/modules/nextflow/src/test/groovy/nextflow/k8s/model/PodSpecBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/k8s/model/PodSpecBuilderTest.groovy
index 79e3919fd7..d04cbc1849 100644
--- a/modules/nextflow/src/test/groovy/nextflow/k8s/model/PodSpecBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/k8s/model/PodSpecBuilderTest.groovy
@@ -1001,23 +1001,24 @@ class PodSpecBuilderTest extends Specification {
                 .buildAsJob()
 
         then:
-        spec ==  [ apiVersion: 'batch/v1',
-                    kind: 'Job',
-                    metadata: [name:'foo', namespace:'default'],
+        spec == [
+            apiVersion: 'batch/v1',
+            kind: 'Job',
+            metadata: [name: 'foo', namespace: 'default'],
+            spec: [
+                backoffLimit: 0,
+                template: [
+                    metadata: [name: 'foo', namespace: 'default'],
                     spec: [
-                            backoffLimit: 0,
-                            template: [
-                                    spec: [
-                                            restartPolicy:'Never',
-                                            containers:[
-                                                    [name:'foo',
-                                                     image:'busybox',
-                                                     command:['echo', 'hello'],
-                                                    ]
-                                            ]
-                                    ]
-                            ]
+                        restartPolicy: 'Never',
+                        containers: [[
+                            name: 'foo',
+                            image: 'busybox',
+                            command: ['echo', 'hello'],
+                        ]]
                     ]
+                ]
+            ]
         ]
     }
 
@@ -1035,37 +1036,40 @@ class PodSpecBuilderTest extends Specification {
                 .withAnnotations([anno2: "val2", anno3: "val3"])
                 .buildAsJob()
 
+        def metadata = [
+            name: 'foo',
+            namespace: 'default',
+            labels: [
+                app: 'someApp',
+                runName: 'someName',
+                version: '3.8.1'
+            ],
+            annotations: [
+                anno1: "val1",
+                anno2: "val2",
+                anno3: "val3"
+            ]
+        ]
+
         then:
-        spec ==  [ apiVersion: 'batch/v1',
-                   kind: 'Job',
-                   metadata: [
-                           name:'foo',
-                           namespace:'default',
-                           labels: [
-                                   app: 'someApp',
-                                   runName: 'someName',
-                                   version: '3.8.1'
-                           ],
-                           annotations: [
-                                   anno1: "val1",
-                                   anno2: "val2",
-                                   anno3: "val3"
-                           ]
-                   ],
-                   spec: [
-                           backoffLimit: 0,
-                           template: [
-                                   spec: [
-                                           restartPolicy:'Never',
-                                           containers:[
-                                                   [name:'foo',
-                                                    image:'busybox',
-                                                    command:['echo', 'hello'],
-                                                   ]
-                                           ]
-                                   ]
-                           ]
-                   ]
+        spec == [
+            apiVersion: 'batch/v1',
+            kind: 'Job',
+            metadata: metadata,
+            spec: [
+                backoffLimit: 0,
+                template: [
+                    metadata: metadata,
+                    spec: [
+                        restartPolicy: 'Never',
+                        containers: [[
+                            name: 'foo',
+                            image: 'busybox',
+                            command: ['echo', 'hello'],
+                        ]]
+                    ]
+                ]
+            ]
         ]
     }
 
@@ -1099,36 +1103,4 @@ class PodSpecBuilderTest extends Specification {
 
     }
 
-    def 'should create job spec with activeDeadlineSeconds' () {
-
-        when:
-        def spec = new PodSpecBuilder()
-                .withPodName('foo')
-                .withImageName('busybox')
-                .withCommand(['echo', 'hello'])
-                .withActiveDeadline(100)
-                .buildAsJob()
-
-        then:
-        spec ==  [ apiVersion: 'batch/v1',
-                   kind: 'Job',
-                   metadata: [name:'foo', namespace:'default'],
-                   spec: [
-                           backoffLimit: 0,
-                           template: [
-                                   spec: [
-                                           restartPolicy:'Never',
-                                           activeDeadlineSeconds: 100,
-                                           containers:[
-                                                   [name:'foo',
-                                                    image:'busybox',
-                                                    command:['echo', 'hello'],
-                                                   ]
-                                           ]
-                                   ]
-                           ]
-                   ]
-        ]
-    }
-
 }

From 2bae5198478857aa0f4c3111967bc444dff98a5a Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Tue, 15 Aug 2023 09:47:41 -0500
Subject: [PATCH 082/350] Remove dockerize launcher classpath file (#4191) [ci
 fast]

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 nextflow       | 7 ++-----
 packing.gradle | 2 +-
 2 files changed, 3 insertions(+), 6 deletions(-)

diff --git a/nextflow b/nextflow
index 75b6424928..7dd0470051 100755
--- a/nextflow
+++ b/nextflow
@@ -385,11 +385,8 @@ EOF
 }
 
 # checked if a cached classpath file exists and it newer that the nextflow boot jar file
-if [[ -f /.nextflow/dockerized ]]; then
-  LAUNCH_FILE=/.nextflow/launch-classpath
-else
-  LAUNCH_FILE="${NXF_LAUNCHER}/classpath-$(env_md5)"
-fi
+LAUNCH_FILE="${NXF_LAUNCHER}/classpath-$(env_md5)"
+
 if [ -s "$LAUNCH_FILE" ] && [ "$LAUNCH_FILE" -nt "$NXF_BIN" ]; then
     declare -a launcher="($(cat "$LAUNCH_FILE"))"
 else
diff --git a/packing.gradle b/packing.gradle
index de6473607e..09993e7844 100644
--- a/packing.gradle
+++ b/packing.gradle
@@ -293,7 +293,7 @@ task dockerPack(type: Exec, dependsOn: ['packOne']) {
     COPY entry.sh /usr/local/bin/entry.sh
     COPY dist/docker /usr/local/bin/docker
     ENV NXF_HOME=/.nextflow
-    RUN touch /.nextflow/dockerized && rm -rf /.nextflow/launch-classpath
+    RUN touch /.nextflow/dockerized
     RUN chmod +x /usr/local/bin/nextflow /usr/local/bin/entry.sh
     RUN nextflow info
     ENTRYPOINT ["/usr/local/bin/entry.sh"]

From 96ab8a69a64f4cbf0274514cbb41b839956512a8 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Tue, 15 Aug 2023 09:48:35 -0500
Subject: [PATCH 083/350] Fix `workflow.container` map resolution (#4190)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 .../src/main/groovy/nextflow/Session.groovy   | 19 ++++++++++++++-----
 .../nextflow/config/ConfigBuilder.groovy      |  4 ++--
 .../test/groovy/nextflow/SessionTest.groovy   | 12 ++++++------
 .../nextflow/config/ConfigBuilderTest.groovy  |  7 ++++---
 4 files changed, 26 insertions(+), 16 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/Session.groovy b/modules/nextflow/src/main/groovy/nextflow/Session.groovy
index 165bb4e5f9..03fc8698c6 100644
--- a/modules/nextflow/src/main/groovy/nextflow/Session.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/Session.groovy
@@ -879,12 +879,13 @@ class Session implements ISession {
         def keys = (config.process as Map).keySet()
         for(String key : keys) {
             String name = null
-            if( key.startsWith('$') ) {
-                name = key.substring(1)
-            }
-            else if( key.startsWith('withName:') ) {
+            if( key.startsWith('withName:') ) {
                 name = key.substring('withName:'.length())
             }
+            else if( key.startsWith('$') ) {
+                name = key.substring(1)
+                log.warn1 "Process config \$${name} is deprecated, use withName:'${name}' instead"
+            }
             if( name )
                 checkValidProcessName(processNames, name, result)
         }
@@ -1268,7 +1269,15 @@ class Session implements ISession {
              * look for `container` definition at process level
              */
             config.process.each { String name, value ->
-                if( name.startsWith('$') && value instanceof Map && value.container ) {
+                if( name.startsWith('withName:') ) {
+                    name = name.substring('withName:'.length())
+                }
+                else if( name.startsWith('$') ) {
+                    name = name.substring(1)
+                    log.warn1 "Process config \$${name} is deprecated, use withName:'${name}' instead"
+                }
+
+                if( value instanceof Map && value.container ) {
                     result[name] = resolveClosure(value.container)
                 }
             }
diff --git a/modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy
index bb963d1684..6cb39fe9d2 100644
--- a/modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy
@@ -787,8 +787,8 @@ class ConfigBuilder {
                 return true
 
             def result = process
-                            .findAll { String name, value -> name.startsWith('$') && value instanceof Map }
-                            .find { String name, Map value -> value.container as boolean }  // the first non-empty `container` string
+                    .findAll { String name, value -> (name.startsWith('withName:') || name.startsWith('$')) && value instanceof Map }
+                    .find { String name, Map value -> value.container as boolean }  // the first non-empty `container` string
 
             return result as boolean
         }
diff --git a/modules/nextflow/src/test/groovy/nextflow/SessionTest.groovy b/modules/nextflow/src/test/groovy/nextflow/SessionTest.groovy
index 6261ace967..71ef367d07 100644
--- a/modules/nextflow/src/test/groovy/nextflow/SessionTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/SessionTest.groovy
@@ -525,25 +525,25 @@ class SessionTest extends Specification {
         when:
         text = '''
                 process {
-                    $proc1 { container = 'alpha' }
-                    $proc2 { container ='beta' }
+                    withName:'proc1' { container = 'alpha' }
+                    withName:'proc2' { container = 'beta' }
                 }
                 '''
         then:
-        new Session(cfg(text)).fetchContainers() == ['$proc1': 'alpha', '$proc2': 'beta']
+        new Session(cfg(text)).fetchContainers() == ['proc1': 'alpha', 'proc2': 'beta']
 
 
         when:
         text = '''
                 process {
-                    $proc1 { container = 'alpha' }
-                    $proc2 { container ='beta' }
+                    withName:'proc1' { container = 'alpha' }
+                    withName:'proc2' { container = 'beta' }
                 }
 
                 process.container = 'gamma'
                 '''
         then:
-        new Session(cfg(text)).fetchContainers() == ['$proc1': 'alpha', '$proc2': 'beta', default: 'gamma']
+        new Session(cfg(text)).fetchContainers() == ['proc1': 'alpha', 'proc2': 'beta', 'default': 'gamma']
 
 
         when:
diff --git a/modules/nextflow/src/test/groovy/nextflow/config/ConfigBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/config/ConfigBuilderTest.groovy
index c5d9b5d6bc..420fe7b54a 100644
--- a/modules/nextflow/src/test/groovy/nextflow/config/ConfigBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/config/ConfigBuilderTest.groovy
@@ -677,14 +677,14 @@ class ConfigBuilderTest extends Specification {
         when:
         file.text =
                 '''
-                process.$test.container = 'busybox'
+                process.'withName:test'.container = 'busybox'
                 '''
         def opt = new CliOptions(config: [file.toFile().canonicalPath])
         def run = new CmdRun(withDocker: '-')
         def config = new ConfigBuilder().setOptions(opt).setCmdRun(run).build()
         then:
         config.docker.enabled
-        config.process.$test.container == 'busybox'
+        config.process.'withName:test'.container == 'busybox'
 
         when:
         file.text =
@@ -709,7 +709,7 @@ class ConfigBuilderTest extends Specification {
         when:
         file.text =
                 '''
-                process.$test.tag = 'tag'
+                process.'withName:test'.tag = 'tag'
                 '''
         opt = new CliOptions(config: [file.toFile().canonicalPath])
         run = new CmdRun(withDocker: '-')
@@ -777,6 +777,7 @@ class ConfigBuilderTest extends Specification {
         !config.hasContainerDirective([foo: 1, bar: 2])
         !config.hasContainerDirective([foo: 1, bar: 2, baz: [container: 'user/repo']])
         config.hasContainerDirective([foo: 1, bar: 2, $baz: [container: 'user/repo']])
+        config.hasContainerDirective([foo: 1, bar: 2, 'withName:baz': [container: 'user/repo']])
 
     }
 

From 552501cefd001ade587394fb3de14633578535ac Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Tue, 15 Aug 2023 10:28:28 -0500
Subject: [PATCH 084/350] Escape semicolons in paths (#4193)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 modules/nf-commons/src/main/nextflow/util/Escape.groovy     | 2 +-
 modules/nf-commons/src/test/nextflow/util/EscapeTest.groovy | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/modules/nf-commons/src/main/nextflow/util/Escape.groovy b/modules/nf-commons/src/main/nextflow/util/Escape.groovy
index 6bef4dce69..5db0682bc6 100644
--- a/modules/nf-commons/src/main/nextflow/util/Escape.groovy
+++ b/modules/nf-commons/src/main/nextflow/util/Escape.groovy
@@ -29,7 +29,7 @@ import nextflow.extension.FilesEx
 @CompileStatic
 class Escape {
 
-    private static List<String> SPECIAL_CHARS = ["'", '"', ' ', '(', ')', '\\', '!', '&', '|', '<', '>', '`', ':']
+    private static List<String> SPECIAL_CHARS = ["'", '"', ' ', '(', ')', '\\', '!', '&', '|', '<', '>', '`', ':', ';']
 
     private static List<String> VAR_CHARS = ['$', "'", '"', '(', ')', '\\', '&', '|', '<', '>', '`']
 
diff --git a/modules/nf-commons/src/test/nextflow/util/EscapeTest.groovy b/modules/nf-commons/src/test/nextflow/util/EscapeTest.groovy
index 59841ba7dc..85f4cf5fb4 100644
--- a/modules/nf-commons/src/test/nextflow/util/EscapeTest.groovy
+++ b/modules/nf-commons/src/test/nextflow/util/EscapeTest.groovy
@@ -55,6 +55,8 @@ class EscapeTest extends Specification {
         Escape.path("hello<3.txt") == "hello\\<3.txt"
         Escape.path("hello>3.txt") == "hello\\>3.txt"
         Escape.path("hello`3.txt") == "hello\\`3.txt"
+        Escape.path('hello:3.txt') == "hello\\:3.txt"
+        Escape.path('hello;3.txt') == "hello\\;3.txt"
         Escape.path("/some'5/data'3/with/quote's/file's.txt") == "/some\\'5/data\\'3/with/quote\\'s/file\\'s.txt"
         Escape.path("Hello '$world'") == "Hello\\ \\'world\\'"
 

From a3a75ea26127e4415d1a6a98ad3e33fdfa5d1931 Mon Sep 17 00:00:00 2001
From: Dr Marco Claudio De La Pierre <marco.delapierre@gmail.com>
Date: Wed, 16 Aug 2023 00:02:15 +0800
Subject: [PATCH 085/350] Use root user in Wave container based on micromamba
 (#4038) [ci fast]

Signed-off-by: Marco De La Pierre <marco.delapierre@gmail.com>
---
 .../resources/templates/conda/dockerfile-conda-file.txt    | 1 +
 .../templates/conda/dockerfile-conda-packages.txt          | 1 +
 .../src/test/io/seqera/wave/plugin/WaveClientTest.groovy   | 2 ++
 .../src/test/io/seqera/wave/util/DockerHelperTest.groovy   | 7 +++++++
 4 files changed, 11 insertions(+)

diff --git a/plugins/nf-wave/src/resources/templates/conda/dockerfile-conda-file.txt b/plugins/nf-wave/src/resources/templates/conda/dockerfile-conda-file.txt
index a7cc7806e8..d9be54e326 100644
--- a/plugins/nf-wave/src/resources/templates/conda/dockerfile-conda-file.txt
+++ b/plugins/nf-wave/src/resources/templates/conda/dockerfile-conda-file.txt
@@ -3,3 +3,4 @@ COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml
 RUN micromamba install -y -n base -f /tmp/conda.yml \
     {{base_packages}}
     && micromamba clean -a -y
+USER root
diff --git a/plugins/nf-wave/src/resources/templates/conda/dockerfile-conda-packages.txt b/plugins/nf-wave/src/resources/templates/conda/dockerfile-conda-packages.txt
index 6885c84ea0..67e01b4378 100644
--- a/plugins/nf-wave/src/resources/templates/conda/dockerfile-conda-packages.txt
+++ b/plugins/nf-wave/src/resources/templates/conda/dockerfile-conda-packages.txt
@@ -4,3 +4,4 @@ RUN \
     {{target}} \
     {{base_packages}}
     && micromamba clean -a -y
+USER root
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
index 4005b1c0b8..8e5bcb31df 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
@@ -476,6 +476,7 @@ class WaveClientTest extends Specification {
                     micromamba install -y -n base -c conda-forge -c defaults \\
                     salmon=1.2.3 \\
                     && micromamba clean -a -y
+                USER root
                     '''.stripIndent()
         and:
         !assets.moduleResources
@@ -544,6 +545,7 @@ class WaveClientTest extends Specification {
                 COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml
                 RUN micromamba install -y -n base -f /tmp/conda.yml \\
                     && micromamba clean -a -y
+                USER root
                     '''.stripIndent()
         and:
         assets.condaFile == condaFile
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/util/DockerHelperTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/util/DockerHelperTest.groovy
index 566838978a..4112c96900 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/util/DockerHelperTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/util/DockerHelperTest.groovy
@@ -41,6 +41,7 @@ class DockerHelperTest extends Specification {
                 RUN micromamba install -y -n base -f /tmp/conda.yml \\
                     && micromamba install -y -n base conda-forge::procps-ng \\
                     && micromamba clean -a -y
+                USER root
                 '''.stripIndent()
     }
 
@@ -52,6 +53,7 @@ class DockerHelperTest extends Specification {
                 COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml
                 RUN micromamba install -y -n base -f /tmp/conda.yml \\
                     && micromamba clean -a -y
+                USER root
                 '''.stripIndent()
     }
 
@@ -67,6 +69,7 @@ class DockerHelperTest extends Specification {
                     micromamba install -y -n base -c conda-forge -c defaults \\
                     bwa=0.7.15 salmon=1.1.1 \\
                     && micromamba clean -a -y
+                USER root
                 '''.stripIndent()
     }
 
@@ -84,6 +87,7 @@ class DockerHelperTest extends Specification {
                     bwa=0.7.15 salmon=1.1.1 \\
                     && micromamba install -y -n base foo::one bar::two \\
                     && micromamba clean -a -y
+                USER root
                 '''.stripIndent()
     }
 
@@ -99,6 +103,7 @@ class DockerHelperTest extends Specification {
                     micromamba install -y -n base -c foo -c bar \\
                     bwa=0.7.15 salmon=1.1.1 \\
                     && micromamba clean -a -y
+                USER root
                 '''.stripIndent()
     }
 
@@ -115,6 +120,7 @@ class DockerHelperTest extends Specification {
                     micromamba install -y -n base -c conda-forge -c defaults \\
                     bwa=0.7.15 salmon=1.1.1 \\
                     && micromamba clean -a -y
+                USER root
                 USER my-user
                 RUN apt-get update -y && apt-get install -y nano
                 '''.stripIndent()
@@ -134,6 +140,7 @@ class DockerHelperTest extends Specification {
                     micromamba install -y -n base -c conda-forge -c defaults \\
                     -f https://foo.com/some/conda-lock.yml \\
                     && micromamba clean -a -y
+                USER root
                 USER my-user
                 RUN apt-get update -y && apt-get install -y procps
                 '''.stripIndent()

From 67980f19c8840d875e29bba3aa2e5e16534b1173 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Tue, 15 Aug 2023 11:03:13 -0500
Subject: [PATCH 086/350] FIx nested InvocationTargetException (#4192) [ci
 fast]

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../src/main/groovy/nextflow/script/BaseScript.groovy      | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/script/BaseScript.groovy b/modules/nextflow/src/main/groovy/nextflow/script/BaseScript.groovy
index 5da185edd6..521d6dca6d 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/BaseScript.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/BaseScript.groovy
@@ -191,9 +191,12 @@ abstract class BaseScript extends Script implements ExecutionContext {
         try {
             run0()
         }
-        catch(InvocationTargetException e) {
+        catch( InvocationTargetException e ) {
             // provide the exception cause which is more informative than InvocationTargetException
-            throw(e.cause ?: e)
+            Throwable target = e
+            do target = target.cause
+            while ( target instanceof InvocationTargetException )
+            throw target
         }
         finally {
             ExecutionStack.pop()

From 50f6f6d598b77010b0bd5e22b05fba0207e153b9 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Wed, 16 Aug 2023 14:11:03 +0200
Subject: [PATCH 087/350] Fix if-guard on log.trace in trask processor inner
 class [ci fast]

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../nextflow/processor/TaskProcessor.groovy    | 18 ++++++++++++++----
 1 file changed, 14 insertions(+), 4 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
index 07fe7a7ef6..166082b9ea 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
@@ -2388,7 +2388,9 @@ class TaskProcessor {
 
         @Override
         List<Object> beforeRun(final DataflowProcessor processor, final List<Object> messages) {
-            log.trace "<${name}> Before run -- messages: ${messages}"
+            // apparently auto if-guard instrumented by @Slf4j is not honoured in inner classes - add it explictly
+            if( log.isTraceEnabled() )
+                log.trace "<${name}> Before run -- messages: ${messages}"
             // the counter must be incremented here, otherwise it won't be consistent
             state.update { StateObj it -> it.incSubmitted() }
             // task index must be created here to guarantee consistent ordering
@@ -2403,12 +2405,15 @@ class TaskProcessor {
 
         @Override
         void afterRun(DataflowProcessor processor, List<Object> messages) {
-            log.trace "<${name}> After run"
+            // apparently auto if-guard instrumented by @Slf4j is not honoured in inner classes - add it explictly
+            if( log.isTraceEnabled() )
+                log.trace "<${name}> After run"
             currentTask.remove()
         }
 
         @Override
         Object messageArrived(final DataflowProcessor processor, final DataflowReadChannel<Object> channel, final int index, final Object message) {
+            // apparently auto if-guard instrumented by @Slf4j is not honoured in inner classes - add it explictly
             if( log.isTraceEnabled() ) {
                 def channelName = config.getInputs()?.names?.get(index)
                 def taskName = currentTask.get()?.name ?: name
@@ -2420,6 +2425,7 @@ class TaskProcessor {
 
         @Override
         Object controlMessageArrived(final DataflowProcessor processor, final DataflowReadChannel<Object> channel, final int index, final Object message) {
+            // apparently auto if-guard instrumented by @Slf4j is not honoured in inner classes - add it explictly
             if( log.isTraceEnabled() ) {
                 def channelName = config.getInputs()?.names?.get(index)
                 def taskName = currentTask.get()?.name ?: name
@@ -2429,7 +2435,9 @@ class TaskProcessor {
             super.controlMessageArrived(processor, channel, index, message)
 
             if( message == PoisonPill.instance ) {
-                log.trace "<${name}> Poison pill arrived; port: $index"
+                // apparently auto if-guard instrumented by @Slf4j is not honoured in inner classes - add it explictly
+                if( log.isTraceEnabled() )
+                    log.trace "<${name}> Poison pill arrived; port: $index"
                 openPorts.set(index, 0) // mark the port as closed
                 state.update { StateObj it -> it.poison() }
             }
@@ -2439,7 +2447,9 @@ class TaskProcessor {
 
         @Override
         void afterStop(final DataflowProcessor processor) {
-            log.trace "<${name}> After stop"
+            // apparently auto if-guard instrumented by @Slf4j is not honoured in inner classes - add it explictly
+            if( log.isTraceEnabled() )
+                log.trace "<${name}> After stop"
         }
 
         /**

From 7b5e50a15cc1e1b7c22a12c1234c9e60c87d4743 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Thu, 17 Aug 2023 09:23:27 -0500
Subject: [PATCH 088/350] Add resource labels support for Azure Batch (#4178)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/executor.md                                 |  6 +++++-
 docs/process.md                                  | 14 ++++++++++++--
 .../cloud/azure/batch/AzBatchService.groovy      | 16 ++++++++++++++--
 .../cloud/azure/batch/AzVmPoolSpec.groovy        |  1 +
 .../cloud/azure/batch/AzBatchServiceTest.groovy  |  4 +++-
 5 files changed, 35 insertions(+), 6 deletions(-)

diff --git a/docs/executor.md b/docs/executor.md
index 1cce5ecd1d..a14d867146 100644
--- a/docs/executor.md
+++ b/docs/executor.md
@@ -28,6 +28,7 @@ Resource requests and other job characteristics can be controlled via the follow
 - {ref}`process-cpus`
 - {ref}`process-memory`
 - {ref}`process-queue`
+- {ref}`process-resourcelabels`
 - {ref}`process-time`
 
 See the {ref}`AWS Batch<aws-batch>` page for further configuration details.
@@ -55,6 +56,7 @@ Resource requests and other job characteristics can be controlled via the follow
 - {ref}`process-machineType`
 - {ref}`process-memory`
 - {ref}`process-queue`
+- {ref}`process-resourcelabels`
 - {ref}`process-time`
 
 See the {ref}`Azure Batch <azure-batch>` page for further configuration details.
@@ -191,8 +193,8 @@ Resource requests and other job characteristics can be controlled via the follow
 - {ref}`process-disk`
 - {ref}`process-machineType`
 - {ref}`process-memory`
-- {ref}`process-time`
 - {ref}`process-resourcelabels`
+- {ref}`process-time`
 
 See the {ref}`Google Cloud Batch <google-batch>` page for further configuration details.
 
@@ -218,6 +220,7 @@ Resource requests and other job characteristics can be controlled via the follow
 - {ref}`process-disk`
 - {ref}`process-machineType`
 - {ref}`process-memory`
+- {ref}`process-resourcelabels`
 - {ref}`process-time`
 
 See the {ref}`Google Life Sciences <google-lifesciences>` page for further configuration details.
@@ -312,6 +315,7 @@ Resource requests and other job characteristics can be controlled via the follow
 - {ref}`process-disk`
 - {ref}`process-memory`
 - {ref}`process-pod`
+- {ref}`process-resourcelabels`
 - {ref}`process-time`
 
 See the {ref}`Kubernetes <k8s-page>` page to learn how to set up a Kubernetes cluster to run Nextflow pipelines.
diff --git a/docs/process.md b/docs/process.md
index db7a594aca..7c4eb7fce0 100644
--- a/docs/process.md
+++ b/docs/process.md
@@ -2121,8 +2121,18 @@ process my_task {
 
 The limits and the syntax of the corresponding cloud provider should be taken into consideration when using resource labels.
 
-:::{note}
-Resource labels are currently only supported by the {ref}`awsbatch-executor`, {ref}`google-lifesciences-executor`, Google Cloud Batch and {ref}`k8s-executor` executors.
+Resource labels are currently supported by the following executors:
+
+- {ref}`awsbatch-executor`
+- {ref}`azurebatch-executor`
+- {ref}`google-batch-executor`
+- {ref}`google-lifesciences-executor`
+- {ref}`k8s-executor`
+
+:::{versionadded} 23.09.0-edge
+Resource labels are supported for Azure Batch when using automatic pool creation.
+
+Resource labels in Azure are added to pools, rather than jobs, in order to facilitate cost analysis. A new pool will be created for each new set of resource labels, therefore it is recommended to also set `azure.batch.deletePoolsOnCompletion = true` when using process-specific resource labels.
 :::
 
 See also: [label](#label)
diff --git a/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchService.groovy b/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchService.groovy
index ddd858991f..a16506e4ad 100644
--- a/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchService.groovy
+++ b/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchService.groovy
@@ -39,6 +39,7 @@ import com.microsoft.azure.batch.protocol.models.ContainerRegistry
 import com.microsoft.azure.batch.protocol.models.ElevationLevel
 import com.microsoft.azure.batch.protocol.models.ImageInformation
 import com.microsoft.azure.batch.protocol.models.JobUpdateParameter
+import com.microsoft.azure.batch.protocol.models.MetadataItem
 import com.microsoft.azure.batch.protocol.models.MountConfiguration
 import com.microsoft.azure.batch.protocol.models.NetworkConfiguration
 import com.microsoft.azure.batch.protocol.models.OnAllTasksComplete
@@ -563,9 +564,10 @@ class AzBatchService implements Closeable {
             throw new IllegalArgumentException(msg)
         }
 
-        final key = CacheHelper.hasher([vmType.name, opts]).hash().toString()
+        final metadata = task.config.getResourceLabels()
+        final key = CacheHelper.hasher([vmType.name, opts, metadata]).hash().toString()
         final poolId = "nf-pool-$key-$vmType.name"
-        return new AzVmPoolSpec(poolId: poolId, vmType: vmType, opts: opts)
+        return new AzVmPoolSpec(poolId: poolId, vmType: vmType, opts: opts, metadata: metadata)
     }
 
     protected void checkPool(CloudPool pool, AzVmPoolSpec spec) {
@@ -698,6 +700,16 @@ class AzBatchService implements Closeable {
                 .withTaskSlotsPerNode(spec.vmType.numberOfCores)
                 .withStartTask(poolStartTask)
 
+        // resource labels
+        if( spec.metadata ) {
+            final metadata = spec.metadata.collect { name, value ->
+                new MetadataItem()
+                    .withName(name)
+                    .withValue(value)
+            }
+            poolParams.withMetadata(metadata)
+        }
+
         // virtual network
         if( spec.opts.virtualNetwork )
             poolParams.withNetworkConfiguration( new NetworkConfiguration().withSubnetId(spec.opts.virtualNetwork) )
diff --git a/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzVmPoolSpec.groovy b/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzVmPoolSpec.groovy
index d9ac092c85..257edb6cfb 100644
--- a/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzVmPoolSpec.groovy
+++ b/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzVmPoolSpec.groovy
@@ -36,4 +36,5 @@ class AzVmPoolSpec {
     String poolId
     AzVmType vmType
     AzPoolOpts opts
+    Map<String,String> metadata
 }
diff --git a/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchServiceTest.groovy b/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchServiceTest.groovy
index 055a795b27..0b00cc9a38 100644
--- a/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchServiceTest.groovy
+++ b/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchServiceTest.groovy
@@ -338,6 +338,7 @@ class AzBatchServiceTest extends Specification {
                 getMemory() >> MEM
                 getCpus() >> CPUS
                 getMachineType() >> TYPE
+                getResourceLabels() >> [foo: 'bar']
             }
         }
 
@@ -346,7 +347,8 @@ class AzBatchServiceTest extends Specification {
         then:
         1 * svc.guessBestVm(LOC, CPUS, MEM, TYPE) >> VM
         and:
-        spec.poolId == 'nf-pool-ddb1223ab79edfe07c0af2be7fceeb13-Standard_X1'
+        spec.poolId == 'nf-pool-9022a3fbfb5f93028d78fefaea5e21ab-Standard_X1'
+        spec.metadata == [foo: 'bar']
 
     }
 

From 6670bb06ec588e9c3dd02f85d6c6f5152f53c913 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Thu, 17 Aug 2023 16:34:40 +0200
Subject: [PATCH 089/350] Bump nf-azure@1.3.0

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-azure/changelog.txt                      | 4 ++++
 plugins/nf-azure/src/resources/META-INF/MANIFEST.MF | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/plugins/nf-azure/changelog.txt b/plugins/nf-azure/changelog.txt
index 27c932bddc..808543c7da 100644
--- a/plugins/nf-azure/changelog.txt
+++ b/plugins/nf-azure/changelog.txt
@@ -1,5 +1,9 @@
 nf-azure changelog
 ===================
+1.3.0 - 17 Aug 2023
+- Add resource labels support for Azure Batch (#4178) [7b5e50a1]
+- Fix typos in source code comments (#4173) [ci fast] [e78bc37e]
+
 1.2.0 - 5 Aug 2023
 - Add deleteTasksOnCompletion to Azure Batch configuration (#4114) [b14674dc]
 
diff --git a/plugins/nf-azure/src/resources/META-INF/MANIFEST.MF b/plugins/nf-azure/src/resources/META-INF/MANIFEST.MF
index 3bf6761375..48a1d75d94 100644
--- a/plugins/nf-azure/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-azure/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: nextflow.cloud.azure.AzurePlugin
 Plugin-Id: nf-azure
-Plugin-Version: 1.2.0
+Plugin-Version: 1.3.0
 Plugin-Provider: Seqera Labs
 Plugin-Requires: >=23.01.0-edge

From fb8f6681ac30f879be586faf97d10c0c32fc3dd3 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Thu, 17 Aug 2023 16:34:53 +0200
Subject: [PATCH 090/350] Bump nf-cloudcache@0.2.0

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-cloudcache/changelog.txt                      | 4 ++++
 plugins/nf-cloudcache/src/resources/META-INF/MANIFEST.MF | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/plugins/nf-cloudcache/changelog.txt b/plugins/nf-cloudcache/changelog.txt
index 0906ab5bb8..2e9af969f8 100644
--- a/plugins/nf-cloudcache/changelog.txt
+++ b/plugins/nf-cloudcache/changelog.txt
@@ -1,4 +1,8 @@
 nf-cloudcache changelog
 =======================
+0.2.0 - 17 Aug 2023
+- Remove lock file from cloudcache (#4167) [6e6ea579]
+- Enable cloud cache based on environment variable (#4160) [a66b0e63]
+
 0.1.0 - 22 Jul 2023
 - Initial version
diff --git a/plugins/nf-cloudcache/src/resources/META-INF/MANIFEST.MF b/plugins/nf-cloudcache/src/resources/META-INF/MANIFEST.MF
index f000ea6e0a..042ea9ff79 100644
--- a/plugins/nf-cloudcache/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-cloudcache/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: nextflow.CloudCachePlugin
 Plugin-Id: nf-cloudcache
-Plugin-Version: 0.1.0
+Plugin-Version: 0.2.0
 Plugin-Provider: Seqera Labs
 Plugin-Requires: >=23.04.0

From d06b83652212feca38f6d0305af09dbcf9136ea0 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Thu, 17 Aug 2023 16:35:09 +0200
Subject: [PATCH 091/350] Bump nf-tower@1.6.1

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-tower/changelog.txt                      | 4 ++++
 plugins/nf-tower/src/resources/META-INF/MANIFEST.MF | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/plugins/nf-tower/changelog.txt b/plugins/nf-tower/changelog.txt
index ce9117eb76..ee8b075f69 100644
--- a/plugins/nf-tower/changelog.txt
+++ b/plugins/nf-tower/changelog.txt
@@ -1,5 +1,9 @@
 nf-tower changelog
 ===================
+1.6.1 -17 Aug 2023
+- Fix checkpoint thread termination (#4166) [2b449daa]
+- Fix typos in source code comments (#4173) [ci fast] [e78bc37e]
+
 1.6.0 - 5 Aug 2023
 - Add Tower logs checkpoint (#4132) [71dfecc2]
 - Restore Tower CacheManager for backward compatibility [6d269070]
diff --git a/plugins/nf-tower/src/resources/META-INF/MANIFEST.MF b/plugins/nf-tower/src/resources/META-INF/MANIFEST.MF
index d31cd40212..2708dd3558 100644
--- a/plugins/nf-tower/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-tower/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: io.seqera.tower.plugin.TowerPlugin
 Plugin-Id: nf-tower
-Plugin-Version: 1.6.0
+Plugin-Version: 1.6.1
 Plugin-Provider: Seqera Labs
 Plugin-Requires: >=23.05.0-edge

From 7555b17daf4afa4d196a21e245c517b3c9d87539 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Thu, 17 Aug 2023 16:35:27 +0200
Subject: [PATCH 092/350] Bump nf-wave@0.11.2

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-wave/changelog.txt                      | 4 ++++
 plugins/nf-wave/src/resources/META-INF/MANIFEST.MF | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/plugins/nf-wave/changelog.txt b/plugins/nf-wave/changelog.txt
index d9c4f7fbde..5d0b016b7c 100644
--- a/plugins/nf-wave/changelog.txt
+++ b/plugins/nf-wave/changelog.txt
@@ -1,5 +1,9 @@
 nf-wave changelog
 ==================
+0.11.2 - 17 Aug 2023
+- Use root user in Wave container based on micromamba (#4038) [ci fast] [a3a75ea2]
+- Add 429 http status code to Wave retriable errors [8eb5f305]
+
 0.11.1 - 5 Aug 2023
 - Improve Wave config logging [547fad62]
 - Increase Wave client max attempts [fe5dd497]
diff --git a/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF b/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF
index 877822c1a2..143419776a 100644
--- a/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: io.seqera.wave.plugin.WavePlugin
 Plugin-Id: nf-wave
-Plugin-Version: 0.11.1
+Plugin-Version: 0.11.2
 Plugin-Provider: Seqera Labs
 Plugin-Requires: >=23.05.0-edge

From 9a595895d035e66dbcd0fca0ee114a03f8f0416c Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Thu, 17 Aug 2023 16:37:20 +0200
Subject: [PATCH 093/350] Update changelog [ci fast]

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 changelog.txt | 31 ++++++++++++++++++++++++++++++-
 1 file changed, 30 insertions(+), 1 deletion(-)

diff --git a/changelog.txt b/changelog.txt
index 9e2995e8f8..359db4221b 100644
--- a/changelog.txt
+++ b/changelog.txt
@@ -1,5 +1,34 @@
 NEXTFLOW CHANGE-LOG
 ===================
+23.08.1-edge - 17 Aug 2023
+- Add 429 http status code to Wave retriable errors [8eb5f305]
+- Add resource labels support for Azure Batch (#4178) [7b5e50a1]
+- Apply K8s Pod metadata to Job (#4057) [4d918627]
+- Document error about trailing backslash with space (#4180) [245afa5d]
+- Enable cloud cache based on environment variable (#4160) [a66b0e63]
+- Escape semicolons in paths (#4193) [552501ce]
+- FIx nested InvocationTargetException (#4192) [67980f19]
+- Fix Execution should fail if report or timeline file already exists [b238d7e2]
+- Fix Process hangs when using flatten and finish errorStrategy [d99b3432]
+- Fix `workflow.container` map resolution (#4190) [96ab8a69]
+- Fix checkpoint thread termination (#4166) [2b449daa]
+- Fix env output when changing task workdir [8e4d7fed]
+- Fix if-guard on log.trace in trask processor inner class [50f6f6d5]
+- Fix typos in source code comments (#4173) [e78bc37e]
+- Improve Conda build error report [7b19fb03]
+- Improve handling of name-only container env variables [3051cd13]
+- Minor changes [7e58c945]
+- Remove dockerize launcher classpath file (#4191) [2bae5198]
+- Remove lock file from cloudcache (#4167) [6e6ea579]
+- Update AWS instructions for creating a custom AMI (#4174) [563bff13]
+- Update changelog [98f88a50]
+- Update tip about modifying maps (#4153) [30036dbf]
+- Use root user in Wave container based on micromamba (#4038) [a3a75ea2]
+- Bump nf-azure@1.3.0 [6670bb06]
+- Bump nf-cloudcache@0.2.0 [fb8f6681]
+- Bump nf-tower@1.6.1 [d06b8365]
+- Bump nf-wave@0.11.2 [7555b17d]
+
 23.04.3 - 11 Aug 2023
 - Increase Wave client max attempts [8c67610a]
 - Fix log typo [03e19ea2]
@@ -51,7 +80,7 @@ NEXTFLOW CHANGE-LOG
 - Allow SLURM executor option `--mem-per-cpu` (#4023) [96c04e3b]
 - Allow disabling the Wave requirement when Fusion is enabled [9180d633]
 - Disable Singularity and Apptainer home mount by default (#4056) [a0ee4657]
-- Document `NXF_WRAPPER_STAGE_FILE_THRESHOLD` environment variable (#4113) [ci skip] [bda47567]
+- Document `NXF_WRAPPER_STAGE_FILE_THRESHOLD` environment variable (#4113) [bda47567]
 - Fix AzFileSystem retry policy [ba9b6d18] [c2f3cc96]
 - Fix Improve error message for invalid Azure URI [0f4d8867]
 - Fix Treat HTTP headers as case insensitive (#4116) [97fd3358]

From 9f1b68900acb29098effd5a57998a15364958207 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Thu, 17 Aug 2023 15:02:53 +0000
Subject: [PATCH 094/350] [release 23.08.1-edge] Update timestamp and build
 number [ci fast]

---
 VERSION                                                   | 2 +-
 docs/conf.py                                              | 2 +-
 .../nextflow/src/main/resources/META-INF/plugins-info.txt | 8 ++++----
 modules/nf-commons/src/main/nextflow/Const.groovy         | 6 +++---
 nextflow                                                  | 2 +-
 nextflow.md5                                              | 2 +-
 nextflow.sha1                                             | 2 +-
 nextflow.sha256                                           | 2 +-
 8 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/VERSION b/VERSION
index 867f7aa69d..ed8e6580ae 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-23.08.0-edge
\ No newline at end of file
+23.08.1-edge
diff --git a/docs/conf.py b/docs/conf.py
index b68f128789..dd9c2a42f6 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -60,7 +60,7 @@
 # The short X.Y version.
 version = '23.08'
 # The full version, including alpha/beta/rc tags.
-release = '23.08.0-edge'
+release = '23.08.1-edge'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
diff --git a/modules/nextflow/src/main/resources/META-INF/plugins-info.txt b/modules/nextflow/src/main/resources/META-INF/plugins-info.txt
index c7fc7ad006..60364143e3 100644
--- a/modules/nextflow/src/main/resources/META-INF/plugins-info.txt
+++ b/modules/nextflow/src/main/resources/META-INF/plugins-info.txt
@@ -1,9 +1,9 @@
 nf-amazon@2.1.1
-nf-azure@1.2.0
-nf-cloudcache@0.1.0
+nf-azure@1.3.0
+nf-cloudcache@0.2.0
 nf-codecommit@0.1.5
 nf-console@1.0.6
 nf-ga4gh@1.1.0
 nf-google@1.8.1
-nf-tower@1.6.0
-nf-wave@0.11.1
\ No newline at end of file
+nf-tower@1.6.1
+nf-wave@0.11.2
\ No newline at end of file
diff --git a/modules/nf-commons/src/main/nextflow/Const.groovy b/modules/nf-commons/src/main/nextflow/Const.groovy
index 23d624ff1a..38687fde5b 100644
--- a/modules/nf-commons/src/main/nextflow/Const.groovy
+++ b/modules/nf-commons/src/main/nextflow/Const.groovy
@@ -52,17 +52,17 @@ class Const {
     /**
      * The application version
      */
-    static public final String APP_VER = "23.08.0-edge"
+    static public final String APP_VER = "23.08.1-edge"
 
     /**
      * The app build time as linux/unix timestamp
      */
-    static public final long APP_TIMESTAMP = 1691246068029
+    static public final long APP_TIMESTAMP = 1692284319999
 
     /**
      * The app build number
      */
-    static public final int APP_BUILDNUM = 5872
+    static public final int APP_BUILDNUM = 5874
 
     /**
      * The app build time string relative to UTC timezone
diff --git a/nextflow b/nextflow
index 7dd0470051..6e3931e648 100755
--- a/nextflow
+++ b/nextflow
@@ -15,7 +15,7 @@
 #  limitations under the License.
 
 [[ "$NXF_DEBUG" == 'x' ]] && set -x
-NXF_VER=${NXF_VER:-'23.08.0-edge'}
+NXF_VER=${NXF_VER:-'23.08.1-edge'}
 NXF_ORG=${NXF_ORG:-'nextflow-io'}
 NXF_HOME=${NXF_HOME:-$HOME/.nextflow}
 NXF_PROT=${NXF_PROT:-'https'}
diff --git a/nextflow.md5 b/nextflow.md5
index 14f8bff303..5aa63f083a 100644
--- a/nextflow.md5
+++ b/nextflow.md5
@@ -1 +1 @@
-e84b9b8b1453bb81540b10e057e126ee
+74e5cedd3fd06021c698fab73cf5f03e
diff --git a/nextflow.sha1 b/nextflow.sha1
index aa412cac8b..d24bb70c95 100644
--- a/nextflow.sha1
+++ b/nextflow.sha1
@@ -1 +1 @@
-f70facf7083770f11d4d915c6f11502302a3aa4a
+fbaa08de20ccc1743711f9d58fc2ada055d79f01
diff --git a/nextflow.sha256 b/nextflow.sha256
index 14fbf058ba..144ff2727b 100644
--- a/nextflow.sha256
+++ b/nextflow.sha256
@@ -1 +1 @@
-1448ebceec2213751c8846f0edc06a6791f2ff0bc996a7553fa7f94bb57c2606
+2b099e5febcc8236308be215936af5ac0af6d9c007e329247f25d4bd9a7cf444

From c30d52113db4f2dbc78ba845740cd285134b0159 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Thu, 17 Aug 2023 18:09:48 +0200
Subject: [PATCH 095/350] Fix security deps in nf-azure plugin

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-azure/build.gradle | 1 +
 1 file changed, 1 insertion(+)

diff --git a/plugins/nf-azure/build.gradle b/plugins/nf-azure/build.gradle
index 0868cdbdbf..ffcfd88869 100644
--- a/plugins/nf-azure/build.gradle
+++ b/plugins/nf-azure/build.gradle
@@ -52,6 +52,7 @@ dependencies {
 
     constraints {
         api 'net.minidev:json-smart:2.4.9'
+        api 'com.google.code.gson:gson:2.8.9'
     }
 
     testImplementation(testFixtures(project(":nextflow")))

From 8a4348939949ce5532179cc8067350c9c2c598ef Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sun, 20 Aug 2023 19:44:47 +0200
Subject: [PATCH 096/350] Add support for Wave native build for singularity

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 build.gradle                                  |   2 +
 .../script/bundle/ResourcesBundle.groovy      |  15 +-
 .../script/bundle/ResourcesBundleTest.groovy  |  27 +-
 plugins/nf-wave/build.gradle                  |   1 +
 .../main/io/seqera/wave/config/CondaOpts.java |  41 --
 .../main/io/seqera/wave/config/SpackOpts.java |  48 ---
 .../plugin/SubmitContainerTokenRequest.groovy |   5 +
 .../io/seqera/wave/plugin/WaveAssets.groovy   |   9 +-
 .../io/seqera/wave/plugin/WaveClient.groovy   |  91 +++--
 .../resolver/WaveContainerResolver.groovy     |  19 +-
 .../io/seqera/wave/util/DockerHelper.java     | 256 ------------
 .../io/seqera/wave/util/TemplateRenderer.java | 150 -------
 .../templates/conda/dockerfile-conda-file.txt |   6 -
 .../conda/dockerfile-conda-packages.txt       |   7 -
 .../templates/spack/dockerfile-spack-file.txt |  18 -
 .../seqera/wave/config/CondaOptsTest.groovy   |  47 ---
 .../seqera/wave/config/SpackOptsTest.groovy   |  48 ---
 .../seqera/wave/plugin/WaveClientTest.groovy  | 174 +++++++-
 .../resolver/WaveContainerResolverTest.groovy |  25 +-
 .../seqera/wave/util/DockerHelperTest.groovy  | 381 ------------------
 .../wave/util/TemplateRendererTest.groovy     | 202 ----------
 21 files changed, 296 insertions(+), 1276 deletions(-)
 delete mode 100644 plugins/nf-wave/src/main/io/seqera/wave/config/CondaOpts.java
 delete mode 100644 plugins/nf-wave/src/main/io/seqera/wave/config/SpackOpts.java
 delete mode 100644 plugins/nf-wave/src/main/io/seqera/wave/util/DockerHelper.java
 delete mode 100644 plugins/nf-wave/src/main/io/seqera/wave/util/TemplateRenderer.java
 delete mode 100644 plugins/nf-wave/src/resources/templates/conda/dockerfile-conda-file.txt
 delete mode 100644 plugins/nf-wave/src/resources/templates/conda/dockerfile-conda-packages.txt
 delete mode 100644 plugins/nf-wave/src/resources/templates/spack/dockerfile-spack-file.txt
 delete mode 100644 plugins/nf-wave/src/test/io/seqera/wave/config/CondaOptsTest.groovy
 delete mode 100644 plugins/nf-wave/src/test/io/seqera/wave/config/SpackOptsTest.groovy
 delete mode 100644 plugins/nf-wave/src/test/io/seqera/wave/util/DockerHelperTest.groovy
 delete mode 100644 plugins/nf-wave/src/test/io/seqera/wave/util/TemplateRendererTest.groovy

diff --git a/build.gradle b/build.gradle
index 82c8422e3d..2b8f83e687 100644
--- a/build.gradle
+++ b/build.gradle
@@ -82,6 +82,8 @@ allprojects {
         mavenCentral()
         maven { url 'https://repo.eclipse.org/content/groups/releases' }
         maven { url 'https://oss.sonatype.org/content/repositories/snapshots' }
+        maven { url = "https://s3-eu-west-1.amazonaws.com/maven.seqera.io/releases" }
+        maven { url = "https://s3-eu-west-1.amazonaws.com/maven.seqera.io/snapshots" }
     }
 
     configurations {
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/bundle/ResourcesBundle.groovy b/modules/nextflow/src/main/groovy/nextflow/script/bundle/ResourcesBundle.groovy
index a0f17094b0..6aa1ef9622 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/bundle/ResourcesBundle.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/bundle/ResourcesBundle.groovy
@@ -45,13 +45,15 @@ class ResourcesBundle {
     private Path root
     private LinkedHashMap<String,Path> content = new LinkedHashMap<>(100)
     private Path dockerfile
+    private Path singularityfile
     private MemoryUnit maxFileSize = MAX_FILE_SIZE
     private MemoryUnit maxBundleSize = MAX_BUNDLE_SIZE
     private String baseDirectory
 
     ResourcesBundle(Path root) {
         this.root = root
-        this.dockerfile = dockefile0(root.resolveSibling('Dockerfile'))
+        this.dockerfile = pathIfExists0(root.resolveSibling('Dockerfile'))
+        this.singularityfile = pathIfExists0(root.resolveSibling('Singularityfile'))
     }
 
     ResourcesBundle withMaxFileSize(MemoryUnit mem) {
@@ -68,7 +70,7 @@ class ResourcesBundle {
 
     Map<String,Path> content() { content }
 
-    static private Path dockefile0(Path path) {
+    static private Path pathIfExists0(Path path) {
         return path?.exists() ? path : null
     }
 
@@ -100,6 +102,10 @@ class ResourcesBundle {
         return dockerfile
     }
 
+    Path getSingularityfile() {
+        return singularityfile
+    }
+
     Set<Path> getPaths() {
         return new HashSet<Path>(content.values())
     }
@@ -125,7 +131,7 @@ class ResourcesBundle {
     }
 
     boolean asBoolean() {
-        return content.size() || dockerfile
+        return content.size() || dockerfile || singularityfile
     }
 
     /**
@@ -189,6 +195,9 @@ class ResourcesBundle {
         if( dockerfile ) {
             allMeta.add(fileMeta(dockerfile.name, dockerfile))
         }
+        if( singularityfile ) {
+            allMeta.add(fileMeta(singularityfile.name, singularityfile))
+        }
 
         return CacheHelper.hasher(allMeta).hash().toString()
     }
diff --git a/modules/nextflow/src/test/groovy/nextflow/script/bundle/ResourcesBundleTest.groovy b/modules/nextflow/src/test/groovy/nextflow/script/bundle/ResourcesBundleTest.groovy
index 655dd82cd3..2ec7a41688 100644
--- a/modules/nextflow/src/test/groovy/nextflow/script/bundle/ResourcesBundleTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/script/bundle/ResourcesBundleTest.groovy
@@ -106,12 +106,31 @@ class ResourcesBundleTest extends Specification {
         then:
         bundle.fingerprint() == '7b2200ff24230f76cea22e5eb15b1701'
 
+    }
+
+    def 'should get singularityfile' () {
+        given:
+        def singularPath = folder.resolve('Singularityfile'); singularPath.text = "I'm the main file"
+        def bundlePath = folder.resolve('bundle')
+        and:
+        singularPath.setLastModified(LAST_MODIFIED)
+        singularPath.setPermissions(6,4,4)
         when:
-        // changing the last modified time, change the fingerprint
-        dockerPath.setLastModified(LAST_MODIFIED +100)
+        def bundle = ResourcesBundle.scan(bundlePath)
         then:
-        bundle.fingerprint() == '7b2200ff24230f76cea22e5eb15b1701'
-        
+        bundle.getSingularityfile() == singularPath
+        and:
+        bundle
+        !bundle.hasEntries()
+        and:
+        bundle.fingerprint() == '6933e9238f3363c8e013a35715fa0540'
+
+        when:
+        // changing file permissions, change the fingerprint
+        singularPath.setPermissions(6,0,0)
+        then:
+        bundle.fingerprint() == '3ffe7f16cd5ae17e6ba7485e01972b20'
+
     }
 
     def 'should check max file size'() {
diff --git a/plugins/nf-wave/build.gradle b/plugins/nf-wave/build.gradle
index 6c37eba4b1..61255db8e3 100644
--- a/plugins/nf-wave/build.gradle
+++ b/plugins/nf-wave/build.gradle
@@ -36,6 +36,7 @@ dependencies {
     api 'org.apache.commons:commons-lang3:3.12.0'
     api 'com.google.code.gson:gson:2.10.1'
     api 'org.yaml:snakeyaml:2.0'
+    api 'io.seqera:wave-utils:0.6.2'
 
     testImplementation(testFixtures(project(":nextflow")))
     testImplementation "org.codehaus.groovy:groovy:3.0.18"
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/config/CondaOpts.java b/plugins/nf-wave/src/main/io/seqera/wave/config/CondaOpts.java
deleted file mode 100644
index fe36f8aa8c..0000000000
--- a/plugins/nf-wave/src/main/io/seqera/wave/config/CondaOpts.java
+++ /dev/null
@@ -1,41 +0,0 @@
-/*
- * Copyright 2013-2023, Seqera Labs
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package io.seqera.wave.config;
-
-import java.util.List;
-import java.util.Map;
-
-/**
- * Conda build options
- *
- * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
- */
-public class CondaOpts {
-    final public static String DEFAULT_MAMBA_IMAGE = "mambaorg/micromamba:1.4.9";
-
-    final public String mambaImage;
-    final public List<String> commands;
-    final public String basePackages;
-
-    public CondaOpts(Map<String,?> opts) {
-        this.mambaImage = opts.containsKey("mambaImage") ? opts.get("mambaImage").toString(): DEFAULT_MAMBA_IMAGE;
-        this.commands = opts.containsKey("commands") ? (List<String>)opts.get("commands") : null;
-        this.basePackages = (String)opts.get("basePackages");
-    }
-
-}
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/config/SpackOpts.java b/plugins/nf-wave/src/main/io/seqera/wave/config/SpackOpts.java
deleted file mode 100644
index 1ccabcf22e..0000000000
--- a/plugins/nf-wave/src/main/io/seqera/wave/config/SpackOpts.java
+++ /dev/null
@@ -1,48 +0,0 @@
-/*
- * Copyright 2013-2023, Seqera Labs
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package io.seqera.wave.config;
-
-import java.util.List;
-import java.util.Map;
-
-/**
- * Spack build options
- *
- * @author Marco De La Pierre <marco.delapierre@gmail.com>
- */
-public class SpackOpts {
-
-    /**
-     * Custom Dockerfile `RUN` commands that can be used to customise the target container
-     */
-    public final List<String> commands;
-
-    /**
-     * Spack packages that should be added to any Spack environment requested via Wave
-     */
-    public final String basePackages;
-
-    public SpackOpts() {
-        this(Map.of());
-    }
-    public SpackOpts(Map<String,?> opts) {
-        this.commands = opts.containsKey("commands") ? (List<String>)opts.get("commands") : null;
-        this.basePackages = opts.containsKey("basePackages") ? opts.get("basePackages").toString() : null;
-    }
-
-}
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/SubmitContainerTokenRequest.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/SubmitContainerTokenRequest.groovy
index 875cdfe338..1a219ef79c 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/SubmitContainerTokenRequest.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/SubmitContainerTokenRequest.groovy
@@ -111,4 +111,9 @@ class SubmitContainerTokenRequest {
      */
     boolean freeze
 
+    /**
+     * Specify the format of the container file
+     */
+    String format
+
 }
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveAssets.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveAssets.groovy
index 4541bf72b0..8201cdafb9 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveAssets.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveAssets.groovy
@@ -36,10 +36,11 @@ class WaveAssets {
     final String containerPlatform
     final ResourcesBundle moduleResources
     final ContainerConfig containerConfig
-    final String dockerFileContent
+    final String containerFile
     final Path condaFile
     final Path spackFile
     final ResourcesBundle projectResources
+    final boolean singularity
 
     static fromImage(String containerImage,String containerPlatform=null) {
         new WaveAssets(containerImage, containerPlatform)
@@ -50,8 +51,8 @@ class WaveAssets {
     }
 
     String dockerFileEncoded() {
-        return dockerFileContent
-                ? dockerFileContent.bytes.encodeBase64()
+        return containerFile
+                ? containerFile.bytes.encodeBase64()
                 : null
     }
 
@@ -73,7 +74,7 @@ class WaveAssets {
         allMeta.add( this.containerImage )
         allMeta.add( this.moduleResources?.fingerprint() )
         allMeta.add( this.containerConfig?.fingerprint() )
-        allMeta.add( this.dockerFileContent )
+        allMeta.add( this.containerFile )
         allMeta.add( this.condaFile?.text )
         allMeta.add( this.spackFile?.text )
         allMeta.add( this.projectResources?.fingerprint() )
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
index d189704e86..bf87c02135 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
@@ -165,10 +165,10 @@ class WaveClient {
             containerConfig.prependLayer(makeLayer(assets.projectResources))
         }
 
-        if( !assets.containerImage && !assets.dockerFileContent )
+        if( !assets.containerImage && !assets.containerFile )
             throw new IllegalArgumentException("Wave container request requires at least a image or container file to build")
 
-        if( assets.containerImage && assets.dockerFileContent )
+        if( assets.containerImage && assets.containerFile )
             throw new IllegalArgumentException("Wave container image and container file cannot be specified in the same request")
 
         return new SubmitContainerTokenRequest(
@@ -182,7 +182,8 @@ class WaveClient {
                 cacheRepository: config.cacheRepository(),
                 timestamp: OffsetDateTime.now().toString(),
                 fingerprint: assets.fingerprint(),
-                freeze: config.freezeMode()
+                freeze: config.freezeMode(),
+                format: assets.singularity ? 'sif' : null
         )
     }
 
@@ -311,24 +312,29 @@ class WaveClient {
     }
 
     protected void checkConflicts(Map<String,String> attrs, String name) {
-        if( attrs.dockerfile && attrs.conda ) {
-            throw new IllegalArgumentException("Process '${name}' declares both a 'conda' directive and a module bundle dockerfile that conflict each other")
-        }
-        if( attrs.container && attrs.dockerfile ) {
-            throw new IllegalArgumentException("Process '${name}' declares both a 'container' directive and a module bundle dockerfile that conflict each other")
-        }
         if( attrs.container && attrs.conda ) {
             throw new IllegalArgumentException("Process '${name}' declares both 'container' and 'conda' directives that conflict each other")
         }
-        if( attrs.dockerfile && attrs.spack ) {
-            throw new IllegalArgumentException("Process '${name}' declares both a 'spack' directive and a module bundle dockerfile that conflict each other")
-        }
         if( attrs.container && attrs.spack ) {
             throw new IllegalArgumentException("Process '${name}' declares both 'container' and 'spack' directives that conflict each other")
         }
         if( attrs.spack && attrs.conda ) {
             throw new IllegalArgumentException("Process '${name}' declares both 'spack' and 'conda' directives that conflict each other")
         }
+        checkConflicts0(attrs, name, 'dockerfile')
+        checkConflicts0(attrs, name, 'singularityfile')
+    }
+
+    protected void checkConflicts0(Map<String,String> attrs, String name, String fileType) {
+        if( attrs.get(fileType) && attrs.conda ) {
+            throw new IllegalArgumentException("Process '${name}' declares both a 'conda' directive and a module bundle $fileType that conflict each other")
+        }
+        if( attrs.container && attrs.get(fileType) ) {
+            throw new IllegalArgumentException("Process '${name}' declares both a 'container' directive and a module bundle $fileType that conflict each other")
+        }
+        if( attrs.get(fileType) && attrs.spack ) {
+            throw new IllegalArgumentException("Process '${name}' declares both a 'spack' directive and a module bundle $fileType that conflict each other")
+        }
     }
 
     Map<String,String> resolveConflicts(Map<String,String> attrs, List<String> strategy) {
@@ -341,6 +347,21 @@ class WaveClient {
         return result
     }
 
+    protected List<String> patchStrategy(List<String> strategy, boolean singularity) {
+        if( !singularity )
+            return strategy
+        // when singularity is enabled, replaces `dockerfile` with `singularityfile`
+        // in the strategy if not specified explicitly
+        final p = strategy.indexOf('dockerfile')
+        if( p!=-1 && !strategy.contains('singularityfile') ) {
+            final result = new ArrayList(strategy)
+            result.remove(p)
+            result.add(p, 'singularityfile')
+            return Collections.<String>unmodifiableList(result)
+        }
+        return strategy
+    }
+
     static Architecture defaultArch() {
         try {
             return new Architecture(SysHelper.getArch())
@@ -352,7 +373,7 @@ class WaveClient {
     }
 
     @Memoized
-    WaveAssets resolveAssets(TaskRun task, String containerImage) {
+    WaveAssets resolveAssets(TaskRun task, String containerImage, boolean singularity) {
         // get the bundle
         final bundle = task.getModuleBundle()
         // get the Spack architecture
@@ -367,49 +388,60 @@ class WaveClient {
         if( bundle!=null && bundle.dockerfile ) {
             attrs.dockerfile = bundle.dockerfile.text
         }
+        if( bundle!=null && bundle.singularityfile ) {
+            attrs.singularityfile = bundle.singularityfile.text
+        }
 
         // validate request attributes
-        if( config().strategy() )
-            attrs = resolveConflicts(attrs, config().strategy())
+        final strategy = config().strategy()
+        if( strategy )
+            attrs = resolveConflicts(attrs, patchStrategy(strategy, singularity))
         else
             checkConflicts(attrs, task.lazyName())
 
         //  resolve the wave assets
-        return resolveAssets0(attrs, bundle, dockerArch, spackArch)
+        return resolveAssets0(attrs, bundle, singularity, dockerArch, spackArch)
     }
 
-    protected WaveAssets resolveAssets0(Map<String,String> attrs, ResourcesBundle bundle, String dockerArch, String spackArch) {
+    protected WaveAssets resolveAssets0(Map<String,String> attrs, ResourcesBundle bundle, boolean singularity, String dockerArch, String spackArch) {
 
-        String dockerScript = attrs.dockerfile
+        final scriptType = singularity ? 'singularityfile' : 'dockerfile'
+        String containerScript = attrs.get(scriptType)
         final containerImage = attrs.container
 
         /*
-         * If 'conda' directive is specified use it to create a Dockefile
+         * If 'conda' directive is specified use it to create a container file
          * to assemble the target container
          */
         Path condaFile = null
         if( attrs.conda ) {
-            if( dockerScript )
-                throw new IllegalArgumentException("Unexpected conda and dockerfile conflict while resolving wave container")
+            if( containerScript )
+                throw new IllegalArgumentException("Unexpected conda and $scriptType conflict while resolving wave container")
 
             // map the recipe to a dockerfile
             if( isCondaLocalFile(attrs.conda) ) {
                 condaFile = Path.of(attrs.conda)
-                dockerScript = condaFileToDockerFile(config.condaOpts())
+                containerScript = singularity
+                        ? condaFileToSingularityFile(config.condaOpts())
+                        : condaFileToDockerFile(config.condaOpts())
             }
             // 'conda' attributes is resolved as the conda packages to be used
             else {
-                dockerScript = condaPackagesToDockerFile(attrs.conda, condaChannels, config.condaOpts())
+                containerScript = singularity
+                        ? condaPackagesToSingularityFile(attrs.conda, condaChannels, config.condaOpts())
+                        : condaPackagesToDockerFile(attrs.conda, condaChannels, config.condaOpts())
             }
         }
 
         /*
-         * If 'spack' directive is specified use it to create a Dockefile
+         * If 'spack' directive is specified use it to create a container file
          * to assemble the target container
          */
         Path spackFile = null
         if( attrs.spack ) {
-            if( dockerScript )
+            if( singularity )
+                throw new IllegalArgumentException("Wave containers do not support (yet) the resolution of Spack package with Singularity")
+            if( containerScript )
                 throw new IllegalArgumentException("Unexpected spack and dockerfile conflict while resolving wave container")
 
             if( isSpackFile(attrs.spack) ) {
@@ -420,14 +452,14 @@ class WaveClient {
                 // create a minimal spack file with package spec from user input
                 spackFile = spackPackagesToSpackFile(attrs.spack, config.spackOpts())
             }
-            dockerScript = spackFileToDockerFile(config.spackOpts())
+            containerScript = spackFileToDockerFile(config.spackOpts())
         }
 
         /*
          * The process should declare at least a container image name via 'container' directive
          * or a dockerfile file to build, otherwise there's no job to be done by wave
          */
-        if( !dockerScript && !containerImage ) {
+        if( !containerScript && !containerImage ) {
             return null
         }
 
@@ -451,10 +483,11 @@ class WaveClient {
                     platform,
                     bundle,
                     containerConfig,
-                    dockerScript,
+                    containerScript,
                     condaFile,
                     spackFile,
-                    projectRes)
+                    projectRes,
+                    singularity)
     }
 
     @Memoized
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/resolver/WaveContainerResolver.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/resolver/WaveContainerResolver.groovy
index 643e8dc755..46b00c464c 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/resolver/WaveContainerResolver.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/resolver/WaveContainerResolver.groovy
@@ -59,17 +59,19 @@ class WaveContainerResolver implements ContainerResolver {
         if( !client().enabled() )
             return defaultResolver.resolveImage(task, imageName)
 
+        final freeze = client().config().freezeMode()
+        final engine= task.getContainerConfig().getEngine()
+        final nativeSingularityBuild = freeze && engine in SINGULARITY_LIKE
         if( !imageName ) {
             // when no image name is provided the module bundle should include a
             // Dockerfile or a Conda recipe or a Spack recipe to build
             // an image on-fly with an automatically assigned name
-            return waveContainer(task, null)
+            return waveContainer(task, null, nativeSingularityBuild)
         }
 
-        final engine= task.getContainerConfig().getEngine()
         if( engine in DOCKER_LIKE ) {
             final image = defaultResolver.resolveImage(task, imageName)
-            return waveContainer(task, image.target)
+            return waveContainer(task, image.target, false)
         }
         else if( engine in SINGULARITY_LIKE ) {
             // remove any `docker://` prefix if any
@@ -80,8 +82,11 @@ class WaveContainerResolver implements ContainerResolver {
                 return defaultResolver.resolveImage(task, imageName)
             }
             // fetch the wave container name
-            final image = waveContainer(task, imageName)
-            // then adapt it to singularity format
+            final image = waveContainer(task, imageName, nativeSingularityBuild)
+            // oras prefixed container are served directly
+            if( image && image.target.startsWith("oras://") )
+                return image
+            // otherwise adapt it to singularity format
             return defaultResolver.resolveImage(task, image.target)
         }
         else
@@ -102,9 +107,9 @@ class WaveContainerResolver implements ContainerResolver {
      *      The container image name returned by the Wave backend or {@code null}
      *      when the task does not request any container or dockerfile to build
      */
-    protected ContainerInfo waveContainer(TaskRun task, String container) {
+    protected ContainerInfo waveContainer(TaskRun task, String container, boolean singularity) {
         validateContainerRepo(container)
-        final assets = client().resolveAssets(task, container)
+        final assets = client().resolveAssets(task, container, singularity)
         if( assets ) {
             return client().fetchContainerImage(assets)
         }
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/util/DockerHelper.java b/plugins/nf-wave/src/main/io/seqera/wave/util/DockerHelper.java
deleted file mode 100644
index 33b844a3c8..0000000000
--- a/plugins/nf-wave/src/main/io/seqera/wave/util/DockerHelper.java
+++ /dev/null
@@ -1,256 +0,0 @@
-/*
- * Copyright 2013-2023, Seqera Labs
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package io.seqera.wave.util;
-
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.net.URL;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.stream.Collectors;
-import java.io.File;
-
-import io.seqera.wave.config.CondaOpts;
-import io.seqera.wave.config.SpackOpts;
-import org.apache.commons.lang3.StringUtils;
-import org.yaml.snakeyaml.Yaml;
-
-/**
- * Helper class to create Dockerfile for Conda and Spack package managers
- *
- * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
- */
-public class DockerHelper {
-
-    static public List<String> spackPackagesToList(String packages) {
-        if( packages==null || packages.isEmpty() )
-            return null;
-        final List<String> entries = Arrays.asList(packages.split(" "));
-        final List<String> result = new ArrayList<>();
-        List<String> current = new ArrayList<>();
-        for( String it : entries ) {
-            if( it==null || it.isEmpty() || it.isBlank() )
-                continue;
-            if( !Character.isLetterOrDigit(it.charAt(0)) || it.contains("=") ) {
-              current.add(it);
-            }
-            else {
-                if( current.size()>0 )
-                    result.add(String.join(" ",current));
-                current = new ArrayList<>();
-                current.add(it);
-            }
-        }
-        // remaining entries
-        if( current.size()>0 )
-            result.add(String.join(" ",current));
-        return result;
-    }
-
-    static public String spackPackagesToSpackYaml(String packages, SpackOpts opts) {
-        final List<String> base = spackPackagesToList(opts.basePackages);
-        final List<String> custom = spackPackagesToList(packages);
-        if( base==null && custom==null )
-            return null;
-
-        final List<String> specs = new ArrayList<>();
-        if( base!=null )
-            specs.addAll(base);
-        if( custom!=null )
-            specs.addAll(custom);
-
-        final Map<String,Object> concretizer = new LinkedHashMap<>();
-        concretizer.put("unify", true);
-        concretizer.put("reuse", false);
-
-        final Map<String,Object> spack = new LinkedHashMap<>();
-        spack.put("specs", specs);
-        spack.put("concretizer", concretizer);
-
-        final Map<String,Object> root = new LinkedHashMap<>();
-        root.put("spack", spack);
-
-        return new Yaml().dump(root);
-    }
-
-    static public Path spackPackagesToSpackFile(String packages, SpackOpts opts) {
-        final String yaml = spackPackagesToSpackYaml(packages, opts);
-        if( yaml==null || yaml.length()==0 )
-            return null;
-        return toYamlFile(yaml);
-    }
-
-    static private Path toYamlFile(String yaml) {
-        try {
-            final File tempFile = File.createTempFile("nf-spack", ".yaml");
-            tempFile.deleteOnExit();
-            final Path result = tempFile.toPath();
-            Files.write(result, yaml.getBytes());
-            return result;
-        }
-        catch (IOException e) {
-            throw new IllegalStateException("Unable to write temporary Spack environment file - Reason: " + e.getMessage(), e);
-        }
-    }
-
-    static public String spackFileToDockerFile(SpackOpts opts) {
-        // create bindings
-        final Map<String,String> binding = spackBinding(opts);
-        // final ignored variables
-        final List<String> ignore = List.of("spack_runner_image");
-        //  return the template
-        return renderTemplate0("/templates/spack/dockerfile-spack-file.txt", binding, ignore);
-    }
-
-    static private Map<String,String> spackBinding(SpackOpts opts) {
-        final Map<String,String> binding = new HashMap<>();
-        binding.put("add_commands", joinCommands(opts.commands));
-        return binding;
-    }
-
-    static public String condaPackagesToDockerFile(String packages, List<String> condaChannels, CondaOpts opts) {
-        final List<String> channels0 = condaChannels!=null ? condaChannels : List.of();
-        final String channelsOpts = channels0.stream().map(it -> "-c "+it).collect(Collectors.joining(" "));
-        final String image = opts.mambaImage;
-        final String target = packages.startsWith("http://") || packages.startsWith("https://")
-                ? "-f " + packages
-                : packages;
-        final Map<String,String> binding = new HashMap<>();
-        binding.put("base_image", image);
-        binding.put("channel_opts", channelsOpts);
-        binding.put("target", target);
-        binding.put("base_packages", mambaInstallBasePackage0(opts.basePackages));
-
-        final String result = renderTemplate0("/templates/conda/dockerfile-conda-packages.txt", binding) ;
-        return addCommands(result, opts.commands);
-    }
-
-    static public String condaFileToDockerFile(CondaOpts opts) {
-        // create the binding map
-        final Map<String,String> binding = new HashMap<>();
-        binding.put("base_image", opts.mambaImage);
-        binding.put("base_packages", mambaInstallBasePackage0(opts.basePackages));
-
-        final String result = renderTemplate0("/templates/conda/dockerfile-conda-file.txt", binding);
-        return addCommands(result, opts.commands);
-    }
-
-    static private String renderTemplate0(String templatePath, Map<String,String> binding) {
-        return renderTemplate0(templatePath, binding, List.of());
-    }
-
-    static private String renderTemplate0(String templatePath, Map<String,String> binding, List<String> ignore) {
-        final URL template = DockerHelper.class.getResource(templatePath);
-        if( template==null )
-            throw new IllegalStateException(String.format("Unable to load template '%s' from classpath", templatePath));
-        try {
-            final InputStream reader = template.openStream();
-            return new TemplateRenderer()
-                    .withIgnore(ignore)
-                    .render(reader, binding);
-        }
-        catch (IOException e) {
-            throw new IllegalStateException(String.format("Unable to read classpath template '%s'", templatePath), e);
-        }
-    }
-
-    private static String mambaInstallBasePackage0(String basePackages) {
-        return !StringUtils.isEmpty(basePackages)
-                ? String.format("&& micromamba install -y -n base %s \\", basePackages)
-                : null;
-    }
-
-    static private String addCommands(String result, List<String> commands) {
-        if( commands==null || commands.isEmpty() )
-            return result;
-        for( String cmd : commands ) {
-            result += cmd + "\n";
-        }
-        return result;
-    }
-
-    static private String joinCommands(List<String> commands) {
-        if( commands==null || commands.size()==0 )
-            return null;
-        StringBuilder result = new StringBuilder();
-        for( String cmd : commands ) {
-            if( result.length()>0 )
-                result.append("\n");
-            result.append(cmd);
-        }
-        return result.toString();
-    }
-
-    public static Path addPackagesToSpackFile(String spackFile, SpackOpts opts) {
-        // Case A - both empty, nothing to do
-        if( StringUtils.isEmpty(spackFile) && StringUtils.isEmpty(opts.basePackages) )
-            return null;
-
-        // Case B - the spack file is empty, but some base package are given
-        // create a spack file with those packages
-        if( StringUtils.isEmpty(spackFile) ) {
-            return spackPackagesToSpackFile(null, opts);
-        }
-
-        final Path spackEnvPath = Path.of(spackFile);
-
-        // make sure the file exists
-        if( !Files.exists(spackEnvPath) ) {
-            throw new IllegalArgumentException("The specific Spack environment file cannot be found: " + spackFile);
-        }
-
-        // Case C - if not base packages are given just return the spack file as a path
-        if( StringUtils.isEmpty(opts.basePackages) ) {
-            return spackEnvPath;
-        }
-
-        // Case D - last case, both spack file and base packages are specified
-        // => parse the spack file yaml, add the base packages to it
-        final Yaml yaml = new Yaml();
-        try {
-            // 1. parse the file
-            Map<String,Object> data = yaml.load(new FileReader(spackFile));
-            // 2. parse the base packages
-            final List<String> base = spackPackagesToList(opts.basePackages);
-            // 3. append to the specs
-            Map<String,Object> spack = (Map<String,Object>) data.get("spack");
-            if( spack==null ) {
-                throw new IllegalArgumentException("The specified Spack environment file does not contain a root entry 'spack:' - offending file path: " + spackFile);
-            }
-            List<String> specs = (List<String>)spack.get("specs");
-            if( specs==null ) {
-                specs = new ArrayList<>();
-                spack.put("specs", specs);
-            }
-            specs.addAll(base);
-            // 5. return it as a new temp file
-            return toYamlFile( yaml.dump(data) );
-        }
-        catch (FileNotFoundException e) {
-            throw new IllegalArgumentException("The specific Spack environment file cannot be found: " + spackFile, e);
-        }
-    }
-}
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/util/TemplateRenderer.java b/plugins/nf-wave/src/main/io/seqera/wave/util/TemplateRenderer.java
deleted file mode 100644
index af9d4b8f95..0000000000
--- a/plugins/nf-wave/src/main/io/seqera/wave/util/TemplateRenderer.java
+++ /dev/null
@@ -1,150 +0,0 @@
-/*
- * Copyright 2013-2023, Seqera Labs
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package io.seqera.wave.util;
-
-import java.io.InputStream;
-import java.util.List;
-import java.util.Map;
-import java.util.Scanner;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-/**
- * Template rendering helper
- *
- * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
- */
-public class TemplateRenderer {
-
-    private static final Pattern PATTERN = Pattern.compile("\\{\\{([^}]+)}}");
-
-    private static final Pattern VAR1 = Pattern.compile("(\\s*)\\{\\{([\\d\\w_-]+)}}(\\s*$)");
-    private static final Pattern VAR2 = Pattern.compile("(?<!\\$)\\{\\{([\\d\\w_-]+)}}");
-
-    private List<String> ignoreNames = List.<String>of();
-
-    public TemplateRenderer withIgnore(String... names) {
-        return withIgnore(List.of(names));
-    }
-
-    public TemplateRenderer withIgnore(List<String> names) {
-        if( names!=null ) {
-            ignoreNames = List.copyOf(names);
-        }
-        return this;
-    }
-
-    public String render(InputStream template, Map<String, String> binding) {
-        String str = new Scanner(template).useDelimiter("\\A").next();
-        return render(str, binding);
-    }
-
-    public String render(String template, Map<String, String> binding) {
-        final String[] lines = template.split("(?<=\n)");
-        final StringBuilder result = new StringBuilder();
-        for( String it : lines ) {
-            if( it==null || it.startsWith("##"))
-                continue;
-            final String resolved = replace0(it, binding);
-            if( resolved!=null )
-                result.append(resolved);
-        }
-        return result.toString();
-    }
-
-    /**
-     * Simple template helper class replacing all variable enclosed by {{..}}
-     * with the corresponding variable specified in a map object
-     *
-     * @param template The template string
-     * @param binding The binding {@link Map}
-     * @return The templated having the variables replaced with the corresponding value
-     */
-     String replace1(CharSequence template, Map<String, ?> binding) {
-        Matcher matcher = PATTERN.matcher(template);
-
-        // Loop through each matched variable placeholder
-        StringBuilder builder = new StringBuilder();
-        boolean isNull=false;
-        while (matcher.find()) {
-            String variable = matcher.group(1);
-
-            // Check if the variable exists in the values map
-            if (binding.containsKey(variable)) {
-                Object value = binding.get(variable);
-                String str = value!=null ? value.toString() : "";
-                isNull |= value==null;
-                matcher.appendReplacement(builder, str);
-            }
-            else if( !ignoreNames.contains(variable) ) {
-                throw new IllegalArgumentException(String.format("Unable to resolve template variable: {{%s}}", variable));
-            }
-        }
-        matcher.appendTail(builder);
-
-        final String result = builder.toString();
-        return !isNull || !result.isBlank() ? result : null;
-    }
-
-    String replace0(String line, Map<String,String> binding) {
-        if( line==null || line.length()==0 )
-            return line;
-
-        Matcher matcher = VAR1.matcher(line);
-        if( matcher.matches() ) {
-            final String name = matcher.group(2);
-            if( ignoreNames.contains(name) )
-                return line;
-            if( !binding.containsKey(name) )
-                throw new IllegalArgumentException("Missing template key: "+name);
-            final String prefix = matcher.group(1);
-            final String value = binding.get(name);
-            if( value==null )
-                return null; // <-- return null to skip this line
-
-            final StringBuilder result = new StringBuilder();
-            final String[] multi = value.split("(?<=\n)");
-            for (String s : multi) {
-                result.append(prefix);
-                result.append(s);
-            }
-            result.append( matcher.group(3) );
-            return result.toString();
-        }
-
-        final StringBuilder result = new StringBuilder();
-        while( (matcher=VAR2.matcher(line)).find() ) {
-            final String name = matcher.group(1);
-            if( !binding.containsKey(name) && !ignoreNames.contains(name)) {
-                throw new IllegalArgumentException("Missing template key: "+name);
-            }
-            final String value = !ignoreNames.contains(name)
-                    ? (binding.get(name)!=null ? binding.get(name) : "")
-                    : "{{"+name+"}}";
-            final int p = matcher.start(1);
-            final int q = matcher.end(1);
-
-            result.append(line.substring(0,p-2));
-            result.append(value);
-            line = line.substring(q+2);
-        }
-        result.append(line);
-        return result.toString();
-    }
-
-}
diff --git a/plugins/nf-wave/src/resources/templates/conda/dockerfile-conda-file.txt b/plugins/nf-wave/src/resources/templates/conda/dockerfile-conda-file.txt
deleted file mode 100644
index d9be54e326..0000000000
--- a/plugins/nf-wave/src/resources/templates/conda/dockerfile-conda-file.txt
+++ /dev/null
@@ -1,6 +0,0 @@
-FROM {{base_image}}
-COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml
-RUN micromamba install -y -n base -f /tmp/conda.yml \
-    {{base_packages}}
-    && micromamba clean -a -y
-USER root
diff --git a/plugins/nf-wave/src/resources/templates/conda/dockerfile-conda-packages.txt b/plugins/nf-wave/src/resources/templates/conda/dockerfile-conda-packages.txt
deleted file mode 100644
index 67e01b4378..0000000000
--- a/plugins/nf-wave/src/resources/templates/conda/dockerfile-conda-packages.txt
+++ /dev/null
@@ -1,7 +0,0 @@
-FROM {{base_image}}
-RUN \
-    micromamba install -y -n base {{channel_opts}} \
-    {{target}} \
-    {{base_packages}}
-    && micromamba clean -a -y
-USER root
diff --git a/plugins/nf-wave/src/resources/templates/spack/dockerfile-spack-file.txt b/plugins/nf-wave/src/resources/templates/spack/dockerfile-spack-file.txt
deleted file mode 100644
index bf6e436b15..0000000000
--- a/plugins/nf-wave/src/resources/templates/spack/dockerfile-spack-file.txt
+++ /dev/null
@@ -1,18 +0,0 @@
-# Runner image
-FROM {{spack_runner_image}}
-
-COPY --from=builder /opt/spack-env /opt/spack-env
-COPY --from=builder /opt/software /opt/software
-COPY --from=builder /opt/._view /opt/._view
-
-# Entrypoint for Singularity
-RUN mkdir -p /.singularity.d/env && \
-    cp -p /opt/spack-env/z10_spack_environment.sh /.singularity.d/env/91-environment.sh
-# Entrypoint for Docker
-RUN echo "#!/usr/bin/env bash\n\nset -ef -o pipefail\nsource /opt/spack-env/z10_spack_environment.sh\nexec \"\$@\"" \
-    >/opt/spack-env/spack_docker_entrypoint.sh && chmod a+x /opt/spack-env/spack_docker_entrypoint.sh
-
-{{add_commands}}
-
-ENTRYPOINT [ "/opt/spack-env/spack_docker_entrypoint.sh" ]
-CMD [ "/bin/bash" ]
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/config/CondaOptsTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/config/CondaOptsTest.groovy
deleted file mode 100644
index 055259888a..0000000000
--- a/plugins/nf-wave/src/test/io/seqera/wave/config/CondaOptsTest.groovy
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * Copyright 2013-2023, Seqera Labs
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package io.seqera.wave.config
-
-import spock.lang.Specification
-
-/**
- *
- * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
- */
-class CondaOptsTest extends Specification {
-
-    def 'check conda options' () {
-        when:
-        def opts = new CondaOpts([:])
-        then:
-        opts.mambaImage == CondaOpts.DEFAULT_MAMBA_IMAGE
-        !opts.basePackages
-        !opts.commands
-
-        when:
-        opts = new CondaOpts([
-                mambaImage:'foo:latest',
-                commands: ['this','that'],
-                basePackages: 'some::more-package'
-        ])
-        then:
-        opts.mambaImage == 'foo:latest'
-        opts.basePackages == 'some::more-package'
-        opts.commands == ['this','that']
-    }
-}
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/config/SpackOptsTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/config/SpackOptsTest.groovy
deleted file mode 100644
index f3e5f5a955..0000000000
--- a/plugins/nf-wave/src/test/io/seqera/wave/config/SpackOptsTest.groovy
+++ /dev/null
@@ -1,48 +0,0 @@
-/*
- * Copyright 2013-2023, Seqera Labs
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package io.seqera.wave.config
-
-import spock.lang.Specification
-
-/**
- *
- * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
- */
-class SpackOptsTest extends Specification {
-
-    def 'check spack default options' () {
-        given:
-        def opts = new SpackOpts()
-        expect:
-        opts.commands == null
-        opts.basePackages == null
-    }
-
-    def 'check spack custom opts' () {
-        given:
-        def opts = new SpackOpts([
-                basePackages: 'foo bar',
-                commands: ['run','--this','--that']
-        ])
-
-        expect:
-        opts.commands == ['run','--this','--that']
-        and:
-        opts.basePackages == 'foo bar'
-    }
-}
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
index 8e5bcb31df..6b6446cc0a 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
@@ -231,6 +231,33 @@ class WaveClientTest extends Specification {
         !req.containerConfig.layers
     }
 
+    def 'should create request object with singularityfile' () {
+        given:
+        def session = Mock(Session) { getConfig() >> [:]}
+        def SINGULARITY_FILE =  'From foo:latest'
+        def wave = new WaveClient(session)
+        and:
+        def assets = new WaveAssets(null,
+                'linux/amd64',
+                null,
+                null,
+                SINGULARITY_FILE,
+                null,
+                null,
+                null,
+                true)
+        when:
+        def req = wave.makeRequest(assets)
+        then:
+        !req.containerImage
+        new String(req.containerFile.decodeBase64()) == SINGULARITY_FILE
+        !req.condaFile
+        !req.spackFile
+        !req.containerConfig.layers
+        and:
+        req.format == 'sif'
+    }
+
     def 'should create request object with build and cache repos' () {
         given:
         def session = Mock(Session) { getConfig() >> [wave:[build:[repository:'some/repo',cacheRepository:'some/cache']]]}
@@ -347,11 +374,11 @@ class WaveClientTest extends Specification {
         def client = new WaveClient(session)
 
         when:
-        def assets = client.resolveAssets(task, IMAGE)
+        def assets = client.resolveAssets(task, IMAGE, false)
         then:
         assets.containerImage == IMAGE
         !assets.moduleResources
-        !assets.dockerFileContent
+        !assets.containerFile
         !assets.containerConfig
         !assets.condaFile
         !assets.spackFile
@@ -369,12 +396,12 @@ class WaveClientTest extends Specification {
         def client = new WaveClient(session)
 
         when:
-        def assets = client.resolveAssets(task, IMAGE)
+        def assets = client.resolveAssets(task, IMAGE, false)
         then:
         assets.containerImage == IMAGE
         assets.containerPlatform == 'linux/arm64'
         !assets.moduleResources
-        !assets.dockerFileContent
+        !assets.containerFile
         !assets.containerConfig
         !assets.condaFile
         !assets.spackFile
@@ -392,11 +419,11 @@ class WaveClientTest extends Specification {
         def client = new WaveClient(session)
 
         when:
-        def assets = client.resolveAssets(task, IMAGE)
+        def assets = client.resolveAssets(task, IMAGE, false)
         then:
         assets.containerImage == IMAGE
         assets.moduleResources == BUNDLE
-        !assets.dockerFileContent
+        !assets.containerFile
         !assets.containerConfig
         !assets.condaFile
         !assets.spackFile
@@ -416,7 +443,7 @@ class WaveClientTest extends Specification {
         WaveClient client = Spy(WaveClient, constructorArgs:[session])
 
         when:
-        def assets = client.resolveAssets(task, IMAGE)
+        def assets = client.resolveAssets(task, IMAGE, false)
         then:
         client.resolveContainerConfig(ARCH) >> CONTAINER_CONFIG
         and:
@@ -424,7 +451,7 @@ class WaveClientTest extends Specification {
         assets.moduleResources == BUNDLE
         assets.containerConfig == CONTAINER_CONFIG
         and:
-        !assets.dockerFileContent
+        !assets.containerFile
         !assets.condaFile
         !assets.spackFile
         !assets.projectResources
@@ -445,9 +472,9 @@ class WaveClientTest extends Specification {
         def client = new WaveClient(session)
 
         when:
-        def assets = client.resolveAssets(task, null)
+        def assets = client.resolveAssets(task, null, false)
         then:
-        assets.dockerFileContent == 'FROM foo\nRUN this/that'
+        assets.containerFile == 'FROM foo\nRUN this/that'
         assets.moduleResources == BUNDLE
         !assets.containerImage
         !assets.containerConfig
@@ -468,9 +495,9 @@ class WaveClientTest extends Specification {
         def client = new WaveClient(session)
 
         when:
-        def assets = client.resolveAssets(task, null)
+        def assets = client.resolveAssets(task, null, false)
         then:
-        assets.dockerFileContent == '''\
+        assets.containerFile == '''\
                 FROM mambaorg/micromamba:1.4.9
                 RUN \\
                     micromamba install -y -n base -c conda-forge -c defaults \\
@@ -496,9 +523,9 @@ class WaveClientTest extends Specification {
         def client = new WaveClient(session)
 
         when:
-        def assets = client.resolveAssets(task, null)
+        def assets = client.resolveAssets(task, null, false)
         then:
-        assets.dockerFileContent == '''\
+        assets.containerFile == '''\
                 # Runner image
                 FROM {{spack_runner_image}}
                 
@@ -538,9 +565,9 @@ class WaveClientTest extends Specification {
         def client = new WaveClient(session)
 
         when:
-        def assets = client.resolveAssets(task, null)
+        def assets = client.resolveAssets(task, null, false)
         then:
-        assets.dockerFileContent == '''\
+        assets.containerFile == '''\
                 FROM mambaorg/micromamba:1.4.9
                 COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml
                 RUN micromamba install -y -n base -f /tmp/conda.yml \\
@@ -571,9 +598,9 @@ class WaveClientTest extends Specification {
         def client = new WaveClient(session)
 
         when:
-        def assets = client.resolveAssets(task, null)
+        def assets = client.resolveAssets(task, null, false)
         then:
-        assets.dockerFileContent == '''\
+        assets.containerFile == '''\
                 # Runner image
                 FROM {{spack_runner_image}}
                 
@@ -605,6 +632,78 @@ class WaveClientTest extends Specification {
         folder?.deleteDir()
     }
 
+    // ==== singularity native build + conda ====
+
+    def 'should create asset with conda recipe and singularity native build' () {
+        given:
+        def session = Mock(Session) { getConfig() >> [:]}
+        and:
+        def task = Mock(TaskRun) {getConfig() >> [conda:'salmon=1.2.3'] }
+        and:
+        def client = new WaveClient(session)
+
+        when:
+        def assets = client.resolveAssets(task, null, true)
+        then:
+        assets.containerFile == '''\
+                BootStrap: docker
+                From: mambaorg/micromamba:1.4.9
+                %post
+                    micromamba install -y -n base -c conda-forge -c defaults \\
+                    salmon=1.2.3 \\
+                    && micromamba clean -a -y
+                %environment
+                    export PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
+                    '''.stripIndent()
+        and:
+        assets.singularity
+        and:
+        !assets.moduleResources
+        !assets.containerImage
+        !assets.containerConfig
+        !assets.condaFile
+        !assets.spackFile
+        !assets.projectResources
+    }
+
+    def 'should create asset with conda file and singularity native build' () {
+        given:
+        def folder = Files.createTempDirectory('test')
+        def condaFile = folder.resolve('conda.yml'); condaFile.text = 'the-conda-recipe-here'
+        and:
+        def session = Mock(Session) { getConfig() >> [:]}
+        def task = Mock(TaskRun) {getConfig() >> [conda:condaFile.toString()] }
+        and:
+        def client = new WaveClient(session)
+
+        when:
+        def assets = client.resolveAssets(task, null, true)
+        then:
+        assets.containerFile == '''\
+                BootStrap: docker
+                From: mambaorg/micromamba:1.4.9
+                %files
+                    {{wave_context_dir}}/conda.yml /tmp/conda.yml
+                %post
+                    micromamba install -y -n base -f /tmp/conda.yml \\
+                    && micromamba clean -a -y
+                %environment
+                    export PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"                    
+                '''.stripIndent()
+        and:
+        assets.condaFile == condaFile
+        assets.singularity
+        and:
+        !assets.moduleResources
+        !assets.containerImage
+        !assets.containerConfig
+        !assets.spackFile
+        !assets.projectResources
+
+        cleanup:
+        folder?.deleteDir()
+    }
+
     def 'should create assets with project resources' () {
         given:
         def MODULE_RES = Mock(ResourcesBundle)
@@ -623,7 +722,7 @@ class WaveClientTest extends Specification {
         WaveClient wave = Spy(WaveClient, constructorArgs: [session])
 
         when:
-        def assets = wave.resolveAssets(task, 'image:latest')
+        def assets = wave.resolveAssets(task, 'image:latest', false)
         then:
         1 * wave.projectResources(BIN_DIR) >> PROJECT_RES
         and:
@@ -666,6 +765,23 @@ class WaveClientTest extends Specification {
         result == [spack:'x']
     }
 
+    def 'should patch strategy for singularity' () {
+        given:
+        def session = Mock(Session) { getConfig() >> [:]}
+        and:
+        def client = new WaveClient(session)
+
+        expect:
+        client.patchStrategy(Collections.unmodifiableList(STRATEGY), SING) == EXPECTED
+
+        where:
+        STRATEGY                                            | SING      | EXPECTED
+        ['conda','dockerfile', 'spack']                     | false     | ['conda','dockerfile', 'spack']
+        ['conda','dockerfile', 'spack']                     | true      | ['conda','singularityfile', 'spack']
+        ['conda','dockerfile', 'spack']                     | true      | ['conda','singularityfile', 'spack']
+        ['conda','singularityfile','dockerfile', 'spack']   | true      | ['conda','singularityfile','dockerfile', 'spack']
+    }
+
     def 'should check conflicts' () {
         given:
         def session = Mock(Session) { getConfig() >> [:]}
@@ -713,6 +829,25 @@ class WaveClientTest extends Specification {
         e = thrown(IllegalArgumentException)
         e.message == "Process 'foo' declares both 'spack' and 'conda' directives that conflict each other"
 
+        // singularity file checks
+        when:
+        client.checkConflicts([conda:'this', singularityfile:'that'], 'foo')
+        then:
+        e = thrown(IllegalArgumentException)
+        e.message == "Process 'foo' declares both a 'conda' directive and a module bundle singularityfile that conflict each other"
+
+        when:
+        client.checkConflicts([container:'this', singularityfile:'that'], 'foo')
+        then:
+        e = thrown(IllegalArgumentException)
+        e.message == "Process 'foo' declares both a 'container' directive and a module bundle singularityfile that conflict each other"
+
+        when:
+        client.checkConflicts([spack:'this', singularityfile:'that'], 'foo')
+        then:
+        e = thrown(IllegalArgumentException)
+        e.message == "Process 'foo' declares both a 'spack' directive and a module bundle singularityfile that conflict each other"
+
     }
 
     def 'should get project resource bundle' () {
@@ -762,7 +897,6 @@ class WaveClientTest extends Specification {
             assert (it[0] as SubmitContainerTokenRequest).towerWorkspaceId == 123
             assert (it[0] as SubmitContainerTokenRequest).towerEndpoint == 'http://foo.com'
         }
-
     }
 
     def 'should send request with tower access token and refresh token' () {
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/resolver/WaveContainerResolverTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/resolver/WaveContainerResolverTest.groovy
index 7825dd0540..da190d728e 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/resolver/WaveContainerResolverTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/resolver/WaveContainerResolverTest.groovy
@@ -18,6 +18,7 @@
 package io.seqera.wave.plugin.resolver
 
 import io.seqera.wave.plugin.WaveClient
+import io.seqera.wave.plugin.config.WaveConfig
 import nextflow.container.ContainerConfig
 import nextflow.container.resolver.ContainerInfo
 import nextflow.container.resolver.DefaultContainerResolver
@@ -35,6 +36,7 @@ class WaveContainerResolverTest extends Specification {
         given:
         def CONTAINER_NAME = "ubuntu:latest"
         def WAVE_CONTAINER = new ContainerInfo(CONTAINER_NAME, "wave.io/ubuntu:latest", "12345")
+        def ORAS_CONTAINER = new ContainerInfo(CONTAINER_NAME, "oras://wave.io/ubuntu:latest", "12345")
         def SINGULARITY_CONTAINER = new ContainerInfo('ubuntu:latest', '/some/singularity/ubuntu.img')
         and:
         def defaultResolver = Spy(DefaultContainerResolver)
@@ -46,27 +48,40 @@ class WaveContainerResolverTest extends Specification {
             }
         }
 
+        // docker images
         when:
         def result = resolver.resolveImage(task, CONTAINER_NAME)
         then:
-        resolver.client() >> Mock(WaveClient) { enabled()>>true }
+        resolver.client() >> Mock(WaveClient) { enabled()>>true; config()>>Mock(WaveConfig) }
         _ * task.getContainerConfig() >> Mock(ContainerConfig) { getEngine()>>'docker' }
         and:
-        1 * resolver.waveContainer(task, CONTAINER_NAME) >> WAVE_CONTAINER
+        1 * resolver.waveContainer(task, CONTAINER_NAME, false) >> WAVE_CONTAINER
         and:
         result == WAVE_CONTAINER
 
-
+        // singularity images
         when:
         result = resolver.resolveImage(task, CONTAINER_NAME)
         then:
-        resolver.client() >> Mock(WaveClient) { enabled()>>true }
+        resolver.client() >> Mock(WaveClient) { enabled()>>true; config()>>Mock(WaveConfig) }
         _ * task.getContainerConfig() >> Mock(ContainerConfig) { getEngine()>>'singularity' }
         and:
-        1 * resolver.waveContainer(task, CONTAINER_NAME) >> WAVE_CONTAINER
+        1 * resolver.waveContainer(task, CONTAINER_NAME, false) >> WAVE_CONTAINER
         1 * defaultResolver.resolveImage(task, WAVE_CONTAINER.target) >> SINGULARITY_CONTAINER
         and:
         result == SINGULARITY_CONTAINER
+
+        // singularity images + oras protocol
+        when:
+        result = resolver.resolveImage(task, CONTAINER_NAME)
+        then:
+        resolver.client() >> Mock(WaveClient) { enabled()>>true; config()>>Mock(WaveConfig) { freezeMode()>>true } }
+        _ * task.getContainerConfig() >> Mock(ContainerConfig) { getEngine()>>'singularity' }
+        and:
+        1 * resolver.waveContainer(task, CONTAINER_NAME, true) >> ORAS_CONTAINER
+        0 * defaultResolver.resolveImage(task, WAVE_CONTAINER.target) >> null
+        and:
+        result == ORAS_CONTAINER
     }
 
     def 'should validate container name' () {
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/util/DockerHelperTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/util/DockerHelperTest.groovy
deleted file mode 100644
index 4112c96900..0000000000
--- a/plugins/nf-wave/src/test/io/seqera/wave/util/DockerHelperTest.groovy
+++ /dev/null
@@ -1,381 +0,0 @@
-/*
- * Copyright 2013-2023, Seqera Labs
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package io.seqera.wave.util
-
-import java.nio.file.Files
-
-import spock.lang.Specification
-
-import io.seqera.wave.config.CondaOpts
-import io.seqera.wave.config.SpackOpts
-
-/**
- *
- * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
- */
-class DockerHelperTest extends Specification {
-
-    def 'should create dockerfile content from conda file' () {
-        given:
-        def CONDA_OPTS = new CondaOpts([basePackages: 'conda-forge::procps-ng'])
-
-        expect:
-        DockerHelper.condaFileToDockerFile(CONDA_OPTS)== '''\
-                FROM mambaorg/micromamba:1.4.9
-                COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml
-                RUN micromamba install -y -n base -f /tmp/conda.yml \\
-                    && micromamba install -y -n base conda-forge::procps-ng \\
-                    && micromamba clean -a -y
-                USER root
-                '''.stripIndent()
-    }
-
-    def 'should create dockerfile content from conda file and base packages' () {
-
-        expect:
-        DockerHelper.condaFileToDockerFile(new CondaOpts([:]))== '''\
-                FROM mambaorg/micromamba:1.4.9
-                COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml
-                RUN micromamba install -y -n base -f /tmp/conda.yml \\
-                    && micromamba clean -a -y
-                USER root
-                '''.stripIndent()
-    }
-
-
-    def 'should create dockerfile content from conda package' () {
-        given:
-        def PACKAGES = 'bwa=0.7.15 salmon=1.1.1'
-        def CHANNELS = ['conda-forge', 'defaults']
-        expect:
-        DockerHelper.condaPackagesToDockerFile(PACKAGES, CHANNELS, new CondaOpts([:])) == '''\
-                FROM mambaorg/micromamba:1.4.9
-                RUN \\
-                    micromamba install -y -n base -c conda-forge -c defaults \\
-                    bwa=0.7.15 salmon=1.1.1 \\
-                    && micromamba clean -a -y
-                USER root
-                '''.stripIndent()
-    }
-
-    def 'should create dockerfile with base packages' () {
-        given:
-        def CHANNELS = ['conda-forge', 'defaults']
-        def CONDA_OPTS = new CondaOpts([basePackages: 'foo::one bar::two'])
-        def PACKAGES = 'bwa=0.7.15 salmon=1.1.1'
-
-        expect:
-        DockerHelper.condaPackagesToDockerFile(PACKAGES, CHANNELS, CONDA_OPTS) == '''\
-                FROM mambaorg/micromamba:1.4.9
-                RUN \\
-                    micromamba install -y -n base -c conda-forge -c defaults \\
-                    bwa=0.7.15 salmon=1.1.1 \\
-                    && micromamba install -y -n base foo::one bar::two \\
-                    && micromamba clean -a -y
-                USER root
-                '''.stripIndent()
-    }
-
-    def 'should create dockerfile content with custom channels' () {
-        given:
-        def CHANNELS = 'foo,bar'.tokenize(',')
-        def PACKAGES = 'bwa=0.7.15 salmon=1.1.1'
-
-        expect:
-        DockerHelper.condaPackagesToDockerFile(PACKAGES, CHANNELS, new CondaOpts([:])) == '''\
-                FROM mambaorg/micromamba:1.4.9
-                RUN \\
-                    micromamba install -y -n base -c foo -c bar \\
-                    bwa=0.7.15 salmon=1.1.1 \\
-                    && micromamba clean -a -y
-                USER root
-                '''.stripIndent()
-    }
-
-    def 'should create dockerfile content with custom conda config' () {
-        given:
-        def CHANNELS = ['conda-forge', 'defaults']
-        def CONDA_OPTS = [mambaImage:'my-base:123', commands: ['USER my-user', 'RUN apt-get update -y && apt-get install -y nano']]
-        def PACKAGES = 'bwa=0.7.15 salmon=1.1.1'
-
-        expect:
-        DockerHelper.condaPackagesToDockerFile(PACKAGES, CHANNELS, new CondaOpts(CONDA_OPTS)) == '''\
-                FROM my-base:123
-                RUN \\
-                    micromamba install -y -n base -c conda-forge -c defaults \\
-                    bwa=0.7.15 salmon=1.1.1 \\
-                    && micromamba clean -a -y
-                USER root
-                USER my-user
-                RUN apt-get update -y && apt-get install -y nano
-                '''.stripIndent()
-    }
-
-
-    def 'should create dockerfile content with remote conda lock' () {
-        given:
-        def CHANNELS = ['conda-forge', 'defaults']
-        def OPTS = [mambaImage:'my-base:123', commands: ['USER my-user', 'RUN apt-get update -y && apt-get install -y procps']]
-        def PACKAGES = 'https://foo.com/some/conda-lock.yml'
-
-        expect:
-        DockerHelper.condaPackagesToDockerFile(PACKAGES, CHANNELS, new CondaOpts(OPTS)) == '''\
-                FROM my-base:123
-                RUN \\
-                    micromamba install -y -n base -c conda-forge -c defaults \\
-                    -f https://foo.com/some/conda-lock.yml \\
-                    && micromamba clean -a -y
-                USER root
-                USER my-user
-                RUN apt-get update -y && apt-get install -y procps
-                '''.stripIndent()
-    }
-
-
-    def 'should create dockerfile content from spack package' () {
-        given:
-        def PACKAGES = 'bwa@0.7.15 salmon@1.1.1'
-
-        expect:
-        DockerHelper.spackPackagesToSpackFile(PACKAGES, Mock(SpackOpts)).text == '''\
-                spack:
-                  specs: [bwa@0.7.15, salmon@1.1.1]
-                  concretizer: {unify: true, reuse: false}
-                '''.stripIndent(true)
-
-        DockerHelper.spackFileToDockerFile(new SpackOpts())== '''\
-                # Runner image
-                FROM {{spack_runner_image}}
-                
-                COPY --from=builder /opt/spack-env /opt/spack-env
-                COPY --from=builder /opt/software /opt/software
-                COPY --from=builder /opt/._view /opt/._view
-                
-                # Entrypoint for Singularity
-                RUN mkdir -p /.singularity.d/env && \\
-                    cp -p /opt/spack-env/z10_spack_environment.sh /.singularity.d/env/91-environment.sh
-                # Entrypoint for Docker
-                RUN echo "#!/usr/bin/env bash\\n\\nset -ef -o pipefail\\nsource /opt/spack-env/z10_spack_environment.sh\\nexec \\"\\\$@\\"" \\
-                    >/opt/spack-env/spack_docker_entrypoint.sh && chmod a+x /opt/spack-env/spack_docker_entrypoint.sh
-                
-                
-                ENTRYPOINT [ "/opt/spack-env/spack_docker_entrypoint.sh" ]
-                CMD [ "/bin/bash" ]
-                '''.stripIndent()
-    }
-
-    def 'should create dockerfile content with custom spack config' () {
-        given:
-        def SPACK_OPTS = [ commands:['USER hola'] ]
-        def PACKAGES = 'bwa@0.7.15 salmon@1.1.1'
-
-        expect:
-        DockerHelper.spackPackagesToSpackFile(PACKAGES, Mock(SpackOpts)).text == '''\
-                spack:
-                  specs: [bwa@0.7.15, salmon@1.1.1]
-                  concretizer: {unify: true, reuse: false}
-                '''.stripIndent(true)
-
-        DockerHelper.spackFileToDockerFile(new SpackOpts(SPACK_OPTS))== '''\
-                # Runner image
-                FROM {{spack_runner_image}}
-                
-                COPY --from=builder /opt/spack-env /opt/spack-env
-                COPY --from=builder /opt/software /opt/software
-                COPY --from=builder /opt/._view /opt/._view
-                
-                # Entrypoint for Singularity
-                RUN mkdir -p /.singularity.d/env && \\
-                    cp -p /opt/spack-env/z10_spack_environment.sh /.singularity.d/env/91-environment.sh
-                # Entrypoint for Docker
-                RUN echo "#!/usr/bin/env bash\\n\\nset -ef -o pipefail\\nsource /opt/spack-env/z10_spack_environment.sh\\nexec \\"\\\$@\\"" \\
-                    >/opt/spack-env/spack_docker_entrypoint.sh && chmod a+x /opt/spack-env/spack_docker_entrypoint.sh
-                
-                USER hola
-                
-                ENTRYPOINT [ "/opt/spack-env/spack_docker_entrypoint.sh" ]
-                CMD [ "/bin/bash" ]
-                '''.stripIndent()
-    }
-
-
-    def 'should create dockerfile content from spack file' () {
-        expect:
-        DockerHelper.spackFileToDockerFile(new SpackOpts())== '''\
-                # Runner image
-                FROM {{spack_runner_image}}
-                
-                COPY --from=builder /opt/spack-env /opt/spack-env
-                COPY --from=builder /opt/software /opt/software
-                COPY --from=builder /opt/._view /opt/._view
-                
-                # Entrypoint for Singularity
-                RUN mkdir -p /.singularity.d/env && \\
-                    cp -p /opt/spack-env/z10_spack_environment.sh /.singularity.d/env/91-environment.sh
-                # Entrypoint for Docker
-                RUN echo "#!/usr/bin/env bash\\n\\nset -ef -o pipefail\\nsource /opt/spack-env/z10_spack_environment.sh\\nexec \\"\\\$@\\"" \\
-                    >/opt/spack-env/spack_docker_entrypoint.sh && chmod a+x /opt/spack-env/spack_docker_entrypoint.sh
-                
-                
-                ENTRYPOINT [ "/opt/spack-env/spack_docker_entrypoint.sh" ]
-                CMD [ "/bin/bash" ]
-                '''.stripIndent()
-    }
-
-    def 'should return empty packages' () {
-        when:
-        def result = DockerHelper.spackPackagesToSpackYaml(null, new SpackOpts())
-        then:
-        result == null
-    }
-
-    def 'should convert a list of packages to a spack yaml' () {
-        when:
-        def result = DockerHelper.spackPackagesToSpackYaml('foo@1.2.3 x=one bar @2', new SpackOpts())
-        then:
-        result == '''\
-            spack:
-              specs: [foo@1.2.3 x=one, bar @2]
-              concretizer: {unify: true, reuse: false}
-            '''.stripIndent(true)
-    }
-
-
-    def 'should add base packages' () {
-        when:
-        def result = DockerHelper.spackPackagesToSpackYaml(null, new SpackOpts(basePackages: 'foo bar'))
-        then:
-        result == '''\
-            spack:
-              specs: [foo, bar]
-              concretizer: {unify: true, reuse: false}
-            '''.stripIndent(true)
-
-        when:
-        result = DockerHelper.spackPackagesToSpackYaml('this that @2', new SpackOpts(basePackages: 'foo bar @1'))
-        then:
-        result == '''\
-            spack:
-              specs: [foo, bar @1, this, that @2]
-              concretizer: {unify: true, reuse: false}
-            '''.stripIndent(true)
-    }
-
-    def 'should convert a list of packages to a spack file' () {
-        when:
-        def result = DockerHelper.spackPackagesToSpackFile('foo@1.2.3 x=one bar @2', new SpackOpts())
-        then:
-        result.text == '''\
-            spack:
-              specs: [foo@1.2.3 x=one, bar @2]
-              concretizer: {unify: true, reuse: false}
-            '''.stripIndent(true)
-    }
-
-    def 'should parse a spack packages string' () {
-        expect:
-        DockerHelper.spackPackagesToList(PACKAGES) == EXPECTED
-
-        where:
-        PACKAGES            | EXPECTED
-         null               | null
-        'alpha'             | ['alpha']
-        'alpha delta'       | ['alpha', 'delta']
-        'alpha delta gamma' | ['alpha', 'delta', 'gamma']
-        'alpha 1aa'         | ['alpha', '1aa']
-        and:
-        'alpha x=1'         | ['alpha x=1']
-        'alpha x=1 delta'   | ['alpha x=1', 'delta']
-        'alpha ^foo delta'  | ['alpha ^foo', 'delta']
-        and:
-        '^alpha ~beta foo'  | ['^alpha ~beta', 'foo']   // <-- this should not be valid
-
-    }
-
-    def 'should merge spack file and base package' () {
-        given:
-        def folder = Files.createTempDirectory('test')
-        and:
-        def SPACK_FILE1 = folder.resolve('spack1.yaml')
-        SPACK_FILE1.text = '''\
-            spack:
-              specs: [foo@1.2.3 x=one, bar @2]
-              concretizer: {unify: true, reuse: false}
-            '''.stripIndent(true)
-        and:
-        def SPACK_FILE2 = folder.resolve('spack2.yaml')
-        SPACK_FILE2.text = '''\
-            spack:
-              concretizer: {unify: true, reuse: false}
-            '''.stripIndent(true)
-        and:
-        def SPACK_FILE3 = folder.resolve('spack3.yaml')
-        SPACK_FILE3.text = '''\
-            foo:
-              concretizer: {unify: true, reuse: false}
-            '''.stripIndent(true)
-
-        when:
-        def result = DockerHelper.addPackagesToSpackFile(null, new SpackOpts())
-        then:
-        result == null
-
-        when:
-        result = DockerHelper.addPackagesToSpackFile(SPACK_FILE1.toString(), new SpackOpts())
-        then:
-        result.toString() == SPACK_FILE1.toString()
-
-        when:
-        result = DockerHelper.addPackagesToSpackFile(SPACK_FILE1.toString(), new SpackOpts(basePackages: 'alpha delta'))
-        then:
-        result.text == '''\
-            spack:
-              specs: [foo@1.2.3 x=one, bar @2, alpha, delta]
-              concretizer: {unify: true, reuse: false}
-            '''.stripIndent(true)
-
-
-        when:
-        result = DockerHelper.addPackagesToSpackFile(SPACK_FILE2.toString(), new SpackOpts(basePackages: 'alpha delta'))
-        then:
-        result.text == '''\
-            spack:
-              concretizer: {unify: true, reuse: false}
-              specs: [alpha, delta]
-            '''.stripIndent(true)
-
-        when:
-        DockerHelper.addPackagesToSpackFile(SPACK_FILE3.toString(), new SpackOpts(basePackages: 'foo'))
-        then:
-        thrown(IllegalArgumentException)
-
-        when:
-        DockerHelper.addPackagesToSpackFile('missing file', new SpackOpts(basePackages: 'foo'))
-        then:
-        thrown(IllegalArgumentException)
-
-        when:
-        DockerHelper.addPackagesToSpackFile('missing file', new SpackOpts())
-        then:
-        thrown(IllegalArgumentException)
-
-        cleanup:
-        folder?.deleteDir()
-    }
-
-}
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/util/TemplateRendererTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/util/TemplateRendererTest.groovy
deleted file mode 100644
index 392893e16c..0000000000
--- a/plugins/nf-wave/src/test/io/seqera/wave/util/TemplateRendererTest.groovy
+++ /dev/null
@@ -1,202 +0,0 @@
-/*
- * Copyright 2013-2023, Seqera Labs
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package io.seqera.wave.util
-
-import spock.lang.Specification
-
-/**
- *
- * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
- */
-class TemplateRendererTest extends Specification {
-
-    def 'should replace vars' () {
-        given:
-        def binding = [foo: 'Hello', bar: 'world']
-        def render = new TemplateRenderer()
-        expect:
-        render.replace0('{{foo}}', binding) == 'Hello'
-        render.replace0('{{foo}} ', binding) == 'Hello '
-        render.replace0('{{foo}}\n', binding) == 'Hello\n'
-        render.replace0('  {{foo}}', binding) == '  Hello'
-        render.replace0('  {{foo}}\n', binding) == '  Hello\n'
-        render.replace0('  ${foo}', binding)  == '  ${foo}'
-        render.replace0('  ${{foo}}', binding) == '  ${{foo}}'
-        render.replace0('{{foo}}', [foo:'']) == ''
-        render.replace0('{{foo}}', [foo:null]) == null
-        render.replace0('  {{foo}}\n', [foo:null]) == null
-        render.replace0('', binding) == ''
-        render.replace0(null, binding) == null
-
-        render.replace0('{{foo}} {{bar}}!', binding) == 'Hello world!'
-        render.replace0('abc {{foo}} pq {{bar}} xyz', binding) == 'abc Hello pq world xyz'
-        render.replace0('{{foo}} 123 {{bar}} xyz {{foo}}', binding) == 'Hello 123 world xyz Hello'
-        render.replace0('1{{foo}}2{{foo}}3', [foo:'']) == '123'
-        render.replace0('1{{foo}}2{{foo}}3', [foo:null]) == '123'
-    }
-
-    def 'should throw an exception when missing variables' () {
-        when:
-        new TemplateRenderer().replace0('{{x1}}', [:])
-        then:
-        def e = thrown(IllegalArgumentException)
-        e.message == 'Missing template key: x1'
-
-        when:
-        new TemplateRenderer().replace0('{{foo}} {{x2}}', [foo:'ciao'])
-        then:
-        e = thrown(IllegalArgumentException)
-        e.message == 'Missing template key: x2'
-    }
-
-    def 'should not throw an exception when missing variables' () {
-        when:
-        def result = new TemplateRenderer().withIgnore("x1").replace0('{{x1}}', [x1:'one'])
-        then:
-        result == '{{x1}}'
-
-        when:
-        result = new TemplateRenderer().withIgnore('x1','x2').replace0('{{x1}} {{x2}}', [x1:'one'])
-        then:
-        result == '{{x1}} {{x2}}'
-    }
-
-    def 'should render template' () {
-        given:
-        def template = "Hello, {{name}}!\n" +
-                "Today is {{day}} and the weather is {{weather}}.";
-        and:
-        def binding = new HashMap<String,String>();
-        binding.put("name", "John");
-        binding.put("day", "Monday");
-        binding.put("weather", "sunny");
-
-        when:
-        def renderer = new TemplateRenderer()
-        and:
-        def result = renderer.render(template, binding);
-
-        then:
-        result == 'Hello, John!\nToday is Monday and the weather is sunny.'
-    }
-
-    def 'should render a template with comment'() {
-        given:
-        def template = """\
-            ## remove this comment
-            1: {{alpha}}
-            2: {{delta}} {{delta}}
-            3: {{gamma}} {{gamma}} {{gamma}} 
-            4: end
-            """.stripIndent()
-        and:
-        def binding = new HashMap<String,String>();
-        binding.put("alpha", "one");
-        binding.put("delta", "two");
-        binding.put("gamma", "three");
-
-        when:
-        def renderer = new TemplateRenderer()
-        and:
-        def result = renderer.render(new ByteArrayInputStream(template.bytes), binding);
-
-        then:
-        result == """\
-            1: one
-            2: two two
-            3: three three three 
-            4: end
-            """.stripIndent()
-    }
-
-
-    def 'should render a template using an input stream'() {
-        given:
-        def template = """\
-            {{one}}
-            {{two}}
-            xxx
-            {{three}}            
-            zzz
-            """.stripIndent()
-        and:
-        def binding = [
-                one: '1',   // this is rendered
-                two:null,   // a line containing a null variable is not rendered
-                three:''    // empty value is considered ok
-        ]
-
-        when:
-        def renderer = new TemplateRenderer()
-        and:
-        def result = renderer.render(new ByteArrayInputStream(template.bytes), binding);
-
-        then:
-        result == """\
-            1
-            xxx
-            
-            zzz
-            """.stripIndent()
-    }
-
-    def 'should render template with indentations' () {
-        given:
-        def binding = [foo: 'Hello', bar: 'world']
-
-        when:
-        def renderer = new TemplateRenderer()
-        and:
-        def result = renderer.render('{{foo}}\n{{bar}}', binding)
-        then:
-        result == 'Hello\nworld'
-
-        when:
-        def template = '''\
-              {{foo}}
-            {{bar}}
-            '''.stripIndent()
-        result = renderer.render(template, [foo:'11\n22\n33', bar:'Hello world'])
-        then:
-        result == '''\
-              11
-              22
-              33
-            Hello world
-            '''.stripIndent()
-
-
-        when:
-        template = '''\
-            {{x1}}
-            {{x2}}
-            {{x3}}
-            '''.stripIndent()
-        result = renderer.render(template, [x1:'aa\nbb\n', x2:null, x3:'pp\nqq'])
-        then:
-        result == '''\
-            aa
-            bb
-            
-            pp
-            qq
-            '''.stripIndent()
-
-    }
-
-}

From cb4112080994a2e749e17f5e0234c1e6d47b55e3 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Wed, 23 Aug 2023 09:01:52 +0200
Subject: [PATCH 097/350] Bump groovy 3.0.19

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 build.gradle                       |  4 ++--
 modules/nextflow/build.gradle      | 14 +++++++-------
 modules/nf-commons/build.gradle    |  4 ++--
 modules/nf-httpfs/build.gradle     |  6 +++---
 plugins/nf-amazon/build.gradle     |  4 ++--
 plugins/nf-azure/build.gradle      |  4 ++--
 plugins/nf-cloudcache/build.gradle |  4 ++--
 plugins/nf-codecommit/build.gradle |  4 ++--
 plugins/nf-console/build.gradle    |  8 ++++----
 plugins/nf-ga4gh/build.gradle      |  4 ++--
 plugins/nf-google/build.gradle     |  4 ++--
 plugins/nf-tower/build.gradle      |  4 ++--
 plugins/nf-wave/build.gradle       |  4 ++--
 13 files changed, 34 insertions(+), 34 deletions(-)

diff --git a/build.gradle b/build.gradle
index 2b8f83e687..438e51dacb 100644
--- a/build.gradle
+++ b/build.gradle
@@ -102,8 +102,8 @@ allprojects {
 
         // Documentation required libraries
         groovyDoc 'org.fusesource.jansi:jansi:1.11'
-        groovyDoc "org.codehaus.groovy:groovy-groovydoc:3.0.18"
-        groovyDoc "org.codehaus.groovy:groovy-ant:3.0.18"
+        groovyDoc "org.codehaus.groovy:groovy-groovydoc:3.0.19"
+        groovyDoc "org.codehaus.groovy:groovy-ant:3.0.19"
     }
 
     test {
diff --git a/modules/nextflow/build.gradle b/modules/nextflow/build.gradle
index 66f39fad28..4b468ecc14 100644
--- a/modules/nextflow/build.gradle
+++ b/modules/nextflow/build.gradle
@@ -17,12 +17,12 @@ compileGroovy {
 dependencies {
     api(project(':nf-commons'))
     api(project(':nf-httpfs'))
-    api "org.codehaus.groovy:groovy:3.0.18"
-    api "org.codehaus.groovy:groovy-nio:3.0.18"
-    api "org.codehaus.groovy:groovy-xml:3.0.18"
-    api "org.codehaus.groovy:groovy-json:3.0.18"
-    api "org.codehaus.groovy:groovy-templates:3.0.18"
-    api "org.codehaus.groovy:groovy-yaml:3.0.18"
+    api "org.codehaus.groovy:groovy:3.0.19"
+    api "org.codehaus.groovy:groovy-nio:3.0.19"
+    api "org.codehaus.groovy:groovy-xml:3.0.19"
+    api "org.codehaus.groovy:groovy-json:3.0.19"
+    api "org.codehaus.groovy:groovy-templates:3.0.19"
+    api "org.codehaus.groovy:groovy-yaml:3.0.19"
     api "org.slf4j:jcl-over-slf4j:2.0.7"
     api "org.slf4j:jul-to-slf4j:2.0.7"
     api "org.slf4j:log4j-over-slf4j:2.0.7"
@@ -48,7 +48,7 @@ dependencies {
     testImplementation 'org.subethamail:subethasmtp:3.1.7'
 
     // test configuration
-    testFixturesApi ("org.codehaus.groovy:groovy-test:3.0.18") { exclude group: 'org.codehaus.groovy' }
+    testFixturesApi ("org.codehaus.groovy:groovy-test:3.0.19") { exclude group: 'org.codehaus.groovy' }
     testFixturesApi ("cglib:cglib-nodep:3.3.0")
     testFixturesApi ("org.objenesis:objenesis:3.2")
     testFixturesApi ("org.spockframework:spock-core:2.3-groovy-3.0") { exclude group: 'org.codehaus.groovy'; exclude group: 'net.bytebuddy' }
diff --git a/modules/nf-commons/build.gradle b/modules/nf-commons/build.gradle
index d42542be3b..e3a00932d9 100644
--- a/modules/nf-commons/build.gradle
+++ b/modules/nf-commons/build.gradle
@@ -26,8 +26,8 @@ sourceSets {
 
 dependencies {
     api "ch.qos.logback:logback-classic:1.4.6"
-    api "org.codehaus.groovy:groovy:3.0.18"
-    api "org.codehaus.groovy:groovy-nio:3.0.18"
+    api "org.codehaus.groovy:groovy:3.0.19"
+    api "org.codehaus.groovy:groovy-nio:3.0.19"
     api "commons-lang:commons-lang:2.6"
     api 'com.google.guava:guava:31.1-jre'
     api 'org.pf4j:pf4j:3.4.1'
diff --git a/modules/nf-httpfs/build.gradle b/modules/nf-httpfs/build.gradle
index e6e9d81ecd..9db2f0da7b 100644
--- a/modules/nf-httpfs/build.gradle
+++ b/modules/nf-httpfs/build.gradle
@@ -30,12 +30,12 @@ sourceSets {
 dependencies {
     api project(':nf-commons')
     api "ch.qos.logback:logback-classic:1.4.6"
-    api "org.codehaus.groovy:groovy:3.0.18"
-    api "org.codehaus.groovy:groovy-nio:3.0.18"
+    api "org.codehaus.groovy:groovy:3.0.19"
+    api "org.codehaus.groovy:groovy-nio:3.0.19"
     api("com.esotericsoftware.kryo:kryo:2.24.0") { exclude group: 'com.esotericsoftware.minlog', module: 'minlog' }
 
     /* testImplementation inherited from top gradle build file */
-    testImplementation "org.codehaus.groovy:groovy-json:3.0.18" // needed by wiremock
+    testImplementation "org.codehaus.groovy:groovy-json:3.0.19" // needed by wiremock
     testImplementation ('com.github.tomakehurst:wiremock:1.57') { exclude module: 'groovy-all' }
     testImplementation ('com.github.tomjankes:wiremock-groovy:0.2.0') { exclude module: 'groovy-all' }
 
diff --git a/plugins/nf-amazon/build.gradle b/plugins/nf-amazon/build.gradle
index 8499e56160..fad4a22db4 100644
--- a/plugins/nf-amazon/build.gradle
+++ b/plugins/nf-amazon/build.gradle
@@ -56,6 +56,6 @@ dependencies {
         
     testImplementation(testFixtures(project(":nextflow")))
     testImplementation project(':nextflow')
-    testImplementation "org.codehaus.groovy:groovy:3.0.18"
-    testImplementation "org.codehaus.groovy:groovy-nio:3.0.18"
+    testImplementation "org.codehaus.groovy:groovy:3.0.19"
+    testImplementation "org.codehaus.groovy:groovy-nio:3.0.19"
 }
diff --git a/plugins/nf-azure/build.gradle b/plugins/nf-azure/build.gradle
index ffcfd88869..c74ef70fe8 100644
--- a/plugins/nf-azure/build.gradle
+++ b/plugins/nf-azure/build.gradle
@@ -57,6 +57,6 @@ dependencies {
 
     testImplementation(testFixtures(project(":nextflow")))
     testImplementation project(':nextflow')
-    testImplementation "org.codehaus.groovy:groovy:3.0.18"
-    testImplementation "org.codehaus.groovy:groovy-nio:3.0.18"
+    testImplementation "org.codehaus.groovy:groovy:3.0.19"
+    testImplementation "org.codehaus.groovy:groovy-nio:3.0.19"
 }
diff --git a/plugins/nf-cloudcache/build.gradle b/plugins/nf-cloudcache/build.gradle
index 977c686c08..d37b5354c9 100644
--- a/plugins/nf-cloudcache/build.gradle
+++ b/plugins/nf-cloudcache/build.gradle
@@ -35,7 +35,7 @@ dependencies {
     compileOnly 'org.pf4j:pf4j:3.4.1'
 
     testImplementation(testFixtures(project(":nextflow")))
-    testImplementation "org.codehaus.groovy:groovy:3.0.18"
-    testImplementation "org.codehaus.groovy:groovy-nio:3.0.18"
+    testImplementation "org.codehaus.groovy:groovy:3.0.19"
+    testImplementation "org.codehaus.groovy:groovy-nio:3.0.19"
 }
 
diff --git a/plugins/nf-codecommit/build.gradle b/plugins/nf-codecommit/build.gradle
index ba425ffebc..0137c25c5a 100644
--- a/plugins/nf-codecommit/build.gradle
+++ b/plugins/nf-codecommit/build.gradle
@@ -42,6 +42,6 @@ dependencies {
         
     testImplementation(testFixtures(project(":nextflow")))
     testImplementation project(':nextflow')
-    testImplementation "org.codehaus.groovy:groovy:3.0.18"
-    testImplementation "org.codehaus.groovy:groovy-nio:3.0.18"
+    testImplementation "org.codehaus.groovy:groovy:3.0.19"
+    testImplementation "org.codehaus.groovy:groovy-nio:3.0.19"
 }
diff --git a/plugins/nf-console/build.gradle b/plugins/nf-console/build.gradle
index 94a6973fb0..9b88a1daf2 100644
--- a/plugins/nf-console/build.gradle
+++ b/plugins/nf-console/build.gradle
@@ -37,11 +37,11 @@ dependencies {
     compileOnly 'org.slf4j:slf4j-api:2.0.7'
     compileOnly 'org.pf4j:pf4j:3.4.1'
 
-    api("org.codehaus.groovy:groovy-console:3.0.18") { transitive=false }
-    api("org.codehaus.groovy:groovy-swing:3.0.18")  { transitive=false }
+    api("org.codehaus.groovy:groovy-console:3.0.19") { transitive=false }
+    api("org.codehaus.groovy:groovy-swing:3.0.19")  { transitive=false }
 
     testImplementation project(':nextflow')
-    testImplementation "org.codehaus.groovy:groovy:3.0.18"
-    testImplementation "org.codehaus.groovy:groovy-nio:3.0.18"
+    testImplementation "org.codehaus.groovy:groovy:3.0.19"
+    testImplementation "org.codehaus.groovy:groovy-nio:3.0.19"
 }
 
diff --git a/plugins/nf-ga4gh/build.gradle b/plugins/nf-ga4gh/build.gradle
index 96302cd9ac..1f87616d4d 100644
--- a/plugins/nf-ga4gh/build.gradle
+++ b/plugins/nf-ga4gh/build.gradle
@@ -45,6 +45,6 @@ dependencies {
     api 'joda-time:joda-time:2.9.9'
 
     testImplementation(testFixtures(project(":nextflow")))
-    testImplementation "org.codehaus.groovy:groovy:3.0.18"
-    testImplementation "org.codehaus.groovy:groovy-nio:3.0.18"
+    testImplementation "org.codehaus.groovy:groovy:3.0.19"
+    testImplementation "org.codehaus.groovy:groovy-nio:3.0.19"
 }
diff --git a/plugins/nf-google/build.gradle b/plugins/nf-google/build.gradle
index c232099166..644aa9502e 100644
--- a/plugins/nf-google/build.gradle
+++ b/plugins/nf-google/build.gradle
@@ -46,8 +46,8 @@ dependencies {
     api 'com.google.code.gson:gson:2.10.1'
 
     testImplementation(testFixtures(project(":nextflow")))
-    testImplementation "org.codehaus.groovy:groovy:3.0.18"
-    testImplementation "org.codehaus.groovy:groovy-nio:3.0.18"
+    testImplementation "org.codehaus.groovy:groovy:3.0.19"
+    testImplementation "org.codehaus.groovy:groovy-nio:3.0.19"
 }
 
 test {
diff --git a/plugins/nf-tower/build.gradle b/plugins/nf-tower/build.gradle
index b3b487be82..bb5980c1a8 100644
--- a/plugins/nf-tower/build.gradle
+++ b/plugins/nf-tower/build.gradle
@@ -37,6 +37,6 @@ dependencies {
     api "com.fasterxml.jackson.core:jackson-databind:2.12.7.1"
 
     testImplementation(testFixtures(project(":nextflow")))
-    testImplementation "org.codehaus.groovy:groovy:3.0.18"
-    testImplementation "org.codehaus.groovy:groovy-nio:3.0.18"
+    testImplementation "org.codehaus.groovy:groovy:3.0.19"
+    testImplementation "org.codehaus.groovy:groovy-nio:3.0.19"
 }
diff --git a/plugins/nf-wave/build.gradle b/plugins/nf-wave/build.gradle
index 61255db8e3..0d161c146b 100644
--- a/plugins/nf-wave/build.gradle
+++ b/plugins/nf-wave/build.gradle
@@ -39,6 +39,6 @@ dependencies {
     api 'io.seqera:wave-utils:0.6.2'
 
     testImplementation(testFixtures(project(":nextflow")))
-    testImplementation "org.codehaus.groovy:groovy:3.0.18"
-    testImplementation "org.codehaus.groovy:groovy-nio:3.0.18"
+    testImplementation "org.codehaus.groovy:groovy:3.0.19"
+    testImplementation "org.codehaus.groovy:groovy-nio:3.0.19"
 }

From 090c31cea264f9578596f08a7f4147fbb9002abc Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Thu, 24 Aug 2023 09:26:26 -0500
Subject: [PATCH 098/350] Add inspect command (#4069)

This commit introduces a new nextflow command named `inspect`.

The inspect command allows resolving a pipeline script or project reporting
all container images used by the pipeline execution.

The main advantage of this command over  the existing `config` command is that
it's able to resolve container names defined "dynamically" or Wave containers that
are only determined at execution time.

The command option `-concretise` when used along with the Wave freeze option
allows building ahead all the container images required by the pipeline execution.


Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/cli.md                                   |  67 +++++++++--
 .../src/main/groovy/nextflow/Session.groovy   |   5 +
 .../groovy/nextflow/cli/CmdInspect.groovy     | 106 ++++++++++++++++
 .../main/groovy/nextflow/cli/CmdRun.groovy    |   7 +-
 .../main/groovy/nextflow/cli/Launcher.groovy  |   3 +-
 .../inspect/ContainersInspector.groovy        | 113 ++++++++++++++++++
 .../nextflow/processor/TaskProcessor.groovy   |  23 ++++
 .../groovy/nextflow/script/BaseScript.groovy  |  15 +++
 .../nextflow/script/ScriptRunner.groovy       |  12 +-
 .../groovy/nextflow/util/LoggerHelper.groovy  |  24 ++--
 .../groovy/nextflow/cli/CmdInspectTest.groovy |  54 +++++++++
 .../inspect/ContainersInspectorTest.groovy    | 109 +++++++++++++++++
 .../processor/TaskProcessorTest.groovy        |  17 +++
 .../plugin/SubmitContainerTokenRequest.groovy |   5 +
 .../io/seqera/wave/plugin/WaveClient.groovy   |   8 +-
 .../wave/plugin/config/WaveConfig.groovy      |   4 +
 .../seqera/wave/plugin/WaveClientTest.groovy  |  23 ++++
 17 files changed, 571 insertions(+), 24 deletions(-)
 create mode 100644 modules/nextflow/src/main/groovy/nextflow/cli/CmdInspect.groovy
 create mode 100644 modules/nextflow/src/main/groovy/nextflow/container/inspect/ContainersInspector.groovy
 create mode 100644 modules/nextflow/src/test/groovy/nextflow/cli/CmdInspectTest.groovy
 create mode 100644 modules/nextflow/src/test/groovy/nextflow/container/inspect/ContainersInspectorTest.groovy

diff --git a/docs/cli.md b/docs/cli.md
index b101b568b9..cfc1c40ef2 100644
--- a/docs/cli.md
+++ b/docs/cli.md
@@ -643,6 +643,57 @@ $ nextflow info nextflow-io/hello
     v1.2 [t]
 ```
 
+### inspect
+
+:::{versionadded} 23.09.0-edge
+:::
+
+Inspect process settings in a pipeline project. Currently only supports the `container` directive.
+
+**Usage**
+
+```console
+$ nextflow inspect [options] [project]
+```
+
+**Description**
+
+The `inspect` command allows you to determine the container for each process in a pipeline without running the pipeline. It prints to stdout a listing of containers for each process, formatted either as JSON or Nextflow configuration.
+
+**Options**
+
+`-concretize`
+: Build the container images resolved by the inspect command.
+
+`-format` (`json`)
+: Inspect output format. Can be `json` or `config`.
+
+`-i, -ignore-errors`
+: Ignore errors while inspecting the pipeline.
+
+`-params-file`
+: Load script parameters from a JSON/YAML file.
+
+`-profile`
+: Use the given configuration profile(s).
+
+`-r, revision`
+: Revision of the project to inspect (either a git branch, tag or commit SHA number).
+
+**Examples**
+
+Get the list of containers used by a pipeline.
+
+```console
+$ nextflow inspect nextflow-io/hello
+```
+
+Specify parameters as with the `run` command:
+
+```console
+$ nextflow inspect main.nf --alpha 1 --beta foo
+```
+
 ### kuberun
 
 Launch a Nextflow pipeline on a Kubernetes cluster.
@@ -1070,7 +1121,7 @@ The `run` command is used to execute a local pipeline script or remote pipeline
 `-preview`
 : :::{versionadded} 22.06.0-edge
   :::
-: Run the workflow script skipping the execution of all processes
+: Run the workflow script skipping the execution of all processes.
 
 `-process.<key>=<value>`
 : Set process config options.
@@ -1106,7 +1157,7 @@ The `run` command is used to execute a local pipeline script or remote pipeline
 `-with-conda`
 : Use the specified Conda environment package or file (must end with `.yml` or `.yaml`)
 
-`-with-dag` (`dag.dot`)
+`-with-dag` (`dag-<timestamp>.dot`)
 : Create pipeline DAG file.
 
 `-with-docker`
@@ -1118,7 +1169,7 @@ The `run` command is used to execute a local pipeline script or remote pipeline
 `-with-podman`
 : Enable process execution in a Podman container.
 
-`-with-report` (`report.html`)
+`-with-report` (`report-<timestamp>.html`)
 : Create workflow execution HTML report.
 
 `-with-singularity`
@@ -1127,19 +1178,19 @@ The `run` command is used to execute a local pipeline script or remote pipeline
 `-with-spack`
 : Use the specified Spack environment package or file (must end with `.yaml`)
 
-`-with-timeline` (`timeline.html`)
+`-with-timeline` (`timeline-<timestamp>.html`)
 : Create workflow execution timeline.
 
-`-with-tower`
+`-with-tower` (`https://api.tower.nf`)
 : Monitor workflow execution with [Tower](https://cloud.tower.nf/).
 
-`-with-trace` (`trace.txt`)
+`-with-trace` (`trace-<timestamp>.txt`)
 : Create workflow execution trace file.
 
-`-with-wave`
+`-with-wave` (`https://wave.seqera.io`)
 : Enable the use of Wave containers.
 
-`-with-weblog`
+`-with-weblog` (`http://localhost`)
 : Send workflow status messages via HTTP to target URL.
 
 `-without-conda`
diff --git a/modules/nextflow/src/main/groovy/nextflow/Session.groovy b/modules/nextflow/src/main/groovy/nextflow/Session.groovy
index 03fc8698c6..c7df94b8c6 100644
--- a/modules/nextflow/src/main/groovy/nextflow/Session.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/Session.groovy
@@ -178,6 +178,11 @@ class Session implements ISession {
      */
     boolean disableRemoteBinDir
 
+    /**
+     * Suppress all output from pipeline script
+     */
+    boolean quiet
+
     /**
      * Local path where script generated classes are saved
      */
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdInspect.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdInspect.groovy
new file mode 100644
index 0000000000..f1f192d031
--- /dev/null
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdInspect.groovy
@@ -0,0 +1,106 @@
+/*
+ * Copyright 2013-2023, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package nextflow.cli
+
+import com.beust.jcommander.DynamicParameter
+import com.beust.jcommander.Parameter
+import com.beust.jcommander.Parameters
+import groovy.transform.CompileStatic
+import groovy.util.logging.Slf4j
+import nextflow.Session
+import nextflow.container.inspect.ContainersInspector
+import nextflow.util.LoggerHelper
+/**
+ * Implement `inspect` command
+ * 
+ * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
+ */
+@Slf4j
+@CompileStatic
+@Parameters(commandDescription = "Inspect process settings in a pipeline project")
+class CmdInspect extends CmdBase {
+
+    @Override
+    String getName() {
+        return 'inspect'
+    }
+
+    @Parameter(names=['-concretize'], description = "Build the container images resolved by the inspect command")
+    boolean concretize
+
+    @Parameter(names=['-c','-config'], hidden = true)
+    List<String> runConfig
+
+    @Parameter(names=['-format'], description = "Inspect output format. Can be 'json' or 'config'")
+    String format = 'json'
+
+    @Parameter(names=['-i','-ignore-errors'], description = 'Ignore errors while inspecting the pipeline')
+    boolean ignoreErrors
+
+    @DynamicParameter(names = '--', hidden = true)
+    Map<String,String> params = new LinkedHashMap<>()
+
+    @Parameter(names='-params-file', description = 'Load script parameters from a JSON/YAML file')
+    String paramsFile
+
+    @Parameter(names=['-profile'], description = 'Use the given configuration profile(s)')
+    String profile
+
+    @Parameter(names=['-r','-revision'], description = 'Revision of the project to inspect (either a git branch, tag or commit SHA number)')
+    String revision
+
+    @Parameter(description = 'Project name or repository url')
+    List<String> args
+
+    @Override
+    void run() {
+        // configure quiet mode
+        LoggerHelper.setQuiet(true)
+        // setup the target run command
+        final target = new CmdRun()
+        target.launcher = this.launcher
+        target.args = args
+        target.profile = this.profile
+        target.revision = this.revision
+        target.runConfig = this.runConfig
+        target.params = this.params
+        target.paramsFile = this.paramsFile
+        target.preview = true
+        target.previewAction = this.&applyInspect
+        target.ansiLog = false
+        // run it
+        target.run()
+    }
+
+    protected void applyInspect(Session session) {
+        // disable wave await mode when running
+        if( session.config.wave instanceof Map )
+            checkWaveConfig(session.config.wave as Map)
+        // run the inspector
+        new ContainersInspector(session.dag)
+                .withFormat(format)
+                .withIgnoreErrors(ignoreErrors)
+                .printContainers()
+    }
+
+    protected void checkWaveConfig(Map wave) {
+        if( wave.enabled && wave.freeze )
+            wave.dryRun = !concretize
+    }
+
+}
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
index d1bb17fe20..4023bb3adc 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
@@ -273,6 +273,11 @@ class CmdRun extends CmdBase implements HubOptions {
                 : sysEnv.get('NXF_DISABLE_JOBS_CANCELLATION') as boolean
     }
 
+    /**
+     * Optional closure modelling an action to be invoked when the preview mode is enabled
+     */
+    Closure<Void> previewAction
+
     @Override
     String getName() { NAME }
 
@@ -343,7 +348,7 @@ class CmdRun extends CmdBase implements HubOptions {
         // -- create a new runner instance
         final runner = new ScriptRunner(config)
         runner.setScript(scriptFile)
-        runner.setPreview(this.preview)
+        runner.setPreview(this.preview, previewAction)
         runner.session.profile = profile
         runner.session.commandLine = launcher.cliString
         runner.session.ansiLog = launcher.options.ansiLog
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy
index 7889d4ffaf..c8986cc5d0 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy
@@ -102,7 +102,8 @@ class Launcher {
                 new CmdHelp(),
                 new CmdSelfUpdate(),
                 new CmdPlugins(),
-                new CmdPlugin()
+                new CmdPlugin(),
+                new CmdInspect()
         ]
 
         if(SecretsLoader.isEnabled())
diff --git a/modules/nextflow/src/main/groovy/nextflow/container/inspect/ContainersInspector.groovy b/modules/nextflow/src/main/groovy/nextflow/container/inspect/ContainersInspector.groovy
new file mode 100644
index 0000000000..b4ee859969
--- /dev/null
+++ b/modules/nextflow/src/main/groovy/nextflow/container/inspect/ContainersInspector.groovy
@@ -0,0 +1,113 @@
+/*
+ * Copyright 2013-2023, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package nextflow.container.inspect
+
+import groovy.json.JsonBuilder
+import groovy.json.JsonOutput
+import groovy.transform.CompileStatic
+import groovy.util.logging.Slf4j
+import nextflow.dag.DAG
+import nextflow.exception.AbortOperationException
+import org.codehaus.groovy.util.ListHashMap
+/**
+ * Preview the list of containers used by a pipeline.
+ *
+ * @author Ben Sherman <bentshermann@gmail.com>
+ */
+@Slf4j
+@CompileStatic
+class ContainersInspector {
+
+    private DAG dag
+
+    private String format
+
+    private boolean ignoreErrors
+
+    ContainersInspector(DAG dag) {
+        this.dag = dag
+    }
+
+    ContainersInspector withFormat(String format) {
+        if( format !in ['config', 'json'] )
+            throw new AbortOperationException("Invalid format for containers inspect '${format}' -- should be 'config' or 'json'")
+        this.format = format
+        return this
+    }
+
+    ContainersInspector withIgnoreErrors(boolean ignore) {
+        this.ignoreErrors = ignore
+        return this
+    }
+
+    String renderContainers() {
+        log.debug "Rendering container preview"
+        final containers = getContainers()
+        if( format == 'config' )
+            return renderConfig(containers)
+        if( format == 'json' )
+            return renderJson(containers)
+        else
+            throw new IllegalStateException("Unknown containers preview format: $format")
+    }
+
+    void printContainers() {
+        final result = renderContainers()
+        if( result )
+            print result
+    }
+
+    protected Map<String,String> getContainers() {
+        final containers = new ListHashMap<String,String>()
+
+        for( def vertex : dag.vertices ) {
+            // skip nodes that are not processes
+            final process = vertex.process
+            if( !process )
+                continue
+
+            try {
+                // get container preview
+                containers[process.name] = process.createTaskPreview().getContainer()
+            }
+            catch( Exception e ) {
+                if( ignoreErrors )
+                    log.warn "Unable to inspect container for task `$process.name` - cause: ${e.message}"
+                else
+                    throw e
+            }
+        }
+
+        return containers
+    }
+
+    protected String renderConfig(Map<String,String> containers) {
+        final result = new StringBuilder()
+        for( Map.Entry<String,String> entry : containers ) {
+            result.append("process { withName: '${entry.key}' { container = '${entry.value}' } }\n")
+        }
+        return result.toString()
+    }
+
+    protected String renderJson(Map<String,String> containers) {
+        final list = containers.collect( (k, v) -> [name: k, container: v] )
+        final result = Map.of("processes", list)
+        return JsonOutput.prettyPrint(new JsonBuilder(result).toString()) + '\n'
+    }
+
+}
diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
index 166082b9ea..bc3ae5e711 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
@@ -367,6 +367,29 @@ class TaskProcessor {
 
     boolean hasErrors() { errorCount>0 }
 
+    /**
+     * Create a "preview" for a task run. This method is only meant for the creation of "mock" task run
+     * to allow the access for the associated {@link TaskConfig} during a pipeline "preview" execution.
+     *
+     * Note this returns an "eventually" task configuration object. Also Inputs ane output parameters are NOT
+     * resolved by this method.
+     *
+     * @return A {@link TaskRun} object holding a reference to the associated {@link TaskConfig}
+     */
+    TaskRun createTaskPreview() {
+        final task = new TaskRun(
+                processor: this,
+                type: scriptType,
+                config: config.createTaskConfig(),
+                context: new TaskContext(this)
+        )
+        task.config.context = task.context
+        task.config.process = task.processor.name
+        task.config.executor = task.processor.executor.name
+
+        return task
+    }
+
     protected void checkWarn(String msg, Map opts=null) {
         if( NF.isStrictMode() )
             throw new ProcessUnrecoverableException(msg)
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/BaseScript.groovy b/modules/nextflow/src/main/groovy/nextflow/script/BaseScript.groovy
index 521d6dca6d..81c7891c6b 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/BaseScript.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/BaseScript.groovy
@@ -207,6 +207,9 @@ abstract class BaseScript extends Script implements ExecutionContext {
 
     @Override
     void print(Object object) {
+        if( session?.quiet )
+            return
+
         if( session?.ansiLog )
             log.info(object?.toString())
         else
@@ -215,6 +218,9 @@ abstract class BaseScript extends Script implements ExecutionContext {
 
     @Override
     void println() {
+        if( session?.quiet )
+            return
+
         if( session?.ansiLog )
             log.info("")
         else
@@ -223,6 +229,9 @@ abstract class BaseScript extends Script implements ExecutionContext {
 
     @Override
     void println(Object object) {
+        if( session?.quiet )
+            return
+
         if( session?.ansiLog )
             log.info(object?.toString())
         else
@@ -231,6 +240,9 @@ abstract class BaseScript extends Script implements ExecutionContext {
 
     @Override
     void printf(String msg, Object arg) {
+        if( session?.quiet )
+            return
+
         if( session?.ansiLog )
             log.info(String.printf(msg, arg))
         else
@@ -239,6 +251,9 @@ abstract class BaseScript extends Script implements ExecutionContext {
 
     @Override
     void printf(String msg, Object[] args) {
+        if( session?.quiet )
+            return
+
         if( session?.ansiLog )
             log.info(String.printf(msg, args))
         else
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/ScriptRunner.groovy b/modules/nextflow/src/main/groovy/nextflow/script/ScriptRunner.groovy
index 3cab2bddb0..7be978e903 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/ScriptRunner.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/ScriptRunner.groovy
@@ -62,6 +62,11 @@ class ScriptRunner {
      */
     private boolean preview
 
+    /**
+     * Optional callback to perform a custom action on a preview event
+     */
+    private Closure previewAction
+
     /**
      * Instantiate the runner object creating a new session
      */
@@ -86,8 +91,9 @@ class ScriptRunner {
         return this
     }
 
-    ScriptRunner setPreview(boolean  value ) {
+    ScriptRunner setPreview(boolean  value, Closure<Void> action) {
         this.preview = value
+        this.previewAction = action
         return this
     }
 
@@ -229,8 +235,10 @@ class ScriptRunner {
     }
 
     protected await() {
-        if( preview )
+        if( preview ) {
+            previewAction?.call(session)
             return
+        }
         log.debug "> Awaiting termination "
         session.await()
     }
diff --git a/modules/nextflow/src/main/groovy/nextflow/util/LoggerHelper.groovy b/modules/nextflow/src/main/groovy/nextflow/util/LoggerHelper.groovy
index 8d995b29b6..1e657d6952 100644
--- a/modules/nextflow/src/main/groovy/nextflow/util/LoggerHelper.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/util/LoggerHelper.groovy
@@ -89,6 +89,8 @@ class LoggerHelper {
 
     static private String logFileName
 
+    static private LoggerHelper INSTANCE
+
     private CliOptions opts
 
     private boolean rolling = false
@@ -153,7 +155,11 @@ class LoggerHelper {
         return false
     }
 
-    void setup() {
+    private void setQuiet0(boolean quiet) {
+        packages[MAIN_PACKAGE] = quiet ? Level.ERROR : Level.INFO
+    }
+
+    LoggerHelper setup() {
         logFileName = opts.logFile ?: System.getenv('NXF_LOG_FILE')
 
         final boolean quiet = opts.quiet
@@ -165,7 +171,7 @@ class LoggerHelper {
         root.detachAndStopAllAppenders()
 
         // -- define the console appender
-        packages[MAIN_PACKAGE] = quiet ? Level.WARN : Level.INFO
+        setQuiet0(quiet)
 
         // -- add the S3 uploader by default
         if( !containsClassName(debugConf,traceConf, 'nextflow.cloud.aws.nio') )
@@ -224,6 +230,8 @@ class LoggerHelper {
 
         if(!consoleAppender)
             logger.debug "Console appender: disabled"
+
+        return this
     }
 
     protected Logger createLogger(String clazz, Level level ) {
@@ -342,19 +350,17 @@ class LoggerHelper {
      */
 
     static void configureLogger( Launcher launcher ) {
-        new LoggerHelper(launcher.options)
+        INSTANCE = new LoggerHelper(launcher.options)
                 .setDaemon(launcher.isDaemon())
                 .setRolling(true)
                 .setSyslog(launcher.options.syslog)
                 .setup()
     }
 
-    static void configureLogger( final CliOptions opts, boolean daemon = false ) {
-        new LoggerHelper(opts)
-                .setDaemon(daemon)
-                .setRolling(true)
-                .setSyslog(opts.syslog)
-                .setup()
+    static setQuiet(boolean quiet) {
+        if( INSTANCE==null )
+            throw new IllegalStateException("Method 'LoggerHelper.setQuiet' must be called after the invocation of 'LoggerHelper.configureLogger'")
+        INSTANCE.setQuiet0(quiet)
     }
 
     /*
diff --git a/modules/nextflow/src/test/groovy/nextflow/cli/CmdInspectTest.groovy b/modules/nextflow/src/test/groovy/nextflow/cli/CmdInspectTest.groovy
new file mode 100644
index 0000000000..c6ed93ca74
--- /dev/null
+++ b/modules/nextflow/src/test/groovy/nextflow/cli/CmdInspectTest.groovy
@@ -0,0 +1,54 @@
+/*
+ * Copyright 2013-2023, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package nextflow.cli
+
+
+import spock.lang.Specification
+import spock.lang.Unroll
+/**
+ *
+ * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
+ */
+class CmdInspectTest extends Specification {
+
+    @Unroll
+    def 'should ask for confirmation' () {
+        given:
+        def cmd = Spy(new CmdInspect(concretize: CONCRETIZE))
+        Map wave
+
+        when:
+        wave = WAVE
+        cmd.checkWaveConfig(wave)
+        then:
+        wave == EXPECTED
+
+        where:
+        WAVE                            | CONCRETIZE    | EXPECTED
+        [:]                             | false         | [:]
+        [:]                             | true          | [:]
+        and:
+        [enabled:true]                  | false         | [enabled:true]
+        [enabled:true]                  | true          | [enabled:true]
+        and:
+        [enabled:true, freeze: true]    | false         | [enabled:true, freeze:true, dryRun: true]
+        [enabled:true, freeze: true]    | true          | [enabled:true, freeze:true, dryRun: false]
+
+    }
+
+}
diff --git a/modules/nextflow/src/test/groovy/nextflow/container/inspect/ContainersInspectorTest.groovy b/modules/nextflow/src/test/groovy/nextflow/container/inspect/ContainersInspectorTest.groovy
new file mode 100644
index 0000000000..039f568ba0
--- /dev/null
+++ b/modules/nextflow/src/test/groovy/nextflow/container/inspect/ContainersInspectorTest.groovy
@@ -0,0 +1,109 @@
+/*
+ * Copyright 2013-2023, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package nextflow.container.inspect
+
+
+import nextflow.dag.DAG
+import nextflow.processor.TaskProcessor
+import nextflow.processor.TaskRun
+import spock.lang.Specification
+/**
+ *
+ * @author Ben Sherman <bentshermann@gmail.com>
+ */
+class ContainersInspectorTest extends Specification {
+
+    def makeVertex(DAG dag, String name, String container) {
+        final processor = Mock(TaskProcessor)
+        processor.name >> name
+        processor.createTaskPreview() >> Mock(TaskRun) {
+            getContainer() >> container
+        }
+
+        final vertex = new DAG.Vertex(dag, DAG.Type.PROCESS)
+        vertex.process = processor
+
+        return vertex
+    }
+
+    def 'should get containers' () {
+        given:
+        def dag = Mock(DAG)
+        dag.vertices >> [
+            makeVertex(dag, 'proc1', 'container1'),
+            makeVertex(dag, 'proc2', 'container2')
+        ]
+
+        when:
+        def observer = new ContainersInspector(dag)
+        then:
+        observer.getContainers() == [
+            'proc1': 'container1',
+            'proc2': 'container2',
+        ]
+    }
+
+    def 'should render containers as json' () {
+        given:
+        def dag = Mock(DAG)
+        dag.vertices >> [
+                makeVertex(dag, 'proc1', 'container1'),
+                makeVertex(dag, 'proc2', 'container2')
+        ]
+
+        when:
+        def result = new ContainersInspector(dag)
+                .withFormat('json')
+                .renderContainers()
+        then:
+        result == '''\
+            {
+                "processes": [
+                    {
+                        "name": "proc2",
+                        "container": "container2"
+                    },
+                    {
+                        "name": "proc1",
+                        "container": "container1"
+                    }
+                ]
+            }
+            '''.stripIndent(true)
+    }
+
+    def 'should render containers as nextflow config' () {
+        given:
+        def dag = Mock(DAG)
+        dag.vertices >> [
+                makeVertex(dag, 'proc1', 'container1'),
+                makeVertex(dag, 'proc2', 'container2')
+        ]
+
+        when:
+        def result = new ContainersInspector(dag)
+                .withFormat('config')
+                .renderContainers()
+        then:
+        result == '''\
+            process { withName: 'proc2' { container = 'container2' } }
+            process { withName: 'proc1' { container = 'container1' } }
+            '''.stripIndent(true)
+    }
+
+}
diff --git a/modules/nextflow/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy b/modules/nextflow/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy
index ab2f3bc511..4a075faa8c 100644
--- a/modules/nextflow/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy
@@ -40,6 +40,7 @@ import nextflow.script.bundle.ResourcesBundle
 import nextflow.script.params.FileOutParam
 import nextflow.util.ArrayBag
 import nextflow.util.CacheHelper
+import nextflow.util.MemoryUnit
 import spock.lang.Specification
 import spock.lang.Unroll
 import test.TestHelper
@@ -940,4 +941,20 @@ class TaskProcessorTest extends Specification {
         then:
         result == [ALPHA:'one', DELTA: "x=y", OMEGA: '']
     }
+
+    def 'should create a task preview' () {
+        given:
+        def config = new ProcessConfig([cpus: 10, memory: '100 GB'])
+        def EXEC = Mock(Executor) { getName()>>'exec-name'}
+        def BODY = Mock(BodyDef) { getType()>>ScriptType.SCRIPTLET }
+        def processor = new TaskProcessor(config: config, name: 'proc-name', executor: EXEC, taskBody: BODY)
+
+        when:
+        def result = processor.createTaskPreview()
+        then:
+        result.config.process == 'proc-name'
+        result.config.executor == 'exec-name'
+        result.config.getCpus() == 10
+        result.config.getMemory() == MemoryUnit.of('100 GB')
+    }
 }
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/SubmitContainerTokenRequest.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/SubmitContainerTokenRequest.groovy
index 1a219ef79c..4530911e0f 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/SubmitContainerTokenRequest.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/SubmitContainerTokenRequest.groovy
@@ -116,4 +116,9 @@ class SubmitContainerTokenRequest {
      */
     String format
 
+    /**
+     * When {@code true} build requests are carried out in dry-run mode.
+     */
+    Boolean dryRun
+
 }
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
index bf87c02135..d01d26acc8 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
@@ -183,7 +183,8 @@ class WaveClient {
                 timestamp: OffsetDateTime.now().toString(),
                 fingerprint: assets.fingerprint(),
                 freeze: config.freezeMode(),
-                format: assets.singularity ? 'sif' : null
+                format: assets.singularity ? 'sif' : null,
+                dryRun: config.dryRun()
         )
     }
 
@@ -206,7 +207,8 @@ class WaveClient {
                 towerWorkspaceId: tower.workspaceId,
                 towerEndpoint: tower.endpoint,
                 workflowId: tower.workflowId,
-                freeze: config.freezeMode()
+                freeze: config.freezeMode(),
+                dryRun: config.dryRun(),
         )
         return sendRequest(request)
     }
@@ -507,7 +509,7 @@ class WaveClient {
             // get from cache or submit a new request
             final response = cache.get(key, { sendRequest(assets) } as Callable )
             if( config.freezeMode() )  {
-                if( response.buildId ) {
+                if( response.buildId && !config.dryRun() ) {
                     // await the image to be available when a new image is being built
                     awaitImage(response.targetImage)
                 }
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/WaveConfig.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/WaveConfig.groovy
index 03c3926574..abdd4e2953 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/WaveConfig.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/WaveConfig.groovy
@@ -48,11 +48,13 @@ class WaveConfig {
     final private RetryOpts retryOpts
     final private HttpOpts httpClientOpts
     final private Boolean freezeMode
+    final private Boolean dryRunMode
 
     WaveConfig(Map opts, Map<String,String> env=System.getenv()) {
         this.enabled = opts.enabled
         this.endpoint = (opts.endpoint?.toString() ?: env.get('WAVE_API_ENDPOINT') ?: DEF_ENDPOINT)?.stripEnd('/')
         this.freezeMode = opts.freeze as Boolean
+        this.dryRunMode = opts.navigate('dryRun', false)
         this.containerConfigUrl = parseConfig(opts, env)
         this.tokensCacheMaxDuration = opts.navigate('tokens.cache.maxDuration', '30m') as Duration
         this.condaOpts = opts.navigate('build.conda', Collections.emptyMap()) as CondaOpts
@@ -84,6 +86,8 @@ class WaveConfig {
 
     boolean freezeMode() { return this.freezeMode }
 
+    boolean dryRun() { return this.dryRunMode }
+
     boolean bundleProjectResources() { bundleProjectResources }
 
     String buildRepository() { buildRepository }
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
index 6b6446cc0a..7bb3aa9522 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
@@ -166,6 +166,7 @@ class WaveClientTest extends Specification {
         !req.spackFile
         !req.containerConfig.layers
         !req.freeze
+        !req.dryRun
         and:
         req.fingerprint == 'bd2cb4b32df41f2d290ce2366609f2ad'
         req.timestamp instanceof String
@@ -193,6 +194,28 @@ class WaveClientTest extends Specification {
         req.timestamp instanceof String
     }
 
+    def 'should create request object with dry-run mode' () {
+        given:
+        def session = Mock(Session) { getConfig() >> [wave:[dryRun:true]]}
+        def IMAGE =  'foo:latest'
+        def wave = new WaveClient(session)
+
+        when:
+        def req = wave.makeRequest(WaveAssets.fromImage(IMAGE))
+        then:
+        req.containerImage == IMAGE
+        !req.containerPlatform
+        !req.containerFile
+        !req.condaFile
+        !req.spackFile
+        !req.containerConfig.layers
+        and:
+        req.dryRun
+        and:
+        req.fingerprint == 'bd2cb4b32df41f2d290ce2366609f2ad'
+        req.timestamp instanceof String
+    }
+
     def 'should create request object and platform' () {
         given:
         def session = Mock(Session) { getConfig() >> [:]}

From 465468b02de9bc08dfb4f531277d529e136e0ce8 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Thu, 24 Aug 2023 09:27:42 -0500
Subject: [PATCH 099/350] Fix printf command with negative exit code (#4213)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 .../src/main/resources/nextflow/executor/command-run.txt        | 2 +-
 .../nextflow/executor/test-bash-wrapper-with-trace.txt          | 2 +-
 .../src/test/resources/nextflow/executor/test-bash-wrapper.txt  | 2 +-
 .../nextflow/cloud/google/lifesciences/bash-wrapper-gcp.txt     | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/nextflow/src/main/resources/nextflow/executor/command-run.txt b/modules/nextflow/src/main/resources/nextflow/executor/command-run.txt
index 1c261c937c..d1f695a022 100644
--- a/modules/nextflow/src/main/resources/nextflow/executor/command-run.txt
+++ b/modules/nextflow/src/main/resources/nextflow/executor/command-run.txt
@@ -100,7 +100,7 @@ nxf_fs_fcp() {
 
 on_exit() {
     exit_status=${nxf_main_ret:=$?}
-    printf $exit_status {{exit_file}}
+    printf -- $exit_status {{exit_file}}
     set +u
     {{cleanup_cmd}}
     {{sync_cmd}}
diff --git a/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper-with-trace.txt b/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper-with-trace.txt
index b0672d36ad..0aaf49f410 100644
--- a/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper-with-trace.txt
+++ b/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper-with-trace.txt
@@ -269,7 +269,7 @@ nxf_fs_fcp() {
 
 on_exit() {
     exit_status=${nxf_main_ret:=$?}
-    printf $exit_status > {{folder}}/.exitcode
+    printf -- $exit_status > {{folder}}/.exitcode
     set +u
     sync || true
     exit $exit_status
diff --git a/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper.txt b/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper.txt
index e855aa1a1e..3c380c4067 100644
--- a/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper.txt
+++ b/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper.txt
@@ -80,7 +80,7 @@ nxf_fs_fcp() {
 
 on_exit() {
     exit_status=${nxf_main_ret:=$?}
-    printf $exit_status > {{folder}}/.exitcode
+    printf -- $exit_status > {{folder}}/.exitcode
     set +u
     sync || true
     exit $exit_status
diff --git a/plugins/nf-google/src/test/nextflow/cloud/google/lifesciences/bash-wrapper-gcp.txt b/plugins/nf-google/src/test/nextflow/cloud/google/lifesciences/bash-wrapper-gcp.txt
index 5cb73b9050..f1ac0b4251 100644
--- a/plugins/nf-google/src/test/nextflow/cloud/google/lifesciences/bash-wrapper-gcp.txt
+++ b/plugins/nf-google/src/test/nextflow/cloud/google/lifesciences/bash-wrapper-gcp.txt
@@ -167,7 +167,7 @@ nxf_fs_fcp() {
 
 on_exit() {
     exit_status=${nxf_main_ret:=$?}
-    printf $exit_status > {{folder}}/.exitcode
+    printf -- $exit_status > {{folder}}/.exitcode
     set +u
     {{sync_cmd}}
     exit $exit_status

From b6721b7128c55df31613d0314a16ab46b0312cee Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Thu, 24 Aug 2023 16:42:23 +0200
Subject: [PATCH 100/350] Remove -dsl1 and -dsl1 rub cli options

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../src/main/groovy/nextflow/cli/CmdRun.groovy         |  9 ---------
 .../main/groovy/nextflow/config/ConfigBuilder.groovy   | 10 ----------
 2 files changed, 19 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
index 4023bb3adc..4da1a3b35c 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
@@ -246,12 +246,6 @@ class CmdRun extends CmdBase implements HubOptions {
     @Parameter(names=['-entry'], description = 'Entry workflow name to be executed', arity = 1)
     String entryName
 
-    @Parameter(names=['-dsl1'], description = 'Execute the workflow using DSL1 syntax')
-    boolean dsl1
-
-    @Parameter(names=['-dsl2'], description = 'Execute the workflow using DSL2 syntax')
-    boolean dsl2
-
     @Parameter(names=['-main-script'], description = 'The script file to be executed when launching a project directory or repository' )
     String mainScript
 
@@ -311,9 +305,6 @@ class CmdRun extends CmdBase implements HubOptions {
         if( offline && latest )
             throw new AbortOperationException("Command line options `-latest` and `-offline` cannot be specified at the same time")
 
-        if( dsl1 && dsl2 )
-            throw new AbortOperationException("Command line options `-dsl1` and `-dsl2` cannot be specified at the same time")
-
         checkRunName()
 
         log.info "N E X T F L O W  ~  version ${Const.APP_VER}"
diff --git a/modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy
index 6cb39fe9d2..03bcf3c3b4 100644
--- a/modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy
@@ -709,16 +709,6 @@ class ConfigBuilder {
             config.fusion.enabled = cmdRun.withFusion == 'true'
         }
 
-        // -- nextflow setting
-        if( cmdRun.dsl1 || cmdRun.dsl2 ) {
-            if( config.nextflow !instanceof Map )
-                config.nextflow = [:]
-            if( cmdRun.dsl1 )
-                config.nextflow.enable.dsl = 1
-            if( cmdRun.dsl2 )
-                config.nextflow.enable.dsl = 2
-        }
-
         // -- add the command line parameters to the 'taskConfig' object
         if( cmdRun.hasParams() )
             config.params = mergeMaps( (Map)config.params, cmdRun.parsedParams(configVars()), NF.strictMode )

From 80c5cb276c6d1857897b7883ef7f01deea8f635c Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Thu, 24 Aug 2023 23:41:14 +0200
Subject: [PATCH 101/350] Deprecated Wave report feature

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../src/main/io/seqera/wave/plugin/WaveObserver.groovy     | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveObserver.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveObserver.groovy
index 1032c873d0..029e034546 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveObserver.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveObserver.groovy
@@ -20,6 +20,7 @@ package io.seqera.wave.plugin
 import java.util.concurrent.ConcurrentHashMap
 
 import groovy.transform.CompileStatic
+import groovy.util.logging.Slf4j
 import io.seqera.wave.plugin.config.ReportOpts
 import nextflow.Session
 import nextflow.file.FileHelper
@@ -30,6 +31,7 @@ import nextflow.trace.TraceRecord
  *
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
  */
+@Slf4j
 @CompileStatic
 class WaveObserver implements TraceObserver {
 
@@ -41,6 +43,11 @@ class WaveObserver implements TraceObserver {
         this.client = new WaveClient(session)
     }
 
+    @Override
+    void onFlowCreate(Session session) {
+        log.warn "Wave report feature has been deprecated in favour of the new 'nextflow inspect' command"
+    }
+
     protected void apply(TaskHandler handler) {
         final process = handler.task.getProcessor().getName()
         containers.computeIfAbsent(process, (String it) -> handler.task.getContainer())

From 736ab9bb8ea7d257491676fa3870c3c486f72ed0 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 26 Aug 2023 11:11:36 +0200
Subject: [PATCH 102/350] Improve Wave handing of Conda envs

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-wave/build.gradle                  |  2 +-
 .../io/seqera/wave/plugin/WaveClient.groovy   | 26 ++++--
 .../seqera/wave/plugin/WaveClientTest.groovy  | 92 ++++++++++++++++++-
 validation/wave-tests/example3/demo.nf        | 12 +++
 .../wave-tests/example3/nextflow.config       | 13 +++
 validation/wave-tests/example3/run.sh         |  2 +
 validation/wave-tests/example4/demo.nf        | 12 +++
 validation/wave-tests/example4/run.sh         |  2 +
 validation/wave.sh                            |  6 ++
 9 files changed, 157 insertions(+), 10 deletions(-)
 create mode 100644 validation/wave-tests/example3/demo.nf
 create mode 100644 validation/wave-tests/example3/nextflow.config
 create mode 100644 validation/wave-tests/example3/run.sh
 create mode 100644 validation/wave-tests/example4/demo.nf
 create mode 100644 validation/wave-tests/example4/run.sh

diff --git a/plugins/nf-wave/build.gradle b/plugins/nf-wave/build.gradle
index 0d161c146b..957ac19c2c 100644
--- a/plugins/nf-wave/build.gradle
+++ b/plugins/nf-wave/build.gradle
@@ -36,7 +36,7 @@ dependencies {
     api 'org.apache.commons:commons-lang3:3.12.0'
     api 'com.google.code.gson:gson:2.10.1'
     api 'org.yaml:snakeyaml:2.0'
-    api 'io.seqera:wave-utils:0.6.2'
+    api 'io.seqera:wave-utils:0.7.0'
 
     testImplementation(testFixtures(project(":nextflow")))
     testImplementation "org.codehaus.groovy:groovy:3.0.19"
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
index d01d26acc8..f979da6d9f 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
@@ -421,17 +421,25 @@ class WaveClient {
                 throw new IllegalArgumentException("Unexpected conda and $scriptType conflict while resolving wave container")
 
             // map the recipe to a dockerfile
-            if( isCondaLocalFile(attrs.conda) ) {
-                condaFile = Path.of(attrs.conda)
+            if( isCondaRemoteFile(attrs.conda) ) {
                 containerScript = singularity
-                        ? condaFileToSingularityFile(config.condaOpts())
-                        : condaFileToDockerFile(config.condaOpts())
+                        ? condaPackagesToSingularityFile(attrs.conda, condaChannels, config.condaOpts())
+                        : condaPackagesToDockerFile(attrs.conda, condaChannels, config.condaOpts())
             }
-            // 'conda' attributes is resolved as the conda packages to be used
             else {
+                if( isCondaLocalFile(attrs.conda) ) {
+                    // 'conda' attribute is the path to the local conda environment
+                    // note: ignore the 'channels' attribute because they are supposed to be provided by the conda file
+                    condaFile = condaFileFromPath(attrs.conda, null, config.condaOpts())
+                }
+                else {
+                    // 'conda' attributes is resolved as the conda packages to be used
+                    condaFile = condaFileFromPackages(attrs.conda, condaChannels, config.condaOpts())
+                }
+                // create the container file to build the container
                 containerScript = singularity
-                        ? condaPackagesToSingularityFile(attrs.conda, condaChannels, config.condaOpts())
-                        : condaPackagesToDockerFile(attrs.conda, condaChannels, config.condaOpts())
+                        ? condaFileToSingularityFile(config.condaOpts())
+                        : condaFileToDockerFile(config.condaOpts())
             }
         }
 
@@ -556,6 +564,10 @@ class WaveClient {
         return value.endsWith('.yaml') || value.endsWith('.yml') || value.endsWith('.txt')
     }
 
+    static protected boolean isCondaRemoteFile(String value) {
+        value.startsWith('http://') || value.startsWith('https://')
+    }
+
     protected boolean isSpackFile(String value) {
         if( value.contains('\n') )
             return false
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
index 7bb3aa9522..6d36e5ffc6 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
@@ -517,6 +517,40 @@ class WaveClientTest extends Specification {
         and:
         def client = new WaveClient(session)
 
+        when:
+        def assets = client.resolveAssets(task, null, false)
+        then:
+        assets.containerFile == '''\
+                FROM mambaorg/micromamba:1.4.9
+                COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml
+                RUN micromamba install -y -n base -f /tmp/conda.yml \\
+                    && micromamba clean -a -y
+                USER root
+                    '''.stripIndent()
+        and:
+        !assets.moduleResources
+        !assets.containerImage
+        !assets.containerConfig
+        !assets.spackFile
+        !assets.projectResources
+        and:
+        assets.condaFile.text == '''\
+                channels:
+                - conda-forge
+                - defaults
+                dependencies:
+                - salmon=1.2.3
+                '''.stripIndent(true)
+    }
+
+    def 'should create asset with conda lock file' () {
+        given:
+        def session = Mock(Session) { getConfig() >> [:]}
+        and:
+        def task = Mock(TaskRun) {getConfig() >> [conda:'https://host.com/conda-lock.yml'] }
+        and:
+        def client = new WaveClient(session)
+
         when:
         def assets = client.resolveAssets(task, null, false)
         then:
@@ -524,7 +558,7 @@ class WaveClientTest extends Specification {
                 FROM mambaorg/micromamba:1.4.9
                 RUN \\
                     micromamba install -y -n base -c conda-forge -c defaults \\
-                    salmon=1.2.3 \\
+                    -f https://host.com/conda-lock.yml \\
                     && micromamba clean -a -y
                 USER root
                     '''.stripIndent()
@@ -665,6 +699,46 @@ class WaveClientTest extends Specification {
         and:
         def client = new WaveClient(session)
 
+        when:
+        def assets = client.resolveAssets(task, null, true)
+        then:
+        assets.containerFile == '''\
+                BootStrap: docker
+                From: mambaorg/micromamba:1.4.9
+                %files
+                    {{wave_context_dir}}/conda.yml /tmp/conda.yml
+                %post
+                    micromamba install -y -n base -f /tmp/conda.yml \\
+                    && micromamba clean -a -y
+                %environment
+                    export PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
+                    '''.stripIndent()
+        and:
+        assets.singularity
+        and:
+        !assets.moduleResources
+        !assets.containerImage
+        !assets.containerConfig
+        !assets.spackFile
+        !assets.projectResources
+        and:
+        assets.condaFile.text == '''\
+                channels:
+                - conda-forge
+                - defaults
+                dependencies:
+                - salmon=1.2.3
+                '''.stripIndent(true)
+    }
+
+    def 'should create asset with conda remote lock file and singularity native build' () {
+        given:
+        def session = Mock(Session) { getConfig() >> [:]}
+        and:
+        def task = Mock(TaskRun) {getConfig() >> [conda:'https://host.com/lock-file.yaml'] }
+        and:
+        def client = new WaveClient(session)
+
         when:
         def assets = client.resolveAssets(task, null, true)
         then:
@@ -673,7 +747,7 @@ class WaveClientTest extends Specification {
                 From: mambaorg/micromamba:1.4.9
                 %post
                     micromamba install -y -n base -c conda-forge -c defaults \\
-                    salmon=1.2.3 \\
+                    -f https://host.com/lock-file.yaml \\
                     && micromamba clean -a -y
                 %environment
                     export PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
@@ -1032,4 +1106,18 @@ class WaveClientTest extends Specification {
         'http://foo.com'    | false
     }
 
+    def 'should check is remote conda file' () {
+        expect:
+        WaveClient.isCondaRemoteFile(CONTENT) == EXPECTED
+
+        where:
+        CONTENT             | EXPECTED
+        'foo'               | false
+        'foo.yml'           | false
+        'foo.txt'           | false
+        'foo\nbar.yml'      | false
+        'http://foo.com'    | true
+        'https://foo.com'   | true
+    }
+
 }
diff --git a/validation/wave-tests/example3/demo.nf b/validation/wave-tests/example3/demo.nf
new file mode 100644
index 0000000000..5f1e9be8ab
--- /dev/null
+++ b/validation/wave-tests/example3/demo.nf
@@ -0,0 +1,12 @@
+process cow {
+  debug true
+  conda 'cowpy=1.1.5'
+
+  '''
+  echo cowpy 'Hello Spack'
+  '''
+}
+
+workflow {
+  cow()
+}
diff --git a/validation/wave-tests/example3/nextflow.config b/validation/wave-tests/example3/nextflow.config
new file mode 100644
index 0000000000..38a0e07f6c
--- /dev/null
+++ b/validation/wave-tests/example3/nextflow.config
@@ -0,0 +1,13 @@
+tower {
+  accessToken = "$TOWER_ACCESS_TOKEN"
+}
+
+wave {
+  enabled = true
+  strategy = ['conda']
+  build.repository = 'docker.io/pditommaso/wave-tests'
+}
+
+docker {
+  enabled = true
+}
diff --git a/validation/wave-tests/example3/run.sh b/validation/wave-tests/example3/run.sh
new file mode 100644
index 0000000000..66148af05b
--- /dev/null
+++ b/validation/wave-tests/example3/run.sh
@@ -0,0 +1,2 @@
+$NXF_CMD run demo.nf -with-wave
+
diff --git a/validation/wave-tests/example4/demo.nf b/validation/wave-tests/example4/demo.nf
new file mode 100644
index 0000000000..3384b942cc
--- /dev/null
+++ b/validation/wave-tests/example4/demo.nf
@@ -0,0 +1,12 @@
+process cow {
+  debug true
+  conda 'https://prefix.dev/envs/pditommaso/wave/conda-lock.yml'
+
+  '''
+  echo cowpy 'Hello Spack'
+  '''
+}
+
+workflow {
+  cow()
+}
diff --git a/validation/wave-tests/example4/run.sh b/validation/wave-tests/example4/run.sh
new file mode 100644
index 0000000000..66148af05b
--- /dev/null
+++ b/validation/wave-tests/example4/run.sh
@@ -0,0 +1,2 @@
+$NXF_CMD run demo.nf -with-wave
+
diff --git a/validation/wave.sh b/validation/wave.sh
index 374e92d16b..6b8953a7f3 100644
--- a/validation/wave.sh
+++ b/validation/wave.sh
@@ -12,6 +12,12 @@ echo "Test Wave accessing private container repository"
 echo "Test Wave building a container"
 (cd wave-tests/example2; bash run.sh)
 
+echo "Test Wave building from Conda package"
+(cd wave-tests/example3; bash run.sh)
+
+echo "Test Wave building from Conda lock file"
+(cd wave-tests/example4; bash run.sh)
+
 echo "Test Wave running rnaseq-nf with Fusion on local executor"
 (cd wave-tests/example6; bash run.sh)
 

From a60ef72b4acc30d2f6d51269f2bb08d75fabe119 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 26 Aug 2023 16:48:16 +0200
Subject: [PATCH 103/350] Fix Wave build for Singularity files

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-wave/build.gradle                              | 2 +-
 .../src/test/io/seqera/wave/plugin/WaveClientTest.groovy  | 8 ++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/plugins/nf-wave/build.gradle b/plugins/nf-wave/build.gradle
index 957ac19c2c..d3a604c19b 100644
--- a/plugins/nf-wave/build.gradle
+++ b/plugins/nf-wave/build.gradle
@@ -36,7 +36,7 @@ dependencies {
     api 'org.apache.commons:commons-lang3:3.12.0'
     api 'com.google.code.gson:gson:2.10.1'
     api 'org.yaml:snakeyaml:2.0'
-    api 'io.seqera:wave-utils:0.7.0'
+    api 'io.seqera:wave-utils:0.7.1'
 
     testImplementation(testFixtures(project(":nextflow")))
     testImplementation "org.codehaus.groovy:groovy:3.0.19"
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
index 6d36e5ffc6..cf19d9a8c2 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
@@ -706,9 +706,9 @@ class WaveClientTest extends Specification {
                 BootStrap: docker
                 From: mambaorg/micromamba:1.4.9
                 %files
-                    {{wave_context_dir}}/conda.yml /tmp/conda.yml
+                    {{wave_context_dir}}/conda.yml /scratch/conda.yml
                 %post
-                    micromamba install -y -n base -f /tmp/conda.yml \\
+                    micromamba install -y -n base -f /scratch/conda.yml \\
                     && micromamba clean -a -y
                 %environment
                     export PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
@@ -780,9 +780,9 @@ class WaveClientTest extends Specification {
                 BootStrap: docker
                 From: mambaorg/micromamba:1.4.9
                 %files
-                    {{wave_context_dir}}/conda.yml /tmp/conda.yml
+                    {{wave_context_dir}}/conda.yml /scratch/conda.yml
                 %post
-                    micromamba install -y -n base -f /tmp/conda.yml \\
+                    micromamba install -y -n base -f /scratch/conda.yml \\
                     && micromamba clean -a -y
                 %environment
                     export PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"                    

From a1e1d3ca322afd64eb6d67bc7bb8e9d2a8ff4c00 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Thu, 31 Aug 2023 10:53:39 +0200
Subject: [PATCH 104/350] Align Singularity experience with Docker (#4230)

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Co-authored-by: Ben Sherman <bentshermann@gmail.com>
---
 docs/config.md                                |  5 +-
 docs/container.md                             |  9 +++
 .../container/SingularityBuilder.groovy       | 19 ++++-
 .../groovy/nextflow/cli/CmdInfoTest.groovy    |  2 +
 .../container/ApptainerBuilderTest.groovy     | 80 +++++++++++++++++--
 .../container/SingularityBuilderTest.groovy   | 80 +++++++++++++++++--
 .../executor/BashWrapperBuilderTest.groovy    |  4 +-
 .../executor/fusion/FusionHelperTest.groovy   |  6 +-
 8 files changed, 183 insertions(+), 22 deletions(-)

diff --git a/docs/config.md b/docs/config.md
index 4c429499a3..34ba2e5b97 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -1294,7 +1294,10 @@ The `singularity` scope controls how [Singularity](https://sylabs.io/singularity
 The following settings are available:
 
 `singularity.autoMounts`
-: When `true` Nextflow automatically mounts host paths in the executed container. It requires the `user bind control` feature to be enabled in your Singularity installation (default: `false`).
+: When `true` Nextflow automatically mounts host paths in the executed container. It requires the `user bind control` feature to be enabled in your Singularity installation (default: `true`).
+: :::{versionchanged} 23.09.0-edge
+  Default value was changed from `false` to `true`.
+  :::
 
 `singularity.cacheDir`
 : The directory where remote Singularity images are stored. When using a computing cluster it must be a shared folder accessible to all compute nodes.
diff --git a/docs/container.md b/docs/container.md
index 5f43db1a31..39281700f7 100644
--- a/docs/container.md
+++ b/docs/container.md
@@ -583,6 +583,15 @@ When a process input is a *symbolic link* file, make sure the linked file is sto
 Nextflow no longer mounts the home directory when launching a Singularity container. To re-enable the old behavior, set the environment variable `NXF_SINGULARITY_HOME_MOUNT` to `true`.
 :::
 
+:::{versionchanged} 23.09.0-edge
+Nextflow automatically mounts the required host paths in the container. To re-enable the old behavior, set the environment variable `NXF_SINGULARITY_AUTO_MOUNTS` to `false` or set `singularity.autoMounts=false` in the Nextflow configuration file.
+:::
+
+:::{versionchanged} 23.09.0-edge
+Nextflow uses the command `run` to carry out the execution of Singularity containers instead of the `exec` command.
+To re-enable the old behavior, set the environment variable `NXF_SINGULARITY_RUN_COMMAND` to `exec`.
+:::
+
 ### Multiple containers
 
 It is possible to specify a different Singularity image for each process definition in your pipeline script. For example, let's suppose you have two processes named `foo` and `bar`. You can specify two different Singularity images specifying them in the `nextflow.config` file as shown below:
diff --git a/modules/nextflow/src/main/groovy/nextflow/container/SingularityBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/container/SingularityBuilder.groovy
index 45426b4360..5e0277ea60 100644
--- a/modules/nextflow/src/main/groovy/nextflow/container/SingularityBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/container/SingularityBuilder.groovy
@@ -37,10 +37,14 @@ class SingularityBuilder extends ContainerBuilder<SingularityBuilder> {
 
     private boolean newPidNamespace
 
+    private String runCmd0
+
     SingularityBuilder(String name) {
         this.image = name
         this.homeMount = defaultHomeMount()
+        this.autoMounts = defaultAutoMounts()
         this.newPidNamespace = defaultNewPidNamespace()
+        this.runCmd0 = defaultRunCommand()
     }
 
     private boolean defaultHomeMount() {
@@ -51,6 +55,17 @@ class SingularityBuilder extends ContainerBuilder<SingularityBuilder> {
         SysEnv.get("NXF_${getBinaryName().toUpperCase()}_NEW_PID_NAMESPACE", 'true').toString() == 'true'
     }
 
+    private boolean defaultAutoMounts() {
+        SysEnv.get("NXF_${getBinaryName().toUpperCase()}_AUTO_MOUNTS", 'true').toString() == 'true'
+    }
+
+    private String defaultRunCommand() {
+        final result = SysEnv.get("NXF_${getBinaryName().toUpperCase()}_RUN_COMMAND", 'run')
+        if( result !in ['run','exec'] )
+            throw new IllegalArgumentException("Invalid singularity launch command '$result' - it should be either 'run' or 'exec'")
+        return result
+    }
+
     protected String getBinaryName() { 'singularity' }
 
     @Override
@@ -68,7 +83,7 @@ class SingularityBuilder extends ContainerBuilder<SingularityBuilder> {
         if( params.containsKey('runOptions') )
             addRunOptions(params.runOptions.toString())
 
-        if( params.autoMounts )
+        if( params.autoMounts!=null )
             autoMounts = params.autoMounts.toString() == 'true'
 
         if( params.newPidNamespace!=null )
@@ -97,7 +112,7 @@ class SingularityBuilder extends ContainerBuilder<SingularityBuilder> {
         if( engineOptions )
             result << engineOptions.join(' ') << ' '
 
-        result << 'exec '
+        result << runCmd0 << ' '
 
         if( !homeMount )
             result << '--no-home '
diff --git a/modules/nextflow/src/test/groovy/nextflow/cli/CmdInfoTest.groovy b/modules/nextflow/src/test/groovy/nextflow/cli/CmdInfoTest.groovy
index bd88b9261d..3ec57a2427 100644
--- a/modules/nextflow/src/test/groovy/nextflow/cli/CmdInfoTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/cli/CmdInfoTest.groovy
@@ -17,6 +17,7 @@
 package nextflow.cli
 
 import nextflow.plugin.Plugins
+import spock.lang.IgnoreIf
 import spock.lang.Requires
 import spock.lang.Shared
 import spock.lang.Specification
@@ -31,6 +32,7 @@ import org.yaml.snakeyaml.Yaml
  *
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
  */
+@IgnoreIf({System.getenv('NXF_SMOKE')})
 @Requires({System.getenv('NXF_GITHUB_ACCESS_TOKEN')})
 class CmdInfoTest extends Specification {
 
diff --git a/modules/nextflow/src/test/groovy/nextflow/container/ApptainerBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/container/ApptainerBuilderTest.groovy
index 436f3e74e6..9aa8199fa2 100644
--- a/modules/nextflow/src/test/groovy/nextflow/container/ApptainerBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/container/ApptainerBuilderTest.groovy
@@ -27,9 +27,10 @@ import spock.lang.Unroll
  */
 class ApptainerBuilderTest extends Specification {
 
-    def 'should get the exec command line' () {
-
+    def 'should get the legacy exec command line' () {
         given:
+        SysEnv.push(NXF_APPTAINER_RUN_COMMAND:'exec', NXF_APPTAINER_AUTO_MOUNTS:'false')
+        and:
         def path1 = Paths.get('/foo/data/file1')
         def path2 = Paths.get('/bar/data/file2')
         def path3 = Paths.get('/bar/data file')
@@ -87,6 +88,71 @@ class ApptainerBuilderTest extends Specification {
                 .build()
                 .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home ubuntu'
 
+        cleanup:
+        SysEnv.pop()
+    }
+
+    def 'should get the run command line' () {
+
+        given:
+        def path1 = Paths.get('/foo/data/file1')
+        def path2 = Paths.get('/bar/data/file2')
+        def path3 = Paths.get('/bar/data file')
+
+        expect:
+        new ApptainerBuilder('busybox')
+                .build()
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B "$PWD" busybox'
+
+        new ApptainerBuilder('busybox')
+                .params(engineOptions: '-q -v')
+                .build()
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer -q -v run --no-home --pid -B "$PWD" busybox'
+
+        new ApptainerBuilder('busybox')
+                .params(runOptions: '--contain --writable')
+                .build()
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B "$PWD" --contain --writable busybox'
+
+        new ApptainerBuilder('ubuntu')
+                .addMount(path1)
+                .params(autoMounts: false)
+                .build()
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid ubuntu'
+
+        new ApptainerBuilder('ubuntu')
+                .addMount(path1)
+                .addMount(path2)
+                .params(autoMounts: true)
+                .build()
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B /foo/data/file1 -B /bar/data/file2 -B "$PWD" ubuntu'
+
+        new ApptainerBuilder('ubuntu')
+                .addMount(path1)
+                .addMount(path1)
+                .params(autoMounts: true)
+                .build()
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B /foo/data/file1 -B "$PWD" ubuntu'
+
+        new ApptainerBuilder('ubuntu')
+                .addMount(path1)
+                .addMount(path1)
+                .params(autoMounts: true)
+                .params(readOnlyInputs: true)
+                .build()
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B /foo/data/file1:/foo/data/file1:ro -B "$PWD" ubuntu'
+
+        new ApptainerBuilder('ubuntu')
+                .addMount(path3)
+                .params(autoMounts: true)
+                .build()
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B /bar/data\\ file -B "$PWD" ubuntu'
+
+        new ApptainerBuilder('ubuntu')
+                .params(newPidNamespace: false)
+                .build()
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home -B "$PWD" ubuntu'
+
     }
 
     def 'should mount home directory if specified' () {
@@ -135,12 +201,12 @@ class ApptainerBuilderTest extends Specification {
                 .addEnv('X=1')
                 .addEnv(ALPHA:'aaa', BETA: 'bbb')
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} APPTAINERENV_X="1" APPTAINERENV_ALPHA="aaa" APPTAINERENV_BETA="bbb" apptainer exec --no-home --pid busybox'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} APPTAINERENV_X="1" APPTAINERENV_ALPHA="aaa" APPTAINERENV_BETA="bbb" apptainer run --no-home --pid -B "$PWD" busybox'
 
         new ApptainerBuilder('busybox')
                 .addEnv('CUDA_VISIBLE_DEVICES')
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} ${CUDA_VISIBLE_DEVICES:+APPTAINERENV_CUDA_VISIBLE_DEVICES="$CUDA_VISIBLE_DEVICES"} apptainer exec --no-home --pid busybox'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} ${CUDA_VISIBLE_DEVICES:+APPTAINERENV_CUDA_VISIBLE_DEVICES="$CUDA_VISIBLE_DEVICES"} apptainer run --no-home --pid -B "$PWD" busybox'
 
     }
 
@@ -150,17 +216,17 @@ class ApptainerBuilderTest extends Specification {
         when:
         def cmd = new ApptainerBuilder('ubuntu.img').build().getRunCommand()
         then:
-        cmd == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid ubuntu.img'
+        cmd == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B "$PWD" ubuntu.img'
 
         when:
         cmd = new ApptainerBuilder('ubuntu.img').build().getRunCommand('bwa --this --that file.fastq')
         then:
-        cmd == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid ubuntu.img bwa --this --that file.fastq'
+        cmd == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B "$PWD" ubuntu.img bwa --this --that file.fastq'
 
         when:
         cmd = new ApptainerBuilder('ubuntu.img').params(entry:'/bin/sh').build().getRunCommand('bwa --this --that file.fastq')
         then:
-        cmd == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid ubuntu.img /bin/sh -c "cd $PWD; bwa --this --that file.fastq"'
+        cmd == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B "$PWD" ubuntu.img /bin/sh -c "cd $PWD; bwa --this --that file.fastq"'
     }
 
     @Unroll
diff --git a/modules/nextflow/src/test/groovy/nextflow/container/SingularityBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/container/SingularityBuilderTest.groovy
index 1614550c29..6b412ea3b1 100644
--- a/modules/nextflow/src/test/groovy/nextflow/container/SingularityBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/container/SingularityBuilderTest.groovy
@@ -28,9 +28,10 @@ import spock.lang.Unroll
  */
 class SingularityBuilderTest extends Specification {
 
-    def 'should get the exec command line' () {
-
+    def 'should get the legacy exec command line' () {
         given:
+        SysEnv.push(NXF_SINGULARITY_RUN_COMMAND:'exec', NXF_SINGULARITY_AUTO_MOUNTS:'false')
+        and:
         def path1 = Paths.get('/foo/data/file1')
         def path2 = Paths.get('/bar/data/file2')
         def path3 = Paths.get('/bar/data file')
@@ -88,6 +89,71 @@ class SingularityBuilderTest extends Specification {
                 .build()
                 .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home ubuntu'
 
+        cleanup:
+        SysEnv.pop()
+    }
+
+    def 'should get the run command line' () {
+
+        given:
+        def path1 = Paths.get('/foo/data/file1')
+        def path2 = Paths.get('/bar/data/file2')
+        def path3 = Paths.get('/bar/data file')
+
+        expect:
+        new SingularityBuilder('busybox')
+                .build()
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity run --no-home --pid -B "$PWD" busybox'
+
+        new SingularityBuilder('busybox')
+                .params(engineOptions: '-q -v')
+                .build()
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity -q -v run --no-home --pid -B "$PWD" busybox'
+
+        new SingularityBuilder('busybox')
+                .params(runOptions: '--contain --writable')
+                .build()
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity run --no-home --pid -B "$PWD" --contain --writable busybox'
+
+        new SingularityBuilder('ubuntu')
+                .params(autoMounts: false)
+                .build()
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity run --no-home --pid ubuntu'
+
+        new SingularityBuilder('ubuntu')
+                .addMount(path1)
+                .addMount(path2)
+                .params(autoMounts: true)
+                .build()
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity run --no-home --pid -B /foo/data/file1 -B /bar/data/file2 -B "$PWD" ubuntu'
+
+        new SingularityBuilder('ubuntu')
+                .addMount(path1)
+                .addMount(path1)
+                .params(autoMounts: true)
+                .build()
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity run --no-home --pid -B /foo/data/file1 -B "$PWD" ubuntu'
+
+        new SingularityBuilder('ubuntu')
+                .addMount(path1)
+                .addMount(path1)
+                .params(autoMounts: true)
+                .params(readOnlyInputs: true)
+                .build()
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity run --no-home --pid -B /foo/data/file1:/foo/data/file1:ro -B "$PWD" ubuntu'
+
+        new SingularityBuilder('ubuntu')
+                .addMount(path3)
+                .params(autoMounts: true)
+                .build()
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity run --no-home --pid -B /bar/data\\ file -B "$PWD" ubuntu'
+
+        new SingularityBuilder('ubuntu')
+                .params(newPidNamespace: false)
+                .params(autoMounts: false)
+                .build()
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity run --no-home ubuntu'
+
     }
 
     def 'should mount home directory if specified' () {
@@ -136,12 +202,12 @@ class SingularityBuilderTest extends Specification {
                 .addEnv('X=1')
                 .addEnv(ALPHA:'aaa', BETA: 'bbb')
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} SINGULARITYENV_X="1" SINGULARITYENV_ALPHA="aaa" SINGULARITYENV_BETA="bbb" singularity exec --no-home --pid busybox'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} SINGULARITYENV_X="1" SINGULARITYENV_ALPHA="aaa" SINGULARITYENV_BETA="bbb" singularity run --no-home --pid -B "$PWD" busybox'
 
         new SingularityBuilder('busybox')
                 .addEnv('CUDA_VISIBLE_DEVICES')
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} ${CUDA_VISIBLE_DEVICES:+SINGULARITYENV_CUDA_VISIBLE_DEVICES="$CUDA_VISIBLE_DEVICES"} singularity exec --no-home --pid busybox'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} ${CUDA_VISIBLE_DEVICES:+SINGULARITYENV_CUDA_VISIBLE_DEVICES="$CUDA_VISIBLE_DEVICES"} singularity run --no-home --pid -B "$PWD" busybox'
 
     }
 
@@ -151,17 +217,17 @@ class SingularityBuilderTest extends Specification {
         when:
         def cmd = new SingularityBuilder('ubuntu.img').build().getRunCommand()
         then:
-        cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid ubuntu.img'
+        cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity run --no-home --pid -B "$PWD" ubuntu.img'
 
         when:
         cmd = new SingularityBuilder('ubuntu.img').build().getRunCommand('bwa --this --that file.fastq')
         then:
-        cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid ubuntu.img bwa --this --that file.fastq'
+        cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity run --no-home --pid -B "$PWD" ubuntu.img bwa --this --that file.fastq'
 
         when:
         cmd = new SingularityBuilder('ubuntu.img').params(entry:'/bin/sh').build().getRunCommand('bwa --this --that file.fastq')
         then:
-        cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid ubuntu.img /bin/sh -c "cd $PWD; bwa --this --that file.fastq"'
+        cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity run --no-home --pid -B "$PWD" ubuntu.img /bin/sh -c "cd $PWD; bwa --this --that file.fastq"'
     }
 
     @Unroll
diff --git a/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
index 15c9965a18..006c2d9c33 100644
--- a/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
@@ -977,7 +977,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [enabled: true, engine: 'singularity'] as ContainerConfig ).makeBinding()
 
         then:
-        binding.launch_cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} ${NXF_TASK_WORKDIR:+SINGULARITYENV_NXF_TASK_WORKDIR="$NXF_TASK_WORKDIR"} singularity exec --no-home --pid docker://ubuntu:latest /bin/bash -c "cd $PWD; eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
+        binding.launch_cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} ${NXF_TASK_WORKDIR:+SINGULARITYENV_NXF_TASK_WORKDIR="$NXF_TASK_WORKDIR"} singularity run --no-home --pid -B /work/dir docker://ubuntu:latest /bin/bash -c "cd $PWD; eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
         binding.cleanup_cmd == ""
         binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
     }
@@ -991,7 +991,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [enabled: true, engine: 'singularity', entrypointOverride: true] as ContainerConfig ).makeBinding()
 
         then:
-        binding.launch_cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} ${NXF_TASK_WORKDIR:+SINGULARITYENV_NXF_TASK_WORKDIR="$NXF_TASK_WORKDIR"} singularity exec --no-home --pid docker://ubuntu:latest /bin/bash -c "cd $PWD; eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
+        binding.launch_cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} ${NXF_TASK_WORKDIR:+SINGULARITYENV_NXF_TASK_WORKDIR="$NXF_TASK_WORKDIR"} singularity run --no-home --pid -B /work/dir docker://ubuntu:latest /bin/bash -c "cd $PWD; eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
         binding.cleanup_cmd == ""
         binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
     }
diff --git a/modules/nextflow/src/test/groovy/nextflow/executor/fusion/FusionHelperTest.groovy b/modules/nextflow/src/test/groovy/nextflow/executor/fusion/FusionHelperTest.groovy
index e1debac016..7dd00bb5b6 100644
--- a/modules/nextflow/src/test/groovy/nextflow/executor/fusion/FusionHelperTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/executor/fusion/FusionHelperTest.groovy
@@ -68,9 +68,9 @@ class FusionHelperTest extends Specification {
         [engine:'docker']       | [FOO:'one']       | 'image:2'     | null          | ['echo', 'hello']     | "docker run -i -e \"FOO=one\" --rm --privileged image:2 echo 'hello'"
         [engine:'docker']       | [FOO:'one']       | 'image:2'     | '--this=that' | ['echo', 'hello']     | "docker run -i -e \"FOO=one\" --this=that --rm --privileged image:2 echo 'hello'"
         and:
-        [engine:'singularity']  | [:]               | 'image:1'     | null          | ['echo', 'hello']     | "set +u; env - PATH=\"\$PATH\" \${TMP:+SINGULARITYENV_TMP=\"\$TMP\"} \${TMPDIR:+SINGULARITYENV_TMPDIR=\"\$TMPDIR\"} singularity exec --no-home --pid image:1 echo 'hello'"
-        [engine:'singularity']  | [FOO:'one']       | 'image:1'     | null          | ['echo', 'hello']     | "set +u; env - PATH=\"\$PATH\" \${TMP:+SINGULARITYENV_TMP=\"\$TMP\"} \${TMPDIR:+SINGULARITYENV_TMPDIR=\"\$TMPDIR\"} SINGULARITYENV_FOO=\"one\" singularity exec --no-home --pid image:1 echo 'hello'"
-        [engine:'singularity']  | [FOO:'one']       | 'image:1'     | '--this=that' | ['echo', 'hello']     | "set +u; env - PATH=\"\$PATH\" \${TMP:+SINGULARITYENV_TMP=\"\$TMP\"} \${TMPDIR:+SINGULARITYENV_TMPDIR=\"\$TMPDIR\"} SINGULARITYENV_FOO=\"one\" singularity exec --no-home --pid --this=that image:1 echo 'hello'"
+        [engine:'singularity']  | [:]               | 'image:1'     | null          | ['echo', 'hello']     | "set +u; env - PATH=\"\$PATH\" \${TMP:+SINGULARITYENV_TMP=\"\$TMP\"} \${TMPDIR:+SINGULARITYENV_TMPDIR=\"\$TMPDIR\"} singularity run --no-home --pid image:1 echo 'hello'"
+        [engine:'singularity']  | [FOO:'one']       | 'image:1'     | null          | ['echo', 'hello']     | "set +u; env - PATH=\"\$PATH\" \${TMP:+SINGULARITYENV_TMP=\"\$TMP\"} \${TMPDIR:+SINGULARITYENV_TMPDIR=\"\$TMPDIR\"} SINGULARITYENV_FOO=\"one\" singularity run --no-home --pid image:1 echo 'hello'"
+        [engine:'singularity']  | [FOO:'one']       | 'image:1'     | '--this=that' | ['echo', 'hello']     | "set +u; env - PATH=\"\$PATH\" \${TMP:+SINGULARITYENV_TMP=\"\$TMP\"} \${TMPDIR:+SINGULARITYENV_TMPDIR=\"\$TMPDIR\"} SINGULARITYENV_FOO=\"one\" singularity run --no-home --pid --this=that image:1 echo 'hello'"
 
     }
 

From d19cb0b704ecf3c8d6d3818e2ff4a928c095a9a1 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 2 Sep 2023 15:19:09 +0200
Subject: [PATCH 105/350] Fix Wave build when Conda package name is quoted

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-wave/build.gradle                       |  2 +-
 .../io/seqera/wave/plugin/WaveClientTest.groovy    | 14 ++++++++++----
 2 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/plugins/nf-wave/build.gradle b/plugins/nf-wave/build.gradle
index d3a604c19b..ce15723239 100644
--- a/plugins/nf-wave/build.gradle
+++ b/plugins/nf-wave/build.gradle
@@ -36,7 +36,7 @@ dependencies {
     api 'org.apache.commons:commons-lang3:3.12.0'
     api 'com.google.code.gson:gson:2.10.1'
     api 'org.yaml:snakeyaml:2.0'
-    api 'io.seqera:wave-utils:0.7.1'
+    api 'io.seqera:wave-utils:0.7.2'
 
     testImplementation(testFixtures(project(":nextflow")))
     testImplementation "org.codehaus.groovy:groovy:3.0.19"
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
index cf19d9a8c2..5dcb1dce33 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
@@ -513,7 +513,7 @@ class WaveClientTest extends Specification {
         given:
         def session = Mock(Session) { getConfig() >> [:]}
         and:
-        def task = Mock(TaskRun) {getConfig() >> [conda:'salmon=1.2.3'] }
+        def task = Mock(TaskRun) {getConfig() >> [conda:"bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'"] }
         and:
         def client = new WaveClient(session)
 
@@ -539,7 +539,8 @@ class WaveClientTest extends Specification {
                 - conda-forge
                 - defaults
                 dependencies:
-                - salmon=1.2.3
+                - bioconda::rseqc=3.0.1
+                - conda-forge::r-base>=3.5
                 '''.stripIndent(true)
     }
 
@@ -575,7 +576,7 @@ class WaveClientTest extends Specification {
         given:
         def session = Mock(Session) { getConfig() >> [:]}
         and:
-        def task = Mock(TaskRun) {getConfig() >> [spack:'salmon@1.2.3', arch:'amd64'] }
+        def task = Mock(TaskRun) {getConfig() >> [spack:"rseqc@3.0.1 'rbase@3.5'", arch:"amd64"] }
         and:
         def client = new WaveClient(session)
 
@@ -607,8 +608,13 @@ class WaveClientTest extends Specification {
         !assets.containerImage
         !assets.containerConfig
         !assets.condaFile
-        assets.spackFile
         !assets.projectResources
+        and:
+        assets.spackFile.text == '''\
+                spack:
+                  specs: [rseqc@3.0.1, rbase@3.5]
+                  concretizer: {unify: true, reuse: false}
+                '''.stripIndent(true)
     }
 
     def 'should create asset with conda file' () {

From fa961e7fadb257b32e8fe19d0d5bf14a7700129f Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 2 Sep 2023 15:47:40 +0200
Subject: [PATCH 106/350] Fix Too long Http connection pool timeout

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../main/groovy/nextflow/cli/Launcher.groovy  | 28 +++++++++++++------
 .../groovy/nextflow/cli/LauncherTest.groovy   | 25 +++++++++++++++--
 2 files changed, 43 insertions(+), 10 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy
index c8986cc5d0..f3f7087cfc 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy
@@ -578,15 +578,28 @@ class Launcher {
      */
     private void setupEnvironment() {
 
-        setProxy('HTTP',System.getenv())
-        setProxy('HTTPS',System.getenv())
-        setProxy('FTP',System.getenv())
+        final env = System.getenv()
+        setProxy('HTTP',env)
+        setProxy('HTTPS',env)
+        setProxy('FTP',env)
 
-        setProxy('http',System.getenv())
-        setProxy('https',System.getenv())
-        setProxy('ftp',System.getenv())
+        setProxy('http',env)
+        setProxy('https',env)
+        setProxy('ftp',env)
 
-        setNoProxy(System.getenv())
+        setNoProxy(env)
+
+        setHttpClientProperties(env)
+    }
+
+    static void setHttpClientProperties(Map<String,String> env) {
+        // Set the httpclient connection pool timeout to 10 seconds.
+        // This required because the default is 20 minutes, which cause the error
+        // "HTTP/1.1 header parser received no bytes" when in some circumstances
+        // https://github.com/nextflow-io/nextflow/issues/3983#issuecomment-1702305137
+        System.setProperty("jdk.httpclient.keepalive.timeout", env.getOrDefault("NXF_JDK_HTTPCLIENT_KEEPALIVE_TIMEOUT","10"))
+        if( env.get("NXF_JDK_HTTPCLIENT_CONNECTIONPOOLSIZE") )
+            System.setProperty("jdk.httpclient.connectionPoolSize", env.get("NXF_JDK_HTTPCLIENT_CONNECTIONPOOLSIZE"))
     }
 
     /**
@@ -650,7 +663,6 @@ class Launcher {
      * @param args The program options as specified by the user on the CLI
      */
     static void main(String... args)  {
-
         final status = new Launcher() .command(args) .run()
         if( status )
             System.exit(status)
diff --git a/modules/nextflow/src/test/groovy/nextflow/cli/LauncherTest.groovy b/modules/nextflow/src/test/groovy/nextflow/cli/LauncherTest.groovy
index 1bd2daff7b..7f97273e42 100644
--- a/modules/nextflow/src/test/groovy/nextflow/cli/LauncherTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/cli/LauncherTest.groovy
@@ -16,12 +16,12 @@
 
 package nextflow.cli
 
-import spock.lang.Specification
-
 import java.nio.file.Files
 
 import com.beust.jcommander.DynamicParameter
 import com.beust.jcommander.Parameter
+import spock.lang.Specification
+import spock.lang.Unroll
 import spock.util.environment.RestoreSystemProperties
 import test.OutputCapture
 /**
@@ -427,6 +427,27 @@ class LauncherTest extends Specification {
 
     }
 
+    @RestoreSystemProperties
+    @Unroll
+    def 'should set http client timeout' () {
+        when:
+        Launcher.setHttpClientProperties(ENV)
+        then:
+        System.getProperty('jdk.httpclient.keepalive.timeout') == TIMEOUT
+        and:
+        System.getProperty('jdk.httpclient.connectionPoolSize') == POOLSIZE
+
+        where:
+        ENV                                             | TIMEOUT   | POOLSIZE
+        [:]                                             | '10'      | null
+        and:
+        [NXF_JDK_HTTPCLIENT_KEEPALIVE_TIMEOUT: '1']     | '1'       | null
+        [NXF_JDK_HTTPCLIENT_KEEPALIVE_TIMEOUT: '100']   | '100'     | null
+        and:
+        [NXF_JDK_HTTPCLIENT_CONNECTIONPOOLSIZE: '0']    | '10'      | '0'
+        [NXF_JDK_HTTPCLIENT_CONNECTIONPOOLSIZE: '99']   | '10'      | '99'
+    }
+
     def 'should make cli' () {
         given:
         def launcher = new Launcher()

From 366eedec9fdda9c98c88390b6b2947fbaf1493c2 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sun, 3 Sep 2023 11:59:58 +0200
Subject: [PATCH 107/350] Fix fs cp command with remote file

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../src/main/groovy/nextflow/cli/CmdFs.groovy | 29 +++++++++++++++++--
 tests/checks/cli-fs.nf/.checks                | 20 +++++++++++++
 2 files changed, 47 insertions(+), 2 deletions(-)
 create mode 100644 tests/checks/cli-fs.nf/.checks

diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdFs.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdFs.groovy
index 5ea9e636a4..2382550ba3 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdFs.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdFs.groovy
@@ -15,22 +15,30 @@
  */
 
 package nextflow.cli
+
 import java.nio.charset.Charset
 import java.nio.file.Files
 import java.nio.file.Path
+import java.nio.file.Paths
 
 import com.beust.jcommander.Parameter
+import groovy.transform.CompileStatic
+import groovy.util.logging.Slf4j
+import nextflow.Global
+import nextflow.Session
+import nextflow.config.ConfigBuilder
 import nextflow.exception.AbortOperationException
 import nextflow.extension.FilesEx
 import nextflow.file.FileHelper
 import nextflow.file.FilePatternSplitter
 import nextflow.plugin.Plugins
-
 /**
  * Implements `fs` command
  *
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
  */
+@CompileStatic
+@Slf4j
 class CmdFs extends CmdBase implements UsageAware {
 
     static final public NAME = 'fs'
@@ -158,6 +166,16 @@ class CmdFs extends CmdBase implements UsageAware {
         return NAME
     }
 
+    private Session createSession() {
+        // create the config
+        final config = new ConfigBuilder()
+                .setOptions(getLauncher().getOptions())
+                .setBaseDir(Paths.get('.'))
+                .build()
+
+        return new Session(config)
+    }
+
     @Override
     void run() {
         if( !args ) {
@@ -166,11 +184,18 @@ class CmdFs extends CmdBase implements UsageAware {
         }
 
         Plugins.setup()
+        final session = createSession()
         try {
             run0()
         }
         finally {
-            Plugins.stop()
+            try {
+                session.destroy()
+                Global.cleanUp()
+                Plugins.stop()
+            } catch (Throwable t) {
+                log.warn "Unexpected error while destroying the session object - cause: ${t.message}"
+            }
         }
     }
 
diff --git a/tests/checks/cli-fs.nf/.checks b/tests/checks/cli-fs.nf/.checks
new file mode 100644
index 0000000000..50da6168aa
--- /dev/null
+++ b/tests/checks/cli-fs.nf/.checks
@@ -0,0 +1,20 @@
+# Skip test if AWS keys are missing
+if [ -z "$AWS_ACCESS_KEY_ID" ]; then
+  echo "Missing AWS credentials -- Skipping test"
+  exit 0
+fi
+
+## random file name
+NAME=test-cmd-$(basename `mktemp`).file
+
+## create random file
+head -c 1000000 </dev/urandom >myfile
+
+## upload it
+$NXF_CMD -log cmd-fs-1.log fs cp myfile s3://nextflow-ci/$NAME
+
+## download it
+$NXF_CMD -log cmd-fs-2.log fs cp s3://nextflow-ci/$NAME $NAME
+
+## check they are equals
+diff myfile $NAME || false

From 976c282c2711305ed115710b8a628a13a5f5c35f Mon Sep 17 00:00:00 2001
From: Jan Philipp Bittner <42641080+najtin@users.noreply.github.com>
Date: Sun, 3 Sep 2023 12:06:29 +0200
Subject: [PATCH 108/350] Fix Parallel execution of Conda corrupts data and
 packages (#4253) [ci fast]

Signed-off-by: Jan Philipp Bittner <42641080+najtin@users.noreply.github.com>
---
 .../src/main/groovy/nextflow/conda/CondaCache.groovy | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/conda/CondaCache.groovy b/modules/nextflow/src/main/groovy/nextflow/conda/CondaCache.groovy
index 451aeecac2..0cc0b86a95 100644
--- a/modules/nextflow/src/main/groovy/nextflow/conda/CondaCache.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/conda/CondaCache.groovy
@@ -41,7 +41,8 @@ import org.yaml.snakeyaml.Yaml
 @Slf4j
 @CompileStatic
 class CondaCache {
-
+    static final private Object condaLock = new Object()
+    
     /**
      * Cache the prefix path for each Conda environment
      */
@@ -273,7 +274,6 @@ class CondaCache {
 
     @PackageScope
     Path createLocalCondaEnv0(String condaEnv, Path prefixPath) {
-
         log.info "Creating env using ${binaryName}: $condaEnv [cache $prefixPath]"
 
         String opts = createOptions ? "$createOptions " : ''
@@ -296,7 +296,13 @@ class CondaCache {
         }
 
         try {
-            runCommand( cmd )
+            // Parallel execution of conda causes data and package corruption.
+            // https://github.com/nextflow-io/nextflow/issues/4233
+            // https://github.com/conda/conda/issues/13037
+            // Should be removed as soon as the upstream bug is fixed and released.
+            synchronized(condaLock) {
+                runCommand( cmd )
+            }
             log.debug "'${binaryName}' create complete env=$condaEnv path=$prefixPath"
         }
         catch( Exception e ){

From c7701e3a1505eb53632306cf1ebeb21e6b37a11d Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Sun, 3 Sep 2023 12:07:03 +0200
Subject: [PATCH 109/350] CI: Add back logic to skip Tests for docs-only PRs.
 (#4250)

Signed-off-by: Phil Ewels <phil.ewels@seqera.io>
---
 .github/workflows/build.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index c27a11929e..a5e1951c22 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -92,7 +92,7 @@ jobs:
       any_changed: ${{ steps.changed-files.outputs.any_changed }}
 
   test:
-    if: ${{ !contains(github.event.head_commit.message, '[ci fast]') }}
+    if: ${{ !contains(github.event.head_commit.message, '[ci fast]') && needs.build.outputs.any_changed == 'true' }}
     needs: build
     runs-on: ubuntu-latest
     strategy:

From a68c1a3efe355c0ea702c362c52e40f276cf2aeb Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Sun, 3 Sep 2023 05:08:35 -0500
Subject: [PATCH 110/350] Add warning about using clusterOptions with process
 directives (#4248)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 docs/process.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/docs/process.md b/docs/process.md
index 7c4eb7fce0..9c71b26897 100644
--- a/docs/process.md
+++ b/docs/process.md
@@ -1314,6 +1314,10 @@ The `clusterOptions` directive allows the usage of any native configuration opti
 This directive is only used by grid executors. Refer to the {ref}`executor-page` page to see which executors support this directive.
 :::
 
+:::{warning}
+While you can use the `clusterOptions` directive to specify options that are supported as process directives (`queue`, `memory`, `time`, etc), you should not use both at the same time, as it will cause undefined behavior. Most HPC schedulers will either fail or simply ignore one or the other.
+:::
+
 (process-conda)=
 
 ### conda

From 1ae70d5d39f68068fa073497d28ced3fed5731e4 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Sun, 3 Sep 2023 05:15:16 -0500
Subject: [PATCH 111/350] Fix Parse negative CLI params as numbers (#4238) [ci
 fast]

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy | 6 +++---
 .../nextflow/src/test/groovy/nextflow/cli/CmdRunTest.groovy | 4 ++++
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
index 4da1a3b35c..890958f270 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
@@ -625,9 +625,9 @@ class CmdRun extends CmdBase implements HubOptions {
         if ( str.toLowerCase() == 'true') return Boolean.TRUE
         if ( str.toLowerCase() == 'false' ) return Boolean.FALSE
 
-        if ( str==~/\d+(\.\d+)?/ && str.isInteger() ) return str.toInteger()
-        if ( str==~/\d+(\.\d+)?/ && str.isLong() ) return str.toLong()
-        if ( str==~/\d+(\.\d+)?/ && str.isDouble() ) return str.toDouble()
+        if ( str==~/-?\d+(\.\d+)?/ && str.isInteger() ) return str.toInteger()
+        if ( str==~/-?\d+(\.\d+)?/ && str.isLong() ) return str.toLong()
+        if ( str==~/-?\d+(\.\d+)?/ && str.isDouble() ) return str.toDouble()
 
         return str
     }
diff --git a/modules/nextflow/src/test/groovy/nextflow/cli/CmdRunTest.groovy b/modules/nextflow/src/test/groovy/nextflow/cli/CmdRunTest.groovy
index 86917bba53..e18b401a76 100644
--- a/modules/nextflow/src/test/groovy/nextflow/cli/CmdRunTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/cli/CmdRunTest.groovy
@@ -49,9 +49,13 @@ class CmdRunTest extends Specification {
         'false'     | false
         'foo'       | 'foo'
         '10'        | 10i
+        '-10'       | -10i
         '20.00'     | 20i
+        '-20.00'    | -20i
         '3000000000'| 3000000000l
         '20.33'     | 20.33d
+        '-20.33'    | -20.33d
+        '-foo'      | '-foo'
         '--foo'     | '--foo'
         '20x0'      | '20x0'
         '20.d'      | '20.d'

From 69d317b6d297c7fd897ffc4cbbc4124efe15594a Mon Sep 17 00:00:00 2001
From: Manuele Simi <2822686+manuelesimi@users.noreply.github.com>
Date: Sun, 3 Sep 2023 12:31:50 +0200
Subject: [PATCH 112/350] Update AZ File share doc. [ci skip] (#4235)

Signed-off-by: Manuele Simi <manuele.simi@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/azure.md | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/docs/azure.md b/docs/azure.md
index aebf7bb9c1..ac8ff1a24d 100644
--- a/docs/azure.md
+++ b/docs/azure.md
@@ -63,7 +63,7 @@ azure {
 }
 ```
 
-The files in the File share are available to the task in the directory: `<YOUR MOUNT DESTINATION>/<YOUR SOURCE FILE SHARE NAME>`.
+The files in the File share are available to the task in the directory: `<YOUR MOUNT DESTINATION>`.
 
 For instance, given the following configuration:
 
@@ -73,15 +73,20 @@ azure {
         // ...
 
         fileShares {
-            dir1 {
-                mountPath = "/mnt/mydata/"
+          rnaseqResources {
+                mountPath = "/mnt/mydata/myresources"
             }
         }
     }
 }
 ```
 
-The task can access the File share in `/mnt/mydata/dir1`.
+The task can access the File share in `/mnt/mydata/myresources`. Note: The string `rnaseqResources` in the above config can be any name of your choice, and it does not affect the underlying mount. 
+
+:::{warning}
+Azure File shares do not support authentication and management with Active Directory. The storage account key must be 
+set in the configuration if a share is mounted.
+:::
 
 (azure-batch)=
 

From 3e8cd4881720b5fd48d4cf2881d331b61c4d3c28 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sun, 3 Sep 2023 13:50:27 +0200
Subject: [PATCH 113/350] Add check for latest version (#4194)

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 nextflow       | 24 +++++++++++++++++++++++-
 packing.gradle |  3 +++
 2 files changed, 26 insertions(+), 1 deletion(-)

diff --git a/nextflow b/nextflow
index 6e3931e648..c7d7b92078 100755
--- a/nextflow
+++ b/nextflow
@@ -85,6 +85,17 @@ function get() {
     fi
 }
 
+function get_ver() {
+    if command -v curl &>/dev/null; then
+        curl -fsSL "$1"
+    elif command -v wget &>/dev/null; then
+        wget "$1" >/dev/null 2>&1
+    else
+        echo_red "ERROR: Cannot find 'curl' nor 'wget' utility --  please install one of them"
+        exit 1
+    fi
+}
+
 function make_temp() {
     local base=${NXF_TEMP:=$PWD}
     if [ "$(uname)" = 'Darwin' ]; then mktemp "${base}/nxf-tmp.XXXXXX" || exit $?
@@ -111,7 +122,7 @@ function resolve_link() {
 }
 
 function current_ver() {
-  [[ $NXF_EDGE == 1 ]] && printf 'edge' || printf 'latest'
+  [[ $NXF_EDGE == 1 || $NXF_VER == *"-edge" ]] && printf 'edge' || printf 'latest'
 }
 
 function install() {
@@ -131,6 +142,15 @@ function install() {
     echo ''
 }
 
+function check_latest() {
+    [[ $cmd != run ]] && return 0
+    [[ $NXF_OFFLINE == true || $NXF_DISABLE_CHECK_LATEST == true ]] && return 0
+    local latest=$(get_ver "$NXF_BASE/$(current_ver)/version?current=$NXF_VER")
+    if [[ -n "$latest" && "$latest" != $NXF_VER ]]; then
+      echo_yellow "Nextflow $latest is available - Please consider updating your version to it"
+    fi
+}
+
 function launch_nextflow() {
     # the launch command line
     local cmdline=()
@@ -445,5 +465,7 @@ else
 
 fi
 
+# check for latest version
+check_latest
 # finally run it
 launch_nextflow
diff --git a/packing.gradle b/packing.gradle
index 09993e7844..efec6214f4 100644
--- a/packing.gradle
+++ b/packing.gradle
@@ -327,6 +327,7 @@ task release(type: Exec, dependsOn: [pack, dockerImage]) {
     def launcherSha1 = file('nextflow.sha1').absoluteFile
     def launcherSha256 = file('nextflow.sha256').absoluteFile
     def nextflowAllFile = file("$releaseDir/nextflow-${version}-all")
+    def versionFile = file('VERSION').absoluteFile
 
     def snapshot = version ==~ /^.+(-RC\d+|-SNAPSHOT)$/
     def edge = version ==~ /^.+(-edge|-EDGE)$/
@@ -350,6 +351,7 @@ task release(type: Exec, dependsOn: [pack, dockerImage]) {
         aws s3 cp $launcherSha1 s3://www2.nextflow.io/releases/edge/nextflow.sha1 $s3CmdOpts
         aws s3 cp $launcherSha256 s3://www2.nextflow.io/releases/edge/nextflow.sha256 $s3CmdOpts
         aws s3 cp $launcherSha256 s3://www2.nextflow.io/releases/edge/nextflow.md5 $s3CmdOpts
+        aws s3 cp $versionFile s3://www2.nextflow.io/releases/edge/version $s3CmdOpts
         """.stripIndent()
         
     else if( isLatest )
@@ -361,6 +363,7 @@ task release(type: Exec, dependsOn: [pack, dockerImage]) {
         aws s3 cp $launcherSha1 s3://www2.nextflow.io/releases/latest/nextflow.sha1 $s3CmdOpts
         aws s3 cp $launcherSha256 s3://www2.nextflow.io/releases/latest/nextflow.sha256 $s3CmdOpts
         aws s3 cp $launcherSha256 s3://www2.nextflow.io/releases/latest/nextflow.md5 $s3CmdOpts
+        aws s3 cp $versionFile s3://www2.nextflow.io/releases/latest/version $s3CmdOpts
         """.stripIndent()
 
     def temp = File.createTempFile('upload',null)

From 1dfb621c12ceda4adbfef9adfec560bb36b7df53 Mon Sep 17 00:00:00 2001
From: Jesse <90865804+dxu104@users.noreply.github.com>
Date: Sun, 3 Sep 2023 08:35:38 -0400
Subject: [PATCH 114/350] Update docs about splitCsv() operator (#4163)

Signed-off-by: Jesse <90865804+dxu104@users.noreply.github.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/operator.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/docs/operator.md b/docs/operator.md
index 636d82cbe7..978fbaf85b 100644
--- a/docs/operator.md
+++ b/docs/operator.md
@@ -1384,6 +1384,10 @@ Channel
     .splitCsv(header: ['col1', 'col2', 'col3'], skip: 1 )
     .view { row -> "${row.col1} - ${row.col2} - ${row.col3}" }
 ```
+:::{note}
+- By default, the `splitCsv` operator returns each row as a *list* object. Items are accessed by using the 0-based column index.
+- When the `header` is specified each row is returned as a *map* object (also known as dictionary). Items are accessed via the corresponding column name. 
+:::
 
 Available options:
 

From 937c8fb7ab72a62152c838c6d7dafe2bb87bfc6d Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sun, 3 Sep 2023 15:20:10 +0200
Subject: [PATCH 115/350] Remove experimental -dockerize option

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../groovy/nextflow/cli/CliOptions.groovy     |  3 ---
 .../executor/BashWrapperBuilder.groovy        |  4 ----
 nextflow                                      | 20 -------------------
 3 files changed, 27 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CliOptions.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CliOptions.groovy
index 8c6f1a445a..c6197b1ea9 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CliOptions.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CliOptions.groovy
@@ -84,9 +84,6 @@ class CliOptions {
     @Parameter(names = ['-self-update'], description = 'Update nextflow to the latest version', arity = 0, hidden = true)
     boolean selfUpdate
 
-    @Parameter(names = ['-d','-dockerize'], description = 'Launch nextflow via Docker (experimental)', arity = 0)
-    boolean dockerize
-
     Boolean ansiLog
 
     boolean getAnsiLog() {
diff --git a/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
index 835739e5ae..b0439ed85f 100644
--- a/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
@@ -593,10 +593,6 @@ class BashWrapperBuilder {
         if( fixOwnership() )
             builder.addEnv( 'NXF_OWNER=$(id -u):$(id -g)' )
 
-        if( engine=='docker' && System.getenv('NXF_DOCKER_OPTS') ) {
-            builder.addRunOptions(System.getenv('NXF_DOCKER_OPTS'))
-        }
-
         for( String var : containerConfig.getEnvWhitelist() ) {
             builder.addEnv(var)
         }
diff --git a/nextflow b/nextflow
index c7d7b92078..727de64bd3 100755
--- a/nextflow
+++ b/nextflow
@@ -194,7 +194,6 @@ unset JAVA_TOOL_OPTIONS
 
 # parse the command line
 bg=''
-dockerize=''
 declare -a jvmopts=()
 declare -a args=("$@")
 declare -a commands=(clone config drop help history info ls pull run view node console kuberun)
@@ -210,11 +209,6 @@ while [[ $# != 0 ]]; do
       jvmopts+=("$1")
       fi
       ;;
-    -d|-dockerize)
-      if [[ ! "$cmd" && ! -f /.nextflow/dockerized ]]; then
-      dockerize=1
-      fi
-      ;;
     -bg)
       if [[ ! -f /.nextflow/dockerized ]]; then
       bg=1
@@ -242,20 +236,6 @@ while [[ $# != 0 ]]; do
     shift
 done
 
-NXF_DOCKER_OPTS=${NXF_DOCKER_OPTS:=''}
-if [[ "$dockerize" ]]; then
-  if [[ "$bg" ]]; then detach='--detach '; else detach=''; fi
-  NXF_ASSETS=${NXF_ASSETS:-${NXF_HOME:-$HOME/.nextflow}/assets}
-  mkdir -p "$NXF_ASSETS"
-  exec docker run $detach --rm --net host \
-   -e NXF_ANSI_LOG=false \
-   -e USER -e HOME -e NXF_ASSETS=$NXF_ASSETS -e NXF_USRMAP=$(id -u) -e NXF_DOCKER_OPTS='-u $(id -u)' \
-   -v /var/run/docker.sock:/var/run/docker.sock \
-   -v $HOME:$HOME:ro,Z -v $NXF_ASSETS:$NXF_ASSETS:Z -v $PWD:$PWD:Z -w $PWD $NXF_DOCKER_OPTS \
-   nextflow/nextflow:$NXF_VER nextflow "${args[@]}"
-  exit 1
-fi
-
 CAPSULE_LOG=${CAPSULE_LOG:=''}
 CAPSULE_RESET=${CAPSULE_RESET:=''}
 CAPSULE_CACHE_DIR=${CAPSULE_CACHE_DIR:="$NXF_HOME/capsule"}

From 7955db8d08dd2a047f58f10e58c609350f849d09 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sun, 3 Sep 2023 15:20:38 +0200
Subject: [PATCH 116/350] Undocument internal NXF_DEBUG variable

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/config.md | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/docs/config.md b/docs/config.md
index 34ba2e5b97..e10b674076 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -1542,9 +1542,6 @@ The following environment variables control the configuration of the Nextflow ru
   :::
 : Enable the use of Conda recipes defined by using the {ref}`process-conda` directive. (default: `false`).
 
-`NXF_DEBUG`
-: Defines scripts debugging level: `1` dump task environment variables in the task log file; `2` enables command script execution tracing; `3` enables command wrapper execution tracing.
-
 `NXF_DEFAULT_DSL`
 : :::{versionadded} 22.03.0-edge
   :::

From 7def554228d5cb039ce97808c90066192bd660e1 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sun, 3 Sep 2023 16:07:03 +0200
Subject: [PATCH 117/350] Remove experimental -dockerize option /2

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docker/Dockerfile | 1 -
 nextflow          | 2 --
 packing.gradle    | 1 -
 3 files changed, 4 deletions(-)

diff --git a/docker/Dockerfile b/docker/Dockerfile
index 5fbe9209ed..e688fa4475 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -11,7 +11,6 @@ COPY nextflow /usr/local/bin/nextflow
 
 # download runtime
 RUN mkdir /.nextflow \
- && touch /.nextflow/dockerized \
  && chmod 755 /usr/local/bin/nextflow \
  && chmod 755 /usr/local/bin/entry.sh \
  && nextflow info
diff --git a/nextflow b/nextflow
index 727de64bd3..496d0f2b86 100755
--- a/nextflow
+++ b/nextflow
@@ -210,9 +210,7 @@ while [[ $# != 0 ]]; do
       fi
       ;;
     -bg)
-      if [[ ! -f /.nextflow/dockerized ]]; then
       bg=1
-      fi
       ;;
     -download)
       if [[ ! "$cmd" ]]; then
diff --git a/packing.gradle b/packing.gradle
index efec6214f4..9131bd7bbc 100644
--- a/packing.gradle
+++ b/packing.gradle
@@ -293,7 +293,6 @@ task dockerPack(type: Exec, dependsOn: ['packOne']) {
     COPY entry.sh /usr/local/bin/entry.sh
     COPY dist/docker /usr/local/bin/docker
     ENV NXF_HOME=/.nextflow
-    RUN touch /.nextflow/dockerized
     RUN chmod +x /usr/local/bin/nextflow /usr/local/bin/entry.sh
     RUN nextflow info
     ENTRYPOINT ["/usr/local/bin/entry.sh"]

From 817aa05bb96e218e0689d3a1aa96c65ce2ba0503 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sun, 3 Sep 2023 16:08:42 +0200
Subject: [PATCH 118/350] Add which to dockerfile build

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docker/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docker/Dockerfile b/docker/Dockerfile
index e688fa4475..de56944d02 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -1,5 +1,5 @@
 FROM amazoncorretto:17.0.8
-RUN yum install -y procps-ng shadow-utils
+RUN yum install -y procps-ng shadow-utils which
 
 ENV NXF_HOME=/.nextflow
 ARG TARGETPLATFORM=linux/amd64

From 7d6ad62476bd43d6e98747cabe8bfe181d5da1e9 Mon Sep 17 00:00:00 2001
From: Robert Syme <rob.syme@gmail.com>
Date: Sun, 3 Sep 2023 13:42:31 -0400
Subject: [PATCH 119/350] Allow setting shell directive when using the trace
 file. (#4210)

Signed-off-by: Rob Syme <rob.syme@gmail.com>
---
 .../main/groovy/nextflow/executor/BashWrapperBuilder.groovy   | 2 +-
 .../groovy/nextflow/executor/BashWrapperBuilderTest.groovy    | 4 ++--
 .../nextflow/executor/test-bash-wrapper-with-trace.txt        | 2 +-
 .../cloud/aws/batch/AwsBatchScriptLauncherTest.groovy         | 2 +-
 .../nextflow/cloud/azure/batch/AzFileCopyStrategyTest.groovy  | 2 +-
 5 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
index b0439ed85f..c37c21ae01 100644
--- a/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
@@ -468,7 +468,7 @@ class BashWrapperBuilder {
         final traceWrapper = isTraceRequired()
         if( traceWrapper ) {
             // executes the stub which in turn executes the target command
-            launcher = "/bin/bash ${fileStr(wrapperFile)} nxf_trace"
+            launcher = "${interpreter} ${fileStr(wrapperFile)} nxf_trace"
         }
         else {
             launcher = "${interpreter} ${fileStr(scriptFile)}"
diff --git a/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
index 006c2d9c33..4ded770ed5 100644
--- a/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
@@ -566,14 +566,14 @@ class BashWrapperBuilderTest extends Specification {
         when:
         binding = newBashWrapperBuilder(statsEnabled: true).makeBinding()
         then:
-        binding.launch_cmd == '/bin/bash /work/dir/.command.run nxf_trace'
+        binding.launch_cmd == '/bin/bash -ue /work/dir/.command.run nxf_trace'
         binding.unstage_controls == null
         binding.containsKey('unstage_controls')
 
         when:
         binding = newBashWrapperBuilder(statsEnabled: true, scratch: true).makeBinding()
         then:
-        binding.launch_cmd == '/bin/bash /work/dir/.command.run nxf_trace'
+        binding.launch_cmd == '/bin/bash -ue /work/dir/.command.run nxf_trace'
         binding.unstage_controls == '''\
                         cp .command.out /work/dir/.command.out || true
                         cp .command.err /work/dir/.command.err || true
diff --git a/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper-with-trace.txt b/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper-with-trace.txt
index 0aaf49f410..b032748ccb 100644
--- a/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper-with-trace.txt
+++ b/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper-with-trace.txt
@@ -281,7 +281,7 @@ on_term() {
 }
 
 nxf_launch() {
-    /bin/bash {{folder}}/.command.run nxf_trace
+    /bin/bash -ue {{folder}}/.command.run nxf_trace
 }
 
 nxf_stage() {
diff --git a/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchScriptLauncherTest.groovy b/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchScriptLauncherTest.groovy
index d2620c2767..5bb60cefa2 100644
--- a/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchScriptLauncherTest.groovy
+++ b/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchScriptLauncherTest.groovy
@@ -232,7 +232,7 @@ class AwsBatchScriptLauncherTest extends Specification {
                     nxf_parallel "${uploads[@]}"
                     '''.stripIndent().leftTrim()
 
-        binding.launch_cmd == '/bin/bash .command.run nxf_trace'
+        binding.launch_cmd == '/bin/bash -ue .command.run nxf_trace'
         
         binding.task_env == ''
 
diff --git a/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzFileCopyStrategyTest.groovy b/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzFileCopyStrategyTest.groovy
index 60eaf1ffb6..bbca973ffd 100644
--- a/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzFileCopyStrategyTest.groovy
+++ b/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzFileCopyStrategyTest.groovy
@@ -385,7 +385,7 @@ class AzFileCopyStrategyTest extends Specification {
                     nxf_parallel "${uploads[@]}"
                     '''.stripIndent().leftTrim()
 
-        binding.launch_cmd == '/bin/bash .command.run nxf_trace'
+        binding.launch_cmd == '/bin/bash -ue .command.run nxf_trace'
 
         binding.task_env == '''\
                     export PATH="$PWD/.nextflow-bin:$AZ_BATCH_NODE_SHARED_DIR/bin/:$PATH"

From 05ff784a130ee1e589924b46e06806d05b0bdf98 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Mon, 4 Sep 2023 11:41:15 -0500
Subject: [PATCH 120/350] Document use of local variables in closures (#4251)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 docs/script.md | 24 +++++++++++++++++-------
 1 file changed, 17 insertions(+), 7 deletions(-)

diff --git a/docs/script.md b/docs/script.md
index 71df9a3487..fc1bc761ef 100644
--- a/docs/script.md
+++ b/docs/script.md
@@ -392,21 +392,31 @@ Mark = Williams
 Sudha = Kumari
 ```
 
-A closure has two other important features. First, it can access variables in the scope where it is defined, so that it can interact with them.
-
-Second, a closure can be defined in an anonymous manner, meaning that it is not given a name, and is defined in the place where it needs to be used.
-
-As an example showing both these features, see the following code fragment:
+Closures can also access variables outside of their scope, and they can be used anonymously, that is without assigning them to a variable. Here is an example that demonstrates both of these things:
 
 ```groovy
-myMap = ["China": 1 , "India" : 2, "USA" : 3]
+myMap = ["China": 1, "India": 2, "USA": 3]
 
 result = 0
-myMap.keySet().each( { result+= myMap[it] } )
+myMap.keySet().each { result += myMap[it] }
 
 println result
 ```
 
+A closure can also declare local variables that exist only for the lifetime of the closure:
+
+```groovy
+result = 0
+myMap.keySet().each {
+  def count = myMap[it]
+  result += count
+}
+```
+
+:::{warning}
+Local variables should be declared using a qualifier such as `def` or a type name, otherwise they will be interpreted as global variables, which could lead to a race condition.
+:::
+
 Learn more about closures in the [Groovy documentation](http://groovy-lang.org/closures.html)
 
 (implicit-variables)=

From 6664b578f09e76bbbb2e69cc97d98edfe97cd043 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Mon, 4 Sep 2023 13:01:53 -0500
Subject: [PATCH 121/350] Fix setting `executor.queueSize = 0` is ignored
 (#4228)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 docs/config.md                                    |  2 +-
 .../processor/ParallelPollingMonitor.groovy       |  4 ++--
 .../main/groovy/nextflow/util/ConfigHelper.groovy |  2 +-
 .../groovy/nextflow/util/ConfigHelperTest.groovy  | 15 +++++++++++++++
 4 files changed, 19 insertions(+), 4 deletions(-)

diff --git a/docs/config.md b/docs/config.md
index e10b674076..5fde00ec5b 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -640,7 +640,7 @@ The following settings are available:
 : Determines how job status is retrieved. When `false` only the queue associated with the job execution is queried. When `true` the job status is queried globally i.e. irrespective of the submission queue (default: `false`).
 
 `executor.queueSize`
-: The number of tasks the executor will handle in a parallel manner. Default varies for each executor (see below).
+: The number of tasks the executor will handle in a parallel manner. A queue size of zero corresponds to no limit. Default varies for each executor (see below).
 
 `executor.queueStatInterval`
 : Determines how often to fetch the queue status from the scheduler (default: `1min`). Used only by grid executors.
diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/ParallelPollingMonitor.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/ParallelPollingMonitor.groovy
index 9c2f687ffb..64b8ee52b6 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/ParallelPollingMonitor.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/ParallelPollingMonitor.groovy
@@ -55,7 +55,7 @@ class ParallelPollingMonitor extends TaskPollingMonitor {
 
     @Override
     protected boolean canSubmit(TaskHandler handler) {
-        return super.canSubmit(handler) && semaphore.tryAcquire()
+        return super.canSubmit(handler) && semaphore?.tryAcquire()
     }
 
     protected RateLimiter createSubmitRateLimit() {
@@ -95,7 +95,7 @@ class ParallelPollingMonitor extends TaskPollingMonitor {
 
     @Override
     boolean evict(TaskHandler handler) {
-        semaphore.release()
+        semaphore?.release()
         return super.evict(handler)
     }
 }
diff --git a/modules/nextflow/src/main/groovy/nextflow/util/ConfigHelper.groovy b/modules/nextflow/src/main/groovy/nextflow/util/ConfigHelper.groovy
index 09a83f0fb9..e4891e7391 100644
--- a/modules/nextflow/src/main/groovy/nextflow/util/ConfigHelper.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/util/ConfigHelper.groovy
@@ -42,7 +42,7 @@ class ConfigHelper {
             result = config['$'+execName][propName]
         }
 
-        if( result==null && config instanceof Map && config[propName] ) {
+        if( result==null && config instanceof Map && config[propName] != null ) {
             result = config[propName]
         }
 
diff --git a/modules/nextflow/src/test/groovy/nextflow/util/ConfigHelperTest.groovy b/modules/nextflow/src/test/groovy/nextflow/util/ConfigHelperTest.groovy
index c8cef55c45..442e8e3488 100644
--- a/modules/nextflow/src/test/groovy/nextflow/util/ConfigHelperTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/util/ConfigHelperTest.groovy
@@ -28,6 +28,21 @@ import spock.lang.Unroll
  */
 class ConfigHelperTest extends Specification {
 
+    @Unroll
+    def "get config property" () {
+
+        expect:
+        ConfigHelper.getConfigProperty(config, execName, 'foo') == value
+
+        where:
+        config               | execName | value
+        [foo: 0]             | null     | 0
+        [foo: 100]           | null     | 100
+        [foo: 'bar']         | null     | 'bar'
+        [$sge: [foo: 'bar']] | 'sge'    | 'bar'
+
+    }
+
     @Unroll
     def "should parse string value: #str" () {
 

From b0bdfd79db7d54993763c4482b58b979ebdf0c76 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Mon, 4 Sep 2023 20:18:03 +0200
Subject: [PATCH 122/350] Fix IOException should be thrown when failing to
 creare Azure directory

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../main/nextflow/cloud/azure/nio/AzFileSystemProvider.groovy   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/plugins/nf-azure/src/main/nextflow/cloud/azure/nio/AzFileSystemProvider.groovy b/plugins/nf-azure/src/main/nextflow/cloud/azure/nio/AzFileSystemProvider.groovy
index f8fd7ab5b7..f77051023f 100644
--- a/plugins/nf-azure/src/main/nextflow/cloud/azure/nio/AzFileSystemProvider.groovy
+++ b/plugins/nf-azure/src/main/nextflow/cloud/azure/nio/AzFileSystemProvider.groovy
@@ -440,7 +440,7 @@ class AzFileSystemProvider extends FileSystemProvider {
             // 409 (CONFLICT) is returned when the path already
             // exists, ignore it
             if( e.statusCode!=409 )
-                throw e
+                throw new IOException("Unable to create Azure blob directory: ${dir.toUriString()} - cause: ${e.message}", e)
         }
     }
 

From c37e00bcf1fb3d1a7f6704db3b457cfd51d0a8e2 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Mon, 4 Sep 2023 13:41:19 -0500
Subject: [PATCH 123/350] Document API differences of process path inputs
 (#4189)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 docs/process.md | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/docs/process.md b/docs/process.md
index 9c71b26897..4cd585ab94 100644
--- a/docs/process.md
+++ b/docs/process.md
@@ -488,6 +488,16 @@ workflow {
 }
 ```
 
+:::{note}
+Process `path` inputs have nearly the same interface as described in {ref}`script-file-io`, with one difference which is relevant when files are staged into a subdirectory. Given the following input:
+
+```groovy
+path x, stageAs: 'my-dir/*'
+```
+
+In this case, `x.name` returns the file name with the parent directory (e.g. `my-dir/file.txt`), whereas normally it would return the file name (e.g. `file.txt`). You can use `x.fileName.name` to get the file name.
+:::
+
 ### Multiple input files
 
 A `path` input can also accept a collection of files instead of a single value. In this case, the input variable will be a Groovy list, and you can use it as such.

From 87e0648a98ec022e6af05b688885d3ce48c85070 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Mon, 4 Sep 2023 23:21:02 +0200
Subject: [PATCH 124/350] Add support for remote debug (#4266)

This commit adds the a possibility to compile nextflow scripts with debugging
information and debug them interactively via a remote debugger commonly available
via IntellJ or similar IDE.

To enable this feature it should the top-level command line option `-remote-debug`,
when specified the execution of nextflow stops and wait for the starting of a debugging session
in the IDE. By default, the TCP port 5005 is used. It can be changed by using the environment
variable NXF_REMOTE_DEBUG_PORT.

Credits: Jorge Aguilera

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/cli.md                                   |  3 +++
 launch.sh                                     |  5 ++--
 .../src/main/groovy/nextflow/Session.groovy   |  5 ++++
 .../groovy/nextflow/cli/CliOptions.groovy     |  3 +++
 .../main/groovy/nextflow/cli/CmdRun.groovy    |  1 +
 .../nextflow/script/ScriptParser.groovy       | 25 +++++++++++--------
 .../nextflow/script/ScriptRunner.groovy       |  2 +-
 nextflow                                      | 21 ++++++++++------
 8 files changed, 43 insertions(+), 22 deletions(-)

diff --git a/docs/cli.md b/docs/cli.md
index cfc1c40ef2..14f9a7bd70 100644
--- a/docs/cli.md
+++ b/docs/cli.md
@@ -42,6 +42,9 @@ Available options:
 `-q, -quiet`
 : Do not print information messages.
 
+`-remote-debug`
+: Enable JVM interactive remote debugging (experimental).
+
 `-syslog`
 : Send logs to syslog server (e.g. localhost:514).
 
diff --git a/launch.sh b/launch.sh
index 5f95d01d41..41e5103c40 100755
--- a/launch.sh
+++ b/launch.sh
@@ -83,6 +83,7 @@ NXF_PLUGINS_DEFAULT=${NXF_PLUGINS_DEFAULT:-true}
 NXF_HOME=${NXF_HOME:-$HOME/.nextflow}
 NXF_OPTS=${NXF_OPTS:-}
 NXF_CLI="$0 $@"
+NXF_REMOTE_DEBUG_PORT=${NXF_REMOTE_DEBUG_PORT:-5005}
 export NXF_CLI
 export COLUMNS
 export NXF_PLUGINS_DIR
@@ -115,8 +116,8 @@ while [ "$*" != "" ]; do
     fi
 
   elif [ "$1" == '-remote-debug' ]; then
-    DEBUG='-agentlib:jdwp=transport=dt_socket,server=y,suspend=y,address=8010'
-
+    DEBUG="-agentlib:jdwp=transport=dt_socket,server=y,suspend=y,address=$NXF_REMOTE_DEBUG_PORT"
+    args+=("$1")
   else
    args+=("$1")
   fi
diff --git a/modules/nextflow/src/main/groovy/nextflow/Session.groovy b/modules/nextflow/src/main/groovy/nextflow/Session.groovy
index c7df94b8c6..9109d503ea 100644
--- a/modules/nextflow/src/main/groovy/nextflow/Session.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/Session.groovy
@@ -183,6 +183,11 @@ class Session implements ISession {
      */
     boolean quiet
 
+    /**
+     * Enable debugging mode
+     */
+    boolean debug
+
     /**
      * Local path where script generated classes are saved
      */
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CliOptions.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CliOptions.groovy
index c6197b1ea9..4781af73c2 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CliOptions.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CliOptions.groovy
@@ -84,6 +84,9 @@ class CliOptions {
     @Parameter(names = ['-self-update'], description = 'Update nextflow to the latest version', arity = 0, hidden = true)
     boolean selfUpdate
 
+    @Parameter(names=['-remote-debug'], description = "Enable JVM interactive remote debugging (experimental)")
+    boolean remoteDebug
+
     Boolean ansiLog
 
     boolean getAnsiLog() {
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
index 890958f270..67b4fba639 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
@@ -343,6 +343,7 @@ class CmdRun extends CmdBase implements HubOptions {
         runner.session.profile = profile
         runner.session.commandLine = launcher.cliString
         runner.session.ansiLog = launcher.options.ansiLog
+        runner.session.debug = launcher.options.remoteDebug
         runner.session.disableJobsCancellation = getDisableJobsCancellation()
 
         final isTowerEnabled = config.navigate('tower.enabled') as Boolean
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/ScriptParser.groovy b/modules/nextflow/src/main/groovy/nextflow/script/ScriptParser.groovy
index 4feb2446c9..53952e3c3b 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/ScriptParser.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/ScriptParser.groovy
@@ -125,7 +125,10 @@ class ScriptParser {
         config.addCompilationCustomizers( new ASTTransformationCustomizer(NextflowXform))
         config.addCompilationCustomizers( new ASTTransformationCustomizer(OpXform))
 
-        if( session && session.classesDir )
+        if( session?.debug )
+            config.debug = true
+
+        if( session?.classesDir )
             config.setTargetDirectory(session.classesDir.toFile())
 
         return config
@@ -154,7 +157,7 @@ class ScriptParser {
         throw new IllegalArgumentException("Unknown script type: ${script?.getClass()?.getName()}")
     }
 
-    GroovyShell getInterpreter() {
+    private GroovyShell getInterpreter() {
         if( !binding && session )
             binding = session.binding
         if( !binding )
@@ -163,10 +166,13 @@ class ScriptParser {
         return new GroovyShell(classLoader, binding, getConfig())
     }
 
-    ScriptParser parse(String scriptText, GroovyShell interpreter) {
-        final String clazzName = computeClassName(scriptText)
+    private ScriptParser parse0(String scriptText, Path scriptPath, GroovyShell interpreter) {
+        this.scriptPath = scriptPath
+        final String className = computeClassName(scriptText)
         try {
-            final parsed = interpreter.parse(scriptText, clazzName)
+            final parsed = scriptPath && session.debug
+                    ? interpreter.parse(scriptPath.toFile())
+                    : interpreter.parse(scriptText, className)
             if( parsed !instanceof BaseScript ){
                throw new CompilationFailedException(0, null)
             }
@@ -183,7 +189,7 @@ class ScriptParser {
             String msg = e.message ?: header
             msg = msg != 'startup failed' ? msg : header
             msg = msg.replaceAll(/startup failed:\n/,'')
-            msg = msg.replaceAll(~/$clazzName(: \d+:\b*)?/, header+'\n- cause:')
+            msg = msg.replaceAll(~/$className(: \d+:\b*)?/, header+'\n- cause:')
             if( msg.contains "Unexpected input: '{'" ) {
                 msg += "\nNOTE: If this is the beginning of a process or workflow, there may be a syntax error in the body, such as a missing or extra comma, for which a more specific error message could not be produced."
             }
@@ -191,16 +197,13 @@ class ScriptParser {
         }
     }
 
-
     ScriptParser parse(String scriptText) {
-        def interpreter = getInterpreter()
-        return parse(scriptText, interpreter)
+        return parse0(scriptText, null, getInterpreter())
     }
 
     ScriptParser parse(Path scriptPath) {
-        this.scriptPath = scriptPath
         try {
-            parse(scriptPath.text)
+            parse0(scriptPath.text, scriptPath, getInterpreter())
         }
         catch (IOException e) {
             throw new ScriptCompilationException("Unable to read script: '$scriptPath' -- cause: $e.message", e)
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/ScriptRunner.groovy b/modules/nextflow/src/main/groovy/nextflow/script/ScriptRunner.groovy
index 7be978e903..aee864c680 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/ScriptRunner.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/ScriptRunner.groovy
@@ -91,7 +91,7 @@ class ScriptRunner {
         return this
     }
 
-    ScriptRunner setPreview(boolean  value, Closure<Void> action) {
+    ScriptRunner setPreview(boolean value, Closure<Void> action) {
         this.preview = value
         this.previewAction = action
         return this
diff --git a/nextflow b/nextflow
index 496d0f2b86..e296c43fbe 100755
--- a/nextflow
+++ b/nextflow
@@ -24,6 +24,7 @@ NXF_TEMP=${NXF_TEMP:-$TMPDIR}
 NXF_DIST=${NXF_DIST:-$NXF_HOME/framework}
 NXF_CLI="$0 $@"
 NXF_CLI_OPTS=${NXF_CLI_OPTS:-}
+NXF_REMOTE_DEBUG_PORT=${NXF_REMOTE_DEBUG_PORT:-5005}
 
 export NXF_CLI
 export NXF_ORG
@@ -91,7 +92,7 @@ function get_ver() {
     elif command -v wget &>/dev/null; then
         wget "$1" >/dev/null 2>&1
     else
-        echo_red "ERROR: Cannot find 'curl' nor 'wget' utility --  please install one of them"
+        echo_red "ERROR: Cannot find 'curl' nor 'wget' utility -- please install one of them"
         exit 1
     fi
 }
@@ -154,7 +155,7 @@ function check_latest() {
 function launch_nextflow() {
     # the launch command line
     local cmdline=()
-    # remove leading and trailing double-quotes 
+    # remove leading and trailing double-quotes
     for x in "${launcher[@]}"; do
         x="${x%\"}"
         x="${x#\"}"
@@ -212,6 +213,10 @@ while [[ $# != 0 ]]; do
     -bg)
       bg=1
       ;;
+    -remote-debug)
+      echo_yellow "Enabling script debugging - continue the execution launching the remote VM debugger in your favourite IDE using port $NXF_REMOTE_DEBUG_PORT"
+      remote_debug=1
+      ;;
     -download)
       if [[ ! "$cmd" ]]; then
       rm -rf "$NXF_DIST/$NXF_VER" || exit $?
@@ -385,7 +390,7 @@ EOF
 # checked if a cached classpath file exists and it newer that the nextflow boot jar file
 LAUNCH_FILE="${NXF_LAUNCHER}/classpath-$(env_md5)"
 
-if [ -s "$LAUNCH_FILE" ] && [ "$LAUNCH_FILE" -nt "$NXF_BIN" ]; then
+if [ -s "$LAUNCH_FILE" ] && [ "$LAUNCH_FILE" -nt "$NXF_BIN" ] && [[ "$remote_debug" -ne 1 ]]; then
     declare -a launcher="($(cat "$LAUNCH_FILE"))"
 else
     # otherwise run the capsule and get the result classpath in the 'launcher' and save it to a file
@@ -400,8 +405,11 @@ else
     cmd_base=(${BASH_REMATCH[1]})
     cmd_tail=(${BASH_REMATCH[2]})
 
+    launcher="${cmd_base[@]}"
+    [[ "$NXF_JVM_ARGS" ]] && launcher+=($NXF_JVM_ARGS)
+    [[ "$remote_debug" ]] && launcher+=(-agentlib:jdwp=transport=dt_socket,server=y,suspend=y,address=$NXF_REMOTE_DEBUG_PORT)
+
     if [[ "$JAVA_VER" =~ ^(9|10|11|12|13|14|15|16|17|18|19|20) ]]; then
-      launcher="${cmd_base[@]}"
       launcher+=(--add-opens=java.base/java.lang=ALL-UNNAMED)
       launcher+=(--add-opens=java.base/java.io=ALL-UNNAMED)
       launcher+=(--add-opens=java.base/java.nio=ALL-UNNAMED)
@@ -419,14 +427,11 @@ else
       launcher+=(--add-opens=java.base/jdk.internal.misc=ALL-UNNAMED)
       launcher+=(--add-opens=java.base/jdk.internal.vm=ALL-UNNAMED)
       launcher+=(--add-opens=java.base/java.util.regex=ALL-UNNAMED)
-      [[ "$NXF_JVM_ARGS" ]] && launcher+=($NXF_JVM_ARGS)
       if [[ "$NXF_ENABLE_VIRTUAL_THREADS" == 'true' ]]; then
         [[ "$JAVA_VER" =~ ^(19|20) ]] && launcher+=(--enable-preview) || die "Virtual threads requires Java 19 or later - current version $JAVA_VER"
       fi
       launcher+=("${cmd_tail[@]}")
     else
-      launcher="${cmd_base[@]}"
-      [[ "$NXF_JVM_ARGS" ]] && launcher+=($NXF_JVM_ARGS)
       launcher+=("${cmd_tail[@]}")
     fi
 
@@ -434,7 +439,7 @@ else
     if mkdir -p "${NXF_LAUNCHER}" 2>/dev/null; then
         STR=''
         for x in "${launcher[@]}"; do
-        [[ "$x" != "\"-Duser.dir=$PWD\"" ]] && STR+="$x "
+        [[ "$x" != "\"-Duser.dir=$PWD\"" ]] && [[ ! "$x" == *"-agentlib:jdwp"* ]] && STR+="$x "
         done
         printf "$STR">"$LAUNCH_FILE"
     else

From db79e13f8f1e9d0e318d7a2e865ea783754eb1b7 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Mon, 4 Sep 2023 22:11:59 +0200
Subject: [PATCH 125/350] Disable version check on CI tests

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 validation/test.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/validation/test.sh b/validation/test.sh
index c9f34225ad..a8734027aa 100755
--- a/validation/test.sh
+++ b/validation/test.sh
@@ -9,6 +9,7 @@ export NXF_IGNORE_WARN_DSL2=true
 export NXF_CMD=${NXF_CMD:-$(get_abs_filename ../launch.sh)}
 # disable ansi log to make log more readable
 export NXF_ANSI_LOG=false
+export NXF_DISABLE_CHECK_LATEST=true
 
 #
 # Integration tests

From a88a4245dc19f36957d7b38e6071639cc5803db2 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Tue, 5 Sep 2023 09:16:02 -0500
Subject: [PATCH 126/350] Update documentation of NXF_DEBUG (#4187)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 .../main/groovy/nextflow/executor/BashWrapperBuilder.groovy  | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
index c37c21ae01..b70675ac88 100644
--- a/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
@@ -75,9 +75,8 @@ class BashWrapperBuilder {
         /*
          * Env variable `NXF_DEBUG` is used to control debug options in executed BASH scripts
          * - 0: no debug
-         * - 1: dump current environment in the `.command.log` file
-         * - 2: trace the execution of user script adding the `set -x` flag
-         * - 3: trace the execution of wrapper scripts
+         * - 1: dump current environment in the `.command.log` file and trace the execution of user script
+         * - 2: trace the execution of wrapper scripts
          */
         def str = System.getenv('NXF_DEBUG')
         try {

From 2daa4172bb679efedd6ea02234535b2237a41478 Mon Sep 17 00:00:00 2001
From: Robert Syme <rob.syme@gmail.com>
Date: Tue, 5 Sep 2023 15:06:54 -0400
Subject: [PATCH 127/350] Docs improvement to clarify the usage of the bin dir
 (#4121)

Signed-off-by: Rob Syme <rob.syme@gmail.com>
Signed-off-by: Robert Syme <rob.syme@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/sharing.md | 67 ++++++++++++++++++++++++++++++++-----------------
 1 file changed, 44 insertions(+), 23 deletions(-)

diff --git a/docs/sharing.md b/docs/sharing.md
index f1291381cc..a3f8a5b864 100644
--- a/docs/sharing.md
+++ b/docs/sharing.md
@@ -440,11 +440,52 @@ The use of a code management system is important to keep together all the depend
 
 Moreover to guarantee that a pipeline is reproducible it should be self-contained i.e. it should have ideally no dependencies on the hosting environment. By using Nextflow you can achieve this goal following these methods:
 
-### Third party scripts
+### Binary applications
+
+Docker allows you to ship any binary dependencies that you may have in your pipeline to a portable image that is downloaded on-demand and can be executed on any platform where a Docker engine is installed.
+
+In order to use it with Nextflow, create a Docker image containing the tools needed by your pipeline and make it available in the [Docker Hub](https://hub.docker.com).
+
+Then declare in the `nextflow.config` file, that you will include in your project, the name of the Docker image you have created. For example:
+
+```groovy
+process.container = 'my-docker-image'
+docker.enabled = true
+```
+
+In this way when you launch the pipeline execution, the Docker image will be automatically downloaded and used to run your tasks.
+
+Read the {ref}`container-page` page to learn more on how to use containers with Nextflow.
+
+This mix of technologies makes it possible to write self-contained and truly reproducible pipelines which require zero configuration and can be reproduced in any system having a Java VM and a Docker engine installed.
+
+[^id2]: BitBucket provides two types of version control system: Git and Mercurial. Nextflow supports only Git repositories.
+
+### Bundling executables in the workflow
+
+In most cases, software dependencies should be provided by the execution environment ([container](./container.md), [conda](./conda.md)/[spack](./spack.md) environment, or host-native [modules](./process.md#module)). 
+
+In cases where you do not wish to modify the execution environment(s), executable scripts can be included in the `bin/` directory in the workflow repository root. This can be useful to make changes that affect task execution across all environments with a single change.
+
+To ensure your scripts can be made available to the task:
+
+1. Write scripts in the `bin/` directory (relative to the project repository root)
+2. Specify a portable shebang (see note below for details).
+3. Ensure the scripts are executable. For example: `chmod a+x bin/my_script.py`
+
+:::{tip}
+To maximize portability of your bundled script, it is recommended to avoid hard-coding the interpreter path in the shebang line. 
 
-Any third party script that does not need to be compiled (Bash, Python, Perl, etc) can be included in the pipeline project repository, so that they are distributed with it.
+For example, shebang definitions `#!/usr/bin/python` and `#!/usr/local/bin/python` both hard-code specific paths to the python interpreter. To improve portability, rely on `env` to dynamically resolve the path to the interpreter. An example of the recommended approach is:
 
-Grant the execute permission to these files and copy them into a folder named `bin/` in the root directory of your project repository. Nextflow will automatically add this folder to the `PATH` environment variable, and the scripts will automatically be accessible in your pipeline without the need to specify an absolute path to invoke them.
+```bash
+#!/usr/bin/env python
+```
+:::
+
+### Using bundled executables in the workflow 
+
+Nextflow will automatically add the `bin/` directory to the `PATH` environment variable, and the scripts will automatically be accessible in your pipeline without the need to specify an absolute path to invoke them.
 
 ### System environment
 
@@ -495,23 +536,3 @@ The actual parameter values can be provided when launching the script execution
 nextflow run <your pipeline> --my_input /path/to/input/file --my_output /other/path --my_flag true
 ```
 
-### Binary applications
-
-Docker allows you to ship any binary dependencies that you may have in your pipeline to a portable image that is downloaded on-demand and can be executed on any platform where a Docker engine is installed.
-
-In order to use it with Nextflow, create a Docker image containing the tools needed by your pipeline and make it available in the [Docker registry](https://registry.hub.docker.com).
-
-Then declare in the `nextflow.config` file, that you will include in your project, the name of the Docker image you have created. For example:
-
-```groovy
-process.container = 'my-docker-image'
-docker.enabled = true
-```
-
-In this way when you launch the pipeline execution, the Docker image will be automatically downloaded and used to run your tasks.
-
-Read the {ref}`container-page` page to learn more on how to use containers with Nextflow.
-
-This mix of technologies makes it possible to write self-contained and truly reproducible pipelines which require zero configuration and can be reproduced in any system having a Java VM and a Docker engine installed.
-
-[^id2]: BitBucket provides two types of version control system: Git and Mercurial. Nextflow supports only Git repositories.

From fce9702e39f8dcf3641e4caa4dc1eb4ea6bb1149 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Tue, 5 Sep 2023 14:41:03 -0500
Subject: [PATCH 128/350] Report an error on duplicate workflow name
 definitions (#4088)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 .../groovy/nextflow/script/ScriptMeta.groovy  | 17 ++----
 .../nextflow/script/ScriptIncludesTest.groovy | 32 +----------
 .../nextflow/script/ScriptMetaTest.groovy     | 57 +++++++++++++++++++
 3 files changed, 66 insertions(+), 40 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/script/ScriptMeta.groovy b/modules/nextflow/src/main/groovy/nextflow/script/ScriptMeta.groovy
index ffecebc534..726253eafe 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/ScriptMeta.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/ScriptMeta.groovy
@@ -150,20 +150,15 @@ class ScriptMeta {
     }
 
     void checkComponentName(ComponentDef component, String name) {
-        if( component !instanceof ProcessDef && component !instanceof FunctionDef ) {
+        if( component !instanceof WorkflowDef && component !instanceof ProcessDef && component !instanceof FunctionDef ) {
             return
         }
-        if (functionsCount.get(name)) {
-            final msg = "A function with name '$name' is defined more than once in module script: $scriptPath -- Make sure to not define the same function as process"
-            if (NF.isStrictMode())
-                throw new DuplicateModuleFunctionException(msg)
-            log.warn(msg)
+        if( functionsCount.get(name) ) {
+            throw new DuplicateModuleFunctionException("A function named '$name' is already defined or included in script: $scriptPath")
         }
-        if (imports.get(name)) {
-            final msg = "A process with name '$name' is defined more than once in module script: $scriptPath -- Make sure to not define the same function as process"
-            if (NF.isStrictMode())
-                throw new DuplicateModuleFunctionException(msg)
-            log.warn(msg)
+        final existing = imports.get(name)
+        if( existing != null ) {
+            throw new DuplicateModuleFunctionException("A ${existing.type} named '$name' is already defined or included in script: $scriptPath")
         }
     }
 
diff --git a/modules/nextflow/src/test/groovy/nextflow/script/ScriptIncludesTest.groovy b/modules/nextflow/src/test/groovy/nextflow/script/ScriptIncludesTest.groovy
index d17af77534..d9e15c5099 100644
--- a/modules/nextflow/src/test/groovy/nextflow/script/ScriptIncludesTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/script/ScriptIncludesTest.groovy
@@ -148,7 +148,7 @@ class ScriptIncludesTest extends Dsl2Spec {
         result.val == 'dlrow olleh'
     }
 
-    def 'should allows duplicate functions' () {
+    def 'should allow duplicate functions' () {
         given:
         NextflowMeta.instance.strictMode(true)
         and:
@@ -184,7 +184,7 @@ class ScriptIncludesTest extends Dsl2Spec {
         NextflowMeta.instance.strictMode(false)
     }
 
-    def 'should allows multiple signatures of function' () {
+    def 'should allow multiple signatures of function' () {
         given:
         NextflowMeta.instance.strictMode(true)
         and:
@@ -221,7 +221,7 @@ class ScriptIncludesTest extends Dsl2Spec {
         NextflowMeta.instance.strictMode(false)
     }
 
-    def 'should fails if no signatures of function founded' () {
+    def 'should fail if no signatures of function founded' () {
         given:
         NextflowMeta.instance.strictMode(true)
         and:
@@ -773,32 +773,6 @@ class ScriptIncludesTest extends Dsl2Spec {
         noExceptionThrown()
     }
 
-    def 'should allows duplicate import' () {
-        given:
-        def folder = TestHelper.createInMemTempDir();
-        def MOD1 = folder.resolve('mod1.nf')
-        def MOD2 = folder.resolve('mod2.nf')
-        def SCRIPT = folder.resolve('main.nf')
-
-        MOD1.text = MOD2.text = '''     
-        process foo {
-            /hello/ 
-        }      
-        '''
-
-        SCRIPT.text = """ 
-        include { foo } from './mod1' 
-        include { foo } from './mod2' 
-        println 'x'
-        """
-
-        when:
-        def runner = new MockScriptRunner()
-        runner.setScript(SCRIPT).execute()
-        then:
-        noExceptionThrown()
-    }
-
     def 'should include only named component' () {
         given:
         def folder = Files.createTempDirectory('test')
diff --git a/modules/nextflow/src/test/groovy/nextflow/script/ScriptMetaTest.groovy b/modules/nextflow/src/test/groovy/nextflow/script/ScriptMetaTest.groovy
index fac10444f1..caf41312f2 100644
--- a/modules/nextflow/src/test/groovy/nextflow/script/ScriptMetaTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/script/ScriptMetaTest.groovy
@@ -1,9 +1,26 @@
+/*
+ * Copyright 2013-2023, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
 package nextflow.script
 
 import java.nio.file.Files
 
 import groovy.transform.InheritConstructors
 import nextflow.NF
+import nextflow.exception.DuplicateModuleFunctionException
 import test.Dsl2Spec
 import test.TestHelper
 
@@ -177,4 +194,44 @@ class ScriptMetaTest extends Dsl2Spec {
         bundle.getEntries() == ['foo.txt', 'bar.txt'] as Set
 
     }
+
+    def 'should throw duplicate name exception' () {
+
+        given:
+        def script1 = new FooScript(new ScriptBinding())
+        def script2 = new FooScript(new ScriptBinding())
+        def meta1 = new ScriptMeta(script1)
+        def meta2 = new ScriptMeta(script2)
+
+        // import module into main script
+        def func2 = new FunctionDef(name: 'func1', alias: 'func1')
+        def proc2 = new ProcessDef(script2, Mock(Closure), 'proc1')
+        def work2 = new WorkflowDef(name: 'work1')
+        meta2.addDefinition(proc2, func2, work2)
+
+        meta1.addModule(meta2, null, null)
+
+        // attempt to define duplicate components in main script
+        def func1 = new FunctionDef(name: 'func1', alias: 'func1')
+        def proc1 = new ProcessDef(script1, Mock(Closure), 'proc1')
+        def work1 = new WorkflowDef(name: 'work1')
+
+        when:
+        meta1.addDefinition(func1)
+        then:
+        def e = thrown(DuplicateModuleFunctionException)
+        e.message.contains "A function named 'func1' is already defined"
+
+        when:
+        meta1.addDefinition(proc1)
+        then:
+        e = thrown(DuplicateModuleFunctionException)
+        e.message.contains "A process named 'proc1' is already defined"
+
+        when:
+        meta1.addDefinition(work1)
+        then:
+        e = thrown(DuplicateModuleFunctionException)
+        e.message.contains "A workflow named 'work1' is already defined"
+    }
 }

From 2785ffe917be9954ec3e5352659765737f4a8022 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Tue, 5 Sep 2023 22:41:12 +0200
Subject: [PATCH 129/350] Fix failing test

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../src/test/groovy/nextflow/script/ScriptMetaTest.groovy     | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/modules/nextflow/src/test/groovy/nextflow/script/ScriptMetaTest.groovy b/modules/nextflow/src/test/groovy/nextflow/script/ScriptMetaTest.groovy
index caf41312f2..d94be89795 100644
--- a/modules/nextflow/src/test/groovy/nextflow/script/ScriptMetaTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/script/ScriptMetaTest.groovy
@@ -209,7 +209,9 @@ class ScriptMetaTest extends Dsl2Spec {
         def work2 = new WorkflowDef(name: 'work1')
         meta2.addDefinition(proc2, func2, work2)
 
-        meta1.addModule(meta2, null, null)
+        meta1.addModule(meta2, 'func1', null)
+        meta1.addModule(meta2, 'proc1', null)
+        meta1.addModule(meta2, 'work1', null)
 
         // attempt to define duplicate components in main script
         def func1 = new FunctionDef(name: 'func1', alias: 'func1')

From c3aa26e1770fc0aff1a96a6b473569d7e6f6b84f Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Thu, 7 Sep 2023 04:15:17 -0500
Subject: [PATCH 130/350] Improve pod options documentation (#4274)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 docs/process.md | 149 ++++++++++++++++++++++++++++++++----------------
 1 file changed, 101 insertions(+), 48 deletions(-)

diff --git a/docs/process.md b/docs/process.md
index 4cd585ab94..a1496033d2 100644
--- a/docs/process.md
+++ b/docs/process.md
@@ -1859,7 +1859,7 @@ See also: [cpus](#cpus), [memory](#memory), [time](#time)
 
 ### pod
 
-The `pod` directive allows the definition of pods specific settings, such as environment variables, secrets and config maps when using the {ref}`k8s-executor` executor.
+The `pod` directive allows the definition of pod specific settings, such as environment variables, secrets, and config maps, when using the {ref}`k8s-executor` executor.
 
 For example:
 
@@ -1873,9 +1873,9 @@ process your_task {
 }
 ```
 
-The above snippet defines an environment variable named `FOO` which value is `bar`.
+The above snippet defines an environment variable named `FOO` whose value is `bar`.
 
-When defined in the Nextflow configuration file, a pod setting can be defined using the canonical associative array syntax. For example:
+When defined in the Nextflow configuration file, pod settings should be defined as maps. For example:
 
 ```groovy
 process {
@@ -1883,106 +1883,159 @@ process {
 }
 ```
 
-When more than one setting needs to be provides they must be enclosed in a list definition as shown below:
+Multiple pod settings can be provided as a list of maps:
 
 ```groovy
 process {
-  pod = [ [env: 'FOO', value: 'bar'], [secret: 'my-secret/key1', mountPath: '/etc/file.txt'] ]
+  pod = [
+      [env: 'FOO', value: 'bar'],
+      [secret: 'my-secret/key1', mountPath: '/etc/file.txt']
+  ]
 }
 ```
 
-The `pod` directive supports the following options:
+The following options are available:
 
-`affinity: <V>`
+`affinity: <config>`
 : :::{versionadded} 22.01.0-edge
   :::
-: Specifies affinity for which nodes the process should run on. See [Kubernetes affinity](https://kubernetes.io/docs/concepts/scheduling-eviction/assign-pod-node/#affinity-and-anti-affinity) for details.
+: Specifies the pod [affinity](https://kubernetes.io/docs/concepts/scheduling-eviction/assign-pod-node/#affinity-and-anti-affinity) with the given configuration.
 
-`annotation: <K>, value: <V>`
+`annotation: '<name>', value: '<value>'`
 : *Can be specified multiple times*
-: Defines a pod annotation with key `K` and value `V`.
+: Defines a pod [annotation](https://kubernetes.io/docs/concepts/overview/working-with-objects/annotations/) with the given name and value.
 
-`automountServiceAccountToken: <V>`
+`automountServiceAccountToken: true | false`
 : :::{versionadded} 22.01.0-edge
   :::
-: Specifies whether to [automount service account token](https://kubernetes.io/docs/tasks/configure-pod-container/configure-service-account/) into process pods. If `V` is true, service account token is automounted into task pods (default).
+: Specifies whether to [automount service account token](https://kubernetes.io/docs/tasks/configure-pod-container/configure-service-account/#opt-out-of-api-credential-automounting) into the pod (default: `true`).
 
-`config: <C/K>, mountPath: </absolute/path>`
+`config: '<configMap>/<key>', mountPath: '</absolute/path>'`
 : *Can be specified multiple times*
-: Mounts a [ConfigMap](https://kubernetes.io/docs/tasks/configure-pod-container/configure-pod-configmap/) with name `C` with key `K` to the path `/absolute/path`. When the key component is omitted the path is interpreted as a directory and all the `ConfigMap` entries are exposed in that path.
+: Mounts a [ConfigMap](https://kubernetes.io/docs/tasks/configure-pod-container/configure-pod-configmap/) with name and optional key to the given path. If the key is omitted, the path is interpreted as a directory and all entries in the `ConfigMap` are exposed in that path.
 
-`csi: <V>, mountPath: </absolute/path>`
+`csi: '<name>', mountPath: '</absolute/path>'`
 : :::{versionadded} 22.11.0-edge
   :::
 : *Can be specified multiple times*
-: Mounts a [CSI ephemeral volume](https://kubernetes.io/docs/concepts/storage/ephemeral-volumes/#csi-ephemeral-volumes) with config `V`to the path `/absolute/path`.
+: Mounts a [CSI ephemeral volume](https://kubernetes.io/docs/concepts/storage/ephemeral-volumes/#csi-ephemeral-volumes) by name to the given path.
 
-`emptyDir: <V>, mountPath: </absolute/path>`
+`emptyDir: <config>, mountPath: '</absolute/path>'`
 : :::{versionadded} 22.11.0-edge
   :::
 : *Can be specified multiple times*
-: Mounts an [emptyDir](https://kubernetes.io/docs/concepts/storage/volumes/#emptydir) with configuration `V` to the path `/absolute/path`.
+: Mounts an [emptyDir](https://kubernetes.io/docs/concepts/storage/volumes/#emptydir) with the given configuration to the given path.
 
-`env: <E>, config: <C/K>`
+`env: '<name>', config: '<configMap>/<key>'`
 : *Can be specified multiple times*
-: Defines an environment variable with name `E` and whose value is given by the entry associated to the key with name `K` in the [ConfigMap](https://kubernetes.io/docs/tasks/configure-pod-container/configure-pod-configmap/) with name `C`.
+: Defines an environment variable whose value is defined by the given [ConfigMap](https://kubernetes.io/docs/tasks/configure-pod-container/configure-pod-configmap/) and key.
 
-`env: <E>, fieldPath: <V>`
+`env: '<name>', fieldPath: '<fieldPath>'`
 : :::{versionadded} 21.09.1-edge
   :::
 : *Can be specified multiple times*
-: Defines an environment variable with name `E` and whose value is given by the `V` [field path](https://kubernetes.io/docs/tasks/inject-data-application/environment-variable-expose-pod-information/).
+: Defines an environment variable whose value is defined by the given [field path](https://kubernetes.io/docs/tasks/inject-data-application/environment-variable-expose-pod-information/#use-pod-fields-as-values-for-environment-variables) value.
 
-`env: <E>, secret: <S/K>`
+: For example, the following pod option:
+
+  ```groovy
+  pod = [env: 'MY_NODE_NAME', fieldPath: 'spec.nodeName']
+  ```
+
+  Maps to the following pod spec:
+
+  ```yaml
+  env:
+    - name: MY_NODE_NAME
+      valueFrom:
+        fieldRef:
+          fieldPath: spec.nodeName
+  ```
+
+`env: '<name>', secret: '<secret>/<key>'`
 : *Can be specified multiple times*
-: Defines an environment variable with name `E` and whose value is given by the entry associated to the key with name `K` in the [Secret](https://kubernetes.io/docs/concepts/configuration/secret/) with name `S`.
+: Defines an environment variable whose value is defined by the given [Secret](https://kubernetes.io/docs/concepts/configuration/secret/) and key.
 
-`env: <E>, value: <V>`
+`env: '<name>', value: '<value>'`
 : *Can be specified multiple times*
-: Defines an environment variable with name `E` and whose value is given by the `V` string.
+: Defines an environment variable with the given name and value.
 
-`imagePullPolicy: <V>`
-: Specifies the strategy to be used to pull the container image e.g. `imagePullPolicy: 'Always'`.
+`imagePullPolicy: 'IfNotPresent' | 'Always' | 'Never'`
+: Specifies the [image pull policy](https://kubernetes.io/docs/concepts/containers/images/#image-pull-policy) used by the pod to pull the container image.
 
-`imagePullSecret: <V>`
-: Specifies the secret name to access a private container image registry. See [Kubernetes documentation](https://kubernetes.io/docs/concepts/containers/images/#specifying-imagepullsecrets-on-a-pod) for details.
+`imagePullSecret: '<name>'`
+: Specifies the [image pull secret](https://kubernetes.io/docs/concepts/containers/images/#specifying-imagepullsecrets-on-a-pod) used to access a private container image registry.
 
-`label: <K>, value: <V>`
+`label: '<name>', value: '<value>'`
 : *Can be specified multiple times*
-: Defines a pod label with key `K` and value `V`.
+: Defines a pod [label](https://kubernetes.io/docs/concepts/overview/working-with-objects/labels/) with the given name and value.
 
-`nodeSelector: <V>`
-: Specifies which node the process will run on. See [Kubernetes nodeSelector](https://kubernetes.io/docs/concepts/scheduling-eviction/assign-pod-node/#nodeselector) for details.
+`nodeSelector: <config>`
+: Specifies the [node selector](https://kubernetes.io/docs/concepts/scheduling-eviction/assign-pod-node/#nodeselector) with the given configuration.
 
-`priorityClassName: <V>`
+: The configuration can be a map or a string:
+
+  ```groovy
+  // map
+  pod = [nodeSelector: [disktype: 'ssd', cpu: 'intel']]
+
+  // string
+  pod = [nodeSelector: 'disktype=ssd,cpu=intel']
+  ```
+
+`priorityClassName: '<name>'`
 : :::{versionadded} 22.01.0-edge
   :::
 : Specifies the [priority class name](https://kubernetes.io/docs/concepts/scheduling-eviction/pod-priority-preemption/) for pods.
 
-`privileged: <B>`
+`privileged: true | false`
 : :::{versionadded} 22.05.0-edge
   :::
-: Whether the process task should run as a *privileged* container (default: `false`)
+: Specifies whether the pod should run as a *privileged* container (default: `false`).
 
-`runAsUser: <UID>`
-: Specifies the user ID to be used to run the container. Shortcut for the `securityContext` option.
+`runAsUser: '<uid>'`
+: Specifies the user ID with which to run the container. Shortcut for the `securityContext` option.
 
-`secret: <S/K>, mountPath: </absolute/path>`
+`secret: '<secret>/<key>', mountPath: '</absolute/path>'`
 : *Can be specified multiple times*
-: Mounts a [Secret](https://kubernetes.io/docs/concepts/configuration/secret/) with name `S` with key `K` to the path `/absolute/path`. When the key component is omitted the path is interpreted as a directory and all the `Secret` entries are exposed in that path.
+: Mounts a [Secret](https://kubernetes.io/docs/concepts/configuration/secret/) with name and optional key to the given path. If the key is omitted, the path is interpreted as a directory and all entries in the `Secret` are exposed in that path.
 
-`securityContext: <V>`
-: Specifies the pod security context. See [Kubernetes security context](https://kubernetes.io/docs/tasks/configure-pod-container/security-context/) for details.
+`securityContext: <config>`
+: Specifies the pod [security context](https://kubernetes.io/docs/tasks/configure-pod-container/security-context/) with the given configuration.
 
-`toleration: <V>`
+`toleration: <config>`
 : :::{versionadded} 22.04.0
   :::
 : *Can be specified multiple times*
-: Specifies a toleration for a node taint. See [Taints and Tolerations](https://kubernetes.io/docs/concepts/scheduling-eviction/taint-and-toleration/) for details.
-
-`volumeClaim: <V>, mountPath: </absolute/path>`
+: Specifies the pod [toleration](https://kubernetes.io/docs/concepts/scheduling-eviction/taint-and-toleration/) with the given configuration.
+
+: The configuration should be a map corresponding to a single toleration rule. For example, the following pod options:
+
+  ```groovy
+  pod = [
+      [toleration: [key: 'key1', operator: 'Equal', value: 'value1', effect: 'NoSchedule']],
+      [toleration: [key: 'key1', operator: 'Exists', effect: 'NoSchedule']],
+  ]
+  ```
+
+  Maps to the following pod spec:
+
+  ```yaml
+  tolerations:
+    - key: "key1"
+      operator: "Equal"
+      value: "value1"
+      effect: "NoSchedule"
+    - key: "key1"
+      operator: "Exists"
+      effect: "NoSchedule"
+  ```
+
+`volumeClaim: '<name>', mountPath: '</absolute/path>' [, subPath: '<path>', readOnly: true | false]`
 : *Can be specified multiple times*
-: Mounts a [Persistent volume claim](https://kubernetes.io/docs/concepts/storage/persistent-volumes/) with name `V` to the specified path location. Use the optional `subPath` parameter to mount a directory inside the referenced volume instead of its root. The volume may be mounted with `readOnly: true`, but is read/write by default.
+: Mounts a [Persistent volume claim](https://kubernetes.io/docs/concepts/storage/persistent-volumes/) with the given name to the given path.
+: The `subPath` option can be used to mount a sub-directory of the volume instead of its root.
+: The `readOnly` option can be used to mount the volume as read-only (default: `false`)
 
 (process-publishdir)=
 

From 62686ce86a8d8f24706fbd57b435e91ab4288891 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Thu, 7 Sep 2023 10:27:30 -0500
Subject: [PATCH 131/350] Always emit publish event for cached task outputs
 (#4227)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 .../src/main/groovy/nextflow/processor/PublishDir.groovy | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/PublishDir.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/PublishDir.groovy
index e6f6b64223..8013f97fea 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/PublishDir.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/PublishDir.groovy
@@ -378,11 +378,10 @@ class PublishDir {
             if( checkSourcePathConflicts(destination))
                 return
             
-            if( !overwrite )
-                return
-
-            FileHelper.deletePath(destination)
-            processFileImpl(source, destination)
+            if( overwrite ) {
+                FileHelper.deletePath(destination)
+                processFileImpl(source, destination)
+            }
         }
 
         notifyFilePublish(destination, source)

From 23c4ec1d551cc55d5c35a70015aa137cfa7d5a56 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Thu, 7 Sep 2023 21:11:10 +0200
Subject: [PATCH 132/350] Add support for Spack to Singularity builds

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-wave/build.gradle                  |  2 +-
 .../io/seqera/wave/plugin/WaveClient.groovy   |  9 +-
 .../seqera/wave/plugin/WaveClientTest.groovy  | 89 +++++++++++++++++++
 3 files changed, 95 insertions(+), 5 deletions(-)

diff --git a/plugins/nf-wave/build.gradle b/plugins/nf-wave/build.gradle
index ce15723239..28f5b904da 100644
--- a/plugins/nf-wave/build.gradle
+++ b/plugins/nf-wave/build.gradle
@@ -36,7 +36,7 @@ dependencies {
     api 'org.apache.commons:commons-lang3:3.12.0'
     api 'com.google.code.gson:gson:2.10.1'
     api 'org.yaml:snakeyaml:2.0'
-    api 'io.seqera:wave-utils:0.7.2'
+    api 'io.seqera:wave-utils:0.7.4'
 
     testImplementation(testFixtures(project(":nextflow")))
     testImplementation "org.codehaus.groovy:groovy:3.0.19"
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
index f979da6d9f..1e02a5f9eb 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
@@ -449,8 +449,6 @@ class WaveClient {
          */
         Path spackFile = null
         if( attrs.spack ) {
-            if( singularity )
-                throw new IllegalArgumentException("Wave containers do not support (yet) the resolution of Spack package with Singularity")
             if( containerScript )
                 throw new IllegalArgumentException("Unexpected spack and dockerfile conflict while resolving wave container")
 
@@ -462,7 +460,10 @@ class WaveClient {
                 // create a minimal spack file with package spec from user input
                 spackFile = spackPackagesToSpackFile(attrs.spack, config.spackOpts())
             }
-            containerScript = spackFileToDockerFile(config.spackOpts())
+            // create the container file to build the container
+            containerScript = singularity
+                    ? spackFileToSingularityFile(config.spackOpts())
+                    : spackFileToDockerFile(config.spackOpts())
         }
 
         /*
@@ -571,7 +572,7 @@ class WaveClient {
     protected boolean isSpackFile(String value) {
         if( value.contains('\n') )
             return false
-        return value.endsWith('.yaml')
+        return value.endsWith('.yaml') || value.endsWith('.yml')
     }
 
     protected boolean refreshJwtToken0(String refresh) {
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
index 5dcb1dce33..62468f8ad7 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
@@ -807,6 +807,95 @@ class WaveClientTest extends Specification {
         folder?.deleteDir()
     }
 
+    def 'should create assets with spack recipe for singularity' () {
+        given:
+        def session = Mock(Session) { getConfig() >> [wave:[build:[spack:[commands: ['cmd-foo','cmd-bar']]]]]}
+        and:
+        def task = Mock(TaskRun) {getConfig() >> [spack:"rseqc@3.0.1 'rbase@3.5'", arch:"amd64"] }
+        and:
+        def client = new WaveClient(session)
+
+        when:
+        def assets = client.resolveAssets(task, null, true)
+        then:
+        assets.containerFile == '''\
+                Bootstrap: docker
+                From: {{spack_runner_image}}
+                stage: final
+                 
+                %files from build
+                    /opt/spack-env /opt/spack-env
+                    /opt/software /opt/software
+                    /opt/._view /opt/._view
+                    /opt/spack-env/z10_spack_environment.sh /.singularity.d/env/91-environment.sh
+                 
+                %post
+                    cmd-foo
+                    cmd-bar
+                '''.stripIndent()
+
+        and:
+        !assets.moduleResources
+        !assets.containerImage
+        !assets.containerConfig
+        !assets.condaFile
+        !assets.projectResources
+        and:
+        assets.spackFile.text == '''\
+                spack:
+                  specs: [rseqc@3.0.1, rbase@3.5]
+                  concretizer: {unify: true, reuse: false}
+                '''.stripIndent(true)
+    }
+
+    def 'should create asset with spack file for singularity' () {
+        given:
+        def folder = Files.createTempDirectory('test')
+        def spackFile = folder.resolve('spack.yml');
+        spackFile.text = '''\
+                spack:
+                  specs: [rseqc@3.0.1, rbase@3.5]
+                  concretizer: {unify: true, reuse: false}
+                '''.stripIndent(true)
+        and:
+        def session = Mock(Session) { getConfig() >> [wave:[build:[spack:[basePackages: 'nano@1.2.3']]]]}
+        def task = Mock(TaskRun) {getConfig() >> [spack:spackFile.toString()] }
+        and:
+        def client = new WaveClient(session)
+
+        when:
+        def assets = client.resolveAssets(task, null, true)
+        then:
+        assets.containerFile == '''\
+                    Bootstrap: docker
+                    From: {{spack_runner_image}}
+                    stage: final
+                     
+                    %files from build
+                        /opt/spack-env /opt/spack-env
+                        /opt/software /opt/software
+                        /opt/._view /opt/._view
+                        /opt/spack-env/z10_spack_environment.sh /.singularity.d/env/91-environment.sh
+                     
+                    %post
+                    '''.stripIndent()
+        and:
+        !assets.moduleResources
+        !assets.containerImage
+        !assets.containerConfig
+        !assets.projectResources
+        !assets.condaFile
+        and:
+        assets.spackFile.text == '''\
+                spack:
+                  specs: [rseqc@3.0.1, rbase@3.5, nano@1.2.3]
+                  concretizer: {unify: true, reuse: false}
+                '''.stripIndent(true)
+
+        cleanup:
+        folder?.deleteDir()
+    }
+
     def 'should create assets with project resources' () {
         given:
         def MODULE_RES = Mock(ResourcesBundle)

From c056a74ec08542f5d232de74f00ec844ae29e4a6 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 9 Sep 2023 08:54:40 +0200
Subject: [PATCH 133/350] Add scripts logging for troubleshooting

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../groovy/nextflow/script/ScriptRunner.groovy | 18 +++++++++++++++---
 1 file changed, 15 insertions(+), 3 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/script/ScriptRunner.groovy b/modules/nextflow/src/main/groovy/nextflow/script/ScriptRunner.groovy
index aee864c680..ea9bae557f 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/ScriptRunner.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/ScriptRunner.groovy
@@ -131,9 +131,14 @@ class ScriptRunner {
         session.start()
         try {
             // parse the script
-            parseScript(scriptFile, entryName)
-            // run the code
-            run()
+            try {
+                parseScript(scriptFile, entryName)
+                // run the code
+                run()
+            }
+            finally {
+                log.debug "Parsed script files:${scriptFiles0()}"
+            }
             // await completion
             await()
             // shutdown session
@@ -151,6 +156,13 @@ class ScriptRunner {
         return result
     }
 
+    protected String scriptFiles0() {
+        def result = ''
+        for( Map.Entry<String,Path> it : ScriptMeta.allScriptNames() )
+            result += "\n  ${it.key}: ${it.value.toUriString()}"
+        return result
+    }
+
     /**
      * Test the name specified by the {@code methodName}
      *

From bb96763f454d806c49411745c9fab5f1a482937c Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 9 Sep 2023 08:55:55 +0200
Subject: [PATCH 134/350] Use sipHash24 in place of deprecated murmur32 for
 script aliasing

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../groovy/nextflow/script/ScriptParser.groovy   |  2 +-
 .../groovy/nextflow/util/LoggerHelper.groovy     |  2 +-
 .../nextflow/script/ScriptParserTest.groovy      |  2 +-
 .../nextflow/script/ScriptRunnerTest.groovy      |  1 +
 .../groovy/nextflow/util/LoggerHelperTest.groovy | 16 ++++++++--------
 5 files changed, 12 insertions(+), 11 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/script/ScriptParser.groovy b/modules/nextflow/src/main/groovy/nextflow/script/ScriptParser.groovy
index 53952e3c3b..e491124003 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/ScriptParser.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/ScriptParser.groovy
@@ -147,7 +147,7 @@ class ScriptParser {
 
         if( script instanceof CharSequence ) {
             final hash = Hashing
-                    .murmur3_32()
+                    .sipHash24()
                     .newHasher()
                     .putUnencodedChars(script.toString())
                     .hash()
diff --git a/modules/nextflow/src/main/groovy/nextflow/util/LoggerHelper.groovy b/modules/nextflow/src/main/groovy/nextflow/util/LoggerHelper.groovy
index 1e657d6952..33e28bc473 100644
--- a/modules/nextflow/src/main/groovy/nextflow/util/LoggerHelper.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/util/LoggerHelper.groovy
@@ -597,7 +597,7 @@ class LoggerHelper {
         }
     }
 
-    static private Pattern ERR_LINE_REGEX = ~/\((Script_[0-9a-f]{8}):(\d*)\)$/
+    static private Pattern ERR_LINE_REGEX = ~/\((Script_[0-9a-f]{16}):(\d*)\)$/
 
     @PackageScope
     static List<String> getErrorLine( String str, Map<String,Path> allNames ) {
diff --git a/modules/nextflow/src/test/groovy/nextflow/script/ScriptParserTest.groovy b/modules/nextflow/src/test/groovy/nextflow/script/ScriptParserTest.groovy
index ab0ccf6a89..8235beb80a 100644
--- a/modules/nextflow/src/test/groovy/nextflow/script/ScriptParserTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/script/ScriptParserTest.groovy
@@ -106,7 +106,7 @@ class ScriptParserTest extends Specification {
         when:
         def result = parser.computeClassName('process foo { etc } ')
         then:
-        result == 'Script_01af1441'
+        result == 'Script_dd540db41b3a8b2a'
     }
 
     def 'should set classpath' () {
diff --git a/modules/nextflow/src/test/groovy/nextflow/script/ScriptRunnerTest.groovy b/modules/nextflow/src/test/groovy/nextflow/script/ScriptRunnerTest.groovy
index 726682fa7c..c2554ff4bf 100644
--- a/modules/nextflow/src/test/groovy/nextflow/script/ScriptRunnerTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/script/ScriptRunnerTest.groovy
@@ -248,6 +248,7 @@ class ScriptRunnerTest extends Dsl2Spec {
         runner.session.fault.error instanceof ProcessUnrecoverableException
         runner.session.fault.error.cause instanceof MissingPropertyException
         runner.session.fault.error.cause.message =~ /Unknown variable 'HELLO' -- .*/
+        // if this fails, likely there's something wrong in the LoggerHelper#getErrorLine method
         runner.session.fault.report =~ /No such variable: HELLO -- .*/
 
     }
diff --git a/modules/nextflow/src/test/groovy/nextflow/util/LoggerHelperTest.groovy b/modules/nextflow/src/test/groovy/nextflow/util/LoggerHelperTest.groovy
index 79d438e6ff..8b4a7169db 100644
--- a/modules/nextflow/src/test/groovy/nextflow/util/LoggerHelperTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/util/LoggerHelperTest.groovy
@@ -41,9 +41,9 @@ class LoggerHelperTest extends Specification {
         given:
         final pwd = System.getProperty("user.dir")
         Map<String,Path> names = [
-                'Script_f1bbc0ef': Paths.get('/some/path/main.nf'),
-                'Script_1b751fe9': Paths.get('/other/path/module.nf'),
-                'Script_12345678': Paths.get("$pwd/foo/script.nf")
+                'Script_f1bbc0eff1bbc0ef': Paths.get('/some/path/main.nf'),
+                'Script_1b751fe91b751fe9': Paths.get('/other/path/module.nf'),
+                'Script_1234567812345678': Paths.get("$pwd/foo/script.nf")
         ]
 
         expect:
@@ -53,11 +53,11 @@ class LoggerHelperTest extends Specification {
         EXPECTED                        | LINE
         null                            | 'at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:289)'
         null                            | 'at nextflow.script.BaseScript.run(BaseScript.groovy:151)'
-        ['/some/path/main.nf', '63']    | 'at Script_f1bbc0ef.runScript(Script_f1bbc0ef:63)'
-        null                            | 'at Script_1b751fe9$_runScript_closure1.doCall(Script_1b751fe9)'
-        ['/other/path/module.nf', '10'] | 'at Script_1b751fe9$_runScript_closure1.doCall(Script_1b751fe9:10)'
-        ['foo/script.nf', '55']         | 'at Script_12345678.runScript(Script_12345678:55)'
-        null                            | 'at Script_12345678.runScript(Script_xxxxxxxx:63)'
+        ['/some/path/main.nf', '63']    | 'at Script_f1bbc0ef.runScript(Script_f1bbc0eff1bbc0ef:63)'
+        null                            | 'at Script_1b751fe9$_runScript_closure1.doCall(Script_1b751fe91b751fe9)'
+        ['/other/path/module.nf', '10'] | 'at Script_1b751fe9$_runScript_closure1.doCall(Script_1b751fe91b751fe9:10)'
+        ['foo/script.nf', '55']         | 'at Script_12345678.runScript(Script_1234567812345678:55)'
+        null                            | 'at Script_12345678.runScript(Script_xxxxxxxxxxxxxxxx:63)'
     }
 
 

From 80f7cd4636cdab929ff5bbb7fcb173e0a8bbcd16 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Sun, 10 Sep 2023 03:24:51 -0500
Subject: [PATCH 135/350] Disable staging script for remote work dir (#4282)

This commit disables the use of separate stage file for executors using
a non-default system, e.g. object storage as work directory (including Fusion
file system). The generation of stage file is still used for local and HPC batch
schedulers.

See https://github.com/nextflow-io/nextflow/issues/4279

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../executor/BashWrapperBuilder.groovy        |  4 +-
 .../batch/AwsBatchScriptLauncherTest.groovy   | 43 +++++++++++++++++++
 .../azure/batch/AzFileCopyStrategyTest.groovy |  5 ++-
 3 files changed, 49 insertions(+), 3 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
index b70675ac88..61eefeeb20 100644
--- a/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
@@ -198,7 +198,9 @@ class BashWrapperBuilder {
             return null
 
         final header = "# stage input files\n"
-        if( stagingScript.size() >= stageFileThreshold.bytes ) {
+        // enable only when the stage uses the default file system, i.e. it's not a remote object storage file
+        // see https://github.com/nextflow-io/nextflow/issues/4279
+        if( stageFile.fileSystem == FileSystems.default && stagingScript.size() >= stageFileThreshold.bytes ) {
             stageScript = stagingScript
             return header + "bash ${stageFile}"
         }
diff --git a/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchScriptLauncherTest.groovy b/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchScriptLauncherTest.groovy
index 5bb60cefa2..9ce7ee13d8 100644
--- a/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchScriptLauncherTest.groovy
+++ b/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchScriptLauncherTest.groovy
@@ -16,11 +16,14 @@
 
 package nextflow.cloud.aws.batch
 
+import java.nio.file.FileSystems
 import java.nio.file.Files
 import java.nio.file.Paths
 
 import nextflow.Session
+import nextflow.SysEnv
 import nextflow.cloud.aws.config.AwsConfig
+import nextflow.cloud.aws.util.S3PathFactory
 import nextflow.processor.TaskBean
 import nextflow.util.Duration
 import spock.lang.Specification
@@ -631,4 +634,44 @@ class AwsBatchScriptLauncherTest extends Specification {
 
     }
 
+    def 'should not create separate stage script' () {
+        given:
+        SysEnv.push([NXF_WRAPPER_STAGE_FILE_THRESHOLD: '100'])
+        and:
+        def workDir = S3PathFactory.parse('s3://my-bucket/work')
+        and:
+        def inputFiles = [
+                'sample_1.fq': Paths.get('/my-bucket/data/sample_1.fq'),
+                'sample_2.fq': Paths.get('/my-bucket/data/sample_2.fq'),
+        ]
+        def stageScript = '''\
+                # stage input files
+                downloads=(true)
+                rm -f sample_1.fq
+                rm -f sample_2.fq
+                rm -f .command.sh
+                downloads+=("nxf_s3_download s3://my-bucket/data/sample_1.fq sample_1.fq")
+                downloads+=("nxf_s3_download s3://my-bucket/data/sample_2.fq sample_2.fq")
+                downloads+=("nxf_s3_download s3://my-bucket/work/.command.sh .command.sh")
+                nxf_parallel "${downloads[@]}"
+                '''.stripIndent()
+        and:
+        def bean = [
+                workDir: workDir,
+                targetDir: workDir,
+                inputFiles: inputFiles,
+                script: 'echo Hello world!'
+        ] as TaskBean
+        def opts = new AwsOptions()
+        def builder = new AwsBatchScriptLauncher(bean, opts)
+
+        when:
+        def binding = builder.makeBinding()
+        then:
+        binding.stage_inputs == stageScript
+
+        cleanup:
+        SysEnv.pop()
+    }
+
 }
diff --git a/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzFileCopyStrategyTest.groovy b/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzFileCopyStrategyTest.groovy
index bbca973ffd..0c710aa320 100644
--- a/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzFileCopyStrategyTest.groovy
+++ b/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzFileCopyStrategyTest.groovy
@@ -1,6 +1,6 @@
 package nextflow.cloud.azure.batch
 
-import java.nio.file.FileSystem
+
 import java.nio.file.Path
 import java.nio.file.Paths
 import java.nio.file.attribute.BasicFileAttributes
@@ -9,6 +9,7 @@ import java.nio.file.spi.FileSystemProvider
 import com.azure.storage.blob.BlobClient
 import nextflow.Session
 import nextflow.cloud.azure.config.AzConfig
+import nextflow.cloud.azure.nio.AzFileSystem
 import nextflow.cloud.azure.nio.AzPath
 import nextflow.processor.TaskBean
 import spock.lang.Specification
@@ -34,7 +35,7 @@ class AzFileCopyStrategyTest extends Specification {
         provider.getScheme() >> 'az'
         provider.readAttributes(_, _, _) >> attr
 
-        def fs = Mock(FileSystem)
+        def fs = Mock(AzFileSystem)
         fs.provider() >> provider
         fs.toString() >> ('az://' + bucket)
         def uri = GroovyMock(URI)

From c1cc60dd48866857460912bd7b20098417c8eb28 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 9 Sep 2023 09:10:23 +0200
Subject: [PATCH 136/350] Revert singularity|apptainer run as default

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../container/SingularityBuilder.groovy       |  2 +-
 .../container/ApptainerBuilderTest.groovy     | 50 +++++++++----------
 .../container/SingularityBuilderTest.groovy   | 50 +++++++++----------
 .../executor/BashWrapperBuilderTest.groovy    |  4 +-
 .../executor/fusion/FusionHelperTest.groovy   |  6 +--
 5 files changed, 56 insertions(+), 56 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/container/SingularityBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/container/SingularityBuilder.groovy
index 5e0277ea60..5c2d74abfc 100644
--- a/modules/nextflow/src/main/groovy/nextflow/container/SingularityBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/container/SingularityBuilder.groovy
@@ -60,7 +60,7 @@ class SingularityBuilder extends ContainerBuilder<SingularityBuilder> {
     }
 
     private String defaultRunCommand() {
-        final result = SysEnv.get("NXF_${getBinaryName().toUpperCase()}_RUN_COMMAND", 'run')
+        final result = SysEnv.get("NXF_${getBinaryName().toUpperCase()}_RUN_COMMAND", 'exec')
         if( result !in ['run','exec'] )
             throw new IllegalArgumentException("Invalid singularity launch command '$result' - it should be either 'run' or 'exec'")
         return result
diff --git a/modules/nextflow/src/test/groovy/nextflow/container/ApptainerBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/container/ApptainerBuilderTest.groovy
index 9aa8199fa2..6552918ea0 100644
--- a/modules/nextflow/src/test/groovy/nextflow/container/ApptainerBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/container/ApptainerBuilderTest.groovy
@@ -27,9 +27,9 @@ import spock.lang.Unroll
  */
 class ApptainerBuilderTest extends Specification {
 
-    def 'should get the legacy exec command line' () {
+    def 'should get the run command line and auto mounts disabled' () {
         given:
-        SysEnv.push(NXF_APPTAINER_RUN_COMMAND:'exec', NXF_APPTAINER_AUTO_MOUNTS:'false')
+        SysEnv.push(NXF_APPTAINER_RUN_COMMAND:'run', NXF_APPTAINER_AUTO_MOUNTS:'false')
         and:
         def path1 = Paths.get('/foo/data/file1')
         def path2 = Paths.get('/bar/data/file2')
@@ -38,36 +38,36 @@ class ApptainerBuilderTest extends Specification {
         expect:
         new ApptainerBuilder('busybox')
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid busybox'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid busybox'
 
         new ApptainerBuilder('busybox')
                 .params(engineOptions: '-q -v')
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer -q -v exec --no-home --pid busybox'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer -q -v run --no-home --pid busybox'
 
         new ApptainerBuilder('busybox')
                 .params(runOptions: '--contain --writable')
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid --contain --writable busybox'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid --contain --writable busybox'
 
         new ApptainerBuilder('ubuntu')
                 .addMount(path1)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid ubuntu'
 
         new ApptainerBuilder('ubuntu')
                 .addMount(path1)
                 .addMount(path2)
                 .params(autoMounts: true)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B /foo/data/file1 -B /bar/data/file2 -B "$PWD" ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B /foo/data/file1 -B /bar/data/file2 -B "$PWD" ubuntu'
 
         new ApptainerBuilder('ubuntu')
                 .addMount(path1)
                 .addMount(path1)
                 .params(autoMounts: true)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B /foo/data/file1 -B "$PWD" ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B /foo/data/file1 -B "$PWD" ubuntu'
 
         new ApptainerBuilder('ubuntu')
                 .addMount(path1)
@@ -75,18 +75,18 @@ class ApptainerBuilderTest extends Specification {
                 .params(autoMounts: true)
                 .params(readOnlyInputs: true)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B /foo/data/file1:/foo/data/file1:ro -B "$PWD" ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B /foo/data/file1:/foo/data/file1:ro -B "$PWD" ubuntu'
 
         new ApptainerBuilder('ubuntu')
                 .addMount(path3)
                 .params(autoMounts: true)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B /bar/data\\ file -B "$PWD" ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B /bar/data\\ file -B "$PWD" ubuntu'
 
         new ApptainerBuilder('ubuntu')
                 .params(newPidNamespace: false)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home ubuntu'
 
         cleanup:
         SysEnv.pop()
@@ -102,37 +102,37 @@ class ApptainerBuilderTest extends Specification {
         expect:
         new ApptainerBuilder('busybox')
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B "$PWD" busybox'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B "$PWD" busybox'
 
         new ApptainerBuilder('busybox')
                 .params(engineOptions: '-q -v')
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer -q -v run --no-home --pid -B "$PWD" busybox'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer -q -v exec --no-home --pid -B "$PWD" busybox'
 
         new ApptainerBuilder('busybox')
                 .params(runOptions: '--contain --writable')
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B "$PWD" --contain --writable busybox'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B "$PWD" --contain --writable busybox'
 
         new ApptainerBuilder('ubuntu')
                 .addMount(path1)
                 .params(autoMounts: false)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid ubuntu'
 
         new ApptainerBuilder('ubuntu')
                 .addMount(path1)
                 .addMount(path2)
                 .params(autoMounts: true)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B /foo/data/file1 -B /bar/data/file2 -B "$PWD" ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B /foo/data/file1 -B /bar/data/file2 -B "$PWD" ubuntu'
 
         new ApptainerBuilder('ubuntu')
                 .addMount(path1)
                 .addMount(path1)
                 .params(autoMounts: true)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B /foo/data/file1 -B "$PWD" ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B /foo/data/file1 -B "$PWD" ubuntu'
 
         new ApptainerBuilder('ubuntu')
                 .addMount(path1)
@@ -140,18 +140,18 @@ class ApptainerBuilderTest extends Specification {
                 .params(autoMounts: true)
                 .params(readOnlyInputs: true)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B /foo/data/file1:/foo/data/file1:ro -B "$PWD" ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B /foo/data/file1:/foo/data/file1:ro -B "$PWD" ubuntu'
 
         new ApptainerBuilder('ubuntu')
                 .addMount(path3)
                 .params(autoMounts: true)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B /bar/data\\ file -B "$PWD" ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B /bar/data\\ file -B "$PWD" ubuntu'
 
         new ApptainerBuilder('ubuntu')
                 .params(newPidNamespace: false)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home -B "$PWD" ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home -B "$PWD" ubuntu'
 
     }
 
@@ -201,12 +201,12 @@ class ApptainerBuilderTest extends Specification {
                 .addEnv('X=1')
                 .addEnv(ALPHA:'aaa', BETA: 'bbb')
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} APPTAINERENV_X="1" APPTAINERENV_ALPHA="aaa" APPTAINERENV_BETA="bbb" apptainer run --no-home --pid -B "$PWD" busybox'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} APPTAINERENV_X="1" APPTAINERENV_ALPHA="aaa" APPTAINERENV_BETA="bbb" apptainer exec --no-home --pid -B "$PWD" busybox'
 
         new ApptainerBuilder('busybox')
                 .addEnv('CUDA_VISIBLE_DEVICES')
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} ${CUDA_VISIBLE_DEVICES:+APPTAINERENV_CUDA_VISIBLE_DEVICES="$CUDA_VISIBLE_DEVICES"} apptainer run --no-home --pid -B "$PWD" busybox'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} ${CUDA_VISIBLE_DEVICES:+APPTAINERENV_CUDA_VISIBLE_DEVICES="$CUDA_VISIBLE_DEVICES"} apptainer exec --no-home --pid -B "$PWD" busybox'
 
     }
 
@@ -216,17 +216,17 @@ class ApptainerBuilderTest extends Specification {
         when:
         def cmd = new ApptainerBuilder('ubuntu.img').build().getRunCommand()
         then:
-        cmd == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B "$PWD" ubuntu.img'
+        cmd == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B "$PWD" ubuntu.img'
 
         when:
         cmd = new ApptainerBuilder('ubuntu.img').build().getRunCommand('bwa --this --that file.fastq')
         then:
-        cmd == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B "$PWD" ubuntu.img bwa --this --that file.fastq'
+        cmd == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B "$PWD" ubuntu.img bwa --this --that file.fastq'
 
         when:
         cmd = new ApptainerBuilder('ubuntu.img').params(entry:'/bin/sh').build().getRunCommand('bwa --this --that file.fastq')
         then:
-        cmd == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B "$PWD" ubuntu.img /bin/sh -c "cd $PWD; bwa --this --that file.fastq"'
+        cmd == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B "$PWD" ubuntu.img /bin/sh -c "cd $PWD; bwa --this --that file.fastq"'
     }
 
     @Unroll
diff --git a/modules/nextflow/src/test/groovy/nextflow/container/SingularityBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/container/SingularityBuilderTest.groovy
index 6b412ea3b1..661f459a29 100644
--- a/modules/nextflow/src/test/groovy/nextflow/container/SingularityBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/container/SingularityBuilderTest.groovy
@@ -28,9 +28,9 @@ import spock.lang.Unroll
  */
 class SingularityBuilderTest extends Specification {
 
-    def 'should get the legacy exec command line' () {
+    def 'should get the run command line and auto mounts disable' () {
         given:
-        SysEnv.push(NXF_SINGULARITY_RUN_COMMAND:'exec', NXF_SINGULARITY_AUTO_MOUNTS:'false')
+        SysEnv.push(NXF_SINGULARITY_RUN_COMMAND:'run', NXF_SINGULARITY_AUTO_MOUNTS:'false')
         and:
         def path1 = Paths.get('/foo/data/file1')
         def path2 = Paths.get('/bar/data/file2')
@@ -39,36 +39,36 @@ class SingularityBuilderTest extends Specification {
         expect:
         new SingularityBuilder('busybox')
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid busybox'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity run --no-home --pid busybox'
 
         new SingularityBuilder('busybox')
                 .params(engineOptions: '-q -v')
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity -q -v exec --no-home --pid busybox'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity -q -v run --no-home --pid busybox'
 
         new SingularityBuilder('busybox')
                 .params(runOptions: '--contain --writable')
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid --contain --writable busybox'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity run --no-home --pid --contain --writable busybox'
 
         new SingularityBuilder('ubuntu')
                 .addMount(path1)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity run --no-home --pid ubuntu'
 
         new SingularityBuilder('ubuntu')
                 .addMount(path1)
                 .addMount(path2)
                 .params(autoMounts: true)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid -B /foo/data/file1 -B /bar/data/file2 -B "$PWD" ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity run --no-home --pid -B /foo/data/file1 -B /bar/data/file2 -B "$PWD" ubuntu'
 
         new SingularityBuilder('ubuntu')
                 .addMount(path1)
                 .addMount(path1)
                 .params(autoMounts: true)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid -B /foo/data/file1 -B "$PWD" ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity run --no-home --pid -B /foo/data/file1 -B "$PWD" ubuntu'
 
         new SingularityBuilder('ubuntu')
                 .addMount(path1)
@@ -76,18 +76,18 @@ class SingularityBuilderTest extends Specification {
                 .params(autoMounts: true)
                 .params(readOnlyInputs: true)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid -B /foo/data/file1:/foo/data/file1:ro -B "$PWD" ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity run --no-home --pid -B /foo/data/file1:/foo/data/file1:ro -B "$PWD" ubuntu'
 
         new SingularityBuilder('ubuntu')
                 .addMount(path3)
                 .params(autoMounts: true)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid -B /bar/data\\ file -B "$PWD" ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity run --no-home --pid -B /bar/data\\ file -B "$PWD" ubuntu'
 
         new SingularityBuilder('ubuntu')
                 .params(newPidNamespace: false)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity run --no-home ubuntu'
 
         cleanup:
         SysEnv.pop()
@@ -103,36 +103,36 @@ class SingularityBuilderTest extends Specification {
         expect:
         new SingularityBuilder('busybox')
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity run --no-home --pid -B "$PWD" busybox'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid -B "$PWD" busybox'
 
         new SingularityBuilder('busybox')
                 .params(engineOptions: '-q -v')
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity -q -v run --no-home --pid -B "$PWD" busybox'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity -q -v exec --no-home --pid -B "$PWD" busybox'
 
         new SingularityBuilder('busybox')
                 .params(runOptions: '--contain --writable')
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity run --no-home --pid -B "$PWD" --contain --writable busybox'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid -B "$PWD" --contain --writable busybox'
 
         new SingularityBuilder('ubuntu')
                 .params(autoMounts: false)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity run --no-home --pid ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid ubuntu'
 
         new SingularityBuilder('ubuntu')
                 .addMount(path1)
                 .addMount(path2)
                 .params(autoMounts: true)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity run --no-home --pid -B /foo/data/file1 -B /bar/data/file2 -B "$PWD" ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid -B /foo/data/file1 -B /bar/data/file2 -B "$PWD" ubuntu'
 
         new SingularityBuilder('ubuntu')
                 .addMount(path1)
                 .addMount(path1)
                 .params(autoMounts: true)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity run --no-home --pid -B /foo/data/file1 -B "$PWD" ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid -B /foo/data/file1 -B "$PWD" ubuntu'
 
         new SingularityBuilder('ubuntu')
                 .addMount(path1)
@@ -140,19 +140,19 @@ class SingularityBuilderTest extends Specification {
                 .params(autoMounts: true)
                 .params(readOnlyInputs: true)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity run --no-home --pid -B /foo/data/file1:/foo/data/file1:ro -B "$PWD" ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid -B /foo/data/file1:/foo/data/file1:ro -B "$PWD" ubuntu'
 
         new SingularityBuilder('ubuntu')
                 .addMount(path3)
                 .params(autoMounts: true)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity run --no-home --pid -B /bar/data\\ file -B "$PWD" ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid -B /bar/data\\ file -B "$PWD" ubuntu'
 
         new SingularityBuilder('ubuntu')
                 .params(newPidNamespace: false)
                 .params(autoMounts: false)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity run --no-home ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home ubuntu'
 
     }
 
@@ -202,12 +202,12 @@ class SingularityBuilderTest extends Specification {
                 .addEnv('X=1')
                 .addEnv(ALPHA:'aaa', BETA: 'bbb')
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} SINGULARITYENV_X="1" SINGULARITYENV_ALPHA="aaa" SINGULARITYENV_BETA="bbb" singularity run --no-home --pid -B "$PWD" busybox'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} SINGULARITYENV_X="1" SINGULARITYENV_ALPHA="aaa" SINGULARITYENV_BETA="bbb" singularity exec --no-home --pid -B "$PWD" busybox'
 
         new SingularityBuilder('busybox')
                 .addEnv('CUDA_VISIBLE_DEVICES')
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} ${CUDA_VISIBLE_DEVICES:+SINGULARITYENV_CUDA_VISIBLE_DEVICES="$CUDA_VISIBLE_DEVICES"} singularity run --no-home --pid -B "$PWD" busybox'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} ${CUDA_VISIBLE_DEVICES:+SINGULARITYENV_CUDA_VISIBLE_DEVICES="$CUDA_VISIBLE_DEVICES"} singularity exec --no-home --pid -B "$PWD" busybox'
 
     }
 
@@ -217,17 +217,17 @@ class SingularityBuilderTest extends Specification {
         when:
         def cmd = new SingularityBuilder('ubuntu.img').build().getRunCommand()
         then:
-        cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity run --no-home --pid -B "$PWD" ubuntu.img'
+        cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid -B "$PWD" ubuntu.img'
 
         when:
         cmd = new SingularityBuilder('ubuntu.img').build().getRunCommand('bwa --this --that file.fastq')
         then:
-        cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity run --no-home --pid -B "$PWD" ubuntu.img bwa --this --that file.fastq'
+        cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid -B "$PWD" ubuntu.img bwa --this --that file.fastq'
 
         when:
         cmd = new SingularityBuilder('ubuntu.img').params(entry:'/bin/sh').build().getRunCommand('bwa --this --that file.fastq')
         then:
-        cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity run --no-home --pid -B "$PWD" ubuntu.img /bin/sh -c "cd $PWD; bwa --this --that file.fastq"'
+        cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid -B "$PWD" ubuntu.img /bin/sh -c "cd $PWD; bwa --this --that file.fastq"'
     }
 
     @Unroll
diff --git a/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
index 4ded770ed5..2b4f290e00 100644
--- a/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
@@ -977,7 +977,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [enabled: true, engine: 'singularity'] as ContainerConfig ).makeBinding()
 
         then:
-        binding.launch_cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} ${NXF_TASK_WORKDIR:+SINGULARITYENV_NXF_TASK_WORKDIR="$NXF_TASK_WORKDIR"} singularity run --no-home --pid -B /work/dir docker://ubuntu:latest /bin/bash -c "cd $PWD; eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
+        binding.launch_cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} ${NXF_TASK_WORKDIR:+SINGULARITYENV_NXF_TASK_WORKDIR="$NXF_TASK_WORKDIR"} singularity exec --no-home --pid -B /work/dir docker://ubuntu:latest /bin/bash -c "cd $PWD; eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
         binding.cleanup_cmd == ""
         binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
     }
@@ -991,7 +991,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [enabled: true, engine: 'singularity', entrypointOverride: true] as ContainerConfig ).makeBinding()
 
         then:
-        binding.launch_cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} ${NXF_TASK_WORKDIR:+SINGULARITYENV_NXF_TASK_WORKDIR="$NXF_TASK_WORKDIR"} singularity run --no-home --pid -B /work/dir docker://ubuntu:latest /bin/bash -c "cd $PWD; eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
+        binding.launch_cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} ${NXF_TASK_WORKDIR:+SINGULARITYENV_NXF_TASK_WORKDIR="$NXF_TASK_WORKDIR"} singularity exec --no-home --pid -B /work/dir docker://ubuntu:latest /bin/bash -c "cd $PWD; eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
         binding.cleanup_cmd == ""
         binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
     }
diff --git a/modules/nextflow/src/test/groovy/nextflow/executor/fusion/FusionHelperTest.groovy b/modules/nextflow/src/test/groovy/nextflow/executor/fusion/FusionHelperTest.groovy
index 7dd00bb5b6..e1debac016 100644
--- a/modules/nextflow/src/test/groovy/nextflow/executor/fusion/FusionHelperTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/executor/fusion/FusionHelperTest.groovy
@@ -68,9 +68,9 @@ class FusionHelperTest extends Specification {
         [engine:'docker']       | [FOO:'one']       | 'image:2'     | null          | ['echo', 'hello']     | "docker run -i -e \"FOO=one\" --rm --privileged image:2 echo 'hello'"
         [engine:'docker']       | [FOO:'one']       | 'image:2'     | '--this=that' | ['echo', 'hello']     | "docker run -i -e \"FOO=one\" --this=that --rm --privileged image:2 echo 'hello'"
         and:
-        [engine:'singularity']  | [:]               | 'image:1'     | null          | ['echo', 'hello']     | "set +u; env - PATH=\"\$PATH\" \${TMP:+SINGULARITYENV_TMP=\"\$TMP\"} \${TMPDIR:+SINGULARITYENV_TMPDIR=\"\$TMPDIR\"} singularity run --no-home --pid image:1 echo 'hello'"
-        [engine:'singularity']  | [FOO:'one']       | 'image:1'     | null          | ['echo', 'hello']     | "set +u; env - PATH=\"\$PATH\" \${TMP:+SINGULARITYENV_TMP=\"\$TMP\"} \${TMPDIR:+SINGULARITYENV_TMPDIR=\"\$TMPDIR\"} SINGULARITYENV_FOO=\"one\" singularity run --no-home --pid image:1 echo 'hello'"
-        [engine:'singularity']  | [FOO:'one']       | 'image:1'     | '--this=that' | ['echo', 'hello']     | "set +u; env - PATH=\"\$PATH\" \${TMP:+SINGULARITYENV_TMP=\"\$TMP\"} \${TMPDIR:+SINGULARITYENV_TMPDIR=\"\$TMPDIR\"} SINGULARITYENV_FOO=\"one\" singularity run --no-home --pid --this=that image:1 echo 'hello'"
+        [engine:'singularity']  | [:]               | 'image:1'     | null          | ['echo', 'hello']     | "set +u; env - PATH=\"\$PATH\" \${TMP:+SINGULARITYENV_TMP=\"\$TMP\"} \${TMPDIR:+SINGULARITYENV_TMPDIR=\"\$TMPDIR\"} singularity exec --no-home --pid image:1 echo 'hello'"
+        [engine:'singularity']  | [FOO:'one']       | 'image:1'     | null          | ['echo', 'hello']     | "set +u; env - PATH=\"\$PATH\" \${TMP:+SINGULARITYENV_TMP=\"\$TMP\"} \${TMPDIR:+SINGULARITYENV_TMPDIR=\"\$TMPDIR\"} SINGULARITYENV_FOO=\"one\" singularity exec --no-home --pid image:1 echo 'hello'"
+        [engine:'singularity']  | [FOO:'one']       | 'image:1'     | '--this=that' | ['echo', 'hello']     | "set +u; env - PATH=\"\$PATH\" \${TMP:+SINGULARITYENV_TMP=\"\$TMP\"} \${TMPDIR:+SINGULARITYENV_TMPDIR=\"\$TMPDIR\"} SINGULARITYENV_FOO=\"one\" singularity exec --no-home --pid --this=that image:1 echo 'hello'"
 
     }
 

From 07582f0b7361745e5ef100598a189c881a033062 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sun, 10 Sep 2023 10:40:14 +0200
Subject: [PATCH 137/350] Make TraceRecord@store field public accessible [ci
 fast]

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../src/main/groovy/nextflow/trace/TraceRecord.groovy        | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/trace/TraceRecord.groovy b/modules/nextflow/src/main/groovy/nextflow/trace/TraceRecord.groovy
index 0662c8fb20..444e185843 100644
--- a/modules/nextflow/src/main/groovy/nextflow/trace/TraceRecord.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/trace/TraceRecord.groovy
@@ -237,10 +237,11 @@ class TraceRecord implements Serializable {
         }
     }
 
-
     @PackageScope
     Map<String,Object> store
 
+    Map<String,Object> getStore() { store }
+
     @Memoized
     Set<String> keySet() {
         FIELDS.keySet()
@@ -401,7 +402,7 @@ class TraceRecord implements Serializable {
     }
 
     String toString() {
-        "${this.class.simpleName} ${store}"
+        "${this.class.simpleName} ${this.store}"
     }
 
 

From 5686bf1da63261d03ff42f3fac3088877d9dc34b Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sun, 10 Sep 2023 14:51:21 +0200
Subject: [PATCH 138/350] Add maxSubmitAwait (#3736)

This commit adds a new directive named `maxSubmitAwait` that allows defining
how long a task can be in a pending status waiting to be scheduled for execution
by the underlying executor.

When the timeout is reached, an execution error is returned. The usual `errorStrategy`
directive can be used to control how handle the error condition and, if required, attempt
a new job submission. The `task.submitAttempt` attribute can be used to determine
which submitted attempt failed.


Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/process.md                               | 27 +++++++++++
 .../ProcessSubmitTimeoutException.groovy      | 29 ++++++++++++
 .../nextflow/processor/TaskConfig.groovy      | 19 ++++++--
 .../nextflow/processor/TaskHandler.groovy     | 17 +++++++
 .../processor/TaskPollingMonitor.groovy       | 14 ++++--
 .../nextflow/processor/TaskProcessor.groovy   | 19 +++++---
 .../groovy/nextflow/processor/TaskRun.groovy  |  5 ++
 .../nextflow/script/ProcessConfig.groovy      |  1 +
 .../nextflow/processor/TaskConfigTest.groovy  | 18 +++++++
 .../nextflow/processor/TaskHandlerTest.groovy | 21 +++++++++
 .../processor/TaskProcessorTest.groovy        | 47 +++++++++++--------
 11 files changed, 184 insertions(+), 33 deletions(-)
 create mode 100644 modules/nextflow/src/main/groovy/nextflow/exception/ProcessSubmitTimeoutException.groovy

diff --git a/docs/process.md b/docs/process.md
index a1496033d2..58a2e1d9cf 100644
--- a/docs/process.md
+++ b/docs/process.md
@@ -1705,6 +1705,33 @@ process foo {
 
 See also: [cpus](#cpus) and [memory](#memory).
 
+(process-maxsubmitawait)=
+
+### maxSubmitAwait (experimental)
+
+The `maxSubmitAwait` directives allows you to specify how long a task can remain in submission queue without being executed.
+Elapsed this time the task execution will fail.
+
+When used along with `retry` error strategy, it can be useful to re-schedule the task to a difference queue or
+resource requirement. For example:
+
+```groovy
+process foo {
+  errorStrategy 'retry'
+  maxSubmitAwait '10 mins'
+  maxRetries 3
+  queue "${task.submitAttempt==1 : 'spot-compute' : 'on-demand-compute'}"
+  script:
+  '''
+  your_job --here
+  '''
+}
+```
+
+In the above example the task is submitted to the `spot-compute` on the first attempt (`task.submitAttempt==1`). If the
+task execution does not start in the 10 minutes, a failure is reported and a new submission is attempted using the
+queue named `on-demand-compute`. 
+
 (process-maxerrors)=
 
 ### maxErrors
diff --git a/modules/nextflow/src/main/groovy/nextflow/exception/ProcessSubmitTimeoutException.groovy b/modules/nextflow/src/main/groovy/nextflow/exception/ProcessSubmitTimeoutException.groovy
new file mode 100644
index 0000000000..e2ccbe923e
--- /dev/null
+++ b/modules/nextflow/src/main/groovy/nextflow/exception/ProcessSubmitTimeoutException.groovy
@@ -0,0 +1,29 @@
+/*
+ * Copyright 2013-2019, Centre for Genomic Regulation (CRG)
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package nextflow.exception
+
+import groovy.transform.InheritConstructors
+
+/**
+ * Exception thrown when a task does not complete within
+ * the `time` requested time requirement
+ *
+ * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
+ */
+@InheritConstructors
+class ProcessSubmitTimeoutException extends ProcessException {
+}
diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskConfig.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskConfig.groovy
index cf88eab3af..3a24dc6c04 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskConfig.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskConfig.groovy
@@ -269,8 +269,8 @@ class TaskConfig extends LazyMap implements Cloneable {
         getDiskResource()?.getRequest()
     }
 
-    Duration getTime() {
-        def value = get('time')
+    private Duration getDuration0(String key) {
+        def value = get(key)
 
         if( !value )
             return null
@@ -285,8 +285,17 @@ class TaskConfig extends LazyMap implements Cloneable {
             new Duration(value.toString().trim())
         }
         catch( Exception e ) {
-            throw new AbortOperationException("Not a valid `time` value in process definition: $value")
+            throw new AbortOperationException("Not a valid `$key` value in process definition: $value")
         }
+
+    }
+
+    Duration getTime() {
+        return getDuration0('time')
+    }
+
+    Duration getMaxSubmitAwait() {
+        return getDuration0('maxSubmitAwait')
     }
 
     boolean hasCpus() {
@@ -406,6 +415,10 @@ class TaskConfig extends LazyMap implements Cloneable {
         }
     }
 
+    Integer getSubmitAttempt() {
+        get('submitAttempt') as Integer ?: 1
+    }
+
     Integer getAttempt() {
         get('attempt') as Integer ?: 1
     }
diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskHandler.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskHandler.groovy
index 3a15b99b57..2db1e00470 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskHandler.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskHandler.groovy
@@ -246,4 +246,21 @@ abstract class TaskHandler {
         task.processor.forksCount?.decrement()
     }
 
+    /**
+     * Check if the task submit could not be accomplished with the time specified via the
+     * `maxWait` directive
+     *
+     * @return
+     *      {@code true} if the task is in `submit` status after the amount of time specified
+     *      via {@code maxAwait} directive has passed, otherwise {@code false} is returned.
+     */
+    boolean isSubmitTimeout() {
+        final maxAwait = task.config.getMaxSubmitAwait()
+        if( !maxAwait )
+            return false
+        final now = System.currentTimeMillis()
+        if( isSubmitted() && now-submitTimeMillis>maxAwait.millis )
+            return true
+        return false
+    }
 }
diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskPollingMonitor.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskPollingMonitor.groovy
index 17c2694c46..6b5d281ba8 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskPollingMonitor.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskPollingMonitor.groovy
@@ -16,7 +16,6 @@
 
 package nextflow.processor
 
-
 import java.util.concurrent.LinkedBlockingQueue
 import java.util.concurrent.TimeUnit
 import java.util.concurrent.locks.Condition
@@ -27,6 +26,7 @@ import com.google.common.util.concurrent.RateLimiter
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import nextflow.Session
+import nextflow.exception.ProcessSubmitTimeoutException
 import nextflow.executor.BatchCleanup
 import nextflow.executor.GridTaskHandler
 import nextflow.util.Duration
@@ -611,14 +611,22 @@ class TaskPollingMonitor implements TaskMonitor {
         }
 
         // check if it is terminated
-        if( handler.checkIfCompleted() ) {
-            log.debug "Task completed > $handler"
+        boolean timeout=false
+        if( handler.checkIfCompleted() || (timeout=handler.isSubmitTimeout()) ) {
+            final state = timeout ? 'timed-out' : 'completed'
+            log.debug "Task $state > $handler"
             // decrement forks count
             handler.decProcessForks()
 
             // since completed *remove* the task from the processing queue
             evict(handler)
 
+            // check if submit timeout is reached
+            if( timeout ) {
+                try { handler.kill() } catch( Throwable t ) { log.warn("Unable to cancel task ${handler.task.lazyName()}", t) }
+                handler.task.error = new ProcessSubmitTimeoutException("Task '${handler.task.lazyName()}' could not be submitted within specified 'maxAwait' time: ${handler.task.config.getMaxSubmitAwait()}")
+            }
+
             // finalize the tasks execution
             final fault = handler.task.processor.finalizeTask(handler.task)
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
index bc3ae5e711..df320fe01f 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
@@ -61,6 +61,7 @@ import nextflow.exception.MissingFileException
 import nextflow.exception.MissingValueException
 import nextflow.exception.ProcessException
 import nextflow.exception.ProcessFailedException
+import nextflow.exception.ProcessSubmitTimeoutException
 import nextflow.exception.ProcessRetryableException
 import nextflow.exception.ProcessUnrecoverableException
 import nextflow.exception.ShowOnlyExceptionMessage
@@ -1037,8 +1038,11 @@ class TaskProcessor {
                 return RETRY
             }
 
-            final int taskErrCount = task ? ++task.failCount : 0
-            final int procErrCount = ++errorCount
+            final submitTimeout = error.cause instanceof ProcessSubmitTimeoutException
+            final submitErrMsg = submitTimeout ? error.cause.message : null
+            final int submitRetries = submitTimeout ? ++task.submitRetries : 0
+            final int taskErrCount = !submitTimeout && task ? ++task.failCount : 0
+            final int procErrCount = !submitTimeout ? ++errorCount : errorCount
 
             // -- when is a task level error and the user has chosen to ignore error,
             //    just report and error message and DO NOT stop the execution
@@ -1048,11 +1052,11 @@ class TaskProcessor {
                 task.config.errorCount = procErrCount
                 task.config.retryCount = taskErrCount
 
-                errorStrategy = checkErrorStrategy(task, error, taskErrCount, procErrCount)
+                errorStrategy = checkErrorStrategy(task, error, taskErrCount, procErrCount, submitRetries)
                 if( errorStrategy.soft ) {
-                    def msg = "[$task.hashLog] NOTE: $error.message"
+                    def msg = "[$task.hashLog] NOTE: ${submitTimeout ? submitErrMsg : error.message}"
                     if( errorStrategy == IGNORE ) msg += " -- Error is ignored"
-                    else if( errorStrategy == RETRY ) msg += " -- Execution is retried ($taskErrCount)"
+                    else if( errorStrategy == RETRY ) msg += " -- Execution is retried (${submitTimeout ? submitRetries : taskErrCount})"
                     log.info msg
                     task.failed = true
                     task.errorAction = errorStrategy
@@ -1107,7 +1111,7 @@ class TaskProcessor {
                 : name
     }
 
-    protected ErrorStrategy checkErrorStrategy( TaskRun task, ProcessException error, final int taskErrCount, final int procErrCount ) {
+    protected ErrorStrategy checkErrorStrategy( TaskRun task, ProcessException error, final int taskErrCount, final int procErrCount, final submitRetries ) {
 
         final action = task.config.getErrorStrategy()
 
@@ -1126,11 +1130,12 @@ class TaskProcessor {
             final int maxErrors = task.config.getMaxErrors()
             final int maxRetries = task.config.getMaxRetries()
 
-            if( (procErrCount < maxErrors || maxErrors == -1) && taskErrCount <= maxRetries ) {
+            if( (procErrCount < maxErrors || maxErrors == -1) && taskErrCount <= maxRetries && submitRetries <= maxRetries ) {
                 final taskCopy = task.makeCopy()
                 session.getExecService().submit({
                     try {
                         taskCopy.config.attempt = taskErrCount+1
+                        taskCopy.config.submitAttempt = submitRetries+1
                         taskCopy.runType = RunType.RETRY
                         taskCopy.resolve(taskBody)
                         checkCachedOrLaunchTask( taskCopy, taskCopy.hash, false )
diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskRun.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskRun.groovy
index fd2099f2f6..d4c8f7da32 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskRun.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskRun.groovy
@@ -304,6 +304,11 @@ class TaskRun implements Cloneable {
      */
     volatile int failCount
 
+    /**
+     * The number of times the submit of the task has been retried
+     */
+    volatile int submitRetries
+
     /**
      * Mark the task as failed
      */
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/ProcessConfig.groovy b/modules/nextflow/src/main/groovy/nextflow/script/ProcessConfig.groovy
index 5e3ddaa42c..d88a11cf1d 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/ProcessConfig.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/ProcessConfig.groovy
@@ -65,6 +65,7 @@ class ProcessConfig implements Map<String,Object>, Cloneable {
             'machineType',
             'queue',
             'label',
+            'maxSubmitAwait',
             'maxErrors',
             'maxForks',
             'maxRetries',
diff --git a/modules/nextflow/src/test/groovy/nextflow/processor/TaskConfigTest.groovy b/modules/nextflow/src/test/groovy/nextflow/processor/TaskConfigTest.groovy
index d290723992..b08595666f 100644
--- a/modules/nextflow/src/test/groovy/nextflow/processor/TaskConfigTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/processor/TaskConfigTest.groovy
@@ -233,6 +233,24 @@ class TaskConfigTest extends Specification {
 
     }
 
+    def 'test max submit await'() {
+
+        when:
+        def config = new TaskConfig()
+        config.maxSubmitAwait = value
+
+        then:
+        config.maxSubmitAwait == expected
+        config.getMaxSubmitAwait() == expected
+
+        where:
+        expected            || value
+        null                || null
+        new Duration('1s')  || 1000
+        new Duration('2h')  || '2h'
+
+    }
+
     def testGetMemory() {
 
         when:
diff --git a/modules/nextflow/src/test/groovy/nextflow/processor/TaskHandlerTest.groovy b/modules/nextflow/src/test/groovy/nextflow/processor/TaskHandlerTest.groovy
index 1846fb0838..0225478a21 100644
--- a/modules/nextflow/src/test/groovy/nextflow/processor/TaskHandlerTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/processor/TaskHandlerTest.groovy
@@ -207,4 +207,25 @@ class TaskHandlerTest extends Specification {
         handler.task.processor.getForksCount().intValue() == COUNTER -1
     }
 
+    def 'should validate is submit timeout' () {
+        given:
+        def handler = Spy(TaskHandler)
+        handler.status = TaskStatus.SUBMITTED
+        handler.task = Mock(TaskRun) {
+            getConfig() >> Mock(TaskConfig) { getMaxSubmitAwait() >> Duration.of('500ms') }
+        }
+
+        when:
+        def timeout = handler.isSubmitTimeout()
+        then:
+        !timeout
+
+        when:
+        sleep 1_000
+        and:
+        timeout = handler.isSubmitTimeout()
+        then:
+        timeout
+
+    }
 }
diff --git a/modules/nextflow/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy b/modules/nextflow/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy
index 4a075faa8c..6d8af3ed75 100644
--- a/modules/nextflow/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy
@@ -483,19 +483,19 @@ class TaskProcessorTest extends Specification {
         task = new TaskRun()
         task.config = new TaskConfig()
         then:
-        proc.checkErrorStrategy(task, error, 1,1) == ErrorStrategy.TERMINATE
+        proc.checkErrorStrategy(task, error, 1, 1, 0) == ErrorStrategy.TERMINATE
 
         when:
         task = new TaskRun()
         task.config = new TaskConfig(errorStrategy: 'ignore')
         then:
-        proc.checkErrorStrategy(task, error, 10, 10) == ErrorStrategy.IGNORE
+        proc.checkErrorStrategy(task, error, 10, 10, 0) == ErrorStrategy.IGNORE
 
         when:
         task = new TaskRun()
         task.config = new TaskConfig(errorStrategy: 'finish')
         then:
-        proc.checkErrorStrategy(task, error, 1, 1) == ErrorStrategy.FINISH
+        proc.checkErrorStrategy(task, error, 1, 1, 0) == ErrorStrategy.FINISH
 
     }
 
@@ -509,19 +509,19 @@ class TaskProcessorTest extends Specification {
         task = new TaskRun()
         task.config = new TaskConfig(errorStrategy: 'retry')
         then:
-        proc.checkErrorStrategy(task, error, 1, 1) == ErrorStrategy.TERMINATE
+        proc.checkErrorStrategy(task, error, 1, 1, 0) == ErrorStrategy.TERMINATE
 
         when:
         task = new TaskRun()
         task.config = new TaskConfig(errorStrategy: 'ignore')
         then:
-        proc.checkErrorStrategy(task, error, 1, 1) == ErrorStrategy.TERMINATE
+        proc.checkErrorStrategy(task, error, 1, 1, 0) == ErrorStrategy.TERMINATE
 
         when:
         task = new TaskRun()
         task.config = new TaskConfig(errorStrategy: 'finish')
         then:
-        proc.checkErrorStrategy(task, error, 1, 1) == ErrorStrategy.FINISH
+        proc.checkErrorStrategy(task, error, 1, 1, 0) == ErrorStrategy.FINISH
 
     }
 
@@ -540,23 +540,30 @@ class TaskProcessorTest extends Specification {
 
         when:
         task = new TaskRun(context: new TaskContext(holder: [:]))
-        task.config = new TaskConfig(errorStrategy:'retry', maxErrors: max_errors, maxRetries: max_retries )
+        task.config = new TaskConfig(errorStrategy: 'retry', maxErrors: MAX_ERRORS, maxRetries: MAX_RETRIES )
         then:
-        proc.checkErrorStrategy(task, error, task_err_count , proc_err_count) == strategy
+        proc.checkErrorStrategy(task, error, TASK_ERR_COUNT , PROC_ERR_COUNT, SUBMIT_RETRIES) == EXPECTED
 
         where:
-        max_retries | max_errors    |   task_err_count  |  proc_err_count   | strategy
-                1   |        3      |               0   |               0   | ErrorStrategy.RETRY
-                1   |        3      |               1   |               0   | ErrorStrategy.RETRY
-                1   |        3      |               2   |               0   | ErrorStrategy.TERMINATE
-                1   |        3      |               0   |               1   | ErrorStrategy.RETRY
-                1   |        3      |               0   |               2   | ErrorStrategy.RETRY
-                1   |        3      |               0   |               3   | ErrorStrategy.TERMINATE
-                3   |       -1      |               0   |               0   | ErrorStrategy.RETRY
-                3   |       -1      |               1   |               1   | ErrorStrategy.RETRY
-                3   |       -1      |               2   |               2   | ErrorStrategy.RETRY
-                3   |       -1      |               3   |               9   | ErrorStrategy.RETRY
-                3   |       -1      |               4   |               9   | ErrorStrategy.TERMINATE
+        MAX_RETRIES | MAX_ERRORS    |   TASK_ERR_COUNT  |  PROC_ERR_COUNT   | SUBMIT_RETRIES    | EXPECTED
+                1   |        3      |               0   |               0   | 0                 | ErrorStrategy.RETRY
+                1   |        3      |               1   |               0   | 0                 | ErrorStrategy.RETRY
+                1   |        3      |               2   |               0   | 0                 | ErrorStrategy.TERMINATE
+                1   |        3      |               0   |               1   | 0                 | ErrorStrategy.RETRY
+                1   |        3      |               0   |               2   | 0                 | ErrorStrategy.RETRY
+                1   |        3      |               0   |               3   | 0                 | ErrorStrategy.TERMINATE
+                3   |       -1      |               0   |               0   | 0                 | ErrorStrategy.RETRY
+                3   |       -1      |               1   |               1   | 0                 | ErrorStrategy.RETRY
+                3   |       -1      |               2   |               2   | 0                 | ErrorStrategy.RETRY
+                3   |       -1      |               3   |               9   | 0                 | ErrorStrategy.RETRY
+                3   |       -1      |               4   |               9   | 0                 | ErrorStrategy.TERMINATE
+         and:
+         // terminates when the submit retries is greater than the max retries
+                1   |       -1      |               0   |               0   | 1                 | ErrorStrategy.RETRY
+                1   |       -1      |               0   |               0   | 2                 | ErrorStrategy.TERMINATE
+                3   |       -1      |               0   |               0   | 2                 | ErrorStrategy.RETRY
+                3   |       -1      |               0   |               0   | 2                 | ErrorStrategy.RETRY
+                3   |       -1      |               0   |               0   | 4                 | ErrorStrategy.TERMINATE
 
     }
 

From 42504d3c83145e16179e22df83e9d35ecc995eca Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sun, 10 Sep 2023 21:27:01 +0200
Subject: [PATCH 139/350] Add support for inputs and outputs arity

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/process.md                               |  59 ++++--
 .../exception/IllegalArityException.groovy    |  31 +++
 .../nextflow/processor/TaskProcessor.groovy   |  28 ++-
 .../nextflow/script/params/ArityParam.groovy  |  97 ++++++++++
 .../nextflow/script/params/BaseInParam.groovy |   2 +-
 .../nextflow/script/params/FileInParam.groovy |   2 +-
 .../script/params/FileOutParam.groovy         |   2 +-
 .../processor/TaskProcessorTest.groovy        | 182 +++++++++++++++++-
 .../script/params/ArityParamTest.groovy       |  64 ++++++
 .../script/params/ParamsInTest.groovy         |  11 +-
 .../script/params/ParamsOutTest.groovy        |   8 +-
 tests/checks/process-arity.nf/.checks         |  16 ++
 tests/process-arity.nf                        |  34 ++++
 13 files changed, 503 insertions(+), 33 deletions(-)
 create mode 100644 modules/nextflow/src/main/groovy/nextflow/exception/IllegalArityException.groovy
 create mode 100644 modules/nextflow/src/main/groovy/nextflow/script/params/ArityParam.groovy
 create mode 100644 modules/nextflow/src/test/groovy/nextflow/script/params/ArityParamTest.groovy
 create mode 100644 tests/checks/process-arity.nf/.checks
 create mode 100644 tests/process-arity.nf

diff --git a/docs/process.md b/docs/process.md
index 58a2e1d9cf..183b0c7f08 100644
--- a/docs/process.md
+++ b/docs/process.md
@@ -471,22 +471,41 @@ workflow {
 }
 ```
 
-The `stageAs` option allows you to control how the file should be named in the task work directory. You can provide a specific name or a pattern as described in the [Multiple input files](#multiple-input-files) section:
+Available options:
 
-```groovy
-process foo {
+`arity`
+: :::{versionadded} 23.09.0-edge
+  :::
+: Specify the number of expected files. Can be a number or a range:
+
+  ```groovy
   input:
-  path x, stageAs: 'data.txt'
+      path('one.txt', arity: '1')         // exactly one file is expected
+      path('pair_*.txt', arity: '2')      // exactly two files are expected
+      path('many_*.txt', arity: '1..*')   // one or more files are expected
+  ```
 
-  """
-  your_command --in data.txt
-  """
-}
+  When a task is created, Nextflow will check whether the received files for each path input match the declared arity, and fail if they do not.
 
-workflow {
-  foo('/some/data/file.txt')
-}
-```
+`stageAs`
+: Specify how the file should be named in the task work directory:
+
+  ```groovy
+  process foo {
+    input:
+    path x, stageAs: 'data.txt'
+
+    """
+    your_command --in data.txt
+    """
+  }
+
+  workflow {
+    foo('/some/data/file.txt')
+  }
+  ```
+
+  Can be a name or a pattern as described in the [Multiple input files](#multiple-input-files) section.
 
 :::{note}
 Process `path` inputs have nearly the same interface as described in {ref}`script-file-io`, with one difference which is relevant when files are staged into a subdirectory. Given the following input:
@@ -922,6 +941,22 @@ In the above example, the `randomNum` process creates a file named `result.txt`
 
 Available options:
 
+`arity`
+: :::{versionadded} 23.09.0-edge
+  :::
+: Specify the number of expected files. Can be a number or a range:
+
+  ```groovy
+  output:
+      path('one.txt', arity: '1')         // exactly one file is expected
+      path('pair_*.txt', arity: '2')      // exactly two files are expected
+      path('many_*.txt', arity: '1..*')   // one or more files are expected
+  ```
+
+  When a task completes, Nextflow will check whether the produced files for each path output match the declared arity,
+  and fail if they do not. If the arity is `1`, a sole file object will be emitted. Otherwise, a list will always be emitted,
+  even if only one file is produced.
+
 `followLinks`
 : When `true` target files are return in place of any matching symlink (default: `true`)
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/exception/IllegalArityException.groovy b/modules/nextflow/src/main/groovy/nextflow/exception/IllegalArityException.groovy
new file mode 100644
index 0000000000..f11f8f3cb2
--- /dev/null
+++ b/modules/nextflow/src/main/groovy/nextflow/exception/IllegalArityException.groovy
@@ -0,0 +1,31 @@
+/*
+ * Copyright 2013-2023, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package nextflow.exception
+
+import groovy.transform.CompileStatic
+import groovy.transform.InheritConstructors
+
+/**
+ * Exception thrown when input/output arity check fails
+ *
+ * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
+ */
+@CompileStatic
+@InheritConstructors
+class IllegalArityException extends ProcessUnrecoverableException {
+}
diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
index df320fe01f..ec00c62d56 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
@@ -57,12 +57,13 @@ import nextflow.ast.TaskTemplateVarsXform
 import nextflow.cloud.CloudSpotTerminationException
 import nextflow.dag.NodeMarker
 import nextflow.exception.FailedGuardException
+import nextflow.exception.IllegalArityException
 import nextflow.exception.MissingFileException
 import nextflow.exception.MissingValueException
 import nextflow.exception.ProcessException
 import nextflow.exception.ProcessFailedException
-import nextflow.exception.ProcessSubmitTimeoutException
 import nextflow.exception.ProcessRetryableException
+import nextflow.exception.ProcessSubmitTimeoutException
 import nextflow.exception.ProcessUnrecoverableException
 import nextflow.exception.ShowOnlyExceptionMessage
 import nextflow.exception.UnexpectedException
@@ -1570,7 +1571,6 @@ class TaskProcessor {
         task.setOutput(param, stdout)
     }
 
-
     protected void collectOutFiles( TaskRun task, FileOutParam param, Path workDir, Map context ) {
 
         final List<Path> allFiles = []
@@ -1594,7 +1594,7 @@ class TaskProcessor {
             else {
                 def path = param.glob ? splitter.strip(filePattern) : filePattern
                 def file = workDir.resolve(path)
-                def exists = param.followLinks ? file.exists() : file.exists(LinkOption.NOFOLLOW_LINKS)
+                def exists = checkFileExists(file, param.followLinks)
                 if( exists )
                     result = [file]
                 else
@@ -1604,7 +1604,7 @@ class TaskProcessor {
             if( result )
                 allFiles.addAll(result)
 
-            else if( !param.optional ) {
+            else if( !param.optional && (!param.arity || param.arity.min > 0) ) {
                 def msg = "Missing output file(s) `$filePattern` expected by process `${safeTaskName(task)}`"
                 if( inputsRemovedFlag )
                     msg += " (note: input files are not included in the default matching set)"
@@ -1612,10 +1612,16 @@ class TaskProcessor {
             }
         }
 
-        task.setOutput( param, allFiles.size()==1 ? allFiles[0] : allFiles )
+        if( !param.isValidArity(allFiles.size()) )
+            throw new IllegalArityException("Incorrect number of output files for process `${safeTaskName(task)}` -- expected ${param.arity}, found ${allFiles.size()}")
+
+        task.setOutput( param, allFiles.size()==1 && param.isSingle() ? allFiles[0] : allFiles )
 
     }
 
+    protected boolean checkFileExists(Path file, boolean followLinks) {
+        followLinks ? file.exists() : file.exists(LinkOption.NOFOLLOW_LINKS)
+    }
 
     protected void collectOutValues( TaskRun task, ValueOutParam param, Map ctx ) {
 
@@ -1814,7 +1820,7 @@ class TaskProcessor {
         if( obj instanceof Path )
             return obj
 
-        if( !obj == null )
+        if( obj == null )
             throw new ProcessUnrecoverableException("Path value cannot be null")
         
         if( !(obj instanceof CharSequence) )
@@ -1856,10 +1862,10 @@ class TaskProcessor {
         return files
     }
 
-    protected singleItemOrList( List<FileHolder> items, ScriptType type ) {
+    protected singleItemOrList( List<FileHolder> items, boolean single, ScriptType type ) {
         assert items != null
 
-        if( items.size() == 1 ) {
+        if( items.size() == 1 && single ) {
             return makePath(items[0],type)
         }
 
@@ -2059,7 +2065,11 @@ class TaskProcessor {
             final fileParam = param as FileInParam
             final normalized = normalizeInputToFiles(val, count, fileParam.isPathQualifier(), batch)
             final resolved = expandWildcards( fileParam.getFilePattern(ctx), normalized )
-            ctx.put( param.name, singleItemOrList(resolved, task.type) )
+
+            if( !param.isValidArity(resolved.size()) )
+                throw new IllegalArityException("Incorrect number of input files for process `${safeTaskName(task)}` -- expected ${param.arity}, found ${resolved.size()}")
+
+            ctx.put( param.name, singleItemOrList(resolved, param.isSingle(), task.type) )
             count += resolved.size()
             for( FileHolder item : resolved ) {
                 Integer num = allNames.getOrCreate(item.stageName, 0) +1
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/params/ArityParam.groovy b/modules/nextflow/src/main/groovy/nextflow/script/params/ArityParam.groovy
new file mode 100644
index 0000000000..3c1a425288
--- /dev/null
+++ b/modules/nextflow/src/main/groovy/nextflow/script/params/ArityParam.groovy
@@ -0,0 +1,97 @@
+/*
+ * Copyright 2023, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package nextflow.script.params
+
+import groovy.transform.CompileStatic
+import groovy.transform.EqualsAndHashCode
+import nextflow.exception.IllegalArityException
+
+/**
+ * Implements an arity option for process inputs and outputs.
+ *
+ * @author Ben Sherman <bentshermann@gmail.com>
+ */
+@CompileStatic
+trait ArityParam {
+
+    Range arity
+
+    Range getArity() { arity }
+
+    def setArity(String value) {
+        if( value.isInteger() ) {
+            def n = value.toInteger()
+            this.arity = new Range(n, n)
+            return this
+        }
+
+        final tokens = value.tokenize('..')
+        if( tokens.size() == 2 ) {
+            final min = tokens[0]
+            final max = tokens[1]
+            if( min.isInteger() && (max == '*' || max.isInteger()) ) {
+                this.arity = new Range(
+                    min.toInteger(),
+                    max == '*' ? Integer.MAX_VALUE : max.toInteger()
+                )
+                return this
+            }
+        }
+
+        throw new IllegalArityException("Path arity should be a number (e.g. '1') or a range (e.g. '1..*')")
+    }
+
+    /**
+     * Determine whether a single output file should be unwrapped.
+     */
+    boolean isSingle() {
+        return !arity || arity.max == 1
+    }
+
+    boolean isValidArity(int size) {
+        return !arity || arity.contains(size)
+    }
+
+    @EqualsAndHashCode
+    static class Range {
+        int min
+        int max
+
+        Range(int min, int max) {
+            if( min<0 )
+                throw new IllegalArityException("Path arity min value must be greater or equals to 0")
+            if( max<1 )
+                throw new IllegalArityException("Path arity max value must be greater or equals to 1")
+            if( min==0 && max==1 )
+                throw new IllegalArityException("Path arity 0..1 is not allowed")
+            this.min = min
+            this.max = max
+        }
+
+        boolean contains(int value) {
+            min <= value && value <= max
+        }
+
+        @Override
+        String toString() {
+            min == max
+                ? min.toString()
+                : "${min}..${max == Integer.MAX_VALUE ? '*' : max}".toString()
+        }
+    }
+
+}
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/params/BaseInParam.groovy b/modules/nextflow/src/main/groovy/nextflow/script/params/BaseInParam.groovy
index f8c40aec2c..12d396414f 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/params/BaseInParam.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/params/BaseInParam.groovy
@@ -54,7 +54,7 @@ abstract class BaseInParam extends BaseParam implements InParam {
         return inChannel
     }
 
-    BaseInParam(ProcessConfig config ) {
+    BaseInParam( ProcessConfig config ) {
         this(config.getOwnerScript().getBinding(), config.getInputs())
     }
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/params/FileInParam.groovy b/modules/nextflow/src/main/groovy/nextflow/script/params/FileInParam.groovy
index b52f8dad39..8bebf83d70 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/params/FileInParam.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/params/FileInParam.groovy
@@ -28,7 +28,7 @@ import nextflow.script.TokenVar
  */
 @Slf4j
 @InheritConstructors
-class FileInParam extends BaseInParam implements PathQualifier {
+class FileInParam extends BaseInParam implements ArityParam, PathQualifier {
 
     protected filePattern
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/params/FileOutParam.groovy b/modules/nextflow/src/main/groovy/nextflow/script/params/FileOutParam.groovy
index e305c46c3e..a55cd957c7 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/params/FileOutParam.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/params/FileOutParam.groovy
@@ -33,7 +33,7 @@ import nextflow.util.BlankSeparatedList
  */
 @Slf4j
 @InheritConstructors
-class FileOutParam extends BaseOutParam implements OutParam, OptionalParam, PathQualifier {
+class FileOutParam extends BaseOutParam implements OutParam, ArityParam, OptionalParam, PathQualifier {
 
     /**
      * ONLY FOR TESTING DO NOT USE
diff --git a/modules/nextflow/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy b/modules/nextflow/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy
index 6d8af3ed75..131cc6d0a9 100644
--- a/modules/nextflow/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy
@@ -26,6 +26,8 @@ import groovyx.gpars.agent.Agent
 import nextflow.Global
 import nextflow.ISession
 import nextflow.Session
+import nextflow.exception.IllegalArityException
+import nextflow.exception.MissingFileException
 import nextflow.exception.ProcessException
 import nextflow.exception.ProcessUnrecoverableException
 import nextflow.executor.Executor
@@ -37,6 +39,7 @@ import nextflow.script.BodyDef
 import nextflow.script.ProcessConfig
 import nextflow.script.ScriptType
 import nextflow.script.bundle.ResourcesBundle
+import nextflow.script.params.FileInParam
 import nextflow.script.params.FileOutParam
 import nextflow.util.ArrayBag
 import nextflow.util.CacheHelper
@@ -44,7 +47,6 @@ import nextflow.util.MemoryUnit
 import spock.lang.Specification
 import spock.lang.Unroll
 import test.TestHelper
-
 /**
  *
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
@@ -186,13 +188,19 @@ class TaskProcessorTest extends Specification {
 
         when:
         def list = [ FileHolder.get(path1, 'x_file_1') ]
-        def result = processor.singleItemOrList(list, ScriptType.SCRIPTLET)
+        def result = processor.singleItemOrList(list, true, ScriptType.SCRIPTLET)
         then:
         result.toString() == 'x_file_1'
 
+        when:
+        list = [ FileHolder.get(path1, 'x_file_1') ]
+        result = processor.singleItemOrList(list, false, ScriptType.SCRIPTLET)
+        then:
+        result*.toString() == ['x_file_1']
+
         when:
         list = [ FileHolder.get(path1, 'x_file_1'), FileHolder.get(path2, 'x_file_2'), FileHolder.get(path3, 'x_file_3') ]
-        result = processor.singleItemOrList(list, ScriptType.SCRIPTLET)
+        result = processor.singleItemOrList(list, false, ScriptType.SCRIPTLET)
         then:
         result*.toString() == [ 'x_file_1',  'x_file_2',  'x_file_3']
 
@@ -964,4 +972,172 @@ class TaskProcessorTest extends Specification {
         result.config.getCpus() == 10
         result.config.getMemory() == MemoryUnit.of('100 GB')
     }
+
+    @Unroll
+    def 'should validate inputs arity' () {
+        given:
+        def executor = Mock(Executor)
+        def session = Mock(Session) {getFilePorter()>>Mock(FilePorter) }
+        def processor = Spy(new TaskProcessor(session:session, executor:executor))
+        and:
+        def context = new TaskContext(holder: new HashMap<String, Object>())
+        def task = new TaskRun(
+                name: 'foo',
+                type: ScriptType.SCRIPTLET,
+                context: context,
+                config: new TaskConfig())
+
+        when:
+        def param = new FileInParam(new Binding(), [])
+                .setPathQualifier(true)
+                .bind(FILE_NAME) as FileInParam
+        if( ARITY )
+            param.setArity(ARITY)
+
+        processor.makeTaskContextStage2(task, [(param):FILE_VALUE], 0 )
+        then:
+        context.get(FILE_NAME) == EXPECTED
+
+        where:
+        FILE_NAME       | FILE_VALUE                                | ARITY     | EXPECTED
+        'file.txt'      | '/some/file.txt'                          | null      | Path.of('/some/file.txt')
+        'file.*'        | '/some/file.txt'                          | null      | Path.of('/some/file.txt')
+        'file.*'        | ['/some/file1.txt','/some/file2.txt']     | null      | [Path.of('/some/file1.txt'), Path.of('/some/file2.txt')]
+        '*'             | ['/some/file1.txt','/some/file2.txt']     | null      | [Path.of('/some/file1.txt'), Path.of('/some/file2.txt')]
+        '*'             | []                                        | null      | []
+
+        and:
+        'file.txt'      | '/some/file.txt'                          | '1'      | Path.of('/some/file.txt')
+        'f*'            | '/some/file.txt'                          | '1'      | Path.of('/some/file.txt')
+        'f*'            | '/some/file.txt'                          | '1..2'   | [Path.of('/some/file.txt')]
+        'f*'            | '/some/file.txt'                          | '1..*'   | [Path.of('/some/file.txt')]
+        'f*'            | '/some/file.txt'                          | '1..*'   | [Path.of('/some/file.txt')]
+        'f*'            | ['/some/file.txt']                        | '1..*'   | [Path.of('/some/file.txt')]
+        'f*'            | ['/some/file1.txt', '/some/file2.txt']    | '1..*'   | [Path.of('/some/file1.txt'), Path.of('/some/file2.txt')]
+    }
+
+    def 'should throw an arity error' () {
+        given:
+        def executor = Mock(Executor)
+        def session = Mock(Session) {getFilePorter()>>Mock(FilePorter) }
+        def processor = Spy(new TaskProcessor(session:session, executor:executor))
+        and:
+        def context = new TaskContext(holder: new HashMap<String, Object>())
+        def task = new TaskRun(
+                name: 'foo',
+                type: ScriptType.SCRIPTLET,
+                context: context,
+                config: new TaskConfig())
+
+        when:
+        def param = new FileInParam(new Binding(), [])
+                .setPathQualifier(true)
+                .bind(FILE_NAME) as FileInParam
+        if( ARITY )
+            param.setArity(ARITY)
+
+        processor.makeTaskContextStage2(task, [(param):FILE_VALUE], 0 )
+        then:
+        def e = thrown(IllegalArityException)
+        e.message == ERROR
+
+        where:
+        FILE_NAME       | FILE_VALUE                                | ARITY     | ERROR
+        'file.txt'      | []                                        | '0'       | 'Path arity max value must be greater or equals to 1'
+        'file.txt'      | []                                        | '1'       | 'Incorrect number of input files for process `foo` -- expected 1, found 0'
+        'f*'            | []                                        | '1..*'    | 'Incorrect number of input files for process `foo` -- expected 1..*, found 0'
+        'f*'            | '/some/file.txt'                          | '2..*'    | 'Incorrect number of input files for process `foo` -- expected 2..*, found 1'
+        'f*'            | ['/some/file.txt']                        | '2..*'    | 'Incorrect number of input files for process `foo` -- expected 2..*, found 1'
+        'f*'            | ['/a','/b']                               | '3'       | 'Incorrect number of input files for process `foo` -- expected 3, found 2'
+    }
+
+    def 'should validate collect output files' () {
+        given:
+        def executor = Mock(Executor)
+        def session = Mock(Session) {getFilePorter()>>Mock(FilePorter) }
+        def processor = Spy(new TaskProcessor(session:session, executor:executor))
+        and:
+        def context = new TaskContext(holder: new HashMap<String, Object>())
+        def task = new TaskRun(
+                name: 'foo',
+                type: ScriptType.SCRIPTLET,
+                context: context,
+                config: new TaskConfig())
+        and:
+        def workDir = Path.of('/work')
+
+        when:
+        def param = new FileOutParam(new Binding(), [])
+                .setPathQualifier(true)
+                .optional(OPTIONAL)
+                .bind(FILE_NAME) as FileOutParam
+        if( ARITY )
+            param.setArity(ARITY)
+        and:
+        processor.collectOutFiles(task, param, workDir, context)
+        then:
+        processor.fetchResultFiles(_,_,_) >> RESULTS
+        processor.checkFileExists(_,_) >> EXISTS
+        and:
+        task.getOutputs().get(param) == EXPECTED
+
+        where:
+        FILE_NAME       | RESULTS                                   | EXISTS    | OPTIONAL  | ARITY         | EXPECTED
+        'file.txt'      | null                                      | true      | false     | null          | Path.of('/work/file.txt')
+        '*'             | [Path.of('/work/file.txt')]               | true      | false     | null          | Path.of('/work/file.txt')
+        '*'             | [Path.of('/work/A'), Path.of('/work/B')]  | true      | false     | null          | [Path.of('/work/A'), Path.of('/work/B')]
+        '*'             | []                                        | true      | true      | null          | []
+        and:
+        'file.txt'      | null                                      | true      | false     | '1'           | Path.of('/work/file.txt')
+        '*'             | [Path.of('/work/file.txt')]               | true      | false     | '1'           | Path.of('/work/file.txt')
+        '*'             | [Path.of('/work/file.txt')]               | true      | false     | '1..*'        | [Path.of('/work/file.txt')]
+        '*'             | [Path.of('/work/A'), Path.of('/work/B')]  | true      | false     | '2'           | [Path.of('/work/A'), Path.of('/work/B')]
+        '*'             | [Path.of('/work/A'), Path.of('/work/B')]  | true      | false     | '1..*'        | [Path.of('/work/A'), Path.of('/work/B')]
+        '*'             | []                                        | true      | false     | '0..*'        | []
+    }
+
+    @Unroll
+    def 'should report output error' () {
+        given:
+        def executor = Mock(Executor)
+        def session = Mock(Session) {getFilePorter()>>Mock(FilePorter) }
+        def processor = Spy(new TaskProcessor(session:session, executor:executor))
+        and:
+        def context = new TaskContext(holder: new HashMap<String, Object>())
+        def task = new TaskRun(
+                name: 'foo',
+                type: ScriptType.SCRIPTLET,
+                context: context,
+                config: new TaskConfig())
+        and:
+        def workDir = Path.of('/work')
+
+        when:
+        def param = new FileOutParam(new Binding(), [])
+                .setPathQualifier(true)
+                .optional(OPTIONAL)
+                .bind(FILE_NAME) as FileOutParam
+        if( ARITY )
+            param.setArity(ARITY)
+        and:
+        processor.collectOutFiles(task, param, workDir, context)
+        then:
+        processor.fetchResultFiles(_,_,_) >> RESULTS
+        processor.checkFileExists(_,_) >> EXISTS
+        and:
+        def e = thrown(EXCEPTION)
+        e.message == ERROR
+
+        where:
+        FILE_NAME       | RESULTS                                   | EXISTS    | OPTIONAL  | ARITY         | EXCEPTION             | ERROR
+        'file.txt'      | null                                      | false     | false     | null          | MissingFileException  | "Missing output file(s) `file.txt` expected by process `foo`"
+        '*'             | []                                        | true      | false     | null          | MissingFileException  | "Missing output file(s) `*` expected by process `foo`"
+        and:
+        'file.txt'      | null                                      | true      | false     | '2'           | IllegalArityException | "Incorrect number of output files for process `foo` -- expected 2, found 1"
+        '*'             | [Path.of('/work/file.txt')]               | true      | false     | '2'           | IllegalArityException | "Incorrect number of output files for process `foo` -- expected 2, found 1"
+        '*'             | [Path.of('/work/file.txt')]               | true      | false     | '2..*'        | IllegalArityException | "Incorrect number of output files for process `foo` -- expected 2..*, found 1"
+        '*'             | []                                        | true      | true      | '1..*'        | IllegalArityException | "Incorrect number of output files for process `foo` -- expected 1..*, found 0"
+
+    }
+
 }
diff --git a/modules/nextflow/src/test/groovy/nextflow/script/params/ArityParamTest.groovy b/modules/nextflow/src/test/groovy/nextflow/script/params/ArityParamTest.groovy
new file mode 100644
index 0000000000..bd4f50ee29
--- /dev/null
+++ b/modules/nextflow/src/test/groovy/nextflow/script/params/ArityParamTest.groovy
@@ -0,0 +1,64 @@
+/*
+ * Copyright 2023, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package nextflow.script.params
+
+import spock.lang.Specification
+import spock.lang.Unroll
+/**
+ *
+ * @author Ben Sherman <bentshermann@gmail.com>
+ */
+class ArityParamTest extends Specification {
+
+    static class DefaultArityParam implements ArityParam {
+        DefaultArityParam() {}
+    }
+
+    @Unroll
+    def testArity () {
+
+        when:
+        def param = new DefaultArityParam()
+        param.setArity(VALUE)
+        then:
+        param.arity.min == MIN
+        param.arity.max == MAX
+        param.isSingle() == SINGLE
+
+        where:
+        VALUE  | SINGLE | MIN | MAX
+        '1'    | true   | 1   | 1
+        '1..*' | false  | 1   | Integer.MAX_VALUE
+        '0..*' | false  | 0   | Integer.MAX_VALUE
+    }
+
+    @Unroll
+    def testArityRange () {
+
+        when:
+        def range = new ArityParam.Range(MIN, MAX)
+        then:
+        range.contains(2) == TWO
+        range.toString() == STRING
+
+        where:
+        MIN | MAX               | TWO   | STRING
+        1   | 1                 | false | '1'
+        1   | Integer.MAX_VALUE | true  | '1..*'
+    }
+
+}
diff --git a/modules/nextflow/src/test/groovy/nextflow/script/params/ParamsInTest.groovy b/modules/nextflow/src/test/groovy/nextflow/script/params/ParamsInTest.groovy
index 60dba152bc..3312a37a3c 100644
--- a/modules/nextflow/src/test/groovy/nextflow/script/params/ParamsInTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/script/params/ParamsInTest.groovy
@@ -707,12 +707,12 @@ class ParamsInTest extends Dsl2Spec {
 
             process hola {
               input:
-              path x
-              path f1
-              path '*.fa' 
+              path x, arity: '1'
+              path f1, arity: '1..2'
+              path '*.fa', arity: '1..*'
               path 'file.txt'
               path f2, name: '*.fa'
-              path f3, stageAs: '*.txt' 
+              path f3, stageAs: '*.txt'
 
               return ''
             }
@@ -738,18 +738,21 @@ class ParamsInTest extends Dsl2Spec {
         in0.inChannel.val == FILE
         in0.index == 0
         in0.isPathQualifier()
+        in0.arity == new ArityParam.Range(1, 1)
 
         in1.name == 'f1'
         in1.filePattern == '*'
         in1.inChannel.val == FILE
         in1.index == 1
         in1.isPathQualifier()
+        in1.arity == new ArityParam.Range(1, 2)
 
         in2.name == '*.fa'
         in2.filePattern == '*.fa'
         in2.inChannel.val == FILE
         in2.index == 2
         in2.isPathQualifier()
+        in2.arity == new ArityParam.Range(1, Integer.MAX_VALUE)
 
         in3.name == 'file.txt'
         in3.filePattern == 'file.txt'
diff --git a/modules/nextflow/src/test/groovy/nextflow/script/params/ParamsOutTest.groovy b/modules/nextflow/src/test/groovy/nextflow/script/params/ParamsOutTest.groovy
index 1c46c898ba..d19820f4f6 100644
--- a/modules/nextflow/src/test/groovy/nextflow/script/params/ParamsOutTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/script/params/ParamsOutTest.groovy
@@ -931,7 +931,8 @@ class ParamsOutTest extends Dsl2Spec {
                 separatorChar: '#',
                 glob: false,
                 optional: false,
-                includeInputs: false
+                includeInputs: false,
+                arity: '1'
                 
               path y, 
                 maxDepth:5,
@@ -941,7 +942,8 @@ class ParamsOutTest extends Dsl2Spec {
                 separatorChar: ':',
                 glob: true,
                 optional: true,
-                includeInputs: true
+                includeInputs: true,
+                arity: '0..*'
 
               return ''
             }
@@ -963,6 +965,7 @@ class ParamsOutTest extends Dsl2Spec {
         !out0.getGlob()
         !out0.getOptional()
         !out0.getIncludeInputs()
+        out0.getArity() == new ArityParam.Range(1, 1)
 
         and:
         out1.getMaxDepth() == 5
@@ -973,6 +976,7 @@ class ParamsOutTest extends Dsl2Spec {
         out1.getGlob()
         out1.getOptional()
         out1.getIncludeInputs()
+        out1.getArity() == new ArityParam.Range(0, Integer.MAX_VALUE)
     }
 
     def 'should set file options' () {
diff --git a/tests/checks/process-arity.nf/.checks b/tests/checks/process-arity.nf/.checks
new file mode 100644
index 0000000000..66e9a3e265
--- /dev/null
+++ b/tests/checks/process-arity.nf/.checks
@@ -0,0 +1,16 @@
+set +e
+
+#
+# run normal mode
+#
+echo ''
+$NXF_RUN 
+[[ $? == 0 ]] || false
+
+
+#
+# RESUME mode
+#
+echo ''
+$NXF_RUN -resume 
+[[ $? == 0 ]] || false
\ No newline at end of file
diff --git a/tests/process-arity.nf b/tests/process-arity.nf
new file mode 100644
index 0000000000..8a750745f0
--- /dev/null
+++ b/tests/process-arity.nf
@@ -0,0 +1,34 @@
+#!/usr/bin/env nextflow
+
+process foo {
+  output:
+    path('one.txt', arity: '1')
+    path('pair_*.txt', arity: '2')
+    path('many_*.txt', arity: '1..*')
+  script:
+    """
+    echo 'one' > one.txt
+    echo 'pair_1' > pair_1.txt
+    echo 'pair_2' > pair_2.txt
+    echo 'many_1' > many_1.txt
+    echo 'many_2' > many_2.txt
+    echo 'many_3' > many_3.txt
+    """
+}
+
+process bar {
+  input:
+    path('one.txt', arity: '1')
+    path('pair_*.txt', arity: '2')
+    path('many_*.txt', arity: '1..*')
+  script:
+    """
+    cat one.txt
+    cat pair_*.txt
+    cat many_*.txt
+    """
+}
+
+workflow {
+    foo | bar
+}

From 7e5d414e81322a5cb1f7e8f0bf2f0a7dc69b1ad0 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Mon, 11 Sep 2023 00:04:49 +0200
Subject: [PATCH 140/350] Bump nf-amazon@2.1.2

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-amazon/changelog.txt                      | 5 +++++
 plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF | 2 +-
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/plugins/nf-amazon/changelog.txt b/plugins/nf-amazon/changelog.txt
index 81af4cb0aa..3fd772a31b 100644
--- a/plugins/nf-amazon/changelog.txt
+++ b/plugins/nf-amazon/changelog.txt
@@ -1,5 +1,10 @@
 nf-amazon changelog
 ===================
+2.1.2 - 10 Sep
+- Disable staging script for remote work dir (#4282) [80f7cd46]
+- Allow setting shell directive when using the trace file. (#4210) [7d6ad624]
+- Bump groovy 3.0.19 [cb411208]
+
 2.1.1 - 5 Aug 2023
 - Fix glob resolution for remove files [19a72c40]
 - Fix Option fixOwnership traverse parent directories [f2a2ea35]
diff --git a/plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF b/plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF
index d7b0cf833b..6ae09958e7 100644
--- a/plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: nextflow.cloud.aws.AmazonPlugin
 Plugin-Id: nf-amazon
-Plugin-Version: 2.1.1
+Plugin-Version: 2.1.2
 Plugin-Provider: Seqera Labs
 Plugin-Requires: >=23.05.0-edge

From 83410f39a35d79d079f32cd5a2e4d7656123245c Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Mon, 11 Sep 2023 00:05:18 +0200
Subject: [PATCH 141/350] Bump nf-azure@1.3.1

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-azure/changelog.txt                      | 6 ++++++
 plugins/nf-azure/src/resources/META-INF/MANIFEST.MF | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/plugins/nf-azure/changelog.txt b/plugins/nf-azure/changelog.txt
index 808543c7da..73e9ea7cc8 100644
--- a/plugins/nf-azure/changelog.txt
+++ b/plugins/nf-azure/changelog.txt
@@ -1,5 +1,11 @@
 nf-azure changelog
 ===================
+1.3.1 - 10 Sep 2023
+- Disable staging script for remote work dir (#4282) [80f7cd46]
+- Fix IOException should be thrown when failing to create Azure directory [b0bdfd79]
+- Fix security deps in nf-azure plugin [c30d5211]
+- Bump groovy 3.0.19 [cb411208]
+
 1.3.0 - 17 Aug 2023
 - Add resource labels support for Azure Batch (#4178) [7b5e50a1]
 - Fix typos in source code comments (#4173) [ci fast] [e78bc37e]
diff --git a/plugins/nf-azure/src/resources/META-INF/MANIFEST.MF b/plugins/nf-azure/src/resources/META-INF/MANIFEST.MF
index 48a1d75d94..73da661c8f 100644
--- a/plugins/nf-azure/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-azure/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: nextflow.cloud.azure.AzurePlugin
 Plugin-Id: nf-azure
-Plugin-Version: 1.3.0
+Plugin-Version: 1.3.1
 Plugin-Provider: Seqera Labs
 Plugin-Requires: >=23.01.0-edge

From a9f6dd6559a436c585cd568d5565ba9200630756 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Mon, 11 Sep 2023 00:05:42 +0200
Subject: [PATCH 142/350] Bump nf-wave@0.12.0

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-wave/changelog.txt                      | 10 ++++++++++
 plugins/nf-wave/src/resources/META-INF/MANIFEST.MF |  2 +-
 2 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/plugins/nf-wave/changelog.txt b/plugins/nf-wave/changelog.txt
index 5d0b016b7c..10992dcad5 100644
--- a/plugins/nf-wave/changelog.txt
+++ b/plugins/nf-wave/changelog.txt
@@ -1,5 +1,15 @@
 nf-wave changelog
 ==================
+0.12.0 - 10 Sep 2023
+- Add support for Spack to Singularity builds [23c4ec1d]
+- Add inspect command (#4069) [090c31ce]
+- Add support for Wave native build for singularity [8a434893]
+- Fix Wave build when Conda package name is quoted [d19cb0b7]
+- Fix Wave build for Singularity files [a60ef72b]
+- Improve Wave handing of Conda envs [736ab9bb]
+- Deprecated Wave report feature [80c5cb27]
+- Bump groovy 3.0.19 [cb411208]
+
 0.11.2 - 17 Aug 2023
 - Use root user in Wave container based on micromamba (#4038) [ci fast] [a3a75ea2]
 - Add 429 http status code to Wave retriable errors [8eb5f305]
diff --git a/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF b/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF
index 143419776a..1ac36f6aac 100644
--- a/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: io.seqera.wave.plugin.WavePlugin
 Plugin-Id: nf-wave
-Plugin-Version: 0.11.2
+Plugin-Version: 0.12.0
 Plugin-Provider: Seqera Labs
 Plugin-Requires: >=23.05.0-edge

From 2a7bd21152e273ca2eaffe9377418a24421c3944 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Mon, 11 Sep 2023 00:09:48 +0200
Subject: [PATCH 143/350] Update changelog

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 changelog.txt | 48 ++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)

diff --git a/changelog.txt b/changelog.txt
index 359db4221b..dfd2d910fc 100644
--- a/changelog.txt
+++ b/changelog.txt
@@ -1,5 +1,53 @@
 NEXTFLOW CHANGE-LOG
 ===================
+23.09.0-edge - 10 Sep 2023
+- Add check for latest version (#4194) [3e8cd488]
+- Add inspect command (#4069) [090c31ce]
+- Add maxSubmitAwait (#3736) [5686bf1d]
+- Add scripts logging for troubleshooting [c056a74e]
+- Add support for Spack to Singularity builds [23c4ec1d]
+- Add support for Wave native build for Singularity [8a434893]
+- Add support for inputs and outputs arity [42504d3c]
+- Add support for remote debug (#4266) [87e0648a]
+- Add warning about using clusterOptions with process directives (#4248) [a68c1a3e]
+- Add which to dockerfile build [817aa05b]
+- Align Singularity experience with Docker (#4230) [a1e1d3ca] [c1cc60dd]
+- Allow setting shell directive when using the trace file (#4210) [7d6ad624]
+- Always emit publish event for cached task outputs (#4227) [62686ce8]
+- Deprecated Wave report feature [80c5cb27]
+- Disable staging script for remote work dir (#4282) [80f7cd46]
+- Disable version check on CI tests [db79e13f]
+- Docs improvement to clarify the usage of the bin dir (#4121) [2daa4172]
+- Document API differences of process path inputs (#4189) [c37e00bc]
+- Document use of local variables in closures (#4251) [05ff784a]
+- Fix IOException should be thrown when failing to creare Azure directory [b0bdfd79]
+- Fix Parallel execution of Conda corrupts data and packages (#4253) [976c282c]
+- Fix Parse negative CLI params as numbers (#4238) [1ae70d5d]
+- Fix Too long Http connection pool timeout [fa961e7f]
+- Fix Wave build for Singularity files [a60ef72b]
+- Fix Wave build when Conda package name is quoted [d19cb0b7]
+- Fix failing test [2785ffe9]
+- Fix fs cp command with remote file [366eedec]
+- Fix printf command with negative exit code (#4213) [465468b0]
+- Fix security deps in nf-azure plugin [c30d5211]
+- Fix setting `executor.queueSize = 0` is ignored (#4228) [6664b578]
+- Improve Wave handing of Conda envs [736ab9bb]
+- Improve pod options documentation (#4274) [c3aa26e1]
+- Make TraceRecord@store field public accessible [07582f0b]
+- Remove -dsl1 and -dsl1 rub cli options [b6721b71]
+- Remove experimental -dockerize option /2 [7def5542]
+- Remove experimental -dockerize option [937c8fb7]
+- Report an error on duplicate workflow name definitions (#4088) [fce9702e]
+- Undocument internal NXF_DEBUG variable [7955db8d]
+- Update AZ File share doc (#4235) [69d317b6]
+- Update docs about splitCsv() operator (#4163) [1dfb621c]
+- Update documentation of NXF_DEBUG (#4187) [a88a4245]
+- Use sipHash24 in place of deprecated murmur32 for script aliasing [bb96763f]
+- Bump groovy 3.0.19 [cb411208]
+- Bump nf-amazon@2.1.2 [7e5d414e]
+- Bump nf-azure@1.3.1 [83410f39]
+- Bump nf-wave@0.12.0 [a9f6dd65]
+
 23.08.1-edge - 17 Aug 2023
 - Add 429 http status code to Wave retriable errors [8eb5f305]
 - Add resource labels support for Azure Batch (#4178) [7b5e50a1]

From f37d51baa80979f359c9dbd87be9564965dcd035 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Mon, 11 Sep 2023 00:10:34 +0200
Subject: [PATCH 144/350] [release 23.09.0-edge] Update timestamp and build
 number

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 VERSION                                                     | 2 +-
 docs/conf.py                                                | 4 ++--
 .../nextflow/src/main/resources/META-INF/plugins-info.txt   | 6 +++---
 modules/nf-commons/src/main/nextflow/Const.groovy           | 6 +++---
 nextflow                                                    | 2 +-
 nextflow.md5                                                | 2 +-
 nextflow.sha1                                               | 2 +-
 nextflow.sha256                                             | 2 +-
 8 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/VERSION b/VERSION
index ed8e6580ae..8aa01d92a9 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-23.08.1-edge
+23.09.0-edge
diff --git a/docs/conf.py b/docs/conf.py
index dd9c2a42f6..659d8609d2 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -58,9 +58,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '23.08'
+version = '23.09'
 # The full version, including alpha/beta/rc tags.
-release = '23.08.1-edge'
+release = '23.09.0-edge'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
diff --git a/modules/nextflow/src/main/resources/META-INF/plugins-info.txt b/modules/nextflow/src/main/resources/META-INF/plugins-info.txt
index 60364143e3..eaad0fec0b 100644
--- a/modules/nextflow/src/main/resources/META-INF/plugins-info.txt
+++ b/modules/nextflow/src/main/resources/META-INF/plugins-info.txt
@@ -1,9 +1,9 @@
-nf-amazon@2.1.1
-nf-azure@1.3.0
+nf-amazon@2.1.2
+nf-azure@1.3.1
 nf-cloudcache@0.2.0
 nf-codecommit@0.1.5
 nf-console@1.0.6
 nf-ga4gh@1.1.0
 nf-google@1.8.1
 nf-tower@1.6.1
-nf-wave@0.11.2
\ No newline at end of file
+nf-wave@0.12.0
\ No newline at end of file
diff --git a/modules/nf-commons/src/main/nextflow/Const.groovy b/modules/nf-commons/src/main/nextflow/Const.groovy
index 38687fde5b..d593e5084f 100644
--- a/modules/nf-commons/src/main/nextflow/Const.groovy
+++ b/modules/nf-commons/src/main/nextflow/Const.groovy
@@ -52,17 +52,17 @@ class Const {
     /**
      * The application version
      */
-    static public final String APP_VER = "23.08.1-edge"
+    static public final String APP_VER = "23.09.0-edge"
 
     /**
      * The app build time as linux/unix timestamp
      */
-    static public final long APP_TIMESTAMP = 1692284319999
+    static public final long APP_TIMESTAMP = 1694383263606
 
     /**
      * The app build number
      */
-    static public final int APP_BUILDNUM = 5874
+    static public final int APP_BUILDNUM = 5879
 
     /**
      * The app build time string relative to UTC timezone
diff --git a/nextflow b/nextflow
index e296c43fbe..53609cc4c7 100755
--- a/nextflow
+++ b/nextflow
@@ -15,7 +15,7 @@
 #  limitations under the License.
 
 [[ "$NXF_DEBUG" == 'x' ]] && set -x
-NXF_VER=${NXF_VER:-'23.08.1-edge'}
+NXF_VER=${NXF_VER:-'23.09.0-edge'}
 NXF_ORG=${NXF_ORG:-'nextflow-io'}
 NXF_HOME=${NXF_HOME:-$HOME/.nextflow}
 NXF_PROT=${NXF_PROT:-'https'}
diff --git a/nextflow.md5 b/nextflow.md5
index 5aa63f083a..cd4dff1322 100644
--- a/nextflow.md5
+++ b/nextflow.md5
@@ -1 +1 @@
-74e5cedd3fd06021c698fab73cf5f03e
+8871d71a561d214566dbc8e33300c8c6
diff --git a/nextflow.sha1 b/nextflow.sha1
index d24bb70c95..bb6635b8f2 100644
--- a/nextflow.sha1
+++ b/nextflow.sha1
@@ -1 +1 @@
-fbaa08de20ccc1743711f9d58fc2ada055d79f01
+8fae253e69459149b039e57ca69f0b5ceb2ec5cf
diff --git a/nextflow.sha256 b/nextflow.sha256
index 144ff2727b..f297c7d37e 100644
--- a/nextflow.sha256
+++ b/nextflow.sha256
@@ -1 +1 @@
-2b099e5febcc8236308be215936af5ac0af6d9c007e329247f25d4bd9a7cf444
+41d0d8a76a49c75f91d4d244ab64bc2e2f96f768828cbdcddd29d527e95bbb99

From 9f9edcdc4b80e1316ed3fb164ef9f350fd641c9a Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Mon, 11 Sep 2023 11:36:25 +0200
Subject: [PATCH 145/350] Revert "Allow setting shell directive when using the
 trace file. (#4210)"

This reverts commit 7d6ad62476bd43d6e98747cabe8bfe181d5da1e9 since it breaks
the execution of command scripts that declares a non-Bash shell interpreter.
---
 .../main/groovy/nextflow/executor/BashWrapperBuilder.groovy   | 2 +-
 .../groovy/nextflow/executor/BashWrapperBuilderTest.groovy    | 4 ++--
 .../nextflow/executor/test-bash-wrapper-with-trace.txt        | 2 +-
 .../cloud/aws/batch/AwsBatchScriptLauncherTest.groovy         | 2 +-
 .../nextflow/cloud/azure/batch/AzFileCopyStrategyTest.groovy  | 2 +-
 5 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
index 61eefeeb20..24b6cbe256 100644
--- a/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
@@ -469,7 +469,7 @@ class BashWrapperBuilder {
         final traceWrapper = isTraceRequired()
         if( traceWrapper ) {
             // executes the stub which in turn executes the target command
-            launcher = "${interpreter} ${fileStr(wrapperFile)} nxf_trace"
+            launcher = "/bin/bash ${fileStr(wrapperFile)} nxf_trace"
         }
         else {
             launcher = "${interpreter} ${fileStr(scriptFile)}"
diff --git a/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
index 2b4f290e00..89a40ca4ea 100644
--- a/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
@@ -566,14 +566,14 @@ class BashWrapperBuilderTest extends Specification {
         when:
         binding = newBashWrapperBuilder(statsEnabled: true).makeBinding()
         then:
-        binding.launch_cmd == '/bin/bash -ue /work/dir/.command.run nxf_trace'
+        binding.launch_cmd == '/bin/bash /work/dir/.command.run nxf_trace'
         binding.unstage_controls == null
         binding.containsKey('unstage_controls')
 
         when:
         binding = newBashWrapperBuilder(statsEnabled: true, scratch: true).makeBinding()
         then:
-        binding.launch_cmd == '/bin/bash -ue /work/dir/.command.run nxf_trace'
+        binding.launch_cmd == '/bin/bash /work/dir/.command.run nxf_trace'
         binding.unstage_controls == '''\
                         cp .command.out /work/dir/.command.out || true
                         cp .command.err /work/dir/.command.err || true
diff --git a/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper-with-trace.txt b/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper-with-trace.txt
index b032748ccb..0aaf49f410 100644
--- a/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper-with-trace.txt
+++ b/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper-with-trace.txt
@@ -281,7 +281,7 @@ on_term() {
 }
 
 nxf_launch() {
-    /bin/bash -ue {{folder}}/.command.run nxf_trace
+    /bin/bash {{folder}}/.command.run nxf_trace
 }
 
 nxf_stage() {
diff --git a/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchScriptLauncherTest.groovy b/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchScriptLauncherTest.groovy
index 9ce7ee13d8..4b09a85d46 100644
--- a/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchScriptLauncherTest.groovy
+++ b/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchScriptLauncherTest.groovy
@@ -235,7 +235,7 @@ class AwsBatchScriptLauncherTest extends Specification {
                     nxf_parallel "${uploads[@]}"
                     '''.stripIndent().leftTrim()
 
-        binding.launch_cmd == '/bin/bash -ue .command.run nxf_trace'
+        binding.launch_cmd == '/bin/bash .command.run nxf_trace'
         
         binding.task_env == ''
 
diff --git a/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzFileCopyStrategyTest.groovy b/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzFileCopyStrategyTest.groovy
index 0c710aa320..436fcb2ce9 100644
--- a/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzFileCopyStrategyTest.groovy
+++ b/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzFileCopyStrategyTest.groovy
@@ -386,7 +386,7 @@ class AzFileCopyStrategyTest extends Specification {
                     nxf_parallel "${uploads[@]}"
                     '''.stripIndent().leftTrim()
 
-        binding.launch_cmd == '/bin/bash -ue .command.run nxf_trace'
+        binding.launch_cmd == '/bin/bash .command.run nxf_trace'
 
         binding.task_env == '''\
                     export PATH="$PWD/.nextflow-bin:$AZ_BATCH_NODE_SHARED_DIR/bin/:$PATH"

From 052b51bd384abe05ae95cf95cdff5c64168a577a Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Mon, 11 Sep 2023 12:11:52 +0200
Subject: [PATCH 146/350] Update changelog

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 changelog.txt | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/changelog.txt b/changelog.txt
index dfd2d910fc..ef5d881bb4 100644
--- a/changelog.txt
+++ b/changelog.txt
@@ -1,5 +1,8 @@
 NEXTFLOW CHANGE-LOG
 ===================
+23.09.1-edge - 11 Sep 2023
+- Revert "Allow setting shell directive when using the trace file (#4210)" [9f9edcdc]
+
 23.09.0-edge - 10 Sep 2023
 - Add check for latest version (#4194) [3e8cd488]
 - Add inspect command (#4069) [090c31ce]

From 79c677a12d82400444fb6221219ce92b7247dcf2 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Mon, 11 Sep 2023 12:12:22 +0200
Subject: [PATCH 147/350] [release 23.09.1-edge] [ci fast] Update timestamp and
 build number

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 VERSION                                           | 2 +-
 docs/conf.py                                      | 2 +-
 launch.sh                                         | 6 ++++++
 modules/nf-commons/src/main/nextflow/Const.groovy | 6 +++---
 nextflow                                          | 2 +-
 nextflow.md5                                      | 2 +-
 nextflow.sha1                                     | 2 +-
 nextflow.sha256                                   | 2 +-
 8 files changed, 15 insertions(+), 9 deletions(-)

diff --git a/VERSION b/VERSION
index 8aa01d92a9..4a719b97aa 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-23.09.0-edge
+23.09.1-edge
diff --git a/docs/conf.py b/docs/conf.py
index 659d8609d2..b9e2ae98df 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -60,7 +60,7 @@
 # The short X.Y version.
 version = '23.09'
 # The full version, including alpha/beta/rc tags.
-release = '23.09.0-edge'
+release = '23.09.1-edge'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
diff --git a/launch.sh b/launch.sh
index 41e5103c40..5bc03f3229 100755
--- a/launch.sh
+++ b/launch.sh
@@ -118,6 +118,12 @@ while [ "$*" != "" ]; do
   elif [ "$1" == '-remote-debug' ]; then
     DEBUG="-agentlib:jdwp=transport=dt_socket,server=y,suspend=y,address=$NXF_REMOTE_DEBUG_PORT"
     args+=("$1")
+  elif [ "$1" == '-enable-checkpoint' ]; then
+    mkdir -p crac-files
+    JVM_ARGS+=" -XX:CRaCCheckpointTo=$PWD/crac-files"
+  elif [ "$1" == '-checkpoint' ]; then
+    jcmd $CLASSPATH JDK.checkpoint
+    exit 0
   else
    args+=("$1")
   fi
diff --git a/modules/nf-commons/src/main/nextflow/Const.groovy b/modules/nf-commons/src/main/nextflow/Const.groovy
index d593e5084f..2fc8eec099 100644
--- a/modules/nf-commons/src/main/nextflow/Const.groovy
+++ b/modules/nf-commons/src/main/nextflow/Const.groovy
@@ -52,17 +52,17 @@ class Const {
     /**
      * The application version
      */
-    static public final String APP_VER = "23.09.0-edge"
+    static public final String APP_VER = "23.09.1-edge"
 
     /**
      * The app build time as linux/unix timestamp
      */
-    static public final long APP_TIMESTAMP = 1694383263606
+    static public final long APP_TIMESTAMP = 1694426936712
 
     /**
      * The app build number
      */
-    static public final int APP_BUILDNUM = 5879
+    static public final int APP_BUILDNUM = 5882
 
     /**
      * The app build time string relative to UTC timezone
diff --git a/nextflow b/nextflow
index 53609cc4c7..c3145509a6 100755
--- a/nextflow
+++ b/nextflow
@@ -15,7 +15,7 @@
 #  limitations under the License.
 
 [[ "$NXF_DEBUG" == 'x' ]] && set -x
-NXF_VER=${NXF_VER:-'23.09.0-edge'}
+NXF_VER=${NXF_VER:-'23.09.1-edge'}
 NXF_ORG=${NXF_ORG:-'nextflow-io'}
 NXF_HOME=${NXF_HOME:-$HOME/.nextflow}
 NXF_PROT=${NXF_PROT:-'https'}
diff --git a/nextflow.md5 b/nextflow.md5
index cd4dff1322..4046935306 100644
--- a/nextflow.md5
+++ b/nextflow.md5
@@ -1 +1 @@
-8871d71a561d214566dbc8e33300c8c6
+c6690f184ec1e95646b6a4d60bb5442a
diff --git a/nextflow.sha1 b/nextflow.sha1
index bb6635b8f2..bc00d398a1 100644
--- a/nextflow.sha1
+++ b/nextflow.sha1
@@ -1 +1 @@
-8fae253e69459149b039e57ca69f0b5ceb2ec5cf
+31e0a8e79b45d605459781fe3d31e70590e3f2e1
diff --git a/nextflow.sha256 b/nextflow.sha256
index f297c7d37e..75fc2abc39 100644
--- a/nextflow.sha256
+++ b/nextflow.sha256
@@ -1 +1 @@
-41d0d8a76a49c75f91d4d244ab64bc2e2f96f768828cbdcddd29d527e95bbb99
+dd82066091517be8562f0fa9af26c272db00b14ce07145d202f1d6619d3e3a7f

From 89ede15c71e79858560f93df71064b74d2da2cf4 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Mon, 11 Sep 2023 21:59:39 +0200
Subject: [PATCH 148/350] Update docs

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/wave.md | 42 +++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 41 insertions(+), 1 deletion(-)

diff --git a/docs/wave.md b/docs/wave.md
index 8eec01b3d5..e95a88cb29 100644
--- a/docs/wave.md
+++ b/docs/wave.md
@@ -43,9 +43,11 @@ The Tower access token is not mandatory, but it is recommended in order to acces
 
 ## Use cases
 
+(wave-authenticate-private-repos)=
+
 ### Authenticate private repositories
 
-Wave allows the use of private repositories in your Nextflow pipelines. The repository access keys must be provided in the form of [Nextflow Tower credentials](https://help.tower.nf/22.2/credentials/overview/).
+Wave allows the use of private repositories in your Nextflow pipelines. The repository access keys must be provided in the form of [Tower credentials](https://help.tower.nf/latest/credentials/overview/).
 
 Once the credentials have been created, simply specify your [Tower account access token](https://help.tower.nf/22.2/api/overview/#authentication) in your pipeline configuration file. If the credentials were created in a Tower organization workspace, specify the workspace ID as well in the config file as shown below:
 
@@ -120,6 +122,36 @@ In order to request the build of containers that are optimised for a specific CP
 If using a Spack YAML file to provide the required packages, you should avoid editing the following sections, which are already configured by the Wave plugin: `packages`, `config`, `view` and `concretizer` (your edits may be ignored), and `compilers` (your edits will be considered, and may interfere with the setup by the Wave plugin).
 :::
 
+### Build Singularity native images
+
+As of version `23.09.0-edge`, Nextflow can build Singularity native images on-demand either using `Singularityfile`,
+Conda packages or Spack packages. The Singularity images are automatically uploaded in a container registry OCI compliant
+of your choice and stored as a [ORAS artefact](https://oras.land/).
+
+:::{note}
+This feature requires of Singularity (or Apptainer) version supporting the pull of images using the `oras:` pseudo-protocol.
+:::
+
+For example to enable the provisioning of Singularity images in your pipeline use the following configuration snippet:
+
+```
+singularity.enabled = true
+wave.enabled = true
+wave.freeze = true
+wave.strategy = ['conda']
+wave.build.repository = 'docker.io/user/repo'
+```
+
+In the above configuration replace `docker.io/user/repo` with a repository of your choice where Singularity image files
+should be uploaded.
+
+:::{note}
+When using a private repository, the repository access keys must be provider via Tower credentials manager (see {ref}`above <wave-authenticate-private-repos>`).
+
+Moreover the access to the repository must be granted in the compute nodes by using the command `singularity remote login <registry>`.
+Please see Singularity documentation for further details.
+:::
+
 ### Push to a private repository
 
 Containers built by Wave are uploaded to the Wave default repository hosted on AWS ECR at `195996028523.dkr.ecr.eu-west-1.amazonaws.com/wave/build`. The images in this repository are automatically deleted 1 week after the date of their push.
@@ -154,6 +186,14 @@ The following configuration options are available:
 `wave.endpoint`
 : The Wave service endpoint (default: `https://wave.seqera.io`).
 
+`wave.freeze`
+: :::{versionadded} 22.09.0-edge
+  :::
+: When enabling the container freeze mode, Wave will provision an non-ephemeral container image
+that will be pushed to a container repository your choice. It requires the use of the `wave.build.repository` setting.
+It is also suggested to specify a custom cache repository via the setting `wave.build.cacheRepository`. Note: when using
+container freeze mode, the container repository authentication needs to be managed by the underlying infrastructure.    
+
 `wave.build.repository`
 : The container repository where images built by Wave are uploaded (note: the corresponding credentials must be provided in your Nextflow Tower account).
 

From b30efe36cb115f05b4481d0b3b18af5384997e79 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 16 Sep 2023 10:57:18 +0200
Subject: [PATCH 149/350] Fix Prevent multi attempts to retrive AWS creds

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../nextflow/cloud/aws/util/S3CredentialsProvider.groovy   | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/util/S3CredentialsProvider.groovy b/plugins/nf-amazon/src/main/nextflow/cloud/aws/util/S3CredentialsProvider.groovy
index da693bfd3e..3228e40102 100644
--- a/plugins/nf-amazon/src/main/nextflow/cloud/aws/util/S3CredentialsProvider.groovy
+++ b/plugins/nf-amazon/src/main/nextflow/cloud/aws/util/S3CredentialsProvider.groovy
@@ -23,7 +23,6 @@ import com.amazonaws.auth.AWSCredentialsProvider
 import com.amazonaws.auth.AnonymousAWSCredentials
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
-
 /**
  * AWS credentials provider that delegates the credentials to the
  * specified provider class and fallback to the {@link AnonymousAWSCredentials}
@@ -39,18 +38,22 @@ class S3CredentialsProvider implements AWSCredentialsProvider {
 
     private AWSCredentialsProvider target
 
+    private volatile AWSCredentials anonymous
+
     S3CredentialsProvider(AWSCredentialsProvider target) {
         this.target = target
     }
 
     @Override
     AWSCredentials getCredentials() {
+        if( anonymous!=null )
+            return anonymous
         try {
             return target.getCredentials();
         } catch (AmazonClientException e) {
             log.debug("No AWS credentials available - falling back to anonymous access");
         }
-        return new AnonymousAWSCredentials()
+        return anonymous=new AnonymousAWSCredentials()
     }
 
     @Override

From fff3d7bd15b1217f7bdd9a915cddad423f74d57f Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 16 Sep 2023 10:57:33 +0200
Subject: [PATCH 150/350] Minor improvements

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../src/main/groovy/nextflow/processor/TaskProcessor.groovy     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
index ec00c62d56..e63624d40e 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
@@ -1596,7 +1596,7 @@ class TaskProcessor {
                 def file = workDir.resolve(path)
                 def exists = checkFileExists(file, param.followLinks)
                 if( exists )
-                    result = [file]
+                    result = List.of(file)
                 else
                     log.debug "Process `${safeTaskName(task)}` is unable to find [${file.class.simpleName}]: `$file` (pattern: `$filePattern`)"
             }

From 16f54a9c1654811ddc328ce03adece34769eda7e Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sun, 17 Sep 2023 11:43:48 +0200
Subject: [PATCH 151/350] Improve error report when exception is thrown in
 operator ctx

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../src/main/groovy/nextflow/extension/DataflowHelper.groovy | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/extension/DataflowHelper.groovy b/modules/nextflow/src/main/groovy/nextflow/extension/DataflowHelper.groovy
index 7dcfa70023..dd4cdd5b5a 100644
--- a/modules/nextflow/src/main/groovy/nextflow/extension/DataflowHelper.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/extension/DataflowHelper.groovy
@@ -16,6 +16,8 @@
 
 package nextflow.extension
 
+import java.lang.reflect.InvocationTargetException
+
 import groovy.transform.CompileStatic
 import groovy.transform.PackageScope
 import groovy.util.logging.Slf4j
@@ -91,7 +93,8 @@ class DataflowHelper {
     @PackageScope
     static DEF_ERROR_LISTENER = new DataflowEventAdapter() {
         @Override
-        boolean onException(final DataflowProcessor processor, final Throwable e) {
+        boolean onException(final DataflowProcessor processor, final Throwable t) {
+            final e = t instanceof InvocationTargetException ? t.cause : t
             OperatorImpl.log.error("@unknown", e)
             session?.abort(e)
             return true;

From 144e0a8a1556c4c559913ef060e7605b75950a7c Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sun, 17 Sep 2023 16:40:14 +0200
Subject: [PATCH 152/350] Fix Prevent false positive resumable task

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../nextflow/processor/TaskProcessor.groovy   |  4 +--
 .../groovy/nextflow/trace/TraceRecord.groovy  |  4 +++
 .../nextflow/trace/TraceRecordTest.groovy     | 33 +++++++++++++++++++
 3 files changed, 39 insertions(+), 2 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
index e63624d40e..b4500a95df 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
@@ -793,13 +793,13 @@ class TaskProcessor {
             Path resumeDir = null
             boolean exists = false
             try {
-                def entry = session.cache.getTaskEntry(hash, this)
+                final entry = session.cache.getTaskEntry(hash, this)
                 resumeDir = entry ? FileHelper.asPath(entry.trace.getWorkDir()) : null
                 if( resumeDir )
                     exists = resumeDir.exists()
 
                 log.trace "[${safeTaskName(task)}] Cacheable folder=${resumeDir?.toUriString()} -- exists=$exists; try=$tries; shouldTryCache=$shouldTryCache; entry=$entry"
-                def cached = shouldTryCache && exists && checkCachedOutput(task.clone(), resumeDir, hash, entry)
+                final cached = shouldTryCache && exists && entry.trace.isCompleted() && checkCachedOutput(task.clone(), resumeDir, hash, entry)
                 if( cached )
                     break
             }
diff --git a/modules/nextflow/src/main/groovy/nextflow/trace/TraceRecord.groovy b/modules/nextflow/src/main/groovy/nextflow/trace/TraceRecord.groovy
index 444e185843..40947760b9 100644
--- a/modules/nextflow/src/main/groovy/nextflow/trace/TraceRecord.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/trace/TraceRecord.groovy
@@ -589,6 +589,10 @@ class TraceRecord implements Serializable {
         store.status == 'CACHED'
     }
 
+    boolean isCompleted() {
+        store.status == 'COMPLETED'
+    }
+
     String getExecutorName() {
         return executorName
     }
diff --git a/modules/nextflow/src/test/groovy/nextflow/trace/TraceRecordTest.groovy b/modules/nextflow/src/test/groovy/nextflow/trace/TraceRecordTest.groovy
index d631fc41d3..16568b7392 100644
--- a/modules/nextflow/src/test/groovy/nextflow/trace/TraceRecordTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/trace/TraceRecordTest.groovy
@@ -18,6 +18,7 @@ package nextflow.trace
 
 import groovy.json.JsonSlurper
 import spock.lang.Specification
+import spock.lang.Unroll
 import test.TestHelper
 
 /**
@@ -300,4 +301,36 @@ class TraceRecordTest extends Specification {
         rec.env == 'aws_key=[secure]'
     }
 
+    @Unroll
+    def 'should validate cached status' () {
+        given:
+        def rec = new TraceRecord([status:STATUS])
+
+        expect:
+        rec.isCached() == EXPECTED
+
+        where:
+        STATUS      | EXPECTED
+        null        | false
+        'NEW'       | false
+        'ABORTED'   | false
+        'CACHED'    | true
+    }
+
+    @Unroll
+    def 'should validate completed status' () {
+        given:
+        def rec = new TraceRecord([status:STATUS])
+
+        expect:
+        rec.isCompleted() == EXPECTED
+
+        where:
+        STATUS      | EXPECTED
+        null        | false
+        'NEW'       | false
+        'ABORTED'   | false
+        'COMPLETED' | true
+    }
+
 }

From 5a43a32bc300e44f027ab828a893f470032b54ed Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Sun, 17 Sep 2023 09:59:45 -0500
Subject: [PATCH 153/350] Improve K8s unit tests (#4196) [ci fast]

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../nextflow/k8s/K8sDriverLauncherTest.groovy |  83 +--
 .../nextflow/k8s/K8sTaskHandlerTest.groovy    | 353 ++--------
 .../k8s/model/PodSpecBuilderTest.groovy       | 632 +++++-------------
 3 files changed, 256 insertions(+), 812 deletions(-)

diff --git a/modules/nextflow/src/test/groovy/nextflow/k8s/K8sDriverLauncherTest.groovy b/modules/nextflow/src/test/groovy/nextflow/k8s/K8sDriverLauncherTest.groovy
index 8696f3a41a..8db49f6664 100644
--- a/modules/nextflow/src/test/groovy/nextflow/k8s/K8sDriverLauncherTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/k8s/K8sDriverLauncherTest.groovy
@@ -138,7 +138,6 @@ class K8sDriverLauncherTest extends Specification {
         def pod = Mock(PodOptions)
         pod.getVolumeClaims() >> [ new PodVolumeClaim('pvc-1', '/mnt/path/data') ]
         pod.getMountConfigMaps() >> [ new PodMountConfig('cfg-2', '/mnt/path/cfg') ]
-        pod.getAutomountServiceAccountToken() >> true
 
         def k8s = Mock(K8sConfig)
         k8s.getNextflowImageName() >> 'the-image'
@@ -163,6 +162,7 @@ class K8sDriverLauncherTest extends Specification {
             kind: 'Pod',
             metadata: [name:'foo-boo', namespace:'foo', labels:[app:'nextflow', runName:'foo-boo']],
             spec: [
+                automountServiceAccountToken: false,
                 restartPolicy: 'Never',
                 containers: [
                     [
@@ -197,7 +197,6 @@ class K8sDriverLauncherTest extends Specification {
         def pod = Mock(PodOptions)
         pod.getVolumeClaims() >> [ new PodVolumeClaim('pvc-1', '/mnt/path/data') ]
         pod.getMountConfigMaps() >> [ new PodMountConfig('cfg-2', '/mnt/path/cfg') ]
-        pod.getAutomountServiceAccountToken() >> true
 
         def k8s = Mock(K8sConfig)
         k8s.getNextflowImageName() >> 'the-image'
@@ -230,6 +229,7 @@ class K8sDriverLauncherTest extends Specification {
                 template: [
                     metadata: metadata,
                     spec: [
+                        automountServiceAccountToken: false,
                         restartPolicy: 'Never',
                         containers: [
                             [
@@ -265,7 +265,6 @@ class K8sDriverLauncherTest extends Specification {
         def pod = Mock(PodOptions)
         pod.getVolumeClaims() >> [ new PodVolumeClaim('pvc-1', '/mnt/path/data') ]
         pod.getMountConfigMaps() >> [ new PodMountConfig('cfg-2', '/mnt/path/cfg') ]
-        pod.getAutomountServiceAccountToken() >> true
 
         def k8s = Mock(K8sConfig)
         k8s.getLaunchDir() >> '/the/user/dir'
@@ -281,40 +280,11 @@ class K8sDriverLauncherTest extends Specification {
         driver.@headImage = 'foo/bar'
 
         when:
-        def spec = driver.makeLauncherSpec()
+        def result = driver.makeLauncherSpec()
         then:
         driver.getLaunchCli() >> 'nextflow run foo'
-
-        spec == [
-            apiVersion: 'v1',
-            kind: 'Pod',
-            metadata: [name:'foo-boo', namespace:'foo', labels:[app:'nextflow', runName:'foo-boo']],
-            spec: [
-                restartPolicy: 'Never',
-                containers: [
-                    [
-                        name: 'foo-boo',
-                        image: 'foo/bar',
-                        command: ['/bin/bash', '-c', "source /etc/nextflow/init.sh; nextflow run foo"],
-                        env: [
-                            [name:'NXF_WORK', value:'/the/work/dir'],
-                            [name:'NXF_ASSETS', value:'/the/project/dir'],
-                            [name:'NXF_EXECUTOR', value:'k8s'],
-                            [name:'NXF_ANSI_LOG', value: 'false']
-                        ],
-                        volumeMounts: [
-                            [name:'vol-1', mountPath:'/mnt/path/data'],
-                            [name:'vol-2', mountPath:'/mnt/path/cfg']
-                        ]
-                    ]
-                ],
-                serviceAccountName: 'bar',
-                volumes: [
-                    [name:'vol-1', persistentVolumeClaim:[claimName:'pvc-1']],
-                    [name:'vol-2', configMap:[name:'cfg-2'] ]
-                ]
-            ]
-        ]
+        and:
+        result.spec.containers[0].image == 'foo/bar'
 
     }
 
@@ -324,9 +294,9 @@ class K8sDriverLauncherTest extends Specification {
         def pod = Mock(PodOptions)
         pod.getVolumeClaims() >> [ new PodVolumeClaim('pvc-1', '/mnt/path/data') ]
         pod.getMountConfigMaps() >> [ new PodMountConfig('cfg-2', '/mnt/path/cfg') ]
-        pod.getAutomountServiceAccountToken() >> true
 
         def k8s = Mock(K8sConfig)
+        k8s.getNextflowImageName() >> 'the-image'
         k8s.getLaunchDir() >> '/the/user/dir'
         k8s.getWorkDir() >> '/the/work/dir'
         k8s.getProjectDir() >> '/the/project/dir'
@@ -337,48 +307,17 @@ class K8sDriverLauncherTest extends Specification {
         driver.@runName = 'foo-boo'
         driver.@k8sClient = new K8sClient(new ClientConfig(namespace: 'foo', serviceAccount: 'bar'))
         driver.@k8sConfig = k8s
-        driver.@headImage = 'foo/bar'
         driver.@headCpus = 2
         driver.@headMemory = '200Mi'
 
         when:
-        def spec = driver.makeLauncherSpec()
+        def result = driver.makeLauncherSpec()
         then:
         driver.getLaunchCli() >> 'nextflow run foo'
-
-        spec == [
-            apiVersion: 'v1',
-            kind: 'Pod',
-            metadata: [name:'foo-boo', namespace:'foo', labels:[app:'nextflow', runName:'foo-boo']],
-            spec: [
-                restartPolicy: 'Never',
-                containers: [
-                    [
-                        name: 'foo-boo',
-                        image: 'foo/bar',
-                        command: ['/bin/bash', '-c', "source /etc/nextflow/init.sh; nextflow run foo"],
-                        env: [
-                            [name:'NXF_WORK', value:'/the/work/dir'],
-                            [name:'NXF_ASSETS', value:'/the/project/dir'],
-                            [name:'NXF_EXECUTOR', value:'k8s'],
-                            [name:'NXF_ANSI_LOG', value: 'false']
-                        ],
-                        resources: [
-                            requests: [cpu: 2, memory: '200Mi'],
-                            limits: [memory: '200Mi']
-                        ],
-                        volumeMounts: [
-                            [name:'vol-1', mountPath:'/mnt/path/data'],
-                            [name:'vol-2', mountPath:'/mnt/path/cfg']
-                        ]
-                    ]
-                ],
-                serviceAccountName: 'bar',
-                volumes: [
-                    [name:'vol-1', persistentVolumeClaim:[claimName:'pvc-1']],
-                    [name:'vol-2', configMap:[name:'cfg-2'] ]
-                ]
-            ]
+        and:
+        result.spec.containers[0].resources == [
+            requests: [cpu: 2, memory: '200Mi'],
+            limits: [memory: '200Mi']
         ]
 
     }
diff --git a/modules/nextflow/src/test/groovy/nextflow/k8s/K8sTaskHandlerTest.groovy b/modules/nextflow/src/test/groovy/nextflow/k8s/K8sTaskHandlerTest.groovy
index 4d6f06af2f..1433ab5b3f 100644
--- a/modules/nextflow/src/test/groovy/nextflow/k8s/K8sTaskHandlerTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/k8s/K8sTaskHandlerTest.groovy
@@ -52,7 +52,7 @@ class K8sTaskHandlerTest extends Specification {
         PodSpecBuilder.VOLUMES.set(0)
     }
 
-    def 'should return a new pod with args' () {
+    def 'should return a new pod request' () {
         given:
         def WORK_DIR = Paths.get('/some/work/dir')
         def config = Mock(TaskConfig)
@@ -79,136 +79,24 @@ class K8sTaskHandlerTest extends Specification {
         1 * config.getCpus() >> 0
         1 * config.getMemory() >> null
         1 * client.getConfig() >> new ClientConfig()
-        result == [ apiVersion: 'v1',
-                    kind: 'Pod',
-                    metadata: [
-                            name:'nf-123',
-                            namespace:'default'
-                    ],
-                    spec: [
-                            restartPolicy:'Never',
-                            containers:[
-                                    [name:'nf-123',
-                                     image:'debian:latest',
-                                     args:['/bin/bash', '-ue','/some/work/dir/.command.run'] ]
-                            ]
-                    ]
-        ]
-
-        when:
-        result = handler.newSubmitRequest(task)
-        then:
-        _ * handler.fusionEnabled() >> false
-        1 * handler.entrypointOverride() >> true
-        1 * handler.getSyntheticPodName(task) >> 'nf-foo'
-        1 * handler.getLabels(task) >> [sessionId:'xxx']
-        1 * handler.getAnnotations() >>  [evict: 'false']
-        1 * handler.getPodOptions() >> new PodOptions()
-        1 * handler.getContainerMounts() >> []
-        1 * handler.fixOwnership() >> true
-        1 * handler.getOwner() >> '501:502'
-        1 * task.getContainer() >> 'debian:latest'
-        1 * task.getWorkDir() >> WORK_DIR
-        1 * task.getConfig() >> config
-        1 * config.getCpus() >> 1
-        1 * config.getMemory() >> null
-        1 * client.getConfig() >> new ClientConfig()
-        result == [ apiVersion: 'v1',
-                    kind: 'Pod',
-                    metadata: [name:'nf-foo', namespace:'default', labels: [sessionId: 'xxx'], annotations: [evict: 'false']],
-                    spec: [
-                            restartPolicy:'Never',
-                            containers:[
-                                    [name:'nf-foo',
-                                     image:'debian:latest',
-                                     command:['/bin/bash', '-ue','/some/work/dir/.command.run'],
-                                     resources:[ requests: [cpu:1] ],
-                                     env: [  [name:'NXF_OWNER', value:'501:502'] ]
-                                    ]
-                            ]
-                    ]
-        ]
-
-
-        when:
-        result = handler.newSubmitRequest(task)
-        then:
-        _ * handler.fusionEnabled() >> false
-        1 * handler.fixOwnership() >> false
-        1 * handler.entrypointOverride() >> true
-        1 * handler.getSyntheticPodName(task) >> 'nf-abc'
-        1 * handler.getLabels(task) >> [:]
-        1 * handler.getAnnotations() >> [:]
-        1 * handler.getPodOptions() >> new PodOptions()
-        1 * handler.getContainerMounts() >> []
-        1 * task.getContainer() >> 'user/alpine:1.0'
-        1 * task.getWorkDir() >> WORK_DIR
-        1 * task.getConfig() >> config
-        1 * config.getCpus() >> 4
-        1 * config.getMemory() >> MemoryUnit.of('16GB')
-        1 * client.getConfig() >> new ClientConfig(namespace: 'namespace-x')
-        result == [ apiVersion: 'v1',
-                    kind: 'Pod',
-                    metadata: [name:'nf-abc', namespace:'namespace-x' ],
-                    spec: [
-                            restartPolicy:'Never',
-                            containers:[
-                                    [name:'nf-abc',
-                                     image:'user/alpine:1.0',
-                                     command:['/bin/bash', '-ue', '/some/work/dir/.command.run'],
-                                     resources:[ requests: [cpu:4, memory:'16384Mi'], limits:[memory:'16384Mi'] ]
-                                    ]
-                            ]
-                    ]
+        and:
+        result == [
+            apiVersion: 'v1',
+            kind: 'Pod',
+            metadata: [
+                name:'nf-123',
+                namespace:'default'
+            ],
+            spec: [
+                restartPolicy:'Never',
+                containers: [[
+                    name:'nf-123',
+                    image:'debian:latest',
+                    args:['/bin/bash', '-ue','/some/work/dir/.command.run']
+                ]]
+            ]
         ]
 
-    }
-
-    def 'should return a new pod request with no storage' () {
-        given:
-        def WORK_DIR = Paths.get('/some/work/dir')
-        def config = Mock(TaskConfig)
-        def task = Mock(TaskRun)
-        def client = Mock(K8sClient)
-        def builder = Mock(K8sWrapperBuilder)
-        def handler = Spy(new K8sTaskHandler(builder: builder, client:client))
-        Map result
-
-        when:
-        result = handler.newSubmitRequest(task)
-        then:
-        _ * handler.fusionEnabled() >> false
-        1 * handler.fixOwnership() >> false
-        1 * handler.entrypointOverride() >> true
-        1 * handler.getPodOptions() >> new PodOptions()
-        1 * handler.getSyntheticPodName(task) >> 'nf-123'
-        1 * handler.getLabels(task) >> [foo: 'bar', hello: 'world']
-        1 * handler.getAnnotations() >> [fooz: 'barz', ciao: 'mondo']
-        1 * handler.getContainerMounts() >> []
-        1 * task.getContainer() >> 'debian:latest'
-        1 * task.getWorkDir() >> WORK_DIR
-        1 * task.getConfig() >> config
-        1 * config.getCpus() >> 0
-        1 * config.getMemory() >> null
-        1 * client.getConfig() >> new ClientConfig()
-        result == [ apiVersion: 'v1',
-                    kind: 'Pod',
-                    metadata: [
-                            name:'nf-123',
-                            namespace:'default',
-                            labels:[ foo:'bar', hello: 'world'],
-                            annotations:[ fooz:'barz', ciao: 'mondo']
-                    ],
-                    spec: [
-                            restartPolicy:'Never',
-                            containers:[
-                                    [name:'nf-123',
-                                     image:'debian:latest',
-                                     command:['/bin/bash', '-ue','/some/work/dir/.command.run'] ]
-                            ]
-                    ]
-                ]
-
         when:
         result = handler.newSubmitRequest(task)
         then:
@@ -227,21 +115,12 @@ class K8sTaskHandlerTest extends Specification {
         1 * config.getCpus() >> 1
         1 * config.getMemory() >> null
         1 * client.getConfig() >> new ClientConfig()
-        result == [ apiVersion: 'v1',
-                    kind: 'Pod',
-                    metadata: [name:'nf-foo', namespace:'default', labels: [sessionId: 'xxx'], annotations: [evict: 'false']],
-                    spec: [
-                            restartPolicy:'Never',
-                            containers:[
-                                    [name:'nf-foo',
-                                     image:'debian:latest',
-                                     command:['/bin/bash', '-ue','/some/work/dir/.command.run'],
-                                     resources:[ requests: [cpu:1] ],
-                                     env: [  [name:'NXF_OWNER', value:'501:502'] ]
-                                    ]
-                            ]
-                    ]
-        ]
+        and:
+        result.metadata.labels == [sessionId: 'xxx']
+        result.metadata.annotations == [evict: 'false']
+        result.spec.containers[0].command == ['/bin/bash', '-ue', '/some/work/dir/.command.run']
+        result.spec.containers[0].resources == [ requests: [cpu:1] ]
+        result.spec.containers[0].env == [ [name:'NXF_OWNER', value:'501:502'] ]
 
         when:
         result = handler.newSubmitRequest(task)
@@ -260,20 +139,11 @@ class K8sTaskHandlerTest extends Specification {
         1 * config.getCpus() >> 4
         1 * config.getMemory() >> MemoryUnit.of('16GB')
         1 * client.getConfig() >> new ClientConfig(namespace: 'namespace-x')
-        result == [ apiVersion: 'v1',
-                    kind: 'Pod',
-                    metadata: [name:'nf-abc', namespace:'namespace-x' ],
-                    spec: [
-                            restartPolicy:'Never',
-                            containers:[
-                                    [name:'nf-abc',
-                                     image:'user/alpine:1.0',
-                                     command:['/bin/bash', '-ue', '/some/work/dir/.command.run'],
-                                     resources:[ requests: [cpu:4, memory:'16384Mi'], limits: [memory:'16384Mi'] ]
-                                    ]
-                            ]
-                    ]
-        ]
+        and:
+        result.metadata.namespace == 'namespace-x'
+        result.spec.containers[0].image == 'user/alpine:1.0'
+        result.spec.containers[0].command == ['/bin/bash', '-ue', '/some/work/dir/.command.run']
+        result.spec.containers[0].resources == [ requests: [cpu:4, memory:'16384Mi'], limits: [memory:'16384Mi'] ]
 
     }
 
@@ -306,22 +176,8 @@ class K8sTaskHandlerTest extends Specification {
         1 * config.getCpus() >> 0
         1 * config.getMemory() >> null
         1 * client.getConfig() >> new ClientConfig()
-        result == [ apiVersion: 'v1',
-                    kind: 'Pod',
-                    metadata: [
-                            name:'nf-123',
-                            namespace:'default'
-                    ],
-                    spec: [
-                            restartPolicy:'Never',
-                            containers:[
-                                    [name:'nf-123',
-                                     image:'debian:latest',
-                                     args:['/bin/bash', '-ue','/some/work/dir/.command.run'],
-                                     env:[[name:'NXF_DEBUG', value:'true']] ]
-                            ]
-                    ]
-        ]
+        and:
+        result.spec.containers[0].env == [[name:'NXF_DEBUG', value:'true']]
 
         cleanup:
         SysEnv.pop()
@@ -355,22 +211,9 @@ class K8sTaskHandlerTest extends Specification {
         1 * client.getConfig() >> config
         1 * config.getNamespace() >> 'just-a-namespace'
         1 * config.getServiceAccount() >> 'pedantic-kallisto'
-
-        result == [ apiVersion: 'v1',
-                    kind: 'Pod',
-                    metadata: [name:'nf-123', namespace:'just-a-namespace' ],
-                    spec: [
-                            serviceAccountName: 'pedantic-kallisto',
-                            restartPolicy:'Never',
-                            containers:[
-                                    [name:'nf-123',
-                                     image:'debian:latest',
-                                     command:['/bin/bash', '-ue','/some/work/dir/.command.run'],
-                                     resources:[requests:[cpu:1]]
-                                    ]
-                            ]
-                    ]
-        ]
+        and:
+        result.metadata.namespace == 'just-a-namespace'
+        result.spec.serviceAccountName == 'pedantic-kallisto'
 
     }
 
@@ -385,7 +228,6 @@ class K8sTaskHandlerTest extends Specification {
         def handler = Spy(new K8sTaskHandler(builder:builder, client:client))
         def podOptions = Mock(PodOptions)
         and:
-        podOptions.automountServiceAccountToken >> true
         Map result
 
         when:
@@ -406,30 +248,15 @@ class K8sTaskHandlerTest extends Specification {
         2 * podOptions.getEnvVars() >> [ PodEnv.value('FOO','bar') ]
         2 * podOptions.getMountSecrets() >> [ new PodMountSecret('my-secret/key-z', '/data/secret.txt') ]
         2 * podOptions.getMountConfigMaps() >> [ new PodMountConfig('my-data/key-x', '/etc/file.txt') ]
-
-        result == [
-            apiVersion: 'v1',
-            kind: 'Pod',
-            metadata: [name:'nf-123', namespace:'default' ],
-            spec: [
-                restartPolicy: 'Never',
-                containers: [
-                    [
-                        name: 'nf-123',
-                        image: 'debian:latest',
-                        command: ['/bin/bash', '-ue','/some/work/dir/.command.run'],
-                        env: [[name:'FOO', value:'bar']],
-                        volumeMounts: [
-                            [name:'vol-1', mountPath:'/etc'],
-                            [name:'vol-2', mountPath:'/data']
-                        ]
-                    ]
-                ],
-                volumes:[
-                    [name:'vol-1', configMap:[name:'my-data', items:[[key:'key-x', path:'file.txt']]]],
-                    [name:'vol-2', secret:[secretName:'my-secret', items:[[key:'key-z', path:'secret.txt']]]]
-                ]
-            ]
+        and:
+        result.spec.containers[0].env == [[name:'FOO', value:'bar']]
+        result.spec.containers[0].volumeMounts == [
+            [name:'vol-1', mountPath:'/etc'],
+            [name:'vol-2', mountPath:'/data']
+        ]
+        result.spec.volumes == [
+            [name:'vol-1', configMap:[name:'my-data', items:[[key:'key-x', path:'file.txt']]]],
+            [name:'vol-2', secret:[secretName:'my-secret', items:[[key:'key-z', path:'secret.txt']]]]
         ]
 
     }
@@ -443,13 +270,10 @@ class K8sTaskHandlerTest extends Specification {
         def client = Mock(K8sClient)
         def builder = Mock(K8sWrapperBuilder)
         def handler = Spy(new K8sTaskHandler(builder:builder, client:client))
+        def podOptions = Mock(PodOptions)
         and:
         Map result
 
-        def podOptions = Mock(PodOptions)
-        def CLAIMS = [ new PodVolumeClaim('first','/work'), new PodVolumeClaim('second','/data') ]
-        podOptions.automountServiceAccountToken >> true
-
         when:
         result = handler.newSubmitRequest(task)
         then:
@@ -467,32 +291,19 @@ class K8sTaskHandlerTest extends Specification {
         1 * config.getCpus() >> 0
         1 * config.getMemory() >> null
         1 * client.getConfig() >> new ClientConfig()
-        2 * podOptions.getVolumeClaims() >> CLAIMS
-
-        result == [
-            apiVersion: 'v1',
-            kind: 'Pod',
-            metadata: [name:'nf-123', namespace:'default'],
-            spec: [
-                restartPolicy: 'Never',
-                containers: [
-                    [
-                        name: 'nf-123',
-                        image: 'debian:latest',
-                        command: ['/bin/bash', '-ue', '/some/work/dir/.command.run'],
-                        volumeMounts: [
-                            [name:'vol-1', mountPath:'/work'],
-                            [name:'vol-2', mountPath:'/data']
-                        ]
-                    ]
-                ],
-                volumes: [
-                    [name:'vol-1', persistentVolumeClaim:[claimName: 'first']],
-                    [name:'vol-2', persistentVolumeClaim:[claimName: 'second']]
-                ]
-            ]
+        2 * podOptions.getVolumeClaims() >> [
+            new PodVolumeClaim('first','/work'),
+            new PodVolumeClaim('second','/data')
+        ]
+        and:
+        result.spec.containers[0].volumeMounts == [
+            [name:'vol-1', mountPath:'/work'],
+            [name:'vol-2', mountPath:'/data']
+        ]
+        result.spec.volumes == [
+            [name:'vol-1', persistentVolumeClaim:[claimName: 'first']],
+            [name:'vol-2', persistentVolumeClaim:[claimName: 'second']]
         ]
-
 
         when:
         result = handler.newSubmitRequest(task)
@@ -511,29 +322,14 @@ class K8sTaskHandlerTest extends Specification {
         1 * config.getCpus() >> 0
         1 * config.getMemory() >> null
         1 * client.getConfig() >> new ClientConfig()
-
-        result == [
-            apiVersion: 'v1',
-            kind: 'Pod',
-            metadata: [name:'nf-123', namespace:'default'],
-            spec: [
-                restartPolicy: 'Never',
-                containers: [
-                    [
-                        name: 'nf-123',
-                        image: 'debian:latest',
-                        command: ['/bin/bash', '-ue', '/some/work/dir/.command.run'],
-                        volumeMounts: [
-                            [name:'vol-3', mountPath:'/tmp'],
-                            [name:'vol-4', mountPath: '/data']
-                        ]
-                    ]
-                ],
-                volumes: [
-                    [name:'vol-3', hostPath:[path:'/tmp']],
-                    [name:'vol-4', hostPath:[path:'/data']]
-                ]
-            ]
+        and:
+        result.spec.containers[0].volumeMounts == [
+            [name:'vol-3', mountPath:'/tmp'],
+            [name:'vol-4', mountPath: '/data']
+        ]
+        result.spec.volumes == [
+            [name:'vol-3', hostPath:[path:'/tmp']],
+            [name:'vol-4', hostPath:[path:'/data']]
         ]
 
     }
@@ -584,7 +380,6 @@ class K8sTaskHandlerTest extends Specification {
         def handler = Spy(new K8sTaskHandler(builder: builder, client: client, executor: executor))
         def podOptions = Mock(PodOptions)
         and:
-        podOptions.automountServiceAccountToken >> true
         Map result
 
         when:
@@ -613,6 +408,7 @@ class K8sTaskHandlerTest extends Specification {
                 template: [
                     metadata: [name: 'nf-123', namespace: 'default'],
                     spec: [
+                        automountServiceAccountToken: false,
                         restartPolicy: 'Never',
                         containers: [[
                             name: 'nf-123',
@@ -1123,23 +919,10 @@ class K8sTaskHandlerTest extends Specification {
         1 * config.getCpus() >> 0
         1 * config.getMemory() >> null
         1 * client.getConfig() >> new ClientConfig()
-        result == [ apiVersion: 'v1',
-                    kind: 'Pod',
-                    metadata: [
-                            name:'nf-123',
-                            namespace:'default'
-                    ],
-                    spec: [
-                            restartPolicy:'Never',
-                            containers:[
-                                    [name:'nf-123',
-                                     image:'debian:latest',
-                                     args:['/usr/bin/fusion', 'bash', '/fusion/http/work/dir/.command.run'],
-                                     securityContext:[privileged:true],
-                                     env:[[name:'FUSION_BUCKETS', value:'this,that']]]
-                            ]
-                    ]
-        ]
+        and:
+        result.spec.containers[0].args == ['/usr/bin/fusion', 'bash', '/fusion/http/work/dir/.command.run']
+        result.spec.containers[0].securityContext == [privileged:true]
+        result.spec.containers[0].env == [[name:'FUSION_BUCKETS', value:'this,that']]
      }
 
     def 'get fusion submit command' () {
diff --git a/modules/nextflow/src/test/groovy/nextflow/k8s/model/PodSpecBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/k8s/model/PodSpecBuilderTest.groovy
index d04cbc1849..e808d0c08e 100644
--- a/modules/nextflow/src/test/groovy/nextflow/k8s/model/PodSpecBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/k8s/model/PodSpecBuilderTest.groovy
@@ -41,19 +41,19 @@ class PodSpecBuilderTest extends Specification {
                 .build()
 
         then:
-        spec ==  [ apiVersion: 'v1',
-                   kind: 'Pod',
-                   metadata: [name:'foo', namespace:'default'],
-                   spec: [
-                           restartPolicy:'Never',
-                           containers:[
-                                   [name:'foo',
-                                    image:'busybox',
-                                    command:['echo', 'hello'],
-                                    workingDir:'/some/work/dir'
-                                   ]
-                           ]
-                   ]
+        spec == [
+                apiVersion: 'v1',
+                kind: 'Pod',
+                metadata: [name:'foo', namespace:'default'],
+                spec: [
+                        restartPolicy:'Never',
+                        containers:[[
+                                name:'foo',
+                                image:'busybox',
+                                command:['echo', 'hello'],
+                                workingDir:'/some/work/dir'
+                        ]]
+                ]
         ]
 
     }
@@ -61,63 +61,35 @@ class PodSpecBuilderTest extends Specification {
     def 'should create pod spec with args' () {
 
         when:
-        def spec = new PodSpecBuilder()
+        def pod = new PodSpecBuilder()
                 .withPodName('foo')
                 .withImageName('busybox')
-                .withWorkDir('/some/work/dir')
                 .withArgs(['echo', 'hello'])
                 .build()
 
         then:
-        spec ==  [ apiVersion: 'v1',
-                   kind: 'Pod',
-                   metadata: [name:'foo', namespace:'default'],
-                   spec: [
-                           restartPolicy:'Never',
-                           containers:[
-                                   [name:'foo',
-                                    image:'busybox',
-                                    args:['echo', 'hello'],
-                                    workingDir:'/some/work/dir'
-                                   ]
-                           ]
-                   ]
-        ]
+        pod.spec.containers[0].args == ['echo', 'hello']
 
     }
 
     def 'should create pod spec with args string' () {
 
         when:
-        def spec = new PodSpecBuilder()
+        def pod = new PodSpecBuilder()
                 .withPodName('foo')
                 .withImageName('busybox')
-                .withWorkDir('/some/work/dir')
                 .withArgs('echo foo')
                 .build()
 
         then:
-        spec ==  [ apiVersion: 'v1',
-                   kind: 'Pod',
-                   metadata: [name:'foo', namespace:'default'],
-                   spec: [
-                           restartPolicy:'Never',
-                           containers:[
-                                   [name:'foo',
-                                    image:'busybox',
-                                    args:['/bin/bash', '-c', 'echo foo'],
-                                    workingDir:'/some/work/dir'
-                                   ]
-                           ]
-                   ]
-        ]
+        pod.spec.containers[0].args == ['/bin/bash', '-c', 'echo foo']
 
     }
 
     def 'should create pod spec with privileged' () {
 
         when:
-        def spec = new PodSpecBuilder()
+        def pod = new PodSpecBuilder()
                 .withPodName('foo')
                 .withImageName('busybox')
                 .withCommand('echo foo')
@@ -125,27 +97,14 @@ class PodSpecBuilderTest extends Specification {
                 .build()
 
         then:
-        spec ==  [ apiVersion: 'v1',
-                   kind: 'Pod',
-                   metadata: [name:'foo', namespace:'default'],
-                   spec: [
-                           restartPolicy:'Never',
-                           containers:[
-                                   [name:'foo',
-                                    image:'busybox',
-                                    command:['/bin/bash', '-c', 'echo foo'],
-                                    securityContext: [privileged: true]
-                                   ]
-                           ]
-                   ]
-        ]
+        pod.spec.containers[0].securityContext == [privileged: true]
 
     }
 
     def 'should create pod spec with device and capabilities' () {
 
         when:
-        def spec = new PodSpecBuilder()
+        def pod = new PodSpecBuilder()
                 .withPodName('foo')
                 .withImageName('busybox')
                 .withCommand('echo foo')
@@ -154,31 +113,17 @@ class PodSpecBuilderTest extends Specification {
                 .build()
 
         then:
-        spec ==  [ apiVersion: 'v1',
-                   kind: 'Pod',
-                   metadata: [name:'foo', namespace:'default'],
-                   spec: [
-                           restartPolicy:'Never',
-                           containers:[
-                                   [name:'foo',
-                                    image:'busybox',
-                                    command:['/bin/bash', '-c', 'echo foo'],
-                                    devices: ['/dev/fuse'],
-                                    securityContext: [capabilities: [add:['SYS_ADMIN']]]
-                                   ]
-                           ]
-                   ]
-        ]
+        pod.spec.containers[0].devices == ['/dev/fuse']
+        pod.spec.containers[0].securityContext == [capabilities: [add:['SYS_ADMIN']]]
 
     }
 
     def 'should set namespace, labels and annotations' () {
 
         when:
-        def spec = new PodSpecBuilder()
+        def pod = new PodSpecBuilder()
                 .withPodName('foo')
                 .withImageName('busybox')
-                .withWorkDir('/some/work/dir')
                 .withCommand(['sh', '-c', 'echo hello'])
                 .withNamespace('xyz')
                 .withLabel('app','myApp')
@@ -189,81 +134,39 @@ class PodSpecBuilderTest extends Specification {
                 .build()
 
         then:
-        spec ==  [ apiVersion: 'v1',
-                   kind: 'Pod',
-                   metadata: [
-                           name:'foo',
-                           namespace:'xyz',
-                           labels: [
-                                   app: 'myApp',
-                                   runName: 'something',
-                                   version: '3.6.1'
-                           ],
-                           annotations: [
-                                   anno1: "value1",
-                                   anno2: "value2",
-                                   anno3: "value3"
-                           ]
-                   ],
-                   spec: [
-                           restartPolicy:'Never',
-                           containers:[
-                                   [name:'foo',
-                                    image:'busybox',
-                                    command: ['sh', '-c', 'echo hello'],
-                                    workingDir:'/some/work/dir'
-                                   ]
-                           ]
-                   ]
+        pod.metadata.namespace == 'xyz'
+        pod.metadata.labels == [
+                app: 'myApp',
+                runName: 'something',
+                version: '3.6.1'
+        ]
+        pod.metadata.annotations == [
+                anno1: "value1",
+                anno2: "value2",
+                anno3: "value3"
         ]
     }
     
     def 'should truncate labels longer than 63 chars' () {
 
         when:
-        def spec = new PodSpecBuilder()
+        def pod = new PodSpecBuilder()
                 .withPodName('foo')
                 .withImageName('busybox')
-                .withWorkDir('/some/work/dir')
                 .withCommand(['sh', '-c', 'echo hello'])
-                .withNamespace('xyz')
                 .withLabel('app','myApp')
                 .withLabel('runName','something')
                 .withLabel('tag','somethingreallylonggggggggggggggggggggggggggggggggggggggggggendEXTRABIT')
                 .withLabels([tag2: 'somethingreallylonggggggggggggggggggggggggggggggggggggggggggendEXTRABIT', tag3: 'somethingreallylonggggggggggggggggggggggggggggggggggggggggggendEXTRABIT'])
-                .withAnnotation("anno1", "value1")
-                .withAnnotations([anno2: "value2", anno3: "value3"])
                 .build()
 
         then:
-        spec ==  [ apiVersion: 'v1',
-                   kind: 'Pod',
-                   metadata: [
-                           name:'foo',
-                           namespace:'xyz',
-                           labels: [
-                                   app: 'myApp',
-                                   runName: 'something',
-                                   tag: 'somethingreallylonggggggggggggggggggggggggggggggggggggggggggend',
-                                   tag2: 'somethingreallylonggggggggggggggggggggggggggggggggggggggggggend',
-                                   tag3: 'somethingreallylonggggggggggggggggggggggggggggggggggggggggggend'
-                           ],
-                           annotations: [
-                                   anno1: "value1",
-                                   anno2: "value2",
-                                   anno3: "value3"
-                           ]
-                   ],
-                   spec: [
-                           restartPolicy:'Never',
-                           containers:[
-                                   [name:'foo',
-                                    image:'busybox',
-                                    command: ['sh', '-c', 'echo hello'],
-                                    workingDir:'/some/work/dir'
-                                   ]
-                           ]
-                   ]
+        pod.metadata.labels == [
+                app: 'myApp',
+                runName: 'something',
+                tag: 'somethingreallylonggggggggggggggggggggggggggggggggggggggggggend',
+                tag2: 'somethingreallylonggggggggggggggggggggggggggggggggggggggggggend',
+                tag3: 'somethingreallylonggggggggggggggggggggggggggggggggggggggggggend'
         ]
     }
 
@@ -271,11 +174,10 @@ class PodSpecBuilderTest extends Specification {
     def 'should set resources and env' () {
 
         when:
-        def spec = new PodSpecBuilder()
+        def pod = new PodSpecBuilder()
                 .withPodName('foo')
                 .withImageName('busybox')
                 .withCommand('echo hello')
-                .withWorkDir('/some/work/dir')
                 .withEnv(PodEnv.value('ALPHA','hello'))
                 .withEnv(PodEnv.value('DELTA', 'world'))
                 .withCpus(8)
@@ -285,64 +187,37 @@ class PodSpecBuilderTest extends Specification {
                 .build()
 
         then:
-        spec ==  [ apiVersion: 'v1',
-                   kind: 'Pod',
-                   metadata: [name:'foo', namespace:'default'],
-                   spec: [
-                           restartPolicy:'Never',
-                           containers:[
-                                   [name:'foo',
-                                    image:'busybox',
-                                    command:['/bin/bash', '-c', 'echo hello'],
-                                    workingDir:'/some/work/dir',
-                                    env: [
-                                            [name:'ALPHA', value:'hello'],
-                                            [name:'DELTA', value:'world']
-                                    ],
-                                    resources:[
-                                            requests: ['foo.org/gpu':5, cpu:8, memory:'100Gi', 'ephemeral-storage':'10Gi'],
-                                            limits: ['foo.org/gpu':10, memory:'100Gi', 'ephemeral-storage':'10Gi']
-                                    ]
-                                   ]
-                           ]
-                   ]
+        pod.spec.containers[0].env == [
+                [name:'ALPHA', value:'hello'],
+                [name:'DELTA', value:'world']
+        ]
+        pod.spec.containers[0].resources == [
+                requests: ['foo.org/gpu':5, cpu:8, memory:'100Gi', 'ephemeral-storage':'10Gi'],
+                limits: ['foo.org/gpu':10, memory:'100Gi', 'ephemeral-storage':'10Gi']
         ]
     }
 
     def 'should get storage spec for volume claims' () {
 
         when:
-        def spec = new PodSpecBuilder()
+        def pod = new PodSpecBuilder()
                     .withPodName('foo')
                     .withImageName('busybox')
-                    .withWorkDir('/path')
                     .withCommand(['echo'])
                     .withVolumeClaim(new PodVolumeClaim('first','/work'))
                     .withVolumeClaim(new PodVolumeClaim('second', '/data', '/foo'))
                     .withVolumeClaim(new PodVolumeClaim('third', '/things', null, true))
                     .build()
         then:
-        spec ==  [ apiVersion: 'v1',
-                   kind: 'Pod',
-                   metadata: [name:'foo', namespace:'default'],
-                   spec: [
-                           restartPolicy:'Never',
-                           containers:[
-                                   [name:'foo',
-                                    image:'busybox',
-                                    command: ['echo'],
-                                    workingDir:'/path',
-                                    volumeMounts:[
-                                            [name:'vol-1', mountPath:'/work'],
-                                            [name:'vol-2', mountPath:'/data', subPath: '/foo'],
-                                            [name:'vol-3', mountPath:'/things', readOnly: true]] ]
-                           ],
-                           volumes:[
-                                   [name:'vol-1', persistentVolumeClaim:[claimName:'first']],
-                                   [name:'vol-2', persistentVolumeClaim:[claimName:'second']],
-                                   [name:'vol-3', persistentVolumeClaim:[claimName:'third']] ]
-                   ]
-
+        pod.spec.containers[0].volumeMounts == [
+                [name:'vol-1', mountPath:'/work'],
+                [name:'vol-2', mountPath:'/data', subPath: '/foo'],
+                [name:'vol-3', mountPath:'/things', readOnly: true]
+        ]
+        pod.spec.volumes == [
+                [name:'vol-1', persistentVolumeClaim:[claimName:'first']],
+                [name:'vol-2', persistentVolumeClaim:[claimName:'second']],
+                [name:'vol-3', persistentVolumeClaim:[claimName:'third']]
         ]
 
     }
@@ -350,10 +225,9 @@ class PodSpecBuilderTest extends Specification {
     def 'should only define one volume per persistentVolumeClaim' () {
 
         when:
-        def spec = new PodSpecBuilder()
+        def pod = new PodSpecBuilder()
                 .withPodName('foo')
                 .withImageName('busybox')
-                .withWorkDir('/path')
                 .withCommand(['echo'])
                 .withVolumeClaim(new PodVolumeClaim('first','/work'))
                 .withVolumeClaim(new PodVolumeClaim('first','/work2', '/bar'))
@@ -361,27 +235,15 @@ class PodSpecBuilderTest extends Specification {
                 .withVolumeClaim(new PodVolumeClaim('second', '/data2', '/fooz'))
                 .build()
         then:
-        spec ==  [ apiVersion: 'v1',
-                   kind: 'Pod',
-                   metadata: [name:'foo', namespace:'default'],
-                   spec: [
-                           restartPolicy:'Never',
-                           containers:[
-                                   [name:'foo',
-                                    image:'busybox',
-                                    command: ['echo'],
-                                    workingDir:'/path',
-                                    volumeMounts:[
-                                            [name:'vol-1', mountPath:'/work'],
-                                            [name:'vol-1', mountPath:'/work2', subPath: '/bar'],
-                                            [name:'vol-2', mountPath:'/data', subPath: '/foo'],
-                                            [name:'vol-2', mountPath:'/data2', subPath: '/fooz']]]
-                           ],
-                           volumes:[
-                                   [name:'vol-1', persistentVolumeClaim:[claimName:'first']],
-                                   [name:'vol-2', persistentVolumeClaim:[claimName:'second']] ]
-                   ]
-
+        pod.spec.containers[0].volumeMounts == [
+                [name:'vol-1', mountPath:'/work'],
+                [name:'vol-1', mountPath:'/work2', subPath: '/bar'],
+                [name:'vol-2', mountPath:'/data', subPath: '/foo'],
+                [name:'vol-2', mountPath:'/data2', subPath: '/fooz']
+        ]
+        pod.spec.volumes == [
+                [name:'vol-1', persistentVolumeClaim:[claimName:'first']],
+                [name:'vol-2', persistentVolumeClaim:[claimName:'second']]
         ]
 
     }
@@ -389,34 +251,21 @@ class PodSpecBuilderTest extends Specification {
     def 'should get config map mounts' () {
 
         when:
-        def spec = new PodSpecBuilder()
+        def pod = new PodSpecBuilder()
                 .withPodName('foo')
                 .withImageName('busybox')
-                .withWorkDir('/path')
                 .withCommand(['echo'])
                 .withConfigMap(new PodMountConfig(config: 'cfg1', mountPath: '/etc/config'))
                 .withConfigMap(new PodMountConfig(config: 'data2', mountPath: '/data/path'))
                 .build()
         then:
-        spec ==  [ apiVersion: 'v1',
-                   kind: 'Pod',
-                   metadata: [name:'foo', namespace:'default'],
-                   spec: [
-                           restartPolicy:'Never',
-                           containers:[
-                                   [name:'foo',
-                                    image:'busybox',
-                                    command: ['echo'],
-                                    workingDir:'/path',
-                                    volumeMounts:[
-                                            [name:'vol-1', mountPath:'/etc/config'],
-                                            [name:'vol-2', mountPath:'/data/path']] ]
-                           ],
-                           volumes:[
-                                   [name:'vol-1', configMap:[name:'cfg1']],
-                                   [name:'vol-2', configMap:[name:'data2']] ]
-                   ]
-
+        pod.spec.containers[0].volumeMounts == [
+                [name:'vol-1', mountPath:'/etc/config'],
+                [name:'vol-2', mountPath:'/data/path']
+        ]
+        pod.spec.volumes == [
+                [name:'vol-1', configMap:[name:'cfg1']],
+                [name:'vol-2', configMap:[name:'data2']]
         ]
 
     }
@@ -424,76 +273,46 @@ class PodSpecBuilderTest extends Specification {
     def 'should get csi ephemeral mounts' () {
 
         when:
-        def spec = new PodSpecBuilder()
+        def pod = new PodSpecBuilder()
                 .withPodName('foo')
                 .withImageName('busybox')
-                .withWorkDir('/path')
                 .withCommand(['echo'])
                 .withCsiEphemeral(new PodMountCsiEphemeral(csi: [driver: 'inline.storage.kubernetes.io', readOnly: true], mountPath: '/data'))
                 .build()
         then:
-        spec ==  [
-                apiVersion: 'v1',
-                kind: 'Pod',
-                metadata: [name: 'foo', namespace: 'default'],
-                spec: [
-                        restartPolicy: 'Never',
-                        containers: [[
-                                name: 'foo',
-                                image: 'busybox',
-                                command: ['echo'],
-                                workingDir: '/path',
-                                volumeMounts: [
-                                        [name: 'vol-1', mountPath: '/data', readOnly: true]
-                                ]
-                        ]],
-                        volumes: [
-                                [name: 'vol-1', csi: [driver: 'inline.storage.kubernetes.io', readOnly: true]]
-                        ]
-                ]
+        pod.spec.containers[0].volumeMounts == [
+                [name: 'vol-1', mountPath: '/data', readOnly: true]
+        ]
+        pod.spec.volumes == [
+                [name: 'vol-1', csi: [driver: 'inline.storage.kubernetes.io', readOnly: true]]
         ]
     }
 
     def 'should get empty dir mounts' () {
 
         when:
-        def spec = new PodSpecBuilder()
+        def pod = new PodSpecBuilder()
                 .withPodName('foo')
                 .withImageName('busybox')
-                .withWorkDir('/path')
                 .withCommand(['echo'])
                 .withEmptyDir(new PodMountEmptyDir(mountPath: '/scratch1', emptyDir: [medium: 'Disk']))
                 .withEmptyDir(new PodMountEmptyDir(mountPath: '/scratch2', emptyDir: [medium: 'Memory']))
                 .build()
         then:
-        spec ==  [
-                apiVersion: 'v1',
-                kind: 'Pod',
-                metadata: [name: 'foo', namespace: 'default'],
-                spec: [
-                        restartPolicy: 'Never',
-                        containers: [[
-                                name: 'foo',
-                                image: 'busybox',
-                                command: ['echo'],
-                                workingDir: '/path',
-                                volumeMounts: [
-                                        [name: 'vol-1', mountPath: '/scratch1'],
-                                        [name: 'vol-2', mountPath: '/scratch2']
-                                ]
-                        ]],
-                        volumes: [
-                                [name: 'vol-1', emptyDir: [medium: 'Disk']],
-                                [name: 'vol-2', emptyDir: [medium: 'Memory']]
-                        ]
-                ]
+        pod.spec.containers[0].volumeMounts == [
+                [name: 'vol-1', mountPath: '/scratch1'],
+                [name: 'vol-2', mountPath: '/scratch2']
+        ]
+        pod.spec.volumes == [
+                [name: 'vol-1', emptyDir: [medium: 'Disk']],
+                [name: 'vol-2', emptyDir: [medium: 'Memory']]
         ]
     }
 
     def 'should consume env secrets' () {
 
         when:
-        def spec = new PodSpecBuilder()
+        def pod = new PodSpecBuilder()
                 .withPodName('foo')
                 .withImageName('busybox')
                 .withCommand(['echo'])
@@ -503,29 +322,17 @@ class PodSpecBuilderTest extends Specification {
                 .build()
 
         then:
-        spec == [ apiVersion: 'v1',
-                  kind: 'Pod',
-                  metadata: [name:'foo', namespace:'default'],
-                  spec: [
-                          restartPolicy:'Never',
-                          containers:[
-                                  [name:'foo',
-                                   image:'busybox',
-                                   command: ['echo'],
-                                   env:[   [name: 'FOO', value: 'abc'],
-                                           [name:'VAR_X', valueFrom: [secretKeyRef: [name:'delta', key:'bar']]],
-                                           [name:'VAR_Y', valueFrom: [secretKeyRef: [name:'gamma', key:'VAR_Y']]] ]
-                                  ]
-                          ]
-                  ]
-
+        pod.spec.containers[0].env == [
+                [name: 'FOO', value: 'abc'],
+                [name: 'VAR_X', valueFrom: [secretKeyRef: [name:'delta', key:'bar']]],
+                [name: 'VAR_Y', valueFrom: [secretKeyRef: [name:'gamma', key:'VAR_Y']]]
         ]
     }
 
     def 'should consume env configMap' () {
 
         when:
-        def spec = new PodSpecBuilder()
+        def pod = new PodSpecBuilder()
                 .withPodName('foo')
                 .withImageName('busybox')
                 .withCommand(['echo'])
@@ -535,29 +342,17 @@ class PodSpecBuilderTest extends Specification {
                 .build()
 
         then:
-        spec == [ apiVersion: 'v1',
-                  kind: 'Pod',
-                  metadata: [name:'foo', namespace:'default'],
-                  spec: [
-                          restartPolicy:'Never',
-                          containers:[
-                                  [name:'foo',
-                                   image:'busybox',
-                                   command: ['echo'],
-                                   env:[   [name: 'FOO', value: 'abc'],
-                                           [name:'VAR_X', valueFrom: [configMapKeyRef: [name:'data', key:'VAR_X']]],
-                                           [name:'VAR_Y', valueFrom: [configMapKeyRef: [name:'omega', key:'bar-2']]] ]
-                                  ]
-                          ]
-                  ]
-
+        pod.spec.containers[0].env == [
+                [name: 'FOO', value: 'abc'],
+                [name: 'VAR_X', valueFrom: [configMapKeyRef: [name:'data', key:'VAR_X']]],
+                [name: 'VAR_Y', valueFrom: [configMapKeyRef: [name:'omega', key:'bar-2']]]
         ]
     }
 
     def 'should consume file secrets' () {
 
         when:
-        def spec = new PodSpecBuilder()
+        def pod = new PodSpecBuilder()
                 .withPodName('foo')
                 .withImageName('busybox')
                 .withCommand(['echo'])
@@ -566,67 +361,40 @@ class PodSpecBuilderTest extends Specification {
                 .build()
 
         then:
-        spec == [ apiVersion: 'v1',
-                  kind: 'Pod',
-                  metadata: [name:'foo', namespace:'default'],
-                  spec: [
-                          restartPolicy:'Never',
-                          containers:[
-                                  [name:'foo',
-                                   image:'busybox',
-                                   command: ['echo'],
-                                   volumeMounts:[
-                                           [name:'vol-1', mountPath:'/this/and/that'],
-                                           [name:'vol-2', mountPath:'/etc/mnt']
-                                   ]
-                                  ]
-                          ],
-                          volumes:[
-                                  [name:'vol-1', secret:[secretName: 'alpha']],
-                                  [name:'vol-2', secret:[
-                                          secretName: 'delta',
-                                          items: [
-                                                  [ key: 'foo', path:'bar.txt' ]
-                                          ]
-                                  ]]
-                          ]
-                  ]
-
+        pod.spec.containers[0].volumeMounts == [
+                [name:'vol-1', mountPath:'/this/and/that'],
+                [name:'vol-2', mountPath:'/etc/mnt']
+        ]
+        pod.spec.volumes == [
+                [name:'vol-1', secret:[secretName: 'alpha']],
+                [name:'vol-2', secret:[
+                        secretName: 'delta',
+                        items: [
+                                [ key: 'foo', path:'bar.txt' ]
+                        ]
+                ]]
         ]
     }
 
     def 'should get host path mounts' () {
 
         when:
-        def spec = new PodSpecBuilder()
+        def pod = new PodSpecBuilder()
                 .withPodName('foo')
                 .withImageName('busybox')
-                .withWorkDir('/path')
                 .withCommand(['echo'])
                 .withHostMount('/tmp','/scratch')
                 .withHostMount('/host/data','/mnt/container')
                 .build()
 
         then:
-        spec ==  [ apiVersion: 'v1',
-                   kind: 'Pod',
-                   metadata: [name:'foo', namespace:'default'],
-                   spec: [
-                           restartPolicy:'Never',
-                           containers:[
-                                   [name:'foo',
-                                    image:'busybox',
-                                    command: ['echo'],
-                                    workingDir:'/path',
-                                    volumeMounts:[
-                                            [name:'vol-1', mountPath:'/scratch'],
-                                            [name:'vol-2', mountPath:'/mnt/container']] ]
-                           ],
-                           volumes:[
-                                   [name:'vol-1', hostPath: [path:'/tmp']],
-                                   [name:'vol-2', hostPath: [path:'/host/data']] ]
-                   ]
-
+        pod.spec.containers[0].volumeMounts == [
+                [name:'vol-1', mountPath:'/scratch'],
+                [name:'vol-2', mountPath:'/mnt/container']
+        ]
+        pod.spec.volumes == [
+                [name:'vol-1', hostPath: [path:'/tmp']],
+                [name:'vol-2', hostPath: [path:'/host/data']]
         ]
 
     }
@@ -711,18 +479,9 @@ class PodSpecBuilderTest extends Specification {
     }
 
 
-    def 'should create pod spec given pod options' () {
+    def 'should create pod spec with pod options' () {
 
         given:
-        def opts = Mock(PodOptions)
-        def builder = new PodSpecBuilder([
-            podName: 'foo',
-            imageName: 'image',
-            command: ['echo'],
-            labels: [runName: 'crazy_john'],
-            annotations: [evict: 'false']
-        ])
-
         def affinity = [
             nodeAffinity: [
                 requiredDuringSchedulingIgnoredDuringExecution: [
@@ -732,15 +491,22 @@ class PodSpecBuilderTest extends Specification {
                 ]
             ]
         ]
-
         def tolerations = [[
             key: 'example-key',
             operator: 'Exists',
             effect: 'NoSchedule'
         ]]
+        def opts = Mock(PodOptions)
+        and:
+        def builder = new PodSpecBuilder()
+                .withPodName('foo')
+                .withImageName('busybox')
+                .withCommand(['echo'])
+                .withLabel('runName', 'crazy_john')
+                .withAnnotation('evict', 'false')
 
         when:
-        def spec = builder.withPodOptions(opts).build()
+        def pod = builder.withPodOptions(opts).build()
         then:
         _ * opts.getAffinity() >> affinity
         _ * opts.getAnnotations() >> [OMEGA:'zzz', SIGMA:'www']
@@ -756,48 +522,51 @@ class PodSpecBuilderTest extends Specification {
         _ * opts.getPriorityClassName() >> 'high-priority'
         _ * opts.getSecurityContext() >> new PodSecurityContext(1000)
         _ * opts.getTolerations() >> tolerations
-
-        spec == [
-            apiVersion: 'v1',
-            kind: 'Pod',
-            metadata: [
+        and:
+        pod.metadata == [
                 name:'foo',
                 namespace:'default',
                 labels:[runName:'crazy_john', ALPHA:'xxx', GAMMA:'yyy'],
                 annotations: [evict: 'false', OMEGA:'zzz', SIGMA:'www']
-            ],
-            spec: [
-                affinity: affinity,
-                automountServiceAccountToken: false,
-                imagePullSecrets: [[ name: 'myPullSecret' ]],
-                nodeSelector: [gpu: 'true', queue: 'fast'],
-                priorityClassName: 'high-priority',
-                restartPolicy:'Never',
-                securityContext: [ runAsUser: 1000 ],
-                tolerations: tolerations,
-
-                containers:[[
-                    name:'foo',
-                    image:'image',
-                    imagePullPolicy: 'always',
-                    command:['echo'],
-                    env:[[name:'HELLO', value:'WORLD']],
-                    volumeMounts:[
-                        [name:'vol-1', mountPath:'/work'],
-                        [name:'vol-2', mountPath:'/home/user'],
-                        [name:'vol-3', mountPath:'/etc/secret.txt']
-                    ],
-                ]],
-                volumes:[
-                    [name:'vol-1', persistentVolumeClaim:[claimName:'pvc1']],
-                    [name:'vol-2', configMap:[name:'data']],
-                    [name:'vol-3', secret:[secretName:'blah']]
-                ]
-            ]
+        ]
+        and:
+        pod.spec.affinity == affinity
+        pod.spec.automountServiceAccountToken == false
+        pod.spec.imagePullSecrets == [[ name: 'myPullSecret' ]]
+        pod.spec.nodeSelector == [gpu: 'true', queue: 'fast']
+        pod.spec.priorityClassName == 'high-priority'
+        pod.spec.securityContext == [ runAsUser: 1000 ]
+        pod.spec.tolerations == tolerations
+        pod.spec.containers[0].imagePullPolicy == 'always'
+        pod.spec.containers[0].env == [[name:'HELLO', value:'WORLD']]
+        pod.spec.containers[0].volumeMounts == [
+                [name:'vol-1', mountPath:'/work'],
+                [name:'vol-2', mountPath:'/home/user'],
+                [name:'vol-3', mountPath:'/etc/secret.txt']
+        ]
+        and:
+        pod.spec.volumes == [
+                [name:'vol-1', persistentVolumeClaim:[claimName:'pvc1']],
+                [name:'vol-2', configMap:[name:'data']],
+                [name:'vol-3', secret:[secretName:'blah']]
         ]
 
     }
 
+    def 'should create pod spec with activeDeadlineSeconds' () {
+
+        when:
+        def pod = new PodSpecBuilder()
+                .withPodName('foo')
+                .withImageName('busybox')
+                .withCommand(['echo', 'hello'])
+                .withActiveDeadline(100)
+                .build()
+
+        then:
+        pod.spec.activeDeadlineSeconds == 100
+
+    }
 
     def 'should create image pull request map' () {
         given:
@@ -1022,18 +791,18 @@ class PodSpecBuilderTest extends Specification {
         ]
     }
 
-    def 'should set labels and annotations for job' () {
+    def 'should create job spec with labels and annotations' () {
 
         when:
-        def spec = new PodSpecBuilder()
+        def job = new PodSpecBuilder()
                 .withPodName('foo')
                 .withImageName('busybox')
                 .withCommand(['echo', 'hello'])
                 .withLabel('app','someApp')
                 .withLabel('runName','someName')
                 .withLabel('version','3.8.1')
-                .withAnnotation("anno1", "val1")
-                .withAnnotations([anno2: "val2", anno3: "val3"])
+                .withAnnotation('anno1', 'val1')
+                .withAnnotations([anno2: 'val2', anno3: 'val3'])
                 .buildAsJob()
 
         def metadata = [
@@ -1045,62 +814,15 @@ class PodSpecBuilderTest extends Specification {
                 version: '3.8.1'
             ],
             annotations: [
-                anno1: "val1",
-                anno2: "val2",
-                anno3: "val3"
-            ]
-        ]
-
-        then:
-        spec == [
-            apiVersion: 'batch/v1',
-            kind: 'Job',
-            metadata: metadata,
-            spec: [
-                backoffLimit: 0,
-                template: [
-                    metadata: metadata,
-                    spec: [
-                        restartPolicy: 'Never',
-                        containers: [[
-                            name: 'foo',
-                            image: 'busybox',
-                            command: ['echo', 'hello'],
-                        ]]
-                    ]
-                ]
+                anno1: 'val1',
+                anno2: 'val2',
+                anno3: 'val3'
             ]
         ]
-    }
-
-    def 'should create pod spec with activeDeadlineSeconds' () {
-
-        when:
-        def spec = new PodSpecBuilder()
-                .withPodName('foo')
-                .withImageName('busybox')
-                .withWorkDir('/some/work/dir')
-                .withCommand(['echo', 'hello'])
-                .withActiveDeadline(100)
-                .build()
 
         then:
-        spec ==  [ apiVersion: 'v1',
-                   kind: 'Pod',
-                   metadata: [name:'foo', namespace:'default'],
-                   spec: [
-                           restartPolicy:'Never',
-                           activeDeadlineSeconds: 100,
-                           containers:[
-                                   [name:'foo',
-                                    image:'busybox',
-                                    command:['echo', 'hello'],
-                                    workingDir:'/some/work/dir'
-                                   ]
-                           ]
-                   ]
-        ]
-
+        job.metadata == metadata
+        job.spec.template.metadata == metadata
     }
 
 }

From 19587f4054475eab515c96b7d2eca0bf415ded43 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Sun, 17 Sep 2023 11:12:26 -0500
Subject: [PATCH 154/350] Improve Mermaid DAG rendering (#4070)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/conf.py                                  |   1 +
 docs/config.md                                |  14 +-
 docs/images/dag-mermaid.png                   | Bin 66033 -> 0 bytes
 docs/images/dag.mmd                           |  25 +
 docs/requirements.txt                         |   3 +-
 docs/tracing.md                               |  41 +-
 .../src/main/groovy/nextflow/Channel.groovy   |   1 +
 .../src/main/groovy/nextflow/dag/DAG.groovy   |   2 +-
 .../nextflow/dag/MermaidRenderer.groovy       | 459 +++++++++++++++++-
 .../test/groovy/nextflow/dag/DAGTest.groovy   |   4 +-
 .../nextflow/dag/DotRendererTest.groovy       |  18 +-
 .../nextflow/dag/MermaidRendererTest.groovy   |  28 +-
 12 files changed, 508 insertions(+), 88 deletions(-)
 delete mode 100755 docs/images/dag-mermaid.png
 create mode 100644 docs/images/dag.mmd

diff --git a/docs/conf.py b/docs/conf.py
index b9e2ae98df..6ef95e6b15 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -29,6 +29,7 @@
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
 extensions = [
   'sphinx.ext.mathjax',
+  'sphinxcontrib.mermaid',
   'sphinx_rtd_theme',
   'myst_parser'
 ]
diff --git a/docs/config.md b/docs/config.md
index 5fde00ec5b..e245ec1375 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -503,18 +503,28 @@ Read the {ref}`conda-page` page to learn more about how to use Conda environment
 
 ### Scope `dag`
 
-The `dag` scope controls the layout of the execution graph diagram generated by Nextflow.
+The `dag` scope controls the workflow diagram generated by Nextflow.
 
 The following settings are available:
 
 `dag.enabled`
 : When `true` turns on the generation of the DAG file (default: `false`).
 
+`dag.depth`
+: :::{versionadded} 23.10.0
+  :::
+: Controls the maximum depth at which to render sub-workflows (default: no limit; only supported by the Mermaid render).
+
 `dag.file`
 : Graph file name (default: `dag-<timestamp>.dot`).
 
 `dag.overwrite`
-: When `true` overwrites any existing DAG file with the same name.
+: When `true` overwrites any existing DAG file with the same name (default: `false`).
+
+`dag.verbose`
+: :::{versionadded} 23.10.0
+  :::
+: When `false`, channel names are omitted, operators are collapsed, and empty workflow inputs are removed (default: `false`; only supported by the Mermaid render).
 
 Read the {ref}`dag-visualisation` page to learn more about the execution graph that can be generated by Nextflow.
 
diff --git a/docs/images/dag-mermaid.png b/docs/images/dag-mermaid.png
deleted file mode 100755
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diff --git a/docs/images/dag.mmd b/docs/images/dag.mmd
new file mode 100644
index 0000000000..388eaf306b
--- /dev/null
+++ b/docs/images/dag.mmd
@@ -0,0 +1,25 @@
+flowchart TD
+    subgraph " "
+    v0["Channel.fromFilePairs"]
+    v1["transcriptome"]
+    v7["config"]
+    end
+    subgraph RNASEQ
+    v2([INDEX])
+    v3([FASTQC])
+    v4([QUANT])
+    end
+    v8([MULTIQC])
+    subgraph " "
+    v9[" "]
+    end
+    v5(( ))
+    v0 --> v3
+    v0 --> v4
+    v1 --> v2
+    v2 --> v4
+    v3 --> v5
+    v4 --> v5
+    v7 --> v8
+    v5 --> v8
+    v8 --> v9
diff --git a/docs/requirements.txt b/docs/requirements.txt
index c04a2bb136..6e887390ed 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -1,3 +1,4 @@
 myst-parser==0.18.1
 sphinx==5.3.0
-sphinx-rtd-theme==1.1.1
\ No newline at end of file
+sphinx-rtd-theme==1.1.1
+sphinxcontrib-mermaid==0.9.2
\ No newline at end of file
diff --git a/docs/tracing.md b/docs/tracing.md
index 686e3173cc..e8515fa870 100644
--- a/docs/tracing.md
+++ b/docs/tracing.md
@@ -385,44 +385,7 @@ The DAG produced by Nextflow for the [Unistrap](https://github.com/cbcrg/unistra
 
 Nextflow can render the DAG as a [Mermaid](https://mermaid-js.github.io/) diagram. Mermaid diagrams are particularly useful because they can be embedded in [GitHub Flavored Markdown](https://github.blog/2022-02-14-include-diagrams-markdown-files-mermaid/) without having to render them yourself. You can customize the diagram with CSS, and you can even add links! Visit the [Mermaid documentation](https://mermaid-js.github.io/mermaid/#/flowchart?id=styling-and-classes) for details.
 
-Here is the Mermaid diagram produced by Nextflow for the above example:
-
-```mermaid
-flowchart TD
-    p0((Channel.fromPath))
-    p1([ifEmpty])
-    p2[get_shuffle_replicates]
-    p3[get_msa_replicates]
-    p4[get_msa_trees]
-    p5([collectFile])
-    p6([first])
-    p7[get_stable_msa_trees]
-    p8(( ))
-    p9[get_seqboot_replicates]
-    p10[get_replicate_trees]
-    p11([collectFile])
-    p12([max])
-    p13[get_shootstrap_tree]
-    p14(( ))
-    p0 --> p1
-    p1 -->|file_names| p2
-    p2 -->|shuffle_replicates| p3
-    p3 -->|msa_replicates| p4
-    p3 -->|msa_replicates2| p9
-    p4 -->|msa_trees| p7
-    p4 -->|msa_trees2| p5
-    p5 --> p6
-    p6 --> p7
-    p7 -->|stable_trees| p8
-    p7 -->|most_stable_tree| p12
-    p9 -->|replicates| p10
-    p10 -->|trees| p11
-    p11 --> p13
-    p12 --> p13
-    p13 -->|shootstrap_tree| p14
-```
-
-And the final image produced with the [Mermaid Live Editor](https://mermaid-js.github.io/mermaid-live-editor/edit) (using the `default` theme):
+Here is the Mermaid diagram produced by Nextflow for the [rnaseq-nf](https://github.com/nextflow-io/rnaseq-nf) pipeline (using the [Mermaid Live Editor](https://mermaid-js.github.io/mermaid-live-editor/edit) with the `default` theme):
 
-```{image} images/dag-mermaid.png
+```{mermaid} images/dag.mmd
 ```
diff --git a/modules/nextflow/src/main/groovy/nextflow/Channel.groovy b/modules/nextflow/src/main/groovy/nextflow/Channel.groovy
index 8c9bafaaf2..822ce03537 100644
--- a/modules/nextflow/src/main/groovy/nextflow/Channel.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/Channel.groovy
@@ -105,6 +105,7 @@ class Channel  {
     static private String nth(int i) {
         if( i==1 ) return '1-st'
         if( i==2 ) return '2-nd'
+        if( i==3 ) return '3-rd'
         return "$i-th"
     }
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/dag/DAG.groovy b/modules/nextflow/src/main/groovy/nextflow/dag/DAG.groovy
index d1ef0c0666..e61dac5985 100644
--- a/modules/nextflow/src/main/groovy/nextflow/dag/DAG.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/dag/DAG.groovy
@@ -426,7 +426,7 @@ class DAG {
         /**
          * @return The unique name for this node
          */
-        String getName() { "p${getOrder()}" }
+        String getName() { "v${getOrder()}" }
 
         boolean isActive() {
             operators?.any { DataflowHelper.isProcessorActive(it) }
diff --git a/modules/nextflow/src/main/groovy/nextflow/dag/MermaidRenderer.groovy b/modules/nextflow/src/main/groovy/nextflow/dag/MermaidRenderer.groovy
index 3afdb7cf42..a1b254cddc 100644
--- a/modules/nextflow/src/main/groovy/nextflow/dag/MermaidRenderer.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/dag/MermaidRenderer.groovy
@@ -15,31 +15,88 @@
  */
 
 package nextflow.dag
+
 import java.nio.file.Path
 
+import groovy.transform.CompileStatic
+import groovy.transform.EqualsAndHashCode
+import groovy.transform.TupleConstructor
+import groovy.util.logging.Slf4j
+import nextflow.Global
+import nextflow.Session
 /**
  * Render the DAG using the Mermaid format to the specified file.
  * See https://mermaid-js.github.io/mermaid/#/ for more info.
  *
  * @author Ben Sherman <bentshermann@gmail.com>
  */
+@Slf4j
+@CompileStatic
 class MermaidRenderer implements DagRenderer {
 
+    static private final String INPUTS = 'inputs'
+
+    static private final String OUTPUTS = 'outputs'
+
+    private Session session = Global.session as Session
+
+    private int depth = session.config.navigate('dag.depth', -1) as int
+
+    private boolean verbose = session.config.navigate('dag.verbose', false)
+
     @Override
     void renderDocument(DAG dag, Path file) {
         file.text = renderNetwork(dag)
     }
 
     String renderNetwork(DAG dag) {
-        def lines = []
+        // construct node lookup from DAG
+        def nodeLookup = getNodeLookup(dag)
+
+        // collapse operator nodes
+        if( !verbose )
+            collapseOperators(nodeLookup)
+
+        // remove empty workflow inputs
+        if( !verbose )
+            removeEmptyInputs(nodeLookup)
+
+        // construct node tree
+        final nodeTree = getNodeTree(nodeLookup)
+
+        // collapse node tree to desired depth
+        if( depth >= 0 )
+            collapseNodeTree(nodeTree, depth, nodeLookup)
+
+        // render diagram
+        def lines = [] as List<String>
         lines << "flowchart TD"
 
-        dag.vertices.each { vertex ->
-            lines << "    ${renderVertex( vertex )}"
+        // render nodes
+        renderNodeTree(lines, null, nodeTree)
+
+        // render edges
+        def edges = [] as Set<Edge>
+
+        for( def node : nodeLookup.values() ) {
+            for( def source : node.inputs )
+                edges << new Edge(source.vertex, node.vertex)
+            for( def target : node.outputs )
+                edges << new Edge(node.vertex, target.vertex)
         }
 
-        dag.edges.each { edge ->
-            lines << "    ${renderEdge( edge )}"
+        for( def edge : edges ) {
+            final source = edge.source
+            final target = edge.target
+            def label = ""
+
+            if( verbose ) {
+                final dagEdges = dag.edges.findAll( e -> e.from == source && e.to == target && e.label )
+                if( dagEdges )
+                    label = "|${dagEdges*.label.join(',')}|".toString()
+            }
+
+            lines << "    ${source.name} -->${label} ${target.name}".toString()
         }
 
         lines << ""
@@ -47,32 +104,394 @@ class MermaidRenderer implements DagRenderer {
         return lines.join('\n')
     }
 
-    private String renderVertex(DAG.Vertex vertex) {
-        final id = vertex.getName()
+    /**
+     * Construct a map of nodes with inputs and outputs.
+     *
+     * @param dag
+     */
+    private Map<DAG.Vertex,Node> getNodeLookup(DAG dag) {
+        def nodeLookup = [:] as Map<DAG.Vertex,Node>
 
-        switch (vertex.type) {
-            case DAG.Type.NODE:
-                return "${id}((${vertex.label ?: ' '}))"
+        // create a node for each DAG vertex
+        for( def v : dag.vertices ) {
+            nodeLookup[v] = new Node(v)
+        }
 
-            case DAG.Type.ORIGIN:
-                return "${id}((${vertex.label ?: ' '}))"
+        // save the inputs and outputs for each node
+        for( def e : dag.edges ) {
+            final source = nodeLookup[e.from]
+            final target = nodeLookup[e.to]
+            source.outputs << target
+            target.inputs << source
 
-            case DAG.Type.OPERATOR:
-                return "${id}([${vertex.label ?: ' '}])"
+            // save labels for workflow inputs and outputs
+            if( !verbose && e.from.type == DAG.Type.ORIGIN )
+                source.label = e.label
+            if( !verbose && e.to.type == DAG.Type.NODE )
+                target.label = e.label
+        }
+
+        return nodeLookup
+    }
+
+    /**
+     * Collapse operator nodes by replacing each operator subgraph
+     * with a summary node.
+     *
+     * @param nodeLookup
+     */
+    private void collapseOperators(Map<DAG.Vertex,Node> nodeLookup) {
+        def queue = nodeLookup
+                .values()
+                .findAll( n -> n.vertex.type == DAG.Type.OPERATOR ) as List<Node>
+
+        while( !queue.isEmpty() ) {
+            final node = queue.pop()
+            final subgraph = findSubgraph(node, (Node n) -> n.vertex.type == DAG.Type.OPERATOR)
+            collapseSubgraph(nodeLookup, subgraph, node.vertex)
+            queue.removeAll(subgraph.nodes)
+        }
+    }
+
+    /**
+     * Remove 'Channel.empty' workflow inputs.
+     *
+     * @param nodeLookup
+     */
+    private void removeEmptyInputs(Map<DAG.Vertex,Node> nodeLookup) {
+        def queue = nodeLookup
+                .values()
+                .findAll( n -> n.vertex.type == DAG.Type.ORIGIN )
+                .findAll( n -> n.vertex.label == 'Channel.empty' ) as List<Node>
+
+        while( !queue.isEmpty() ) {
+            final node = queue.pop()
+            final subgraph = findSubgraph(node, (Node n) -> n.vertex.type != DAG.Type.PROCESS)
+
+            final hasProcessNeighbors = (subgraph.inputs + subgraph.outputs).any( (Node n) -> n.vertex.type == DAG.Type.PROCESS )
+            if( hasProcessNeighbors )
+                removeSubgraph(nodeLookup, new Subgraph([node], node.inputs, node.outputs))
+            else {
+                removeSubgraph(nodeLookup, subgraph)
+                queue.removeAll(subgraph.nodes)
+            }
+        }
+    }
+
+    /**
+     * Find the subgraph of all nodes connected to a seed node
+     * that satisfy a predicate.
+     *
+     * @param seedNode
+     * @param predicate
+     */
+    private Subgraph findSubgraph(Node seedNode, Closure predicate) {
+        def queue = [seedNode] as List<Node>
+        def subgraph = new Subgraph()
+
+        while( !queue.isEmpty() ) {
+            final v = queue.pop()
+
+            for( def w : v.inputs + v.outputs ) {
+                if( w in subgraph.nodes )
+                    continue
+
+                if( predicate(w) )
+                    queue << w
+                else if( w in v.inputs )
+                    subgraph.inputs << w
+                else  // w in v.outputs
+                    subgraph.outputs << w
+            }
+
+            subgraph.nodes << v
+        }
+
+        return subgraph
+    }
+
+    /**
+     * Collapse a subgraph by replacing it with a summary node.
+     *
+     * @param nodeLookup
+     * @param subgraph
+     * @param vertex
+     */
+    private void collapseSubgraph(Map<DAG.Vertex,Node> nodeLookup, Subgraph subgraph, DAG.Vertex vertex) {
+        // remove subgraph
+        removeSubgraph(nodeLookup, subgraph)
+
+        // add summary node
+        final summaryNode = new Node(vertex, null, subgraph.inputs, subgraph.outputs)
+        nodeLookup[vertex] = summaryNode
+
+        for( def w : subgraph.inputs )
+            w.outputs << summaryNode
+
+        for( def w : subgraph.outputs )
+            w.inputs << summaryNode
+    }
+
+    /**
+     * Remove a subgraph of nodes.
+     *
+     * @param nodeLookup
+     * @param subgraph
+     */
+    private void removeSubgraph(Map<DAG.Vertex,Node> nodeLookup, Subgraph subgraph) {
+        for( def w : subgraph.nodes )
+            nodeLookup.remove(w.vertex)
+
+        for( def w : subgraph.inputs )
+            w.outputs -= subgraph.nodes
+
+        for( def w : subgraph.outputs )
+            w.inputs -= subgraph.nodes
+    }
 
+    /**
+     * Construct a node tree with a subgraph for each subworkflow.
+     *
+     * @param nodeLookup
+     */
+    private Map getNodeTree(Map<DAG.Vertex,Node> nodeLookup) {
+        // infer subgraphs of operator nodess
+        final inferredKeys = inferSubgraphKeys(nodeLookup)
+
+        // construct node tree
+        def nodeTree = [:]
+
+        for( def node : nodeLookup.values() ) {
+            final vertex = node.vertex
+
+            // determine the vertex subgraph
+            def keys = []
+
+            if( vertex.type == DAG.Type.PROCESS ) {
+                // extract keys from fully qualified name
+                final result = getSubgraphKeys(vertex.label)
+                keys = (List)result[0]
+                node.label = (String)result[1]
+            }
+            else if( vertex.type == DAG.Type.OPERATOR ) {
+                // use inferred subgraph keys
+                keys = inferredKeys[node]
+            }
+            else if( vertex.type == DAG.Type.ORIGIN ) {
+                keys = [INPUTS]
+            }
+            else if( vertex.type == DAG.Type.NODE ) {
+                keys = [OUTPUTS]
+            }
+
+            // navigate to given subgraph
+            def subgraph = nodeTree
+            for( def key : keys ) {
+                if( key !in subgraph )
+                    subgraph[key] = [:]
+                subgraph = subgraph[key]
+            }
+
+            // add vertex to tree
+            subgraph[vertex.name] = node
+        }
+
+        return nodeTree
+    }
+
+    /**
+     * Infer the subgraph of each operator node from neighboring
+     * processes.
+     *
+     * @param nodeLookup
+     */
+    private Map<Node,List> inferSubgraphKeys(Map<DAG.Vertex,Node> nodeLookup) {
+        def inferredKeys = [:]
+        def queue = nodeLookup
+                .values()
+                .findAll( n -> n.vertex.type == DAG.Type.OPERATOR ) as List<Node>
+
+        while( !queue.isEmpty() ) {
+            // find subgraph of operator nodes
+            final node = queue.pop()
+            final subgraph = findSubgraph(node, (Node n) -> n.vertex.type == DAG.Type.OPERATOR)
+
+            // select a neighboring process
+            final inputs = subgraph.inputs.findAll( n -> n.vertex.type == DAG.Type.PROCESS )
+            final outputs = subgraph.outputs.findAll( n -> n.vertex.type == DAG.Type.PROCESS )
+
+            Node process = null
+            if( inputs.size() == 1 )
+                process = inputs[0]
+            else if( outputs.size() == 1 )
+                process = outputs[0]
+            else if( inputs.size() > 0 )
+                process = inputs[0]
+            else if( outputs.size() > 0 )
+                process = outputs[0]
+
+            // extract keys from fully qualified process name
+            final keys = process
+                ? getSubgraphKeys(process.vertex.label)[0]
+                : []
+
+            // save inferred keys
+            for( def w : subgraph.nodes )
+                inferredKeys[w] = keys
+
+            // update queue
+            queue.removeAll(subgraph.nodes)
+        }
+
+        return inferredKeys
+    }
+
+    /**
+     * Get the subgraph keys from a fully qualified process name.
+     *
+     * @param name
+     */
+    private List getSubgraphKeys(String name) {
+        final tokens = name.tokenize(':')
+        return [
+            tokens[0..<tokens.size()-1],
+            tokens.last()
+        ]
+    }
+
+    /**
+     * Collapse a node tree to the desired depth.
+     *
+     * @param nodeTree
+     * @param depth
+     * @param nodeLookup
+     */
+    private void collapseNodeTree(Map<String,Object> nodeTree, int depth, Map<DAG.Vertex,Node> nodeLookup) {
+        nodeTree.each { key, value ->
+            if( value !instanceof Map || key in [INPUTS, OUTPUTS] )
+                return
+
+            if( depth > 0 ) {
+                collapseNodeTree((Map)value, depth - 1, nodeLookup)
+                return
+            }
+
+            // collect subgraph
+            final nodes = collectSubtree((Map)value)
+            final inputs = nodes
+                    .collect( n -> n.inputs )
+                    .flatten()
+                    .findAll( n -> n !in nodes ) as Set<Node>
+            final outputs = nodes
+                    .collect( n -> n.outputs )
+                    .flatten()
+                    .findAll( n -> n !in nodes ) as Set<Node>
+
+            // remove subgraph
+            removeSubgraph(nodeLookup, new Subgraph(nodes, inputs, outputs))
+
+            // add summary node
+            final vertex = nodes.first().vertex
+            final summaryNode = new Node(vertex, key, inputs, outputs)
+            nodeTree[key] = summaryNode
+            nodeLookup[vertex] = summaryNode
+
+            for( def w : inputs )
+                w.outputs << summaryNode
+
+            for( def w : outputs )
+                w.inputs << summaryNode
+        }
+    }
+
+    /**
+     * Collect the nodes in a subtree.
+     *
+     * @param nodeTree
+     */
+    private List<Node> collectSubtree(Map<String,Object> nodeTree) {
+        nodeTree.collect { key, value ->
+                    value instanceof Map
+                        ? collectSubtree(value)
+                        : value
+                }
+                .flatten() as List<Node>
+    }
+
+    /**
+     * Render a tree of nodes and subgraphs.
+     *
+     * @param lines
+     * @param name
+     * @param nodeTree
+     */
+    private void renderNodeTree(List<String> lines, String name, Map<String,Object> nodeTree) {
+        if( name ) {
+            final label = name in [INPUTS, OUTPUTS] ? '" "' : name
+            lines << "    subgraph ${label}".toString()
+        }
+
+        nodeTree.each { key, value ->
+            if( value instanceof Map )
+                renderNodeTree(lines, key, value)
+            else if( value instanceof Node ) {
+                // skip node if it is disconnected
+                if( !value.inputs && !value.outputs )
+                    return
+                lines << "    ${renderNode(value)}".toString()
+            }
+        }
+
+        if( name )
+            lines << "    end"
+    }
+
+    /**
+     * Render a node.
+     *
+     * @param node
+     */
+    private String renderNode(Node node) {
+        final id = node.vertex.name
+
+        switch( node.vertex.type ) {
             case DAG.Type.PROCESS:
-                return "${id}[${vertex.label ?: ' '}]"
+                return "${id}([${node.label}])"
+
+            case DAG.Type.OPERATOR:
+                return verbose
+                    ? "${id}([${node.vertex.label}])"
+                    : "${id}(( ))"
+
+            case DAG.Type.ORIGIN:
+            case DAG.Type.NODE:
+                final label = node.vertex.label ?: node.label ?: ' '
+                return "${id}[\"${label}\"]"
 
             default:
-                return "${id}[${vertex.label ?: ' '}]"
+                return null
         }
     }
 
-    private String renderEdge(DAG.Edge edge) {
-        assert edge.from != null && edge.to != null
+    @TupleConstructor
+    private static class Node {
+        DAG.Vertex vertex
+        String label
+        Set<Node> inputs = []
+        Set<Node> outputs = []
+    }
 
-        String label = edge.label ? "|${edge.label}|" : ""
+    @EqualsAndHashCode
+    @TupleConstructor
+    private static class Edge {
+        DAG.Vertex source
+        DAG.Vertex target
+    }
 
-        return "${edge.from.name} -->${label} ${edge.to.name}"
+    @TupleConstructor
+    private static class Subgraph {
+        List<Node> nodes = []
+        Set<Node> inputs = []
+        Set<Node> outputs = []
     }
 }
diff --git a/modules/nextflow/src/test/groovy/nextflow/dag/DAGTest.groovy b/modules/nextflow/src/test/groovy/nextflow/dag/DAGTest.groovy
index 1e95f57dce..77cd0fde44 100644
--- a/modules/nextflow/src/test/groovy/nextflow/dag/DAGTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/dag/DAGTest.groovy
@@ -48,12 +48,12 @@ class DAGTest extends Specification {
         then:
         v1.label == 'Label A'
         v1.order == 0
-        v1.name == 'p0'
+        v1.name == 'v0'
         v1.type == DAG.Type.PROCESS
 
         v2.label == 'Label B'
         v2.order == 1
-        v2.name == 'p1'
+        v2.name == 'v1'
         v2.type == DAG.Type.OPERATOR
         v1.id != v2.id
     }
diff --git a/modules/nextflow/src/test/groovy/nextflow/dag/DotRendererTest.groovy b/modules/nextflow/src/test/groovy/nextflow/dag/DotRendererTest.groovy
index 2ff86ebaf7..77f7eb8c7a 100644
--- a/modules/nextflow/src/test/groovy/nextflow/dag/DotRendererTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/dag/DotRendererTest.groovy
@@ -59,17 +59,17 @@ class DotRendererTest extends Specification {
         file.text ==
             '''
             digraph "TheGraph" {
-            p0 [shape=point,label="",fixedsize=true,width=0.1];
-            p1 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="Op1"];
-            p0 -> p1;
+            v0 [shape=point,label="",fixedsize=true,width=0.1];
+            v1 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="Op1"];
+            v0 -> v1;
 
-            p1 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="Op1"];
-            p2 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="Op2"];
-            p1 -> p2;
+            v1 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="Op1"];
+            v2 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="Op2"];
+            v1 -> v2;
 
-            p2 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="Op2"];
-            p3 [shape=point];
-            p2 -> p3;
+            v2 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="Op2"];
+            v3 [shape=point];
+            v2 -> v3;
 
             }
             '''
diff --git a/modules/nextflow/src/test/groovy/nextflow/dag/MermaidRendererTest.groovy b/modules/nextflow/src/test/groovy/nextflow/dag/MermaidRendererTest.groovy
index 220422ac77..0c61713b77 100644
--- a/modules/nextflow/src/test/groovy/nextflow/dag/MermaidRendererTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/dag/MermaidRendererTest.groovy
@@ -15,23 +15,18 @@
  */
 
 package nextflow.dag
+
 import java.nio.file.Files
 
 import groovyx.gpars.dataflow.DataflowQueue
-import spock.lang.Specification
-
 import nextflow.Session
-
+import spock.lang.Specification
 /**
  *
  * @author Ben Sherman <bentshermann@gmail.com>
  */
 class MermaidRendererTest extends Specification {
 
-    def setupSpec() {
-        new Session()
-    }
-
     def 'should render a graph using the `mmd` format' () {
         given:
         def file = Files.createTempFile('test', null)
@@ -39,6 +34,7 @@ class MermaidRendererTest extends Specification {
         def ch2 = new DataflowQueue()
         def ch3 = new DataflowQueue()
 
+        def session = new Session([dag: [verbose: true]])
         def dag = new DAG()
         dag.addOperatorNode('Op1', ch1, ch2)
         dag.addOperatorNode('Op2', ch2, ch3)
@@ -51,13 +47,17 @@ class MermaidRendererTest extends Specification {
         file.text ==
             '''
             flowchart TD
-                p0(( ))
-                p1([Op1])
-                p2([Op2])
-                p3(( ))
-                p0 --> p1
-                p1 --> p2
-                p2 --> p3
+                subgraph " "
+                v0[" "]
+                end
+                v1([Op1])
+                v2([Op2])
+                subgraph " "
+                v3[" "]
+                end
+                v0 --> v1
+                v1 --> v2
+                v2 --> v3
             '''
             .stripIndent().leftTrim()
 

From 06843d8767ccf54c8e0a354d94406bd0d41eaaa1 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Sun, 17 Sep 2023 12:29:52 -0500
Subject: [PATCH 155/350] Add developer docs (#4065)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/.dockerignore                            |   1 +
 docs/_static/theme.css                        |  12 ++
 docs/developer/diagrams/.gitignore            |   1 +
 docs/developer/diagrams/README.md             |  17 ++
 docs/developer/diagrams/merge-diagrams.sh     |  35 ++++
 docs/developer/diagrams/nextflow.ast.mmd      |   7 +
 docs/developer/diagrams/nextflow.cache.mmd    |  23 +++
 docs/developer/diagrams/nextflow.cli.mmd      |  29 +++
 .../developer/diagrams/nextflow.cloud.aws.mmd |  21 +++
 .../diagrams/nextflow.cloud.aws.nio.mmd       |  31 ++++
 .../diagrams/nextflow.cloud.azure.mmd         |  17 ++
 .../diagrams/nextflow.cloud.google.mmd        |  13 ++
 docs/developer/diagrams/nextflow.config.mmd   |  10 ++
 .../developer/diagrams/nextflow.container.mmd |  16 ++
 docs/developer/diagrams/nextflow.dag.mmd      |  33 ++++
 docs/developer/diagrams/nextflow.executor.mmd |  82 +++++++++
 .../developer/diagrams/nextflow.extension.mmd |  28 +++
 docs/developer/diagrams/nextflow.ga4gh.mmd    |  14 ++
 docs/developer/diagrams/nextflow.k8s.mmd      |  57 ++++++
 docs/developer/diagrams/nextflow.mmd          |  21 +++
 docs/developer/diagrams/nextflow.plugin.mmd   |  14 ++
 .../developer/diagrams/nextflow.processor.mmd |  44 +++++
 docs/developer/diagrams/nextflow.scm.mmd      |  26 +++
 docs/developer/diagrams/nextflow.script.mmd   | 136 ++++++++++++++
 docs/developer/diagrams/nextflow.secret.mmd   |  10 ++
 docs/developer/diagrams/nextflow.trace.mmd    |  22 +++
 docs/developer/index.md                       |  99 +++++++++++
 docs/developer/nextflow.ast.md                | 168 ++++++++++++++++++
 docs/developer/nextflow.cache.md              |  21 +++
 docs/developer/nextflow.cli.md                |  17 ++
 docs/developer/nextflow.cloud.aws.md          |  13 ++
 docs/developer/nextflow.cloud.aws.nio.md      |  17 ++
 docs/developer/nextflow.cloud.azure.md        |  13 ++
 docs/developer/nextflow.cloud.google.md       |  13 ++
 docs/developer/nextflow.config.md             |  19 ++
 docs/developer/nextflow.container.md          |  19 ++
 docs/developer/nextflow.dag.md                |  19 ++
 docs/developer/nextflow.executor.md           |  21 +++
 docs/developer/nextflow.extension.md          |  19 ++
 docs/developer/nextflow.ga4gh.md              |  13 ++
 docs/developer/nextflow.k8s.md                |  17 ++
 docs/developer/nextflow.md                    |  21 +++
 docs/developer/nextflow.plugin.md             |  17 ++
 docs/developer/nextflow.processor.md          |  21 +++
 docs/developer/nextflow.scm.md                |  17 ++
 docs/developer/nextflow.script.md             |  21 +++
 docs/developer/nextflow.secret.md             |  17 ++
 docs/developer/nextflow.trace.md              |  17 ++
 docs/developer/packages.md                    |  12 ++
 docs/getstarted.md                            |   2 +-
 docs/index.md                                 |  65 +++++--
 51 files changed, 1403 insertions(+), 15 deletions(-)
 create mode 100644 docs/developer/diagrams/.gitignore
 create mode 100644 docs/developer/diagrams/README.md
 create mode 100755 docs/developer/diagrams/merge-diagrams.sh
 create mode 100644 docs/developer/diagrams/nextflow.ast.mmd
 create mode 100644 docs/developer/diagrams/nextflow.cache.mmd
 create mode 100644 docs/developer/diagrams/nextflow.cli.mmd
 create mode 100644 docs/developer/diagrams/nextflow.cloud.aws.mmd
 create mode 100644 docs/developer/diagrams/nextflow.cloud.aws.nio.mmd
 create mode 100644 docs/developer/diagrams/nextflow.cloud.azure.mmd
 create mode 100644 docs/developer/diagrams/nextflow.cloud.google.mmd
 create mode 100644 docs/developer/diagrams/nextflow.config.mmd
 create mode 100644 docs/developer/diagrams/nextflow.container.mmd
 create mode 100644 docs/developer/diagrams/nextflow.dag.mmd
 create mode 100644 docs/developer/diagrams/nextflow.executor.mmd
 create mode 100644 docs/developer/diagrams/nextflow.extension.mmd
 create mode 100644 docs/developer/diagrams/nextflow.ga4gh.mmd
 create mode 100644 docs/developer/diagrams/nextflow.k8s.mmd
 create mode 100644 docs/developer/diagrams/nextflow.mmd
 create mode 100644 docs/developer/diagrams/nextflow.plugin.mmd
 create mode 100644 docs/developer/diagrams/nextflow.processor.mmd
 create mode 100644 docs/developer/diagrams/nextflow.scm.mmd
 create mode 100644 docs/developer/diagrams/nextflow.script.mmd
 create mode 100644 docs/developer/diagrams/nextflow.secret.mmd
 create mode 100644 docs/developer/diagrams/nextflow.trace.mmd
 create mode 100644 docs/developer/index.md
 create mode 100644 docs/developer/nextflow.ast.md
 create mode 100644 docs/developer/nextflow.cache.md
 create mode 100644 docs/developer/nextflow.cli.md
 create mode 100644 docs/developer/nextflow.cloud.aws.md
 create mode 100644 docs/developer/nextflow.cloud.aws.nio.md
 create mode 100644 docs/developer/nextflow.cloud.azure.md
 create mode 100644 docs/developer/nextflow.cloud.google.md
 create mode 100644 docs/developer/nextflow.config.md
 create mode 100644 docs/developer/nextflow.container.md
 create mode 100644 docs/developer/nextflow.dag.md
 create mode 100644 docs/developer/nextflow.executor.md
 create mode 100644 docs/developer/nextflow.extension.md
 create mode 100644 docs/developer/nextflow.ga4gh.md
 create mode 100644 docs/developer/nextflow.k8s.md
 create mode 100644 docs/developer/nextflow.md
 create mode 100644 docs/developer/nextflow.plugin.md
 create mode 100644 docs/developer/nextflow.processor.md
 create mode 100644 docs/developer/nextflow.scm.md
 create mode 100644 docs/developer/nextflow.script.md
 create mode 100644 docs/developer/nextflow.secret.md
 create mode 100644 docs/developer/nextflow.trace.md
 create mode 100644 docs/developer/packages.md

diff --git a/docs/.dockerignore b/docs/.dockerignore
index 550793affd..8896a7a43b 100644
--- a/docs/.dockerignore
+++ b/docs/.dockerignore
@@ -1 +1,2 @@
+**
 !requirements.txt
\ No newline at end of file
diff --git a/docs/_static/theme.css b/docs/_static/theme.css
index fc8ef01f3b..27d788d7e8 100644
--- a/docs/_static/theme.css
+++ b/docs/_static/theme.css
@@ -1,6 +1,18 @@
 
 /* navbar -- Seqera logo */
 
+.wy-side-nav-search {
+    background-color: #27ae60;
+}
+
+.wy-menu-vertical p.caption {
+    color: #27ae60;
+}
+
+.wy-menu-vertical a:active {
+    background-color: #27ae60;
+}
+
 .nav-footer-logo {
     width: 300px;
     margin-top: 2rem;
diff --git a/docs/developer/diagrams/.gitignore b/docs/developer/diagrams/.gitignore
new file mode 100644
index 0000000000..657f47cd79
--- /dev/null
+++ b/docs/developer/diagrams/.gitignore
@@ -0,0 +1 @@
+nextflow-merged.mmd
diff --git a/docs/developer/diagrams/README.md b/docs/developer/diagrams/README.md
new file mode 100644
index 0000000000..392029fbe3
--- /dev/null
+++ b/docs/developer/diagrams/README.md
@@ -0,0 +1,17 @@
+# Class Diagrams
+
+This directory contains class diagrams of the Nextflow source code, abridged and annotated for relevance and ease of use.
+
+Each node is a class. Fields are selectively documented in order to show only core data structures and the classes that "own" them. Methods are not explicitly documented, but they are mentioned in certain links where appropriate.
+
+Links between classes denote one of the following relationships:
+
+- Inheritance (`A <|-- B`): `B` is a subclass of `A`
+- Composition (`A --* B`): `A` contains `B`
+- Instantiation (`A --> B : f`): `A` creates instance(s) of `B` at runtime via `A::f()`
+
+Some links are commented out or not included at all, in order to focus on the most important classes and relationships. You can view these "hidden" links by simply uncommenting them, but I have found that their significance is sufficiently clear from the description files.
+
+A separate diagram description is provided for each package. These files are interoperable, which means that you can combine any subset of files into a larger diagram description. The `merge-diagrams.sh` can create a merged file for you automatically, and it includes a sensible default set of packages.
+
+You can use the [Mermaid Live Editor](https://mermaid-js.github.io/mermaid-live-editor/edit) or the [Mermaid CLI](https://github.com/mermaid-js/mermaid-cli) to render the diagram in a variety of image formats.
diff --git a/docs/developer/diagrams/merge-diagrams.sh b/docs/developer/diagrams/merge-diagrams.sh
new file mode 100755
index 0000000000..a76321ca92
--- /dev/null
+++ b/docs/developer/diagrams/merge-diagrams.sh
@@ -0,0 +1,35 @@
+#!/bin/bash
+
+packages=()
+packages+=("nextflow")
+# packages+=("nextflow.ast")
+packages+=("nextflow.cache")
+packages+=("nextflow.cli")
+# packages+=("nextflow.cloud.aws")
+# packages+=("nextflow.cloud.aws.nio")
+# packages+=("nextflow.cloud.azure")
+# packages+=("nextflow.cloud.google")
+# packages+=("nextflow.config")
+# packages+=("nextflow.container")
+packages+=("nextflow.dag")
+# packages+=("nextflow.executor")
+# packages+=("nextflow.extension")
+# packages+=("nextflow.ga4gh")
+# packages+=("nextflow.k8s")
+# packages+=("nextflow.plugin")
+packages+=("nextflow.processor")
+# packages+=("nextflow.scm")
+packages+=("nextflow.script")
+# packages+=("nextflow.secret")
+# packages+=("nextflow.trace")
+
+outfile="nextflow-merged.mmd"
+
+echo "classDiagram" > ${outfile}
+
+for package in "${packages[@]}"; do
+    echo "${package}"
+
+    tail -n +2 "${package}.mmd" >> ${outfile}
+    echo >> ${outfile}
+done
diff --git a/docs/developer/diagrams/nextflow.ast.mmd b/docs/developer/diagrams/nextflow.ast.mmd
new file mode 100644
index 0000000000..fab36a2c21
--- /dev/null
+++ b/docs/developer/diagrams/nextflow.ast.mmd
@@ -0,0 +1,7 @@
+classDiagram
+    %%
+    %% nextflow.ast
+    %%
+    ScriptParser --> NextflowDSLImpl : parse
+    ScriptParser --> NextflowXformImpl : parse
+    ScriptParser --> OpXformImpl : parse
diff --git a/docs/developer/diagrams/nextflow.cache.mmd b/docs/developer/diagrams/nextflow.cache.mmd
new file mode 100644
index 0000000000..105fd444f8
--- /dev/null
+++ b/docs/developer/diagrams/nextflow.cache.mmd
@@ -0,0 +1,23 @@
+classDiagram
+    %%
+    %% nextflow.cache
+    %%
+    Session --* CacheDB
+    %% CacheFactory --> CacheDB : createInstance
+
+    CacheDB --* CacheStore
+
+    CacheStore <|-- DefaultCacheStore
+    CacheStore <|-- CloudCacheStore
+
+    class DefaultCacheStore {
+        uniqueId : UUID
+        runName : String
+        baseDir : Path
+    }
+
+    class CloudCacheStore {
+        uniqueId : UUID
+        runName : String
+        basePath : Path
+    }
\ No newline at end of file
diff --git a/docs/developer/diagrams/nextflow.cli.mmd b/docs/developer/diagrams/nextflow.cli.mmd
new file mode 100644
index 0000000000..228acacd37
--- /dev/null
+++ b/docs/developer/diagrams/nextflow.cli.mmd
@@ -0,0 +1,29 @@
+classDiagram
+    %%
+    %% nextflow.cli
+    %%
+    class Launcher {
+        cliOptions : CliOptions
+        command : CmdBase
+    } 
+    Launcher --* CliOptions
+    Launcher --* CmdBase
+
+    %% CmdBase <|-- CmdClean
+    %% CmdBase <|-- CmdClone
+    %% CmdBase <|-- CmdConfig
+    CmdBase <|-- CmdConsole
+    %% CmdBase <|-- CmdDrop
+    %% CmdBase <|-- CmdFs
+    CmdBase <|-- CmdHelp
+    CmdBase <|-- CmdInfo
+    %% CmdBase <|-- CmdKubeRun
+    %% CmdBase <|-- CmdList
+    %% CmdBase <|-- CmdLog
+    %% CmdBase <|-- CmdNode
+    %% CmdBase <|-- CmdPlugin
+    %% CmdBase <|-- CmdPull
+    CmdBase <|-- CmdRun
+    %% CmdBase <|-- CmdSecret
+    %% CmdBase <|-- CmdSelfUpdate
+    %% CmdBase <|-- CmdView
diff --git a/docs/developer/diagrams/nextflow.cloud.aws.mmd b/docs/developer/diagrams/nextflow.cloud.aws.mmd
new file mode 100644
index 0000000000..d3adbc00f4
--- /dev/null
+++ b/docs/developer/diagrams/nextflow.cloud.aws.mmd
@@ -0,0 +1,21 @@
+classDiagram
+    %%
+    %% nextflow.cloud.aws
+    %%
+    Executor <|-- AwsBatchExecutor
+    TaskHandler <|-- AwsBatchTaskHandler
+    BashWrapperBuilder <|-- AwsBatchScriptLauncher
+
+    AwsBatchExecutor --* AwsOptions
+    AwsOptions --* AwsConfig
+    AwsConfig --* AwsBatchConfig
+    AwsConfig --* AwsS3Config
+
+    AwsBatchExecutor --> ParallelPollingMonitor : init
+    AwsBatchExecutor --> AwsBatchTaskHandler : submit
+    AwsBatchTaskHandler --> AwsBatchScriptLauncher : submit
+
+    %% TaskPollingMonitor <|-- ParallelPollingMonitor
+
+    SimpleFileCopyStrategy <|-- AwsBatchFileCopyStrategy
+    AwsBatchScriptLauncher --* AwsBatchFileCopyStrategy
diff --git a/docs/developer/diagrams/nextflow.cloud.aws.nio.mmd b/docs/developer/diagrams/nextflow.cloud.aws.nio.mmd
new file mode 100644
index 0000000000..523c5f971a
--- /dev/null
+++ b/docs/developer/diagrams/nextflow.cloud.aws.nio.mmd
@@ -0,0 +1,31 @@
+classDiagram
+    %%
+    %% nextflow.cloud.aws.nio
+    %%
+    S3FileSystemProvider --> S3FileSystem : newFileSystem
+
+    class S3FileSystem {
+        client : S3Client
+        endpoint : String
+    }
+    S3FileSystem --* S3Client
+
+    class S3Client {
+        client : AmazonS3
+        cannedAcl : CannedAccessControlList
+        kmsKeyId : String
+        storageEncryption : SSEAlgorithm
+        transferManager : TransferManager
+        transferPool : ExecutorService
+        uploadChunkSize : Long
+        uploadMaxThreads : Integer
+    }
+
+    Path <|-- S3Path
+
+    class S3Path {
+        bucket : String
+        parts : List~String~
+        fileSystem : S3FileSystem
+    }
+    S3Path --* S3FileSystem
diff --git a/docs/developer/diagrams/nextflow.cloud.azure.mmd b/docs/developer/diagrams/nextflow.cloud.azure.mmd
new file mode 100644
index 0000000000..6993609b33
--- /dev/null
+++ b/docs/developer/diagrams/nextflow.cloud.azure.mmd
@@ -0,0 +1,17 @@
+classDiagram
+    %%
+    %% nextflow.cloud.azure
+    %%
+    Executor <|-- AzBatchExecutor
+    TaskHandler <|-- AzBatchTaskHandler
+    BashWrapperBuilder <|-- AzBatchScriptLauncher
+
+    AzBatchExecutor --* AzConfig
+    AzBatchExecutor --> AzBatchService : register
+
+    AzBatchExecutor --> TaskPollingMonitor : init
+    AzBatchExecutor --> AzBatchTaskHandler : submit
+    AzBatchTaskHandler --> AzBatchScriptLauncher : submit
+
+    SimpleFileCopyStrategy <|-- AzFileCopyStrategy
+    AzBatchScriptLauncher --* AzFileCopyStrategy
diff --git a/docs/developer/diagrams/nextflow.cloud.google.mmd b/docs/developer/diagrams/nextflow.cloud.google.mmd
new file mode 100644
index 0000000000..bd428f7586
--- /dev/null
+++ b/docs/developer/diagrams/nextflow.cloud.google.mmd
@@ -0,0 +1,13 @@
+classDiagram
+    %%
+    %% nextflow.cloud.google
+    %%
+    Executor <|-- GoogleBatchExecutor
+    TaskHandler <|-- GoogleBatchTaskHandler
+    BashWrapperBuilder <|-- GoogleBatchScriptLauncher
+
+    GoogleBatchExecutor --* BatchConfig
+
+    GoogleBatchExecutor --> TaskPollingMonitor : init
+    GoogleBatchExecutor --> GoogleBatchTaskHandler : submit
+    GoogleBatchTaskHandler --> GoogleBatchScriptLauncher : submit
diff --git a/docs/developer/diagrams/nextflow.config.mmd b/docs/developer/diagrams/nextflow.config.mmd
new file mode 100644
index 0000000000..611c19a413
--- /dev/null
+++ b/docs/developer/diagrams/nextflow.config.mmd
@@ -0,0 +1,10 @@
+classDiagram
+    %%
+    %% nextflow.config
+    %%
+    CmdRun --> ConfigMap : run
+    Session --* ConfigMap
+
+    ConfigBuilder --> ConfigParser : build
+    ConfigBuilder --> ConfigMap : build
+    ConfigParser --> ConfigBase : parse
diff --git a/docs/developer/diagrams/nextflow.container.mmd b/docs/developer/diagrams/nextflow.container.mmd
new file mode 100644
index 0000000000..f2ce814750
--- /dev/null
+++ b/docs/developer/diagrams/nextflow.container.mmd
@@ -0,0 +1,16 @@
+classDiagram
+    %%
+    %% nextflow.container
+    %%
+    direction LR
+
+    BashWrapperBuilder --> ContainerBuilder : build
+
+    ContainerBuilder <|-- CharliecloudBuilder
+    ContainerBuilder <|-- DockerBuilder
+    ContainerBuilder <|-- PodmanBuilder
+    ContainerBuilder <|-- ShifterBuilder
+    ContainerBuilder <|-- SingularityBuilder
+    ContainerBuilder <|-- UdockerBuilder
+
+    SingularityBuilder <|-- ApptainerBuilder
diff --git a/docs/developer/diagrams/nextflow.dag.mmd b/docs/developer/diagrams/nextflow.dag.mmd
new file mode 100644
index 0000000000..6858074e33
--- /dev/null
+++ b/docs/developer/diagrams/nextflow.dag.mmd
@@ -0,0 +1,33 @@
+classDiagram
+    %%
+    %% nextflow.dag
+    %%
+    Session --* DAG
+
+    class DAG {
+        vertices : List~Vertex~
+        edges : List~Edge~
+    }
+    DAG "1" --* "*" Vertex
+    DAG "1" --* "*" Edge
+
+    class Vertex {
+        label : String
+        type : Type
+        operators : List~DataflowProcessor~
+        process : TaskProcessor
+    }
+
+    class Edge {
+        channel : Object
+        from : Vertex
+        to : Vertex
+        label : String
+    }
+
+    %% DagRenderer <|-- CytoscapeHtmlRenderer
+    %% DagRenderer <|-- CytoscapeJsRenderer
+    %% DagRenderer <|-- DotRenderer
+    %% DagRenderer <|-- GexfRenderer
+    %% DagRenderer <|-- GraphvizRenderer
+    %% DagRenderer <|-- MermaidRenderer
diff --git a/docs/developer/diagrams/nextflow.executor.mmd b/docs/developer/diagrams/nextflow.executor.mmd
new file mode 100644
index 0000000000..4044bbced4
--- /dev/null
+++ b/docs/developer/diagrams/nextflow.executor.mmd
@@ -0,0 +1,82 @@
+classDiagram
+    %%
+    %% nextflow.executor
+    %%
+    ProcessDef --> Executor : run
+    %% ExecutorFactory --> Executor : getExecutor
+
+    TaskProcessor --* Executor
+
+    %% class Executor {
+    %%     name : String
+    %%     monitor : TaskMonitor
+    %% }
+    %% Executor --* TaskMonitor
+    %% Executor --> TaskHandler : submit
+
+    %% TaskMonitor <|-- TaskPollingMonitor
+
+    class TaskPollingMonitor {
+        capacity : int
+        submitRateLimit : RateLimiter
+        pollIntervalMillis : long
+        dumpInterval : Duration
+    }
+
+    %% TaskPollingMonitor <|-- LocalPollingMonitor
+
+    class LocalPollingMonitor {
+        maxCpus : int
+        maxMemory : long
+    }
+
+    %% class TaskHandler {
+    %%     task : TaskRun
+    %% }
+
+    Executor <|-- AbstractGridExecutor
+    Executor <|-- LocalExecutor
+    %% Executor <|-- NopeExecutor
+    %% AbstractGridExecutor <|-- CondorExecutor
+    %% AbstractGridExecutor <|-- HyperQueueExecutor
+    %% AbstractGridExecutor <|-- LsfExecutor
+    %% AbstractGridExecutor <|-- MoabExecutor
+    %% AbstractGridExecutor <|-- NqsiiExecutor
+    %% AbstractGridExecutor <|-- OarExecutor
+    %% AbstractGridExecutor <|-- PbsExecutor
+    %% AbstractGridExecutor <|-- SgeExecutor
+    %% AbstractGridExecutor <|-- SlurmExecutor
+    %% PbsExecutor <|-- PbsProExecutor
+    %% SgeExecutor <|-- CrgExecutor
+
+    LocalExecutor --> LocalPollingMonitor : init
+    LocalExecutor --> LocalTaskHandler : submit
+    LocalExecutor --> NativeTaskHandler : submit
+    LocalTaskHandler --> BashWrapperBuilder : submit
+
+    AbstractGridExecutor --> TaskPollingMonitor : init
+    AbstractGridExecutor --> GridTaskHandler : submit
+    GridTaskHandler --> BashWrapperBuilder : submit
+
+    %% TaskHandler <|-- CachedTaskHandler
+    %% TaskHandler <|-- GridTaskHandler
+    %% TaskHandler <|-- LocalTaskHandler
+    %% TaskHandler <|-- NativeTaskHandler
+    %% TaskHandler <|-- NopeTaskHandler
+    %% TaskHandler <|-- StoredTaskHandler
+
+    class BashWrapperBuilder {
+        bean : TaskBean
+        copyStrategy : ScriptFileCopyStrategy
+    }
+    BashWrapperBuilder --* TaskBean
+    BashWrapperBuilder --* ScriptFileCopyStrategy
+
+    ScriptFileCopyStrategy <|-- SimpleFileCopyStrategy
+
+    class SimpleFileCopyStrategy {
+        stageinMode : String
+        stageoutMode : String
+        targetDir : Path
+        workDir : Path
+    }
diff --git a/docs/developer/diagrams/nextflow.extension.mmd b/docs/developer/diagrams/nextflow.extension.mmd
new file mode 100644
index 0000000000..4cb817c2e7
--- /dev/null
+++ b/docs/developer/diagrams/nextflow.extension.mmd
@@ -0,0 +1,28 @@
+classDiagram
+    %%
+    %% nextflow.extension
+    %%
+    direction LR
+
+    ChannelEx --> DumpOp : dump
+    Nextflow --> GroupKey : groupKey
+
+    OperatorImpl --> BranchOp : branch
+    OperatorImpl --> BufferOp : buffer
+    OperatorImpl --> CollectFileOp : collectFile
+    OperatorImpl --> CollectOp : collect
+    OperatorImpl --> CombineOp : combine
+    OperatorImpl --> ConcatOp : concat
+    OperatorImpl --> CrossOp : cross
+    OperatorImpl --> GroupTupleOp : groupTuple
+    OperatorImpl --> JoinOp : join
+    OperatorImpl --> MapOp : map
+    OperatorImpl --> MergeOp : merge
+    OperatorImpl --> MixOp : mix
+    OperatorImpl --> MultiMapOp : multiMap
+    OperatorImpl --> RandomSampleOp : randomSample
+    OperatorImpl --> SplitOp : splitCsv, splitFasta, splitFastq, splitText
+    OperatorImpl --> TakeOp : take
+    OperatorImpl --> ToListOp : toList, toSortedList
+    OperatorImpl --> TransposeOp : transpose
+    OperatorImpl --> UntilOp : until
diff --git a/docs/developer/diagrams/nextflow.ga4gh.mmd b/docs/developer/diagrams/nextflow.ga4gh.mmd
new file mode 100644
index 0000000000..7f2c508b3d
--- /dev/null
+++ b/docs/developer/diagrams/nextflow.ga4gh.mmd
@@ -0,0 +1,14 @@
+classDiagram
+    %%
+    %% nextflow.ga4gh
+    %%
+    Executor <|-- TesExecutor
+    %% TaskHandler <|-- TesTaskHandler
+    %% BashWrapperBuilder <|-- TesBashBuilder
+
+    TesExecutor --> TaskPollingMonitor : init
+    TesExecutor --> TesTaskHandler : submit
+    TesTaskHandler --> TesBashBuilder : submit
+
+    %% ScriptFileCopyStrategy <|-- TesFileCopyStrategy
+    TesBashBuilder --* TesFileCopyStrategy
diff --git a/docs/developer/diagrams/nextflow.k8s.mmd b/docs/developer/diagrams/nextflow.k8s.mmd
new file mode 100644
index 0000000000..e329942fb3
--- /dev/null
+++ b/docs/developer/diagrams/nextflow.k8s.mmd
@@ -0,0 +1,57 @@
+classDiagram
+    %%
+    %% nextflow.k8s
+    %%
+    Executor <|-- K8sExecutor
+    TaskHandler <|-- K8sTaskHandler
+    BashWrapperBuilder <|-- K8sWrapperBuilder
+
+    K8sExecutor --> TaskPollingMonitor : init
+    K8sExecutor --> K8sTaskHandler : submit
+    K8sExecutor --* K8sClient
+    K8sTaskHandler --> K8sWrapperBuilder : submit
+
+    CmdKubeRun --> K8sDriverLauncher : run
+
+    class K8sDriverLauncher {
+        args : List~String~
+        cmd : CmdKubeRun
+        config : ConfigObject
+        configMapName : String
+        headCpus : int
+        headImage : String
+        headMemory : String
+        headPreScript : String
+        paramsFile : String
+        pipelineName : String
+        runName : String
+    }
+    K8sDriverLauncher --* K8sClient
+    K8sDriverLauncher --* K8sConfig
+
+    K8sClient --* ClientConfig
+    %% ConfigDiscovery --> ClientConfig : discover
+
+    class K8sConfig {
+        target : Map
+        podOptions : PodOptions
+    }
+    K8sConfig --* PodOptions
+
+    class PodOptions {
+        affinity : Map
+        annotations : Map
+        automountServiceAccountToken : boolean
+        configMaps : Collection~PodMountConfig~
+        envVars : Collection~PodEnv~
+        imagePullPolicy : String
+        imagePullSecret : String
+        labels : Map
+        nodeSelector : PodNodeSelector
+        priorityClassName : String
+        privileged : Boolean
+        secrets : Collection~PodMountSecret~
+        securityContext : PodSecurityContext
+        tolerations : List~Map~
+        volumeClaims : Collection~PodVolumeClaim~
+    }
diff --git a/docs/developer/diagrams/nextflow.mmd b/docs/developer/diagrams/nextflow.mmd
new file mode 100644
index 0000000000..c683746488
--- /dev/null
+++ b/docs/developer/diagrams/nextflow.mmd
@@ -0,0 +1,21 @@
+classDiagram
+    %%
+    %% nextflow
+    %%
+    class Nextflow
+    class Channel
+    class Session {
+        baseDir : Path
+        binding : ScriptBinding
+        cache : CacheDB
+        commandLine : String
+        commitId : String
+        config : Map
+        configFiles : List~Path~
+        dag : DAG
+        profile : String
+        runName : String
+        script : BaseScript
+        uniqueId : UUID
+        workDir : Path
+    }
diff --git a/docs/developer/diagrams/nextflow.plugin.mmd b/docs/developer/diagrams/nextflow.plugin.mmd
new file mode 100644
index 0000000000..83926f39f7
--- /dev/null
+++ b/docs/developer/diagrams/nextflow.plugin.mmd
@@ -0,0 +1,14 @@
+classDiagram
+    %%
+    %% nextflow.plugin
+    %%
+    CmdRun --> Plugins : run
+
+    Plugins --> PluginsFacade : init
+
+    PluginsFacade "1" --> "*" PluginSpec : load
+
+    class PluginSpec {
+        id : String
+        version : String
+    }
diff --git a/docs/developer/diagrams/nextflow.processor.mmd b/docs/developer/diagrams/nextflow.processor.mmd
new file mode 100644
index 0000000000..196433ff69
--- /dev/null
+++ b/docs/developer/diagrams/nextflow.processor.mmd
@@ -0,0 +1,44 @@
+classDiagram
+    %%
+    %% nextflow.processor
+    %%
+    %% ProcessDef --> TaskProcessor : run
+
+    class TaskProcessor {
+        config : ProcessConfig
+        executor : Executor
+        id : int
+        name : String
+        operator : DataflowProcessor
+        taskBody : BodyDef
+    }
+    TaskProcessor --> TaskRun : invokeTask
+    TaskProcessor --> PublishDir : finalizeTask
+
+    class TaskRun {
+        config : TaskConfig
+        context : TaskContext
+        hash : HashCode
+        id : TaskId
+        index : int
+        inputs : Map
+        name : String
+        outputs : Map
+        runType : RunType
+        type : ScriptType
+        workDir : Path
+    }
+    TaskRun --* TaskConfig
+    TaskRun --* TaskContext
+    TaskRun --> TaskBean : toTaskBean
+
+    class TaskConfig {
+        target : Map
+        binding : Map
+    }
+
+    class TaskContext {
+        holder : Map
+        script : Script
+        name : String
+    }
diff --git a/docs/developer/diagrams/nextflow.scm.mmd b/docs/developer/diagrams/nextflow.scm.mmd
new file mode 100644
index 0000000000..1c52075372
--- /dev/null
+++ b/docs/developer/diagrams/nextflow.scm.mmd
@@ -0,0 +1,26 @@
+classDiagram
+    %%
+    %% nextflow.scm
+    %%
+    direction LR
+
+    CmdRun --> AssetManager : run
+
+    class AssetManager {
+        project : String
+        localPath : File
+        mainScript : String
+        repositoryProvider : RepositoryProvider
+        hub : String
+        providerConfigs : List~ProviderConfig~
+    }
+    AssetManager --* RepositoryProvider
+    AssetManager "1" --* "*" ProviderConfig
+
+    RepositoryProvider <|-- AzureRepositoryProvider
+    RepositoryProvider <|-- BitbucketRepositoryProvider
+    RepositoryProvider <|-- BitbucketServerRepositoryProvider
+    RepositoryProvider <|-- GiteaRepositoryProvider
+    RepositoryProvider <|-- GithubRepositoryProvider
+    RepositoryProvider <|-- GitlabRepositoryProvider
+    RepositoryProvider <|-- LocalRepositoryProvider
diff --git a/docs/developer/diagrams/nextflow.script.mmd b/docs/developer/diagrams/nextflow.script.mmd
new file mode 100644
index 0000000000..aa6869d0cd
--- /dev/null
+++ b/docs/developer/diagrams/nextflow.script.mmd
@@ -0,0 +1,136 @@
+classDiagram
+    %%
+    %% nextflow.script
+    %%
+    CmdRun --> ScriptRunner : run
+
+    class ScriptRunner {
+        scriptFile : ScriptFile
+        session : Session
+    }
+    ScriptRunner --* ScriptFile
+    ScriptRunner --* Session
+    ScriptRunner --> ScriptParser : execute
+    ScriptParser --> BaseScript : parse
+
+    class ScriptFile {
+        source : Path
+        main : Path
+        repository : String
+        revisionInfo : AssetManager.RevisionInfo
+        localPath : Path
+        projectName : String
+    }
+
+    Session --* BaseScript
+    Session --* ScriptBinding
+
+    class ScriptBinding {
+        scriptPath : Path
+        args : List~String~
+        params : ParamsMap
+        configEnv : Map
+        entryName : String
+    }
+
+    IncludeDef --> BaseScript : load0
+
+    class BaseScript {
+        meta : ScriptMeta
+        entryFlow : WorkflowDef
+    }
+    BaseScript --* ScriptMeta
+    %% BaseScript --> ProcessDef : process
+    %% BaseScript --> WorkflowDef : workflow
+
+    class ScriptMeta {
+        scriptPath : Path
+        definitions : Map
+        imports : Map
+        module : boolean
+    }
+    ScriptMeta "1" --* "*" ComponentDef : definitions
+    ScriptMeta "1" --* "*" ComponentDef : imports
+
+    ComponentDef <|-- FunctionDef
+    ComponentDef <|-- ProcessDef
+    ComponentDef <|-- WorkflowDef
+
+    class FunctionDef {
+        target : Object
+        name : String
+        alias : String
+    }
+
+    class ProcessDef {
+        processName : String
+        simpleName : String
+        baseName : String
+        rawBody : Closure~BodyDef~
+    }
+    ProcessDef --> ProcessConfig : run
+    ProcessDef --> BodyDef : run
+    ProcessDef --> Executor : run
+    ProcessDef --> TaskProcessor : run
+    ProcessDef --> ChannelOut : run
+
+    class WorkflowDef {
+        name : String
+        body : BodyDef
+        declaredInputs : List~String~
+        declaredOutputs : List~String~
+        variableNames : Set~String~
+    }
+    WorkflowDef --* BodyDef
+    WorkflowDef --> WorkflowBinding : run
+    WorkflowDef --> ChannelOut : run
+
+    class ProcessConfig {
+        configProperties : Map
+        inputs : InputsList
+        outputs : OutputsList
+    }
+    ProcessConfig --* InputsList
+    ProcessConfig --* OutputsList
+
+    class BodyDef {
+        closure : Closure
+        source : String
+        type : ScriptType
+        isShell : boolean
+    }
+
+    class ChannelOut {
+        target : List~DataflowWriteChannel~
+        channels : Map
+    }
+
+    class WorkflowBinding {
+        vars : Map
+    }
+
+    class InputsList {
+        target : List~InParam~
+    }
+    InputsList "1" --* "*" InParam
+
+    class OutputsList {
+        target : List~OutParam~
+    }
+    OutputsList "1" --* "*" OutParam
+
+    %% InParam <|-- BaseInParam
+    %% BaseInParam <|-- EachInParam
+    %% BaseInParam <|-- EnvInParam
+    %% BaseInParam <|-- FileInParam
+    %% BaseInParam <|-- StdInParam
+    %% BaseInParam <|-- TupleInParam
+    %% BaseInParam <|-- ValueInParam
+
+    %% OutParam <|-- BaseOutParam
+    %% BaseOutParam <|-- EachOutParam
+    %% BaseOutParam <|-- EnvOutParam
+    %% BaseOutParam <|-- FileOutParam
+    %% BaseOutParam <|-- StdOutParam
+    %% BaseOutParam <|-- TupleOutParam
+    %% BaseOutParam <|-- ValueOutParam
diff --git a/docs/developer/diagrams/nextflow.secret.mmd b/docs/developer/diagrams/nextflow.secret.mmd
new file mode 100644
index 0000000000..547ade7b93
--- /dev/null
+++ b/docs/developer/diagrams/nextflow.secret.mmd
@@ -0,0 +1,10 @@
+classDiagram
+    %%
+    %% nextflow.secret
+    %%
+    CmdRun --> SecretsProvider : run
+
+    SecretsLoader --> SecretsProvider : load
+    SecretsProvider --> Secret : getSecret
+    SecretsProvider <|-- LocalSecretsProvider
+    Secret <|-- SecretImpl
diff --git a/docs/developer/diagrams/nextflow.trace.mmd b/docs/developer/diagrams/nextflow.trace.mmd
new file mode 100644
index 0000000000..891cfcc698
--- /dev/null
+++ b/docs/developer/diagrams/nextflow.trace.mmd
@@ -0,0 +1,22 @@
+classDiagram
+    %%
+    %% nextflow.trace
+    %%
+    direction LR
+
+    %% TraceObserverFactory "1" --> "*" TraceObserver : create
+    %% TraceObserver <|-- AnsiLogObserver
+    %% TraceObserver <|-- GraphObserver
+    %% TraceObserver <|-- ReportObserver
+    %% TraceObserver <|-- TimelineObserver
+    %% TraceObserver <|-- TraceFileObserver
+    %% TraceObserver <|-- WebLogObserver
+    %% TraceObserver <|-- WorkflowStatsObserver
+
+    Session --> AnsiLogObserver : init
+    Session --> GraphObserver : init
+    Session --> ReportObserver : init
+    Session --> TimelineObserver : init
+    Session --> TraceFileObserver : init
+    Session --> WebLogObserver : init
+    Session --> WorkflowStatsObserver : init
diff --git a/docs/developer/index.md b/docs/developer/index.md
new file mode 100644
index 0000000000..6426feaab2
--- /dev/null
+++ b/docs/developer/index.md
@@ -0,0 +1,99 @@
+# Overview
+
+This section is intended to explain the Nextflow source code at a high level for users who want to understand or contribute to it. Rather than a comprehensive API documentation, these docs simply provide a conceptual map to help you understand the key concepts of the Nextflow implementation, and to quickly find code sections of interest for further investigation.
+
+## Programming Languages
+
+Nextflow is written in [Groovy](http://groovy-lang.org/), which is itself a programming language based on [Java](https://www.java.com/). Groovy is designed to be highly interoperable with Java -- Groovy programs compile to Java bytecode, and nearly any Java program is also a valid Groovy program. However, Groovy adds several language features (e.g. closures, list and map literals, optional typing, optional semicolons, meta-programming) and standard libraries (e.g. JSON and XML parsing) that greatly improve the overall experience of developing for the Java virtual machine.
+
+Recommended resources for Groovy, from most reference-complete to most user-friendly, are listed below:
+
+- [Groovy documentation](http://groovy-lang.org/documentation.html)
+- [Groovy in Action](https://www.manning.com/books/groovy-in-action-second-edition)
+- [Groovy: The Awesome Parts](https://www.slideshare.net/paulk_asert/awesome-groovy)
+- [Groovy cheat sheet](http://www.cheat-sheets.org/saved-copy/rc015-groovy_online.pdf)
+
+## Software Dependencies
+
+Nextflow depends on a variety of libraries and frameworks, the most prominent of which are listed below:
+
+- [AWS SDK for Java 1.x](https://aws.amazon.com/sdk-for-java/): AWS integration
+- [Azure SDK for Java](https://learn.microsoft.com/en-us/azure/developer/java/sdk/): Azure integration
+- [Google Cloud Client Libraries for Java](https://cloud.google.com/java/docs/reference): Google Cloud integration
+- [GPars](http://gpars.org/1.2.1/guide/guide/dataflow.html): dataflow concurrency
+- [Gradle](https://gradle.org/): build automation
+- [JCommander](https://jcommander.org/): command line interface
+- [JGit](https://www.eclipse.org/jgit/): Git integration
+- [Kryo](https://github.com/EsotericSoftware/kryo): serialization
+- [LevelDB](https://mvnrepository.com/artifact/org.iq80.leveldb/leveldb): key-value store for the cache database
+- [Logback](https://logback.qos.ch/): application logging
+- [PF4J](https://pf4j.org/): plugin extensions
+- [Spock](https://spockframework.org/): unit testing framework
+
+Any other integrations are likely implemented using a CLI (e.g. Conda, Docker, HPC schedulers) or REST API (e.g. Kubernetes).
+
+## Class Diagrams
+
+Each package has a class diagram, abridged and annotated for relevance and ease of use.
+
+Each node is a class. Fields are selectively documented in order to show only the core data structures and the classes that "own" them. Methods are not explicitly documented, but they are mentioned in certain links where appropriate. Links are selectively documented in order to show only the most important classes and relationships.
+
+Links between classes denote one of the following relationships:
+
+- Inheritance (`A <|-- B`): `B` is a subclass of `A`
+- Composition (`A --* B`): `A` contains `B`
+- Instantiation (`A --> B : f`): `A` creates instance(s) of `B` at runtime via `A::f()`
+
+See {ref}`packages-page` for the list of Nextflow packages.
+
+```{warning}
+Class diagrams are manually curated, so they might not always reflect the latest version of the source code.
+```
+
+## Building and Testing
+
+The only dependency that you need to build Nextflow is Java. In other words, if you can run Nextflow, then you can probably build it too!
+
+Build and test locally from a branch (useful for testing PRs):
+
+```bash
+# build
+git clone -b <branch> git@github.com:nextflow-io/nextflow.git
+cd nextflow
+make compile
+
+# test
+./launch.sh run <script> ...
+```
+
+Run tests locally:
+
+```bash
+# run all tests
+make test
+
+# run individual test
+make test module=<nextflow|plugins:nf-amazon|...> class=<package>.<class>
+
+# view the Makefile for all build rules
+```
+
+When a test fails, it will give you a report that you can open in your browser to view the stack trace for each failed test. The "Standard output" tab is particularly useful as it shows the console output of each test. You also can view this console output in the terminal by adding `--info` to the `./gradlew` command generated by the Makefile.
+
+## Installing from source
+
+The `nextflow` command is just a Bash script that downloads and executes the Nextflow JAR. When you install Nextflow using `get.nextflow.io`, it only downloads this launcher script, while the Nextflow JAR is downloaded on the first Nextflow run.
+
+You can run `make install` to install a local build of the Nextflow JAR to `$NXF_HOME`. Note that it will overwrite any existing JAR with the same version. This approach is useful for testing non-core plugins with a local build of Nextflow.
+
+If you need to test changes to the `nextflow` launcher script, you can run it directly as `./nextflow`, or you can install it using `cp nextflow $(which nextflow)` and then run it as `nextflow`.
+
+## Debugging
+
+The `groovysh` command provides a command-line REPL that you can use to play around with Groovy code independently of Nextflow. The `groovyConsole` command provides a graphical REPL similar to `nextflow console`. These commands require a standalone Groovy distribution, which can be installed as described for Java in {ref}`Getting started <getstarted-requirement>`.
+
+:::{note}
+If you are using WSL, you must also install an X server for Windows, such as [VcXsrv](https://sourceforge.net/projects/vcxsrv/) or [Xming](http://www.straightrunning.com/XmingNotes/), in order to use these commands.
+:::
+
+For more advanced Groovy debugging capabilities, consider using [IntelliJ IDEA](https://www.jetbrains.com/idea/).
diff --git a/docs/developer/nextflow.ast.md b/docs/developer/nextflow.ast.md
new file mode 100644
index 0000000000..e6c99f5bec
--- /dev/null
+++ b/docs/developer/nextflow.ast.md
@@ -0,0 +1,168 @@
+
+# `nextflow.ast`
+
+The `nextflow.ast` package implements the Nextflow language extensions as AST transforms.
+
+## Class Diagram
+
+```{mermaid} diagrams/nextflow.ast.mmd
+```
+
+```{note}
+Some classes may be excluded from the above diagram for brevity.
+```
+
+## Notes
+
+The Nextflow scripting language is essentially Groovy with some extensions, implemented as transformations to the abstract syntax tree (AST). Every Nextflow script is syntactically (but not semantically) valid Groovy.
+
+You can see the effect of Nextflow's AST transforms by using the Nextflow console:
+
+1. Run `nextflow console` to open the console
+2. Enter a Nextflow script
+3. Execute the script
+4. Go to **Script** > **Inspect AST**
+
+Here is the example from {ref}`getstarted-first`:
+
+```groovy
+params.str = 'Hello world!'
+
+process splitLetters {
+  output:
+    path 'chunk_*'
+
+  """
+  printf '${params.str}' | split -b 6 - chunk_
+  """
+}
+
+process convertToUpper {
+  input:
+    path x
+  output:
+    stdout
+
+  """
+  cat $x | tr '[a-z]' '[A-Z]'
+  """
+}
+
+workflow {
+  splitLetters | flatten | convertToUpper | view { it.trim() }
+}
+```
+
+Here it is after being parsed and de-sugared by Groovy:
+
+```groovy
+params.str = 'Hello world!'
+
+process( splitLetters( {
+  output:
+    path('chunk_*')
+
+  """
+  printf '${params.str}' | split -b 6 - chunk_
+  """
+} ))
+
+process( convertToUpper( {
+  input:
+    path(x)
+  output:
+    stdout
+
+  """
+  cat $x | tr '[a-z]' '[A-Z]'
+  """
+} ))
+
+workflow({
+  splitLetters | flatten | convertToUpper | view { it.trim() }
+})
+```
+
+Here it is after being transformed by Nextflow (whitespace edited for readability):
+
+```groovy
+import static nextflow.Nextflow.*
+
+import org.apache.commons.lang.StringUtils as StringUtils
+import groovy.transform.Field as Field
+import java.nio.file.Path as Path
+import nextflow.Channel as Channel
+import nextflow.util.Duration as Duration
+import nextflow.util.MemoryUnit as MemoryUnit
+import nextflow.io.ValueObject as ValueObject
+import nextflow.Channel as channel
+
+@groovy.transform.BaseScript
+public class script1677225313239 extends nextflow.script.BaseScript { 
+
+    public script1677225313239() {
+        nextflow.script.ScriptMeta.get(this).setDsl1ProcessNames(['splitLetters', 'convertToUpper'])
+    }
+
+    public script1677225313239(final groovy.lang.Binding context) {
+        super.setBinding(context)
+        nextflow.script.ScriptMeta.get(this).setDsl1ProcessNames(['splitLetters', 'convertToUpper'])
+    }
+
+    public static void main(final java.lang.String[] args) {
+        org.codehaus.groovy.runtime.InvokerHelper.runScript(script1677225313239, args)
+    }
+
+    @groovy.transform.Generated
+    protected java.lang.Object runScript() {
+        params.str = 'Hello world!'
+
+        this.process('splitLetters', { 
+            this._out_path('chunk_*')
+            new nextflow.script.BodyDef(
+                {
+                    "printf '$params.str' | split -b 6 - chunk_"
+                },
+                '"""\n  printf \'${params.str}\' | split -b 6 - chunk_\n  """\n',
+                'script',
+                [
+                    new nextflow.script.TokenValRef('params.str', 8, 13)
+                ]
+            )
+        })
+
+        this.process('convertToUpper', { 
+            this._in_path(new nextflow.script.TokenVar('x'))
+            this._out_stdout()
+            new nextflow.script.BodyDef(
+                { 
+                    "cat $x | tr '[a-z]' '[A-Z]'"
+                },
+                '"""\n  cat $x | tr \'[a-z]\' \'[A-Z]\'\n  """\n',
+                'script',
+                [
+                    new nextflow.script.TokenValRef('x', 19, 8)
+                ]
+            )
+        })
+
+        this.workflow({ 
+            new nextflow.script.BodyDef(
+                {
+                    splitLetters | flatten | convertToUpper | this.view({ 
+                        it.trim()
+                    })
+                },
+                '  splitLetters | flatten | convertToUpper | view { it.trim() }\n',
+                'workflow',
+                [
+                    new nextflow.script.TokenValRef('flatten', 24, 18),
+                    new nextflow.script.TokenValRef('splitLetters', 24, 3),
+                    new nextflow.script.TokenValRef('convertToUpper', 24, 28)
+                ]
+            )
+        })
+    }
+
+}
+```
diff --git a/docs/developer/nextflow.cache.md b/docs/developer/nextflow.cache.md
new file mode 100644
index 0000000000..eb96603937
--- /dev/null
+++ b/docs/developer/nextflow.cache.md
@@ -0,0 +1,21 @@
+
+# `nextflow.cache`
+
+The `nextflow.cache` package implements the cache database of previously executed tasks.
+
+## Class Diagram
+
+```{mermaid} diagrams/nextflow.cache.mmd
+```
+
+```{note}
+Some classes may be excluded from the above diagram for brevity.
+```
+
+## Notes
+
+The cache database uses [Kryo](https://github.com/EsotericSoftware/kryo) to serialize and deserialize task data. Each key-value pair in the cache database corresponds to a task. The key is the task hash, and the value consists of (1) the task `TraceRecord`, (2) the `TaskContext`, and (3) the task reference count.
+
+The default cache store is backed by [LevelDB](https://mvnrepository.com/artifact/org.iq80.leveldb/leveldb) and is stored in `.nextflow/cache/<session-id>` relative to the launch directory.
+
+The cloud cache store is backed by remote object storage such as Amazon S3, Azure Blob Storage, and Google Cloud Storage. It stores each task entry as a separate object.
diff --git a/docs/developer/nextflow.cli.md b/docs/developer/nextflow.cli.md
new file mode 100644
index 0000000000..8a93b5c76c
--- /dev/null
+++ b/docs/developer/nextflow.cli.md
@@ -0,0 +1,17 @@
+
+# `nextflow.cli`
+
+The `nextflow.cli` package implements the command line interface.
+
+## Class Diagram
+
+```{mermaid} diagrams/nextflow.cli.mmd
+```
+
+```{note}
+Some classes may be excluded from the above diagram for brevity.
+```
+
+## Notes
+
+The `Launcher` class is the entrypoint for Nextflow. It uses [JCommander](https://jcommander.org/) to parse the command-line arguments. Additionally, there is a class for each subcommand which implements the application logic of that command. By far the most complex command is `CmdRun`.
diff --git a/docs/developer/nextflow.cloud.aws.md b/docs/developer/nextflow.cloud.aws.md
new file mode 100644
index 0000000000..30195218b2
--- /dev/null
+++ b/docs/developer/nextflow.cloud.aws.md
@@ -0,0 +1,13 @@
+
+# `nextflow.cloud.aws`
+
+The `nextflow.cloud.aws` package implements the AWS Batch executor.
+
+## Class Diagram
+
+```{mermaid} diagrams/nextflow.cloud.aws.mmd
+```
+
+```{note}
+Some classes may be excluded from the above diagrams for brevity.
+```
diff --git a/docs/developer/nextflow.cloud.aws.nio.md b/docs/developer/nextflow.cloud.aws.nio.md
new file mode 100644
index 0000000000..78bf60525f
--- /dev/null
+++ b/docs/developer/nextflow.cloud.aws.nio.md
@@ -0,0 +1,17 @@
+
+# `nextflow.cloud.aws.nio`
+
+The `nextflow.cloud.aws.nio` package implements the S3 filesystem.
+
+## Class Diagram
+
+```{mermaid} diagrams/nextflow.cloud.aws.nio.mmd
+```
+
+```{note}
+Some classes may be excluded from the above diagrams for brevity.
+```
+
+## Notes
+
+The S3 filesystem translates Java Path API calls into S3 API calls, which allows Nextflow to interact with S3 objects through the same interface for local files.
diff --git a/docs/developer/nextflow.cloud.azure.md b/docs/developer/nextflow.cloud.azure.md
new file mode 100644
index 0000000000..649e243cc0
--- /dev/null
+++ b/docs/developer/nextflow.cloud.azure.md
@@ -0,0 +1,13 @@
+
+# `nextflow.cloud.azure`
+
+The `nextflow.cloud.azure` package implements the Azure Batch executor.
+
+## Class Diagram
+
+```{mermaid} diagrams/nextflow.cloud.azure.mmd
+```
+
+```{note}
+Some classes may be excluded from the above diagrams for brevity.
+```
diff --git a/docs/developer/nextflow.cloud.google.md b/docs/developer/nextflow.cloud.google.md
new file mode 100644
index 0000000000..bf793fb6ce
--- /dev/null
+++ b/docs/developer/nextflow.cloud.google.md
@@ -0,0 +1,13 @@
+
+# `nextflow.cloud.google`
+
+The `nextflow.cloud.google` package implements the Google Batch executor.
+
+## Class Diagram
+
+```{mermaid} diagrams/nextflow.cloud.google.mmd
+```
+
+```{note}
+Some classes may be excluded from the above diagrams for brevity.
+```
diff --git a/docs/developer/nextflow.config.md b/docs/developer/nextflow.config.md
new file mode 100644
index 0000000000..e4db3ed87a
--- /dev/null
+++ b/docs/developer/nextflow.config.md
@@ -0,0 +1,19 @@
+
+# `nextflow.config`
+
+The `nextflow.config` package contains the implementation of the Nextflow configuration.
+
+## Class Diagram
+
+```{mermaid} diagrams/nextflow.config.mmd
+```
+
+```{note}
+Some classes may be excluded from the above diagram for brevity.
+```
+
+## Notes
+
+Any command that parses Nextflow config files (`config`, `run`, etc) uses the `ConfigBuilder` to build a `ConfigMap` from a set of config files. The `ConfigBuilder` itself uses a `ConfigParser` to parse the config files.
+
+The Nextflow configuration language is essentially Groovy with some extensions. These extensions are implemented in `ConfigBase` and `ConfigTransformImpl`.
diff --git a/docs/developer/nextflow.container.md b/docs/developer/nextflow.container.md
new file mode 100644
index 0000000000..facdf75f7b
--- /dev/null
+++ b/docs/developer/nextflow.container.md
@@ -0,0 +1,19 @@
+
+# `nextflow.container`
+
+The `nextflow.container` package implements the integration with container runtimes.
+
+## Class Diagram
+
+```{mermaid} diagrams/nextflow.container.mmd
+```
+
+```{note}
+Some classes may be excluded from the above diagram for brevity.
+```
+
+## Notes
+
+The `ContainerBuilder` class is the base class for all container runtimes supported by Nextflow. It produces the container wrapper command for a given task run.
+
+Executors that support containerized tasks insert this wrapper command into the task wrapper script (`.command.run`). Executors that are *container-native*, i.e. that launch the task wrapper itself inside a container, don't need to generate a container wrapper command.
diff --git a/docs/developer/nextflow.dag.md b/docs/developer/nextflow.dag.md
new file mode 100644
index 0000000000..2a79127f08
--- /dev/null
+++ b/docs/developer/nextflow.dag.md
@@ -0,0 +1,19 @@
+
+# `nextflow.dag`
+
+The `nextflow.dag` package implements the workflow DAG and renderers for several diagram formats.
+
+## Class Diagram
+
+```{mermaid} diagrams/nextflow.dag.mmd
+```
+
+```{note}
+Some classes may be excluded from the above diagram for brevity.
+```
+
+## Notes
+
+The workflow DAG defines the network of processes, channels, and operators that comprise a workflow. It is produced by the execution of the Nextflow script. See [nextflow.script](nextflow.script.md) for more details.
+
+Implementations of the `DagRenderer` interface define how to render the workflow DAG to a particular diagram format. See {ref}`dag-visualisation` for more details.
diff --git a/docs/developer/nextflow.executor.md b/docs/developer/nextflow.executor.md
new file mode 100644
index 0000000000..65c0771549
--- /dev/null
+++ b/docs/developer/nextflow.executor.md
@@ -0,0 +1,21 @@
+
+# `nextflow.executor`
+
+The `nextflow.executor` package defines the executor interface and implements several built-in executors.
+
+## Class Diagram
+
+```{mermaid} diagrams/nextflow.executor.mmd
+```
+
+```{note}
+Some classes may be excluded from the above diagram for brevity.
+```
+
+## Notes
+
+The `Executor` class is the base class for all Nextflow executors. The main purpose of an `Executor` is to submit tasks to an underlying compute environment, such as an HPC scheduler or cloud batch executor. It uses a `TaskMonitor` to manage the lifecycle of all tasks and `TaskHandler`s to manage each individual task. Most executors use the same polling monitor, but each executor implements its own task handler to customize it for a particular compute environment. See [nextflow.processor](nextflow.processor.md) for more details about these classes.
+
+The built-in executors include the local executor (`LocalExecutor`) and the various grid executors (SLURM, PBS, LSF, etc), all of which extend `AbstractGridExecutor`. The `LocalExecutor` implements both "local" tasks (processes with a `script` or `shell` block) and "native" tasks (processes with an `exec` block).
+
+The `BashWrapperBuilder` is used by executors to generate the wrapper script (`.command.run`) for a task, from a template script called `command-run.txt`, as well as the task configuration and the execution environment.
diff --git a/docs/developer/nextflow.extension.md b/docs/developer/nextflow.extension.md
new file mode 100644
index 0000000000..7bafc14a81
--- /dev/null
+++ b/docs/developer/nextflow.extension.md
@@ -0,0 +1,19 @@
+
+# `nextflow.extension`
+
+The `nextflow.extension` package implements the channel operators and other extension methods.
+
+## Class Diagram
+
+```{mermaid} diagrams/nextflow.extension.mmd
+```
+
+```{note}
+Some classes may be excluded from the above diagram for brevity.
+```
+
+## Notes
+
+Operators are implemented using the [GPars](http://gpars.org/1.2.1/guide/guide/dataflow.html) dataflow library. In general, an operator consumes one or more `DataflowReadChannel`s and produces one or more `DataflowWriteChannel`s. See {ref}`operator-page` for details about each operator.
+
+Other notable classes include `Bolts` and `FilesEx`, which implement various extension methods used throughout the Nextflow codebase. If you see a method that doesn't appear to be implemented by the calling object, it may be implemented in one of these extension classes.
diff --git a/docs/developer/nextflow.ga4gh.md b/docs/developer/nextflow.ga4gh.md
new file mode 100644
index 0000000000..11d7c70a29
--- /dev/null
+++ b/docs/developer/nextflow.ga4gh.md
@@ -0,0 +1,13 @@
+
+# `nextflow.ga4gh`
+
+The `nextflow.ga4gh` package implements an executor for the [GA4GH TES API](https://github.com/ga4gh/task-execution-schemas).
+
+## Class Diagram
+
+```{mermaid} diagrams/nextflow.ga4gh.mmd
+```
+
+```{note}
+Some classes may be excluded from the above diagram for brevity.
+```
diff --git a/docs/developer/nextflow.k8s.md b/docs/developer/nextflow.k8s.md
new file mode 100644
index 0000000000..99168b0d6c
--- /dev/null
+++ b/docs/developer/nextflow.k8s.md
@@ -0,0 +1,17 @@
+
+# `nextflow.k8s`
+
+The `nextflow.k8s` package implements the Kubernetes executor and the `kuberun` command.
+
+## Class Diagram
+
+```{mermaid} diagrams/nextflow.k8s.mmd
+```
+
+```{note}
+Some classes may be excluded from the above diagram for brevity.
+```
+
+## Notes
+
+The Kubernetes integration uses the K8s REST API to interact with K8s clusters, and relies on the `kubectl` command and `~/.kube/config` file for authentication.
diff --git a/docs/developer/nextflow.md b/docs/developer/nextflow.md
new file mode 100644
index 0000000000..457df76a8c
--- /dev/null
+++ b/docs/developer/nextflow.md
@@ -0,0 +1,21 @@
+
+# `nextflow`
+
+The `nextflow` package contains various top-level classes.
+
+## Class Diagram
+
+```{mermaid} diagrams/nextflow.mmd
+```
+
+```{note}
+Some classes may be excluded from the above diagram for brevity.
+```
+
+## Notes
+
+The `Nextflow` class implements several methods that are exposed to Nextflow scripts. See {ref}`implicit-functions` for details.
+
+The `Channel` class implements the channel factory methods, and it is exposed directly to Nextflow scripts. See {ref}`channel-page` for details.
+
+The `Session` class is the top-level representation of a Nextflow run, or "session". See [nextflow.script](nextflow.script.md) for more details about how a `Session` is created.
diff --git a/docs/developer/nextflow.plugin.md b/docs/developer/nextflow.plugin.md
new file mode 100644
index 0000000000..e95fd307bc
--- /dev/null
+++ b/docs/developer/nextflow.plugin.md
@@ -0,0 +1,17 @@
+
+# `nextflow.plugin`
+
+The `nextflow.plugin` package implements the plugin manager.
+
+## Class Diagram
+
+```{mermaid} diagrams/nextflow.plugin.mmd
+```
+
+```{note}
+Some classes may be excluded from the above diagram for brevity.
+```
+
+## Notes
+
+The plugin system uses the [PF4J](https://pf4j.org/) library, which allows for extension classes to be loaded at runtime. Each plugin includes a manifest of extension classes, all of which extend or implement some base class in Nextflow. The `Plugins` class can be used to query the available extensions for a given base class. Extensions can be assigned a priority using the `@Priority` annotation, to ensure that certain extensions are used over others when available.
diff --git a/docs/developer/nextflow.processor.md b/docs/developer/nextflow.processor.md
new file mode 100644
index 0000000000..e58125954f
--- /dev/null
+++ b/docs/developer/nextflow.processor.md
@@ -0,0 +1,21 @@
+
+# `nextflow.processor`
+
+The `nextflow.processor` package implements the execution and monitoring of tasks.
+
+## Class Diagram
+
+```{mermaid} diagrams/nextflow.processor.mmd
+```
+
+```{note}
+Some classes may be excluded from the above diagram for brevity.
+```
+
+## Notes
+
+While the [`executor`](nextflow.executor.md) package defines how tasks are submitted to a particular execution environment (such as an HPC scheduler), the `processor` package defines how tasks are created and executed. As such, these packages work closely together, and in fact several components of the `Executor` interface, specifically the `TaskHandler` and `TaskMonitor`, are defined in this package.
+
+The `TaskProcessor` is by far the largest and most complex class in this package. It implements both the dataflow operator for a given process as well as the task execution logic. In other words, it defines the mapping from an abstract process definition with concrete channel inputs into concrete task executions.
+
+A `TaskRun` represents a particular task execution. There is also `TaskBean`, which is a serializable representation of a task. Legends say that `TaskBean` was originally created to support a "daemon" mode in which Nextflow would run on both the head node and the worker nodes, so the Nextflow "head" would need to send tasks to the Nextflow "workers". This daemon mode was never completed, but echoes of it remain (see `CmdNode`, `DaemonLauncher`, and the `nf-ignite` plugin).
diff --git a/docs/developer/nextflow.scm.md b/docs/developer/nextflow.scm.md
new file mode 100644
index 0000000000..ee7a4e0146
--- /dev/null
+++ b/docs/developer/nextflow.scm.md
@@ -0,0 +1,17 @@
+
+# `nextflow.scm`
+
+The `nextflow.scm` package defines the Git provider interface and implements several built-in Git providers.
+
+## Class Diagram
+
+```{mermaid} diagrams/nextflow.scm.mmd
+```
+
+```{note}
+Some classes may be excluded from the above diagram for brevity.
+```
+
+## Notes
+
+The `RepositoryProvider` class is the base class for all Git providers. It defines how to authenticate with the provider, clone a Git repository, inspect branches and tags, etc.
diff --git a/docs/developer/nextflow.script.md b/docs/developer/nextflow.script.md
new file mode 100644
index 0000000000..2757987c3f
--- /dev/null
+++ b/docs/developer/nextflow.script.md
@@ -0,0 +1,21 @@
+
+# `nextflow.script`
+
+The `nextflow.script` package implements the parsing and execution of Nextflow scripts.
+
+## Class Diagram
+
+```{mermaid} diagrams/nextflow.script.mmd
+```
+
+```{note}
+Some classes may be excluded from the above diagram for brevity.
+```
+
+## Notes
+
+The execution of a Nextflow pipeline occurs in two phases. In the first phase, Nextflow parses and runs the script (using the language extensions in [nextflow.ast](nextflow.ast.md) and [nextflow.extension](nextflow.extension.md)), which constructs the workflow DAG. In the second phase, Nextflow executes the workflow.
+
+```{note}
+In DSL1, there was no separation between workflow construction and execution -- dataflow operators were executed as soon as they were constructed. DSL2 introduced lazy execution in order to separate process definition from execution, and thereby facilitate subworkflows and modules.
+```
diff --git a/docs/developer/nextflow.secret.md b/docs/developer/nextflow.secret.md
new file mode 100644
index 0000000000..db7b84f1a8
--- /dev/null
+++ b/docs/developer/nextflow.secret.md
@@ -0,0 +1,17 @@
+
+# `nextflow.secret`
+
+The `nextflow.secret` package defines the secrets provider interface and implements the built-in local secrets store.
+
+## Class Diagram
+
+```{mermaid} diagrams/nextflow.secret.mmd
+```
+
+```{note}
+Some classes may be excluded from the above diagram for brevity.
+```
+
+## Notes
+
+The default secrets provider simply stores key-value pairs in a local JSON file.
diff --git a/docs/developer/nextflow.trace.md b/docs/developer/nextflow.trace.md
new file mode 100644
index 0000000000..ae90c9be4d
--- /dev/null
+++ b/docs/developer/nextflow.trace.md
@@ -0,0 +1,17 @@
+
+# `nextflow.trace`
+
+The `nextflow.trace` package defines the trace observer interface and implements several built-in trace observers.
+
+## Class Diagram
+
+```{mermaid} diagrams/nextflow.trace.mmd
+```
+
+```{note}
+Some classes may be excluded from the above diagram for brevity.
+```
+
+## Notes
+
+The `TraceObserver` interface defines a set of hooks into the workflow execution, such as when a workflow starts and completes, when a task starts and completes, and when an output file is published. The `Session` maintains a list of all observers and triggers each hook when the corresponding event occurs. Implementing classes can use these hooks to perform custom behaviors. In fact, this interface is used to implemented several core features, including the various execution reports, DAG renderer, and the integration with Nextflow Tower.
diff --git a/docs/developer/packages.md b/docs/developer/packages.md
new file mode 100644
index 0000000000..364d61960b
--- /dev/null
+++ b/docs/developer/packages.md
@@ -0,0 +1,12 @@
+(packages-page)=
+
+# Packages
+
+The following subpages correspond to packages in the Nextflow source code:
+
+```{toctree}
+:glob:
+:maxdepth: 1
+
+nextflow*
+```
diff --git a/docs/getstarted.md b/docs/getstarted.md
index d2ef3a5aeb..4049a0e694 100644
--- a/docs/getstarted.md
+++ b/docs/getstarted.md
@@ -1,6 +1,6 @@
 (getstarted-page)=
 
-# Get started
+# Getting started
 
 (getstarted-requirement)=
 
diff --git a/docs/index.md b/docs/index.md
index 95ce5773ad..6b76b83ca4 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -1,38 +1,75 @@
 
 # Nextflow's documentation!
 
-Contents:
-
 ```{toctree}
-:maxdepth: 2
+:caption: Introduction
+:maxdepth: 1
 
 getstarted
 basic
+```
+
+```{toctree}
+:caption: Language
+:maxdepth: 1
+
 script
 process
 channel
 operator
-executor
 config
 dsl2
+```
+
+```{toctree}
+:caption: Execution
+:maxdepth: 1
+
 cli
+executor
+tracing
+metrics
+sharing
+metadata
+mail
+plugins
+secrets
+```
+
+```{toctree}
+:caption: Software dependencies
+:maxdepth: 1
+
 container
 conda
 spack
 wave
-fusion
+```
+
+```{toctree}
+:caption: Compute & storage platforms
+:maxdepth: 1
+
 aws
 amazons3
 azure
-flux
+fusion
 google
-ignite
 kubernetes
-tracing
-metrics
-sharing
-metadata
-mail
-plugins
-secrets
+```
+
+```{toctree}
+:caption: Additional integrations
+:maxdepth: 1
+
+flux
+ignite
+```
+
+```{toctree}
+:caption: Contributing
+:maxdepth: 1
+
+developer/index
+developer/packages
 ```

From 03752815c26b0aaf5477e70f87ce30d999e2c1ce Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Mon, 18 Sep 2023 05:58:17 +0200
Subject: [PATCH 156/350] Fix support for S3 custom endpoint with anonymous
 access

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../cloud/aws/AwsClientFactory.groovy         |  8 +++++---
 .../cloud/aws/config/AwsS3Config.groovy       |  7 +++++++
 .../cloud/aws/nio/S3FileSystemProvider.java   | 19 +++++--------------
 .../cloud/aws/config/AwsS3ConfigTest.groovy   |  5 ++++-
 4 files changed, 21 insertions(+), 18 deletions(-)

diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/AwsClientFactory.groovy b/plugins/nf-amazon/src/main/nextflow/cloud/aws/AwsClientFactory.groovy
index 2c49df323c..b60c1d794b 100644
--- a/plugins/nf-amazon/src/main/nextflow/cloud/aws/AwsClientFactory.groovy
+++ b/plugins/nf-amazon/src/main/nextflow/cloud/aws/AwsClientFactory.groovy
@@ -21,6 +21,7 @@ import com.amazonaws.ClientConfiguration
 import com.amazonaws.auth.AWSCredentialsProvider
 import com.amazonaws.auth.AWSCredentialsProviderChain
 import com.amazonaws.auth.AWSStaticCredentialsProvider
+import com.amazonaws.auth.AnonymousAWSCredentials
 import com.amazonaws.auth.BasicAWSCredentials
 import com.amazonaws.auth.EC2ContainerCredentialsProviderWrapper
 import com.amazonaws.auth.EnvironmentVariableCredentialsProvider
@@ -256,9 +257,10 @@ class AwsClientFactory {
         else
             builder.withRegion(region)
 
-        final credentials = new S3CredentialsProvider(getCredentialsProvider0())
-        if( credentials )
-            builder.withCredentials(credentials)
+        final credentials = config.s3Config.anonymous
+                ? new AWSStaticCredentialsProvider(new AnonymousAWSCredentials())
+                : new S3CredentialsProvider(getCredentialsProvider0())
+        builder.withCredentials(credentials)
 
         if( clientConfig )
             builder.withClientConfiguration(clientConfig)
diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/config/AwsS3Config.groovy b/plugins/nf-amazon/src/main/nextflow/cloud/aws/config/AwsS3Config.groovy
index e479925314..6f052d6cb7 100644
--- a/plugins/nf-amazon/src/main/nextflow/cloud/aws/config/AwsS3Config.groovy
+++ b/plugins/nf-amazon/src/main/nextflow/cloud/aws/config/AwsS3Config.groovy
@@ -46,6 +46,8 @@ class AwsS3Config {
 
     private Boolean pathStyleAccess
 
+    private Boolean anonymous
+
     AwsS3Config(Map opts) {
         this.debug = opts.debug as Boolean
         this.endpoint = opts.endpoint ?: SysEnv.get('AWS_S3_ENDPOINT')
@@ -53,6 +55,7 @@ class AwsS3Config {
         this.storageEncryption = parseStorageEncryption(opts.storageEncryption as String)
         this.storageKmsKeyId = opts.storageKmsKeyId
         this.pathStyleAccess = opts.s3PathStyleAccess as Boolean
+        this.anonymous = opts.anonymous as Boolean
         this.s3Acl = parseS3Acl(opts.s3Acl as String)
     }
 
@@ -104,4 +107,8 @@ class AwsS3Config {
     Boolean getPathStyleAccess() {
         return pathStyleAccess
     }
+
+    Boolean getAnonymous() {
+        return anonymous
+    }
 }
diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3FileSystemProvider.java b/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3FileSystemProvider.java
index 1c84c707fb..f79d563f0b 100644
--- a/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3FileSystemProvider.java
+++ b/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3FileSystemProvider.java
@@ -62,9 +62,7 @@
 
 import com.amazonaws.ClientConfiguration;
 import com.amazonaws.Protocol;
-import com.amazonaws.auth.AnonymousAWSCredentials;
 import com.amazonaws.regions.Regions;
-import com.amazonaws.services.s3.AmazonS3Client;
 import com.amazonaws.services.s3.model.AccessControlList;
 import com.amazonaws.services.s3.model.AmazonS3Exception;
 import com.amazonaws.services.s3.model.CopyObjectRequest;
@@ -79,11 +77,11 @@
 import com.google.common.collect.ImmutableList;
 import com.google.common.collect.ImmutableSet;
 import com.google.common.collect.Sets;
+import nextflow.cloud.aws.AwsClientFactory;
+import nextflow.cloud.aws.config.AwsConfig;
 import nextflow.cloud.aws.nio.util.IOUtils;
 import nextflow.cloud.aws.nio.util.S3MultipartOptions;
 import nextflow.cloud.aws.nio.util.S3ObjectSummaryLookup;
-import nextflow.cloud.aws.AwsClientFactory;
-import nextflow.cloud.aws.config.AwsConfig;
 import nextflow.extension.FilesEx;
 import nextflow.file.CopyOptions;
 import nextflow.file.FileHelper;
@@ -833,16 +831,9 @@ protected S3FileSystem createFileSystem(URI uri, AwsConfig awsConfig) {
 		ClientConfiguration clientConfig = createClientConfig(props);
 
 		final String bucketName = S3Path.bucketName(uri);
-		final boolean anonymous = "true".equals(props.getProperty("anonymous"));
-		if( anonymous ) {
-			log.debug("Creating AWS S3 client with anonymous credentials");
-			client = new S3Client(new AmazonS3Client(new AnonymousAWSCredentials(), clientConfig));
-		}
-		else {
-			final boolean global = bucketName!=null;
-			final AwsClientFactory factory = new AwsClientFactory(awsConfig, Regions.US_EAST_1.getName());
-			client = new S3Client(factory.getS3Client(clientConfig, global));
-		}
+		final boolean global = bucketName!=null;
+		final AwsClientFactory factory = new AwsClientFactory(awsConfig, Regions.US_EAST_1.getName());
+		client = new S3Client(factory.getS3Client(clientConfig, global));
 
 		// set the client acl
 		client.setCannedAcl(getProp(props, "s_3_acl", "s3_acl", "s3Acl"));
diff --git a/plugins/nf-amazon/src/test/nextflow/cloud/aws/config/AwsS3ConfigTest.groovy b/plugins/nf-amazon/src/test/nextflow/cloud/aws/config/AwsS3ConfigTest.groovy
index 116a64456b..96fbda3acb 100644
--- a/plugins/nf-amazon/src/test/nextflow/cloud/aws/config/AwsS3ConfigTest.groovy
+++ b/plugins/nf-amazon/src/test/nextflow/cloud/aws/config/AwsS3ConfigTest.groovy
@@ -38,6 +38,7 @@ class AwsS3ConfigTest extends Specification {
         !client.debug
         !client.s3Acl
         !client.pathStyleAccess
+        !client.anonymous
     }
 
     def 'should set config' () {
@@ -48,7 +49,8 @@ class AwsS3ConfigTest extends Specification {
                 storageKmsKeyId: 'key-1',
                 storageEncryption: 'AES256',
                 s3Acl: 'public-read',
-                s3PathStyleAccess: true
+                s3PathStyleAccess: true,
+                anonymous: true
         ]
 
         when:
@@ -60,6 +62,7 @@ class AwsS3ConfigTest extends Specification {
         client.storageEncryption == 'AES256'
         client.s3Acl == CannedAccessControlList.PublicRead
         client.pathStyleAccess
+        client.anonymous
     }
 
     def 'should use legacy upload storage class' () {

From 29ab2f247104f2b79a10f94f38a3090788d3675e Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Mon, 18 Sep 2023 06:38:53 +0200
Subject: [PATCH 157/350] Fix fs list command [ci fast]

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../nextflow/src/main/groovy/nextflow/cli/CmdFs.groovy | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdFs.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdFs.groovy
index 2382550ba3..b4f237c47e 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdFs.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdFs.groovy
@@ -16,6 +16,8 @@
 
 package nextflow.cli
 
+import static nextflow.file.FileHelper.toCanonicalPath
+
 import java.nio.charset.Charset
 import java.nio.file.Files
 import java.nio.file.Path
@@ -233,14 +235,14 @@ class CmdFs extends CmdBase implements UsageAware {
         def splitter = FilePatternSplitter.glob().parse(source)
         if( splitter.isPattern() ) {
             final scheme = splitter.scheme
-            final folder = splitter.parent
+            final target = scheme ? "$scheme://$splitter.parent" : splitter.parent
+            final folder = toCanonicalPath(target)
             final pattern = splitter.fileName
-            final fs = FileHelper.fileSystemForScheme(scheme)
 
             def opts = [:]
-            opts.type = 'file'
+            opts.type = 'any'
 
-            FileHelper.visitFiles(opts, fs.getPath(folder), pattern, op)
+            FileHelper.visitFiles(opts, folder, pattern, op)
         }
         else {
             def normalised = splitter.strip(source)

From 4327fa58639881e18d2461e1a902f3d7a7ea7e13 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Mon, 18 Sep 2023 08:00:36 +0200
Subject: [PATCH 158/350] Fix List of S3 bucket for custom endpoint

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../main/nextflow/cloud/aws/nio/S3FileSystemProvider.java   | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3FileSystemProvider.java b/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3FileSystemProvider.java
index f79d563f0b..2e8f818c33 100644
--- a/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3FileSystemProvider.java
+++ b/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3FileSystemProvider.java
@@ -679,7 +679,11 @@ public <A extends BasicFileAttributes> A readAttributes(Path path, Class<A> type
 				"path must be an instance of %s", S3Path.class.getName());
 		S3Path s3Path = (S3Path) path;
 		if (type.isAssignableFrom(BasicFileAttributes.class)) {
-			return (A) readAttr0(s3Path);
+			return (A) ("".equals(s3Path.getKey())
+					// the root bucket is implicitly a directory
+					? new S3FileAttributes("/", null, 0, true, false)
+					// read the target path attributes
+					: readAttr0(s3Path));
 		}
 		// not support attribute class
 		throw new UnsupportedOperationException(format("only %s supported", BasicFileAttributes.class));

From a79056b7f702d3f284a431223b9eafae268ec597 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Tue, 19 Sep 2023 09:00:41 +0200
Subject: [PATCH 159/350] Add fs stat command [ci fast]

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../src/main/groovy/nextflow/cli/CmdFs.groovy | 30 +++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdFs.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdFs.groovy
index b4f237c47e..10464cd533 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdFs.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdFs.groovy
@@ -22,6 +22,7 @@ import java.nio.charset.Charset
 import java.nio.file.Files
 import java.nio.file.Path
 import java.nio.file.Paths
+import java.nio.file.attribute.BasicFileAttributes
 
 import com.beust.jcommander.Parameter
 import groovy.transform.CompileStatic
@@ -53,6 +54,7 @@ class CmdFs extends CmdBase implements UsageAware {
         commands << new CmdList()
         commands << new CmdCat()
         commands << new CmdRemove()
+        commands << new CmdStat()
     }
 
     trait SubCmd {
@@ -141,6 +143,34 @@ class CmdFs extends CmdBase implements UsageAware {
 
     }
 
+    static class CmdStat implements SubCmd {
+        @Override
+        int getArity() { 1 }
+
+        @Override
+        String getName() { 'stat' }
+
+        @Override
+        String getDescription() { 'Print file to meta info' }
+
+        @Override
+        void apply(Path source, Path target) {
+            try {
+                final attr = Files.readAttributes(source, BasicFileAttributes)
+                print """\
+                    name          : ${source.name}
+                    size          : ${attr.size()}
+                    is directory  : ${attr.isDirectory()}
+                    last modified : ${attr.lastModifiedTime() ?: '-'}
+                    creation time : ${attr.creationTime() ?: '-'}                    
+                    """.stripIndent()
+            }
+            catch (IOException e) {
+                log.warn "Unable to read attributes for file: ${source.toUriString()} - cause: $e.message", e
+            }
+        }
+    }
+
     static class CmdRemove implements SubCmd {
 
         @Override

From 0b74c4e28131566f61afcb1dc4c3c2490379ec23 Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Tue, 19 Sep 2023 17:19:14 +0200
Subject: [PATCH 160/350] Add conda.enabled to conda config scope docs (#4320)

Signed-off-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
---
 docs/config.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/docs/config.md b/docs/config.md
index e245ec1375..bd544f25c6 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -480,6 +480,9 @@ The `conda` scope controls the creation of a Conda environment by the Conda pack
 
 The following settings are available:
 
+`conda.enabled`
+: Enable Conda execution (default: `false`).
+
 `conda.cacheDir`
 : Defines the path where Conda environments are stored. When using a compute cluster make sure to provide a shared file system path accessible from all compute nodes.
 

From 4ce9f1df5de5c9e407c0afcce203304ac3cf7ee1 Mon Sep 17 00:00:00 2001
From: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
Date: Tue, 19 Sep 2023 13:48:21 -0300
Subject: [PATCH 161/350] Fix minor typos in changelogs/source code (#4319)

Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 README.md                                     |  2 +-
 build.gradle                                  |  2 +-
 changelog.txt                                 | 34 +++++++++----------
 .../nextflow/dag/MermaidRenderer.groovy       |  2 +-
 .../nextflow/processor/TaskProcessor.groovy   | 14 ++++----
 .../UnmodifiableCollectionsSerializer.java    |  2 +-
 plugins/nf-amazon/changelog.txt               |  2 +-
 .../main/nextflow/cloud/aws/nio/S3Client.java |  2 +-
 .../nextflow/cloud/aws/nio/S3Iterator.java    |  2 +-
 .../cloud/aws/nio/S3OutputStream.java         |  4 +--
 .../cloud/aws/nio/util/S3CopyStream.java      |  4 +--
 .../ga4gh/tes/client/ApiCallback.java         |  4 +--
 .../nextflow/ga4gh/tes/client/ApiClient.java  |  6 ++--
 .../ga4gh/tes/client/model/TesExecutor.java   |  4 +--
 tests/rnaseq-toy-dsl2.nf                      |  2 +-
 15 files changed, 43 insertions(+), 43 deletions(-)

diff --git a/README.md b/README.md
index 4f17f1c934..b079cf49e8 100644
--- a/README.md
+++ b/README.md
@@ -184,7 +184,7 @@ Community
 You can post questions, or report problems by using the Nextflow [discussions](https://github.com/nextflow-io/nextflow/discussions)
 or the Nextflow [Slack community chat](https://www.nextflow.io/slack-invite.html).
 
-*Nextflow* also hosts a yearly workshop showcasing researcher's workflows and advancements in the langauge. Talks from the past workshops are available on the [Nextflow YouTube Channel](https://www.youtube.com/channel/UCB-5LCKLdTKVn2F4V4KlPbQ)
+*Nextflow* also hosts a yearly workshop showcasing researcher's workflows and advancements in the language. Talks from the past workshops are available on the [Nextflow YouTube Channel](https://www.youtube.com/channel/UCB-5LCKLdTKVn2F4V4KlPbQ)
 
 The [nf-core](https://nf-co.re/) project is a community effort aggregating high quality *Nextflow* workflows which can be used by the community. 
 
diff --git a/build.gradle b/build.gradle
index 438e51dacb..d8c9a80f18 100644
--- a/build.gradle
+++ b/build.gradle
@@ -24,7 +24,7 @@ plugins {
 def groovyVer = System.getenv('CI_GROOVY_VERSION')
 if (groovyVer) {
     def repo = groovyVer.startsWith('com.github.apache:') ? 'https://jitpack.io' : 'https://oss.jfrog.org/oss-snapshot-local/'
-    logger.lifecycle "Overriden Groovy dependency to use $groovyVer - repository: $repo"
+    logger.lifecycle "Overridden Groovy dependency to use $groovyVer - repository: $repo"
     allprojects {
         repositories {
             maven { url repo }
diff --git a/changelog.txt b/changelog.txt
index ef5d881bb4..2b75169a91 100644
--- a/changelog.txt
+++ b/changelog.txt
@@ -164,7 +164,7 @@ NEXTFLOW CHANGE-LOG
 - Add Wave containers reports (preview) [9d9e2758]
 - Add disk resource with type option for google batch (#3861) [166b3638]
 - Add httpConnectTimeout and httpReadTimeout to Google options (#3974) [49fa15f7]
-- Add plugin cmd help descrption [d3788f9f]
+- Add plugin cmd help description [d3788f9f]
 - Add retry policy on Az blob operations [295bc1ff]
 - Add retry policy to Wave http client [1daebeef]
 - Add support for AWS SES as mail sending provider [df85d443]
@@ -188,7 +188,7 @@ NEXTFLOW CHANGE-LOG
 - Improve description of channels and channel types (#4120) [8975734d]
 - Improve "Unexpected input: '{'" error message (#4122) [ef9d3cf0]
 - Minor change in Wave config [4da0442a]
-- Prevent null exit code when Google batch is unable to acces exit status [f68a39ec]
+- Prevent null exit code when Google batch is unable to access exit status [f68a39ec]
 - Refactor Conda and Spack support for Wave to Java [36b9e226]
 - Remove `--no-home` default option from charliecloud builder (#3956) [915074a4]
 - Update workflow.revision max length to match the one in Tower (#4010) [1433a903]
@@ -225,7 +225,7 @@ NEXTFLOW CHANGE-LOG
 - Enable static compilation to missing classes (#3906) [c3c4b2f0]
 - Fix -with-conda option in the docs (#3867) [9b350ba8]
 - Fix AWS SSE env propagation to Fusion [e24608c3]
-- Fix Apptainer rendering by removing superflous space [36607ed1]
+- Fix Apptainer rendering by removing superfluous space [36607ed1]
 - Fix Azure jobs correctly deleted after completion (#3927) [b173a983]
 - Fix Azure pool creation when using scaling formula (#3868) [79984a87]
 - Fix DSL2 support in nextflow console (#3864) [0253f8d7]
@@ -787,7 +787,7 @@ NEXTFLOW CHANGE-LOG
 - Fix unit test setting explicit permissions for test files [1c821139] <Jorge Aguilera>
 - Fix Default plugins are overridden by config plugins [46cf3bfa] <Paolo Di Tommaso>
 - Fix S3 transfer download directory [b7bf9fe5]
-- Fix NPE while setting S3 ObjectMetada #3031 [d6163431] <Jorge Aguilera>
+- Fix NPE while setting S3 ObjectMetadata #3031 [d6163431] <Jorge Aguilera>
 - Fix Unable to retrieve AWS batch instance type #1658 [3c4d4d3b]
 - Fix AWS Batch job definition conflict (#3048) [e5084418]
 - Fix JAVA_TOOL_OPTIONS breaking launch #1716 [0e7b416d]
@@ -847,7 +847,7 @@ NEXTFLOW CHANGE-LOG
 - Add DirWatcher v2 [209c82cd]
 - Add Moriondo in the list of random names [e0abca58]
 - Add preview CLI option (#2914) [aa8f1aa4]
-- Fix Git config resultion error [64436697]
+- Fix Git config resolution error [64436697]
 - Fix StackOverflowError when dump all profiles (#2922) [28cd11a2] <Jorge Aguilera>
 - Fix gradle warning message in nf-sqldb (#2921) [b09ceabe] <Jorge Aguilera>
 - Fix log for LsfExecutror perTaskReserve attribute [7c3ec874] <Prete>
@@ -862,14 +862,14 @@ NEXTFLOW CHANGE-LOG
 - Add Hyperqueue executor (#2896) [ffa5712e] <Henrik Nortamo>
 - Add support for K8s Job resource [c70eb12d] <xhejtman>
 - Add support for time process directive in GLS executor (#2880) [1402e183] <Florian De Temmerman>
-- Add support for priviledge option for K8s containers [7ffe3a02]
+- Add support for privilege option for K8s containers [7ffe3a02]
 - Add DSL1 option to docs (#2836) [d30841a5] <Jose Espinosa-Carrasco>
 - Add support for container options to Azure Batch [3f4f00f9] 
 - Add support for move operation to AWS S3 [8c0ddfd5] 
 - Add K8s execution hostname in the trace file (#2828) [ebaef92a] <Fabian Lehmann>
-- Add support for AWS S3 encyption using a custom KMS key [c1e45aa9] <Paolo Di Tommaso>
+- Add support for AWS S3 encryption using a custom KMS key [c1e45aa9] <Paolo Di Tommaso>
 - Add support for Micromamba [383e023f]
-- Add jaxb-api dependecy to nf-amazon [c1a09f87]
+- Add jaxb-api dependency to nf-amazon [c1a09f87]
 - Add strict mode config setting [696e70b5]
 - Add -head-prescript option to kuberun (#2830) [9e387055] 
 - Fix missing err message on submit failure [233e67f0] (#2899)
@@ -974,7 +974,7 @@ NEXTFLOW CHANGE-LOG
 - Prevent invalid use of large maxForks values [5de0c200]
 - Prevent race condition on thread pool creation [3e707a1d]
 - Refactor AWS batch job unique token generation [d64f5a21]
-- Decrese log verbosity [9237d587] [d1a5e5a8]
+- Decrease log verbosity [9237d587] [d1a5e5a8]
 - Throw an error if a required secret is missing [8e5129d6]
 - Wait for pod to stop running before shutdown (#2667) [505c5ad6]) <kfrancisdev>
 - Restore AZ tests [858a4568]
@@ -985,7 +985,7 @@ NEXTFLOW CHANGE-LOG
 22.02.0-edge - 25 Feb 2022
 - Fix Prevent S3 tagging with empty list [ae7db466]
 - Fix Azure repos tests [856aacf0]
-- Fix isse on includeConfig resolution #2675 [6591a9e1]
+- Fix issue on includeConfig resolution #2675 [6591a9e1]
 - Fix NPE when accessing not existing Git file [6c79f8fd]
 - Fix Batch Job name exceed max allowed size [e8b70ca3]
 - Fix detect and skip bom mark in files (#2645) [02b06ba3] <Jorge Aguilera>
@@ -1145,7 +1145,7 @@ NEXTFLOW CHANGE-LOG
 - Fix verbose logging [92b113134]
 - Fix docker image url [ed24a475d]
 - Fix Temporary directories not deleted in on_exit #2406 [181bdf528] <Lukas Jelonek>
-- Fix implict authentication for resources served by Tower [e30310b4f]
+- Fix implicit authentication for resources served by Tower [e30310b4f]
 - Fix No more of 255 channels can be defined into a workflow context #2417 [7f91ecb39]
 - Add tip about escaping variables in env scope #2366 <Ben Shealy>
 - Add K8s env fieldPath option to pod directive #2363 <Ben Shealy>
@@ -1233,7 +1233,7 @@ NEXTFLOW CHANGE-LOG
 21.06.0-edge - 3 Jul 2021
 - Add Keep alive option to Google LS executor [994222074]
 - Add support for FTP proxy and proxy servers authentication [8ec33b04d]
-- Add support for plugins groupping [aa5bc7d34]
+- Add support for plugins grouping [aa5bc7d34]
 - Add More details about the reason why a AWS Batch job has failed #2146 [27a4e88b2]
 - Add support for extensions priority [ae083f1aa]
 - Add stubRun attribute to workflow metadata #2164 [86cfc66fd]
@@ -1298,7 +1298,7 @@ NEXTFLOW CHANGE-LOG
 - Add readOnly flag to k8s volume mounts (#2013) [33bd24ac]
 - Add Start default plugins on-demand #1964 [cf2a9d73]
 - Add support for tower workspaceId [e2977688]
-- Improve suppor for BitBucket server repos [eb946e27]
+- Improve support for BitBucket server repos [eb946e27]
 - Fix toInt/Long/Float/Double operator hangs with value channel [7c35d985]
 - Fix regression caused by nested params handling #1923 [b25af49b]
 - Fix Cache invalidation when repo is cloned between runs #1989 [ac526f38]
@@ -1444,7 +1444,7 @@ NEXTFLOW CHANGE-LOG
 - Remove unneeded parentheses from stdout declaration [dc029c04]
 - Merge execution logs command docs [577ec744]
 - Passing exact memory to TES executor in GiB #1696 [c8a15545]
-- Improve docs replacing suscribe{println it} with view() [f84ccb6f] [cb2d607d]
+- Improve docs replacing subscribe{println it} with view() [f84ccb6f] [cb2d607d]
 - Use current environment Bash #1598 #1614 [e70ef87a]
 - Include GA4GH support into the standalone binary (make pack) #1666 [e2175d45]
 - Update Bitbucket docs [b9b57f83]
@@ -1884,7 +1884,7 @@ NEXTFLOW CHANGE-LOG
 - Fixed remote bin directory when using bucketDir option [6d796783]
 - Fixed foreign file system detection [1489cc72]
 - Fixed Ansi logger division by zero [ae2b1380]
-- Fixed Unparseable Data format on http file #962
+- Fixed Unparsable Data format on http file #962
 - Fixed Log command history #405
 - Fixed Too long process tag name can cause SLURM failure #941
 - Fixed LSF can return an inconsistent jobs status #927
@@ -1936,7 +1936,7 @@ NEXTFLOW CHANGE-LOG
 - Fixed remote bin directory when using buckerDir option [6d796783]
 - Fixed foreign file system detection [1489cc72]
 - Fixed Ansi logger division by zero [ae2b1380]
-- Fixed Unparseable Data format on http file #962
+- Fixed Unparsable Data format on http file #962
 - Fixed Log command history #405
 - Fixed Too long process tag name can cause SLURM failure #941
 - Fixed LSF can return an inconsistent jobs status #927
@@ -2438,7 +2438,7 @@ NEXTFLOW CHANGE-LOG
 0.23.3 - 9 Feb 2017
 - Fixed Job termination is not recognised if the starter file is not created #268
 - Fixed Allow NF console to resume process executions (second take) #280
-- Fixed PublishDir may throw a FileAlredyExistsException #283
+- Fixed PublishDir may throw a FileAlreadyExistsException #283
 - Increased logger file appender buffer size to 64kb
 - Updated Logback to version 1.1.10
 - Updated copyright info
diff --git a/modules/nextflow/src/main/groovy/nextflow/dag/MermaidRenderer.groovy b/modules/nextflow/src/main/groovy/nextflow/dag/MermaidRenderer.groovy
index a1b254cddc..76507c4ab4 100644
--- a/modules/nextflow/src/main/groovy/nextflow/dag/MermaidRenderer.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/dag/MermaidRenderer.groovy
@@ -255,7 +255,7 @@ class MermaidRenderer implements DagRenderer {
      * @param nodeLookup
      */
     private Map getNodeTree(Map<DAG.Vertex,Node> nodeLookup) {
-        // infer subgraphs of operator nodess
+        // infer subgraphs of operator nodes
         final inferredKeys = inferSubgraphKeys(nodeLookup)
 
         // construct node tree
diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
index b4500a95df..4e2639d257 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
@@ -373,7 +373,7 @@ class TaskProcessor {
      * Create a "preview" for a task run. This method is only meant for the creation of "mock" task run
      * to allow the access for the associated {@link TaskConfig} during a pipeline "preview" execution.
      *
-     * Note this returns an "eventually" task configuration object. Also Inputs ane output parameters are NOT
+     * Note this returns an "eventually" task configuration object. Also Inputs and output parameters are NOT
      * resolved by this method.
      *
      * @return A {@link TaskRun} object holding a reference to the associated {@link TaskConfig}
@@ -2426,7 +2426,7 @@ class TaskProcessor {
 
         @Override
         List<Object> beforeRun(final DataflowProcessor processor, final List<Object> messages) {
-            // apparently auto if-guard instrumented by @Slf4j is not honoured in inner classes - add it explictly
+            // apparently auto if-guard instrumented by @Slf4j is not honoured in inner classes - add it explicitly
             if( log.isTraceEnabled() )
                 log.trace "<${name}> Before run -- messages: ${messages}"
             // the counter must be incremented here, otherwise it won't be consistent
@@ -2443,7 +2443,7 @@ class TaskProcessor {
 
         @Override
         void afterRun(DataflowProcessor processor, List<Object> messages) {
-            // apparently auto if-guard instrumented by @Slf4j is not honoured in inner classes - add it explictly
+            // apparently auto if-guard instrumented by @Slf4j is not honoured in inner classes - add it explicitly
             if( log.isTraceEnabled() )
                 log.trace "<${name}> After run"
             currentTask.remove()
@@ -2451,7 +2451,7 @@ class TaskProcessor {
 
         @Override
         Object messageArrived(final DataflowProcessor processor, final DataflowReadChannel<Object> channel, final int index, final Object message) {
-            // apparently auto if-guard instrumented by @Slf4j is not honoured in inner classes - add it explictly
+            // apparently auto if-guard instrumented by @Slf4j is not honoured in inner classes - add it explicitly
             if( log.isTraceEnabled() ) {
                 def channelName = config.getInputs()?.names?.get(index)
                 def taskName = currentTask.get()?.name ?: name
@@ -2463,7 +2463,7 @@ class TaskProcessor {
 
         @Override
         Object controlMessageArrived(final DataflowProcessor processor, final DataflowReadChannel<Object> channel, final int index, final Object message) {
-            // apparently auto if-guard instrumented by @Slf4j is not honoured in inner classes - add it explictly
+            // apparently auto if-guard instrumented by @Slf4j is not honoured in inner classes - add it explicitly
             if( log.isTraceEnabled() ) {
                 def channelName = config.getInputs()?.names?.get(index)
                 def taskName = currentTask.get()?.name ?: name
@@ -2473,7 +2473,7 @@ class TaskProcessor {
             super.controlMessageArrived(processor, channel, index, message)
 
             if( message == PoisonPill.instance ) {
-                // apparently auto if-guard instrumented by @Slf4j is not honoured in inner classes - add it explictly
+                // apparently auto if-guard instrumented by @Slf4j is not honoured in inner classes - add it explicitly
                 if( log.isTraceEnabled() )
                     log.trace "<${name}> Poison pill arrived; port: $index"
                 openPorts.set(index, 0) // mark the port as closed
@@ -2485,7 +2485,7 @@ class TaskProcessor {
 
         @Override
         void afterStop(final DataflowProcessor processor) {
-            // apparently auto if-guard instrumented by @Slf4j is not honoured in inner classes - add it explictly
+            // apparently auto if-guard instrumented by @Slf4j is not honoured in inner classes - add it explicitly
             if( log.isTraceEnabled() )
                 log.trace "<${name}> After stop"
         }
diff --git a/modules/nextflow/src/main/java/de/javakaffee/kryoserializers/UnmodifiableCollectionsSerializer.java b/modules/nextflow/src/main/java/de/javakaffee/kryoserializers/UnmodifiableCollectionsSerializer.java
index 5971ecd4a9..c98eb4420a 100644
--- a/modules/nextflow/src/main/java/de/javakaffee/kryoserializers/UnmodifiableCollectionsSerializer.java
+++ b/modules/nextflow/src/main/java/de/javakaffee/kryoserializers/UnmodifiableCollectionsSerializer.java
@@ -78,7 +78,7 @@ public Object read(final Kryo kryo, final Input input, final Class<Object> clazz
     public void write(final Kryo kryo, final Output output, final Object object) {
         try {
             final UnmodifiableCollection unmodifiableCollection = UnmodifiableCollection.valueOfType( object.getClass() );
-            // the ordinal could be replaced by s.th. else (e.g. a explicitely managed "id")
+            // the ordinal could be replaced by s.th. else (e.g. a explicitly managed "id")
             output.writeInt( unmodifiableCollection.ordinal(), true );
             kryo.writeClassAndObject( output, unmodifiableCollection.sourceCollectionField.get( object ) );
         } catch ( final RuntimeException e ) {
diff --git a/plugins/nf-amazon/changelog.txt b/plugins/nf-amazon/changelog.txt
index 3fd772a31b..7e783ff79f 100644
--- a/plugins/nf-amazon/changelog.txt
+++ b/plugins/nf-amazon/changelog.txt
@@ -115,7 +115,7 @@ nf-amazon changelog
 
 1.9.0 - 1 Aug 2022
 - Fix Unable to disable scratch attribute with AWS Batch [1770f73a]
-- Fix NPE while setting S3 ObjectMetada #3031 [d6163431] <Jorge Aguilera>
+- Fix NPE while setting S3 ObjectMetadata #3031 [d6163431] <Jorge Aguilera>
 - Fix Unable to retrieve AWS batch instance type #1658 [3c4d4d3b] <Paolo Di Tommaso>
 - Fix AWS Batch job definition conflict (#3048) [e5084418] <Paolo Di Tommaso>
 - Improve S3 file upload/download via Transfer manager [7e8d2a5a] [b7bf9fe5] <Jorge Aguilera>
diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3Client.java b/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3Client.java
index 3386fdd63e..e980be5453 100644
--- a/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3Client.java
+++ b/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3Client.java
@@ -226,7 +226,7 @@ public void copyObject(CopyObjectRequest req, List<Tag> tags, String contentType
 		if( cannedAcl != null ) {
 			req.withCannedAccessControlList(cannedAcl);
 		}
-		// getNewObjectMetada returns null if no object metadata has been specified.
+		// getNewObjectMetadata returns null if no object metadata has been specified.
 		ObjectMetadata meta = req.getNewObjectMetadata() != null ? req.getNewObjectMetadata() : new ObjectMetadata();
 		if( storageEncryption != null ) {
 			meta.setSSEAlgorithm(storageEncryption.toString());
diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3Iterator.java b/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3Iterator.java
index c6411f73dd..ac1df0d30a 100644
--- a/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3Iterator.java
+++ b/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3Iterator.java
@@ -29,7 +29,7 @@
 
 /**
  * S3 iterator over folders at first level.
- * Future verions of this class should be return the elements
+ * Future versions of this class should be return the elements
  * in a incremental way when the #next() method is called.
  */
 public class S3Iterator implements Iterator<Path> {
diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3OutputStream.java b/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3OutputStream.java
index b592772776..56454b186a 100644
--- a/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3OutputStream.java
+++ b/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3OutputStream.java
@@ -235,7 +235,7 @@ private MessageDigest createMd5() {
 
     /**
      * Writes a byte into the uploader buffer. When it is full starts the upload process
-     * in a asynchornous manner
+     * in a asynchronous manner
      *
      * @param b The byte to be written
      * @throws IOException
@@ -384,7 +384,7 @@ public void run() {
     }
 
     /**
-     * Close the stream uploading any remaning buffered data
+     * Close the stream uploading any remaining buffered data
      *
      * @throws IOException
      */
diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/util/S3CopyStream.java b/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/util/S3CopyStream.java
index 583a9356b4..d927f6519f 100644
--- a/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/util/S3CopyStream.java
+++ b/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/util/S3CopyStream.java
@@ -150,7 +150,7 @@ public void write(byte b[], int off, int len) throws IOException {
 
     /**
      * Writes a byte into the uploader buffer. When it is full starts the upload process
-     * in a asynchornous manner
+     * in a asynchronous manner
      *
      * @param b The byte to be written
      * @throws IOException
@@ -166,7 +166,7 @@ public void write (int b) throws IOException {
 
 
     /**
-     * Close the stream uploading any remaning buffered data
+     * Close the stream uploading any remaining buffered data
      *
      * @throws IOException
      */
diff --git a/plugins/nf-ga4gh/src/main/nextflow/ga4gh/tes/client/ApiCallback.java b/plugins/nf-ga4gh/src/main/nextflow/ga4gh/tes/client/ApiCallback.java
index 48ced73c7f..f1e07a2412 100644
--- a/plugins/nf-ga4gh/src/main/nextflow/ga4gh/tes/client/ApiCallback.java
+++ b/plugins/nf-ga4gh/src/main/nextflow/ga4gh/tes/client/ApiCallback.java
@@ -66,10 +66,10 @@ public interface ApiCallback<T> {
     void onUploadProgress(long bytesWritten, long contentLength, boolean done);
 
     /**
-     * This is called when the API downlond processing.
+     * This is called when the API download processing.
      *
      * @param bytesRead bytes Read
-     * @param contentLength content lenngth of the response
+     * @param contentLength content length of the response
      * @param done Read end
      */
     void onDownloadProgress(long bytesRead, long contentLength, boolean done);
diff --git a/plugins/nf-ga4gh/src/main/nextflow/ga4gh/tes/client/ApiClient.java b/plugins/nf-ga4gh/src/main/nextflow/ga4gh/tes/client/ApiClient.java
index 422b08143e..b32863234f 100644
--- a/plugins/nf-ga4gh/src/main/nextflow/ga4gh/tes/client/ApiClient.java
+++ b/plugins/nf-ga4gh/src/main/nextflow/ga4gh/tes/client/ApiClient.java
@@ -606,7 +606,7 @@ public ApiClient setDebugging(boolean debugging) {
     /**
      * The path of temporary folder used to store downloaded files from endpoints
      * with file response. The default value is <code>null</code>, i.e. using
-     * the system's default tempopary folder.
+     * the system's default temporary folder.
      *
      * @see <a href="https://docs.oracle.com/javase/7/docs/api/java/io/File.html#createTempFile">createTempFile</a>
      * @return Temporary folder path
@@ -616,7 +616,7 @@ public String getTempFolderPath() {
     }
 
     /**
-     * Set the tempoaray folder path (for downloading files)
+     * Set the temporary folder path (for downloading files)
      *
      * @param tempFolderPath Temporary folder path
      * @return ApiClient
@@ -1195,7 +1195,7 @@ public String buildUrl(String path, List<Pair> queryParams) {
      * Set header parameters to the request builder, including default headers.
      *
      * @param headerParams Header parameters in the ofrm of Map
-     * @param reqBuilder Reqeust.Builder
+     * @param reqBuilder Request.Builder
      */
     public void processHeaderParams(Map<String, String> headerParams, Request.Builder reqBuilder) {
         for (Entry<String, String> param : headerParams.entrySet()) {
diff --git a/plugins/nf-ga4gh/src/main/nextflow/ga4gh/tes/client/model/TesExecutor.java b/plugins/nf-ga4gh/src/main/nextflow/ga4gh/tes/client/model/TesExecutor.java
index a93f9ebf61..1d3fb95cdd 100644
--- a/plugins/nf-ga4gh/src/main/nextflow/ga4gh/tes/client/model/TesExecutor.java
+++ b/plugins/nf-ga4gh/src/main/nextflow/ga4gh/tes/client/model/TesExecutor.java
@@ -197,10 +197,10 @@ public TesExecutor putEnvItem(String key, String envItem) {
   }
 
    /**
-   * Enviromental variables to set within the container.
+   * Environmental variables to set within the container.
    * @return env
   **/
-  @ApiModelProperty(value = "Enviromental variables to set within the container.")
+  @ApiModelProperty(value = "Environmental variables to set within the container.")
   public Map<String, String> getEnv() {
     return env;
   }
diff --git a/tests/rnaseq-toy-dsl2.nf b/tests/rnaseq-toy-dsl2.nf
index 2acc205f22..94e76aae20 100644
--- a/tests/rnaseq-toy-dsl2.nf
+++ b/tests/rnaseq-toy-dsl2.nf
@@ -1,7 +1,7 @@
 #!/usr/bin/env nextflow
 
 /*
- * Defines pipeline parameters in order to specify the refence genomes
+ * Defines pipeline parameters in order to specify the reference genomes
  * and read pairs by using the command line options
  */
 params.reads = "$baseDir/data/ggal/*_{1,2}.fq"

From 73eb5a02a16eb30ffd5d2e713d6c610ae94aedda Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Wed, 20 Sep 2023 08:12:52 +0200
Subject: [PATCH 162/350] Improve wave container name validation

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../io/seqera/wave/plugin/WaveAssets.groovy   | 11 +++++++++
 .../io/seqera/wave/plugin/WaveClient.groovy   |  2 ++
 .../resolver/WaveContainerResolver.groovy     | 11 ---------
 .../seqera/wave/plugin/WaveAssetsTest.groovy  | 23 +++++++++++++++++++
 .../resolver/WaveContainerResolverTest.groovy | 21 -----------------
 5 files changed, 36 insertions(+), 32 deletions(-)

diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveAssets.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveAssets.groovy
index 8201cdafb9..2b7e6fb6e7 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveAssets.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveAssets.groovy
@@ -24,6 +24,8 @@ import groovy.transform.CompileStatic
 import groovy.transform.Memoized
 import nextflow.script.bundle.ResourcesBundle
 import nextflow.util.CacheHelper
+import nextflow.util.StringUtils
+
 /**
  * Hold assets required to fulfill wave container image build
  * 
@@ -81,4 +83,13 @@ class WaveAssets {
         allMeta.add( this.containerPlatform )
         return CacheHelper.hasher(allMeta).hash().toString()
     }
+
+
+    static void validateContainerRepo(String name) {
+        if( !name )
+            return
+        final scheme = StringUtils.getUrlProtocol(name)
+        if( scheme )
+            throw new IllegalArgumentException("Container repository should not start with URL like prefix - offending value: $name")
+    }
 }
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
index 1e02a5f9eb..f2e3aa475b 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
@@ -487,6 +487,8 @@ class WaveClient {
          */
         final platform = dockerArch
 
+        // check is a valid container image
+        WaveAssets.validateContainerRepo(containerImage)
         // read the container config and go ahead
         final containerConfig = this.resolveContainerConfig(platform)
         return new WaveAssets(
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/resolver/WaveContainerResolver.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/resolver/WaveContainerResolver.groovy
index 46b00c464c..44cae4f476 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/resolver/WaveContainerResolver.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/resolver/WaveContainerResolver.groovy
@@ -30,8 +30,6 @@ import nextflow.container.resolver.ContainerResolver
 import nextflow.container.resolver.DefaultContainerResolver
 import nextflow.plugin.Priority
 import nextflow.processor.TaskRun
-import nextflow.util.StringUtils
-
 /**
  * Implement Wave container resolve logic
  *
@@ -108,7 +106,6 @@ class WaveContainerResolver implements ContainerResolver {
      *      when the task does not request any container or dockerfile to build
      */
     protected ContainerInfo waveContainer(TaskRun task, String container, boolean singularity) {
-        validateContainerRepo(container)
         final assets = client().resolveAssets(task, container, singularity)
         if( assets ) {
             return client().fetchContainerImage(assets)
@@ -118,12 +115,4 @@ class WaveContainerResolver implements ContainerResolver {
         return null
     }
 
-    static protected void validateContainerRepo(String name) {
-        if( !name )
-            return 
-        final scheme = StringUtils.getUrlProtocol(name)
-        if( scheme )
-            throw new IllegalArgumentException("Container repository should not start with URL like prefix - offending value: $name")
-    }
-
 }
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveAssetsTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveAssetsTest.groovy
index d322791489..8ecf593e61 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveAssetsTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveAssetsTest.groovy
@@ -17,6 +17,7 @@
 
 package io.seqera.wave.plugin
 
+
 import nextflow.script.bundle.ResourcesBundle
 import nextflow.util.CacheHelper
 import spock.lang.Specification
@@ -36,4 +37,26 @@ class WaveAssetsTest extends Specification {
 
     }
 
+    def 'should validate container name' () {
+        when:
+        WaveAssets.validateContainerRepo('ubuntu')
+        then:
+        noExceptionThrown()
+
+        when:
+        WaveAssets.validateContainerRepo('ubuntu:latest')
+        then:
+        noExceptionThrown()
+
+        when:
+        WaveAssets.validateContainerRepo('quay.io/wtsicgp/nanoseq:3.3.0')
+        then:
+        noExceptionThrown()
+
+        when:
+        WaveAssets.validateContainerRepo('docker://quay.io/wtsicgp/nanoseq:3.3.0')
+        then:
+        thrown(IllegalArgumentException)
+    }
+
 }
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/resolver/WaveContainerResolverTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/resolver/WaveContainerResolverTest.groovy
index da190d728e..8f46949bf4 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/resolver/WaveContainerResolverTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/resolver/WaveContainerResolverTest.groovy
@@ -84,25 +84,4 @@ class WaveContainerResolverTest extends Specification {
         result == ORAS_CONTAINER
     }
 
-    def 'should validate container name' () {
-        when:
-        WaveContainerResolver.validateContainerRepo('ubuntu')
-        then:
-        noExceptionThrown()
-
-        when:
-        WaveContainerResolver.validateContainerRepo('ubuntu:latest')
-        then:
-        noExceptionThrown()
-
-        when:
-        WaveContainerResolver.validateContainerRepo('quay.io/wtsicgp/nanoseq:3.3.0')
-        then:
-        noExceptionThrown()
-
-        when:
-        WaveContainerResolver.validateContainerRepo('docker://quay.io/wtsicgp/nanoseq:3.3.0')
-        then:
-        thrown(IllegalArgumentException)
-    }
 }

From 4e3e9aca77e30acd8cb54274d51d188a91afb1a9 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Thu, 21 Sep 2023 14:24:08 -0500
Subject: [PATCH 163/350] Document `NXF_DISABLE_CHECK_LATEST` environment var
 (#4327)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 docs/cli.md     |  6 ++++++
 docs/config.md  | 12 ++++++++++--
 docs/plugins.md |  1 +
 docs/wave.md    |  9 ++++++---
 4 files changed, 23 insertions(+), 5 deletions(-)

diff --git a/docs/cli.md b/docs/cli.md
index 14f9a7bd70..2b15253bf4 100644
--- a/docs/cli.md
+++ b/docs/cli.md
@@ -31,6 +31,8 @@ Available options:
 : Add the specified file to configuration set.
 
 `-d, -dockerize`
+: :::{deprecated} 23.09.0-edge
+  :::
 : Launch nextflow via Docker (experimental).
 
 `-h`
@@ -1075,9 +1077,13 @@ The `run` command is used to execute a local pipeline script or remote pipeline
 : Prevent the cancellation of child jobs on execution termination
 
 `-dsl1`
+: :::{deprecated} 23.09.0-edge
+  :::
 : Execute the workflow using DSL1 syntax.
 
 `-dsl2`
+: :::{deprecated} 23.09.0-edge
+  :::
 : Execute the workflow using DSL2 syntax.
 
 `-dump-channels`
diff --git a/docs/config.md b/docs/config.md
index bd544f25c6..c013547aaf 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -1560,6 +1560,11 @@ The following environment variables control the configuration of the Nextflow ru
   :::
 : Defines the DSL version that should be used in not specified otherwise in the script of config file (default: `2`)
 
+`NXF_DISABLE_CHECK_LATEST`
+: :::{versionadded} 23.09.0-edge
+  :::
+: Nextflow automatically checks for a newer version of itself unless this option is enabled (default: `false`).
+
 `NXF_DISABLE_JOBS_CANCELLATION`
 : :::{versionadded} 21.12.0-edge
   :::
@@ -1567,12 +1572,12 @@ The following environment variables control the configuration of the Nextflow ru
 
 `NXF_DISABLE_PARAMS_TYPE_DETECTION`
 : :::{versionadded} 23.07.0-edge
-:::
+  :::
 : Disables the automatic type detection of command line parameters.
 
 `NXF_DISABLE_WAVE_SERVICE`
 : :::{versionadded} 23.08.0-edge
-:::
+  :::
 : Disables the requirement for Wave service when enabling the Fusion file system.
 
 `NXF_ENABLE_SECRETS`
@@ -1607,6 +1612,9 @@ The following environment variables control the configuration of the Nextflow ru
 
 `NXF_OFFLINE`
 : When `true` disables the project automatic download and update from remote repositories (default: `false`).
+: :::{versionchanged} 23.09.0-edge
+  This option also disables the automatic version check (see `NXF_DISABLE_CHECK_LATEST`).
+  :::
 
 `NXF_OPTS`
 : Provides extra options for the Java and Nextflow runtime. It must be a blank separated list of `-Dkey[=value]` properties.
diff --git a/docs/plugins.md b/docs/plugins.md
index f7f1c22d69..66734f5551 100644
--- a/docs/plugins.md
+++ b/docs/plugins.md
@@ -10,6 +10,7 @@ The following functionalities are provided via plugin components, and they make
 
 - `nf-amazon`: Support for Amazon cloud.
 - `nf-azure`: Support for Azure cloud.
+- `nf-cloudcache`: Support for the cloud cache (see `NXF_CLOUDCACHE_PATH` under {ref}`config-env-vars`).
 - `nf-console`: Implement Nextflow [REPL console](https://www.nextflow.io/blog/2015/introducing-nextflow-console.html).
 - `nf-ga4gh`: Support [GA4GH APIs](https://www.ga4gh.org/).
 - `nf-google`: Support for Google cloud.
diff --git a/docs/wave.md b/docs/wave.md
index e95a88cb29..2a7b1a1c86 100644
--- a/docs/wave.md
+++ b/docs/wave.md
@@ -124,7 +124,10 @@ If using a Spack YAML file to provide the required packages, you should avoid ed
 
 ### Build Singularity native images
 
-As of version `23.09.0-edge`, Nextflow can build Singularity native images on-demand either using `Singularityfile`,
+:::{versionadded} 23.09.0-edge
+:::
+
+Nextflow can build Singularity native images on-demand either using `Singularityfile`,
 Conda packages or Spack packages. The Singularity images are automatically uploaded in a container registry OCI compliant
 of your choice and stored as a [ORAS artefact](https://oras.land/).
 
@@ -134,7 +137,7 @@ This feature requires of Singularity (or Apptainer) version supporting the pull
 
 For example to enable the provisioning of Singularity images in your pipeline use the following configuration snippet:
 
-```
+```groovy
 singularity.enabled = true
 wave.enabled = true
 wave.freeze = true
@@ -187,7 +190,7 @@ The following configuration options are available:
 : The Wave service endpoint (default: `https://wave.seqera.io`).
 
 `wave.freeze`
-: :::{versionadded} 22.09.0-edge
+: :::{versionadded} 23.07.0-edge
   :::
 : When enabling the container freeze mode, Wave will provision an non-ephemeral container image
 that will be pushed to a container repository your choice. It requires the use of the `wave.build.repository` setting.

From 6525b0a1c50c3c92cb4d53c2870acadae34df4ae Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Thu, 21 Sep 2023 15:17:29 -0500
Subject: [PATCH 164/350] Document source of `vol_ctxt` and `inv_ctxt` trace
 metrics (#4333)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 docs/tracing.md                                               | 4 ++--
 .../src/main/groovy/nextflow/trace/TraceRecord.groovy         | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/docs/tracing.md b/docs/tracing.md
index e8515fa870..6d7647bbd1 100644
--- a/docs/tracing.md
+++ b/docs/tracing.md
@@ -282,10 +282,10 @@ The following table shows the fields that can be included in the execution repor
 : Number of bytes the process originally dirtied in the page-cache (assuming they will go to disk later). This data is read from file `/proc/$pid/io`.
 
 `vol_ctxt`
-: Number of voluntary context switches.
+: Number of voluntary context switches. This data is read from field `voluntary_ctxt_switches` in `/proc/$pid/status` file.
 
 `inv_ctxt`
-: Number of involuntary context switches.
+: Number of involuntary context switches. This data is read from field `nonvoluntary_ctxt_switches` in `/proc/$pid/status` file.
 
 `env`
 : The variables defined in task execution environment.
diff --git a/modules/nextflow/src/main/groovy/nextflow/trace/TraceRecord.groovy b/modules/nextflow/src/main/groovy/nextflow/trace/TraceRecord.groovy
index 40947760b9..93b5b6856b 100644
--- a/modules/nextflow/src/main/groovy/nextflow/trace/TraceRecord.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/trace/TraceRecord.groovy
@@ -98,8 +98,8 @@ class TraceRecord implements Serializable {
             time:       'time',
             env:        'str',
             error_action:'str',
-            vol_ctxt: 'num',
-            inv_ctxt: 'num',
+            vol_ctxt: 'num',        // -- /proc/$pid/status field 'voluntary_ctxt_switches'
+            inv_ctxt: 'num',        // -- /proc/$pid/status field 'nonvoluntary_ctxt_switches'
             hostname: 'str',
             cpu_model:  'str'
     ]

From 66b2d2d27c4529d7310714209e7510f45e50bbc9 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Thu, 21 Sep 2023 22:38:58 +0200
Subject: [PATCH 165/350] Add procps by default to Conda-based Wave builds

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-wave/build.gradle                  |  2 +-
 .../seqera/wave/plugin/WaveClientTest.groovy  | 22 +++++++++++--------
 2 files changed, 14 insertions(+), 10 deletions(-)

diff --git a/plugins/nf-wave/build.gradle b/plugins/nf-wave/build.gradle
index 28f5b904da..521a0a335f 100644
--- a/plugins/nf-wave/build.gradle
+++ b/plugins/nf-wave/build.gradle
@@ -36,7 +36,7 @@ dependencies {
     api 'org.apache.commons:commons-lang3:3.12.0'
     api 'com.google.code.gson:gson:2.10.1'
     api 'org.yaml:snakeyaml:2.0'
-    api 'io.seqera:wave-utils:0.7.4'
+    api 'io.seqera:wave-utils:0.7.5'
 
     testImplementation(testFixtures(project(":nextflow")))
     testImplementation "org.codehaus.groovy:groovy:3.0.19"
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
index 62468f8ad7..755ff11c67 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
@@ -524,6 +524,7 @@ class WaveClientTest extends Specification {
                 FROM mambaorg/micromamba:1.4.9
                 COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml
                 RUN micromamba install -y -n base -f /tmp/conda.yml \\
+                    && micromamba install -y -n base conda-forge::procps-ng \\
                     && micromamba clean -a -y
                 USER root
                     '''.stripIndent()
@@ -558,8 +559,8 @@ class WaveClientTest extends Specification {
         assets.containerFile == '''\
                 FROM mambaorg/micromamba:1.4.9
                 RUN \\
-                    micromamba install -y -n base -c conda-forge -c defaults \\
-                    -f https://host.com/conda-lock.yml \\
+                    micromamba install -y -n base -c conda-forge -c defaults -f https://host.com/conda-lock.yml \\
+                    && micromamba install -y -n base conda-forge::procps-ng \\
                     && micromamba clean -a -y
                 USER root
                     '''.stripIndent()
@@ -634,6 +635,7 @@ class WaveClientTest extends Specification {
                 FROM mambaorg/micromamba:1.4.9
                 COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml
                 RUN micromamba install -y -n base -f /tmp/conda.yml \\
+                    && micromamba install -y -n base conda-forge::procps-ng \\
                     && micromamba clean -a -y
                 USER root
                     '''.stripIndent()
@@ -714,8 +716,9 @@ class WaveClientTest extends Specification {
                 %files
                     {{wave_context_dir}}/conda.yml /scratch/conda.yml
                 %post
-                    micromamba install -y -n base -f /scratch/conda.yml \\
-                    && micromamba clean -a -y
+                    micromamba install -y -n base -f /scratch/conda.yml
+                    micromamba install -y -n base conda-forge::procps-ng
+                    micromamba clean -a -y
                 %environment
                     export PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
                     '''.stripIndent()
@@ -752,9 +755,9 @@ class WaveClientTest extends Specification {
                 BootStrap: docker
                 From: mambaorg/micromamba:1.4.9
                 %post
-                    micromamba install -y -n base -c conda-forge -c defaults \\
-                    -f https://host.com/lock-file.yaml \\
-                    && micromamba clean -a -y
+                    micromamba install -y -n base -c conda-forge -c defaults -f https://host.com/lock-file.yaml
+                    micromamba install -y -n base conda-forge::procps-ng
+                    micromamba clean -a -y
                 %environment
                     export PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
                     '''.stripIndent()
@@ -788,8 +791,9 @@ class WaveClientTest extends Specification {
                 %files
                     {{wave_context_dir}}/conda.yml /scratch/conda.yml
                 %post
-                    micromamba install -y -n base -f /scratch/conda.yml \\
-                    && micromamba clean -a -y
+                    micromamba install -y -n base -f /scratch/conda.yml
+                    micromamba install -y -n base conda-forge::procps-ng
+                    micromamba clean -a -y
                 %environment
                     export PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"                    
                 '''.stripIndent()

From 9b3741e3c1432170a60891b3d6da154af9b55b41 Mon Sep 17 00:00:00 2001
From: Brandon Price <baceprice@gmail.com>
Date: Thu, 21 Sep 2023 17:06:18 -0400
Subject: [PATCH 166/350] Fix allow_other vulnerability preventing google-batch
 submissions (#4332)

---
 .../cloud/google/batch/GoogleBatchScriptLauncher.groovy       | 2 +-
 .../cloud/google/batch/GoogleBatchScriptLauncherTest.groovy   | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchScriptLauncher.groovy b/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchScriptLauncher.groovy
index ae4dc6b5f6..c9ed889685 100644
--- a/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchScriptLauncher.groovy
+++ b/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchScriptLauncher.groovy
@@ -134,7 +134,7 @@ class GoogleBatchScriptLauncher extends BashWrapperBuilder implements GoogleBatc
                             .setRemotePath(it)
                     )
                     .setMountPath( "${MOUNT_ROOT}/${it}".toString() )
-                    .addAllMountOptions( ['-o rw,allow_other', '-implicit-dirs'] )
+                    .addAllMountOptions( ['-o rw', '-implicit-dirs'] )
                     .build()
             )
         }
diff --git a/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchScriptLauncherTest.groovy b/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchScriptLauncherTest.groovy
index 62dfe74e04..7375728245 100644
--- a/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchScriptLauncherTest.groovy
+++ b/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchScriptLauncherTest.groovy
@@ -71,10 +71,10 @@ class GoogleBatchScriptLauncherTest extends Specification{
         volumes.size() == 2
         volumes[0].getGcs().getRemotePath() == 'alpha'
         volumes[0].getMountPath() == '/mnt/disks/alpha'
-        volumes[0].getMountOptionsList() == ['-o rw,allow_other', '-implicit-dirs']
+        volumes[0].getMountOptionsList() == ['-o rw', '-implicit-dirs']
         volumes[1].getGcs().getRemotePath() == 'omega'
         volumes[1].getMountPath() == '/mnt/disks/omega'
-        volumes[1].getMountOptionsList() == ['-o rw,allow_other', '-implicit-dirs']
+        volumes[1].getMountOptionsList() == ['-o rw', '-implicit-dirs']
     }
 
 }

From 1a68049562d892a852ed09cc85f91349f0f51964 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Thu, 21 Sep 2023 16:07:28 -0500
Subject: [PATCH 167/350] Document `fs` CLI command (#4328)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 docs/cli.md                                   | 60 +++++++++++++++++++
 .../src/main/groovy/nextflow/cli/CmdFs.groovy |  4 +-
 2 files changed, 62 insertions(+), 2 deletions(-)

diff --git a/docs/cli.md b/docs/cli.md
index 2b15253bf4..89b274d881 100644
--- a/docs/cli.md
+++ b/docs/cli.md
@@ -550,6 +550,66 @@ Forcefully drop the `nextflow-io/hello` pipeline, ignoring any local changes.
 $ nextflow drop nextflow-io/hello -f
 ```
 
+### fs
+
+Perform basic filesystem operations.
+
+**Usage**
+
+```console
+$ nextflow fs [subcommands]
+```
+
+**Description**
+
+The `fs` command is used to perform filesystem operations like copy, move, delete, list directory, etc. Like the `file()` method, it can work with local files, remote URLs, and remote object storage. Storage credentials can be provided through the same manner as launching a pipeline (Nextflow config, environment vars, etc).
+
+**Options**
+
+`-h, -help`
+: Print the command usage.
+
+**Examples**
+
+List a directory.
+
+```console
+$ nextflow fs list <directory>
+```
+
+Print the contents of a file to standard output.
+
+```console
+$ nextflow fs cat <file>
+```
+
+Copy a file or directory.
+
+```console
+$ nextflow fs cp <source> <target>
+```
+
+Move a file or directory.
+
+```console
+$ nextflow fs mv <source> <target>
+```
+
+Delete a file or directory.
+
+```console
+$ nextflow fs rm <path>
+```
+
+:::{versionadded} 23.10.0
+:::
+
+Print file or directory attributes.
+
+```console
+$ nextflow fs stat <path>
+```
+
 ### help
 
 Print the top-level help or specific help for a command.
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdFs.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdFs.groovy
index 10464cd533..78daaa5ea6 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdFs.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdFs.groovy
@@ -234,7 +234,7 @@ class CmdFs extends CmdBase implements UsageAware {
     private void run0() {
         final cmd = findCmd(args[0])
         if( !cmd ) {
-            throw new AbortOperationException("Unknown file system command: `$cmd`")
+            throw new AbortOperationException("Unknown fs sub-command: `$cmd`")
         }
 
         Path target
@@ -311,7 +311,7 @@ class CmdFs extends CmdBase implements UsageAware {
             if( sub )
                 println sub.usage()
             else {
-                throw new AbortOperationException("Unknown cloud sub-command: ${args[0]}")
+                throw new AbortOperationException("Unknown fs sub-command: ${args[0]}")
             }
         }
 

From aabb6c19c909b4ba07509e2e0ab0ae3aa720841c Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 23 Sep 2023 12:11:19 +0200
Subject: [PATCH 168/350] Prevent cache invalidation for task directives
 (#4339)

This commit prevents the cache invalidation then a process directive is modified
over a resume, as introduced by PR #2382, since they are configured hints for the process
execution. When the task has been successfully completed, should not be re-executed if a
directive value changes e.g. `cpus` or `memory`.

The extension directive i.e. with the prefix `ext.` is an exception to this rule and will invalidate
the cache in any case.

The experimental variable `NXF_ENABLE_CACHE_INVALIDATION_ON_TASK_DIRECTIVE_CHANGE`
has been removed in favour of the above logic.

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../nextflow/processor/TaskProcessor.groovy      | 16 ++++------------
 .../nextflow/processor/TaskProcessorTest.groovy  |  3 +--
 2 files changed, 5 insertions(+), 14 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
index 4e2639d257..8e71969661 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
@@ -131,12 +131,6 @@ class TaskProcessor {
 
     final private static Pattern QUESTION_MARK = ~/(\?+)/
 
-    @Memoized
-    static boolean getInvalidateCacheOnTaskDirectiveChange() {
-        final value = System.getenv("NXF_ENABLE_CACHE_INVALIDATION_ON_TASK_DIRECTIVE_CHANGE")
-        return value==null || value =='true'
-    }
-
     @TestOnly private static volatile TaskProcessor currentProcessor0
 
     @TestOnly static TaskProcessor currentProcessor() { currentProcessor0 }
@@ -2210,19 +2204,17 @@ class TaskProcessor {
 
     protected Map<String,Object> getTaskGlobalVars(TaskRun task) {
         final result = task.getGlobalVars(ownerScript.binding)
-        if( invalidateCacheOnTaskDirectiveChange ) {
-            final directives = getTaskDirectiveVars(task)
-            result.putAll(directives)
-        }
+        final directives = getTaskExtensionDirectiveVars(task)
+        result.putAll(directives)
         return result
     }
 
-    protected Map<String,Object> getTaskDirectiveVars(TaskRun task) {
+    protected Map<String,Object> getTaskExtensionDirectiveVars(TaskRun task) {
         final variableNames = task.getVariableNames()
         final result = new HashMap(variableNames.size())
         final taskConfig = task.config
         for( String key : variableNames ) {
-            if( !key.startsWith('task.') ) continue
+            if( !key.startsWith('task.ext.') ) continue
             final value = taskConfig.eval(key.substring(5))
             result.put(key, value)
         }
diff --git a/modules/nextflow/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy b/modules/nextflow/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy
index 131cc6d0a9..4307c7edb4 100644
--- a/modules/nextflow/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy
@@ -864,13 +864,12 @@ class TaskProcessorTest extends Specification {
         config.setContext( foo: 'DDDD', bar: 'OOOO' )
 
         when:
-        def result = processor.getTaskDirectiveVars(task)
+        def result = processor.getTaskExtensionDirectiveVars(task)
         then:
         1 * task.getVariableNames() >> {[ 'task.cpus', 'task.ext.alpha', 'task.ext.delta', 'task.ext.omega' ] as Set}
         1 * task.getConfig() >> config
         then:
         result == [
-                'task.cpus': 4,
                 'task.ext.alpha': 'AAAA',
                 'task.ext.delta': 'DDDD',
                 'task.ext.omega': 'OOOO',

From ac1fc9ee87510bedd9edc510610391d9825b913b Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 23 Sep 2023 12:49:12 +0200
Subject: [PATCH 169/350] Add support for Java 21 (#4338) [ci fast]

This commit adds the support for Java 21. Moreover, it enables virtual threads
by default when using Java 21. It's still possible to rollback to platform threads
by setting the environment variable NXF_ENABLE_VIRTUAL_THREADS=false.


Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/getstarted.md |  2 +-
 launch.sh          |  8 +++++---
 nextflow           | 16 ++++++++++------
 3 files changed, 16 insertions(+), 10 deletions(-)

diff --git a/docs/getstarted.md b/docs/getstarted.md
index 4049a0e694..40651b5edb 100644
--- a/docs/getstarted.md
+++ b/docs/getstarted.md
@@ -6,7 +6,7 @@
 
 ## Requirements
 
-Nextflow can be used on any POSIX compatible system (Linux, OS X, etc). It requires Bash 3.2 (or later) and [Java 11 (or later, up to 20)](http://www.oracle.com/technetwork/java/javase/downloads/index.html) to be installed.
+Nextflow can be used on any POSIX compatible system (Linux, OS X, etc). It requires Bash 3.2 (or later) and [Java 11 (or later, up to 21)](http://www.oracle.com/technetwork/java/javase/downloads/index.html) to be installed.
 
 For the execution in a cluster of computers, the use of a shared file system is required to allow the sharing of tasks input/output files.
 
diff --git a/launch.sh b/launch.sh
index 5bc03f3229..b910384518 100755
--- a/launch.sh
+++ b/launch.sh
@@ -66,14 +66,15 @@ fi
 JAVA_VER=$(echo "$JAVA_VER" | awk '/version/ {gsub(/"/, "", $3); print $3}')
 major=${BASH_REMATCH[1]}
 minor=${BASH_REMATCH[2]}
-version_check="^(1.8|9|10|11|12|13|14|15|16|17|18|19|20)"
+version_check="^(1.8|9|10|11|12|13|14|15|16|17|18|19|20|21)"
 if [[ ! $JAVA_VER =~ $version_check ]]; then
     echo "Error: cannot find Java or it's a wrong version -- please make sure that Java 8 or higher is installed"
     exit 1
 fi
 JVM_ARGS+=" -Dfile.encoding=UTF-8 -XX:+TieredCompilation -XX:TieredStopAtLevel=1"
-[[ $JAVA_VER =~ ^(9|10|11|12|13|14|15|16|17|18|19|20) ]] && JVM_ARGS+=" --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.io=ALL-UNNAMED --add-opens=java.base/java.nio=ALL-UNNAMED --add-opens=java.base/java.net=ALL-UNNAMED --add-opens=java.base/java.nio.file.spi=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED --add-opens=java.base/java.util.concurrent.locks=ALL-UNNAMED --add-opens=java.base/java.util.concurrent.atomic=ALL-UNNAMED --add-opens=java.base/sun.nio.ch=ALL-UNNAMED --add-opens=java.base/sun.nio.fs=ALL-UNNAMED --add-opens=java.base/sun.net.www.protocol.http=ALL-UNNAMED --add-opens=java.base/sun.net.www.protocol.https=ALL-UNNAMED --add-opens=java.base/sun.net.www.protocol.ftp=ALL-UNNAMED --add-opens=java.base/sun.net.www.protocol.file=ALL-UNNAMED --add-opens=java.base/jdk.internal.misc=ALL-UNNAMED --add-opens=java.base/jdk.internal.vm=ALL-UNNAMED --add-opens=java.base/java.util.regex=ALL-UNNAMED"
-[[ $NXF_ENABLE_VIRTUAL_THREADS == 'true' ]] && JVM_ARGS+=" --enable-preview"
+[[ $JAVA_VER =~ ^(9|10|11|12|13|14|15|16|17|18|19|20|21) ]] && JVM_ARGS+=" --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.io=ALL-UNNAMED --add-opens=java.base/java.nio=ALL-UNNAMED --add-opens=java.base/java.net=ALL-UNNAMED --add-opens=java.base/java.nio.file.spi=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED --add-opens=java.base/java.util.concurrent.locks=ALL-UNNAMED --add-opens=java.base/java.util.concurrent.atomic=ALL-UNNAMED --add-opens=java.base/sun.nio.ch=ALL-UNNAMED --add-opens=java.base/sun.nio.fs=ALL-UNNAMED --add-opens=java.base/sun.net.www.protocol.http=ALL-UNNAMED --add-opens=java.base/sun.net.www.protocol.https=ALL-UNNAMED --add-opens=java.base/sun.net.www.protocol.ftp=ALL-UNNAMED --add-opens=java.base/sun.net.www.protocol.file=ALL-UNNAMED --add-opens=java.base/jdk.internal.misc=ALL-UNNAMED --add-opens=java.base/jdk.internal.vm=ALL-UNNAMED --add-opens=java.base/java.util.regex=ALL-UNNAMED"
+[[ $NXF_ENABLE_VIRTUAL_THREADS == 'true' ]] && [[ "$JAVA_VER" =~ ^(19|20) ]] && JVM_ARGS+=" --enable-preview"
+[[ "$JAVA_VER" =~ ^(21) ]] && [[ ! "$NXF_ENABLE_VIRTUAL_THREADS" ]] && NXF_ENABLE_VIRTUAL_THREADS=true
 
 ## flight recorded -- http://docs.oracle.com/javacomponents/jmc-5-4/jfr-runtime-guide/run.htm
 ##JVM_ARGS+=" -XX:+UnlockCommercialFeatures -XX:+FlightRecorder -XX:StartFlightRecording=duration=60s,filename=myrecording.jfr"
@@ -89,6 +90,7 @@ export COLUMNS
 export NXF_PLUGINS_DIR
 export NXF_PLUGINS_MODE
 export NXF_PLUGINS_DEFAULT
+export NXF_ENABLE_VIRTUAL_THREADS
 
 # Yourkit profiling library
 YOURKIT_AGENT=${YOURKIT_AGENT:-/Applications/YourKit-Java-Profiler-2021.11.app/Contents/Resources/bin/mac/libyjpagent.dylib}
diff --git a/nextflow b/nextflow
index c3145509a6..b6983744eb 100755
--- a/nextflow
+++ b/nextflow
@@ -305,8 +305,8 @@ else
     version_check="^(1.7|1.8)"
     version_message="Java 7 or 8"
   else
-    version_check="^(1.8|9|10|11|12|13|14|15|16|17|18|19|20)"
-    version_message="Java 8 or later (up to 20)"
+    version_check="^(1.8|9|10|11|12|13|14|15|16|17|18|19|20|21)"
+    version_message="Java 8 or later (up to 21)"
   fi
   if [[ ! $JAVA_VER =~ $version_check ]]; then
       echo_red "ERROR: Cannot find Java or it's a wrong version -- please make sure that $version_message is installed"
@@ -317,8 +317,8 @@ else
       fi
       exit 1
   fi
-  if [[ ! $JAVA_VER =~ ^(11|12|13|14|15|16|17|18|19|20) ]]; then
-      echo_yellow "NOTE: Nextflow is not tested with Java $JAVA_VER -- It's recommended the use of version 11 up to 20\n"
+  if [[ ! $JAVA_VER =~ ^(11|12|13|14|15|16|17|18|19|20|21) ]]; then
+      echo_yellow "NOTE: Nextflow is not tested with Java $JAVA_VER -- It's recommended the use of version 11 up to 21\n"
   fi
   mkdir -p $(dirname "$JAVA_KEY")
   [[ -f $JAVA_VER ]] && echo $JAVA_VER > "$JAVA_KEY"
@@ -340,6 +340,7 @@ if [[ $cmd == console ]]; then bg=1;
 else JAVA_OPTS+=(-Djava.awt.headless=true)
 fi
 
+[[ "$JAVA_VER" =~ ^(21) ]] && [[ ! "$NXF_ENABLE_VIRTUAL_THREADS" ]] && NXF_ENABLE_VIRTUAL_THREADS=true
 [[ "$JAVA_HOME" ]] && JAVA_OPTS+=(-Dcapsule.java.home="$JAVA_HOME")
 [[ "$CAPSULE_LOG" ]] && JAVA_OPTS+=(-Dcapsule.log=$CAPSULE_LOG)
 [[ "$CAPSULE_RESET" ]] && JAVA_OPTS+=(-Dcapsule.reset=true)
@@ -356,6 +357,7 @@ export NXF_PLUGINS_DIR
 export NXF_PLUGINS_MODE
 export NXF_PLUGINS_DEFAULT
 export NXF_PACK
+export NXF_ENABLE_VIRTUAL_THREADS
 
 # lookup the a `md5` command
 if hash md5sum 2>/dev/null; then MD5=md5sum;
@@ -409,7 +411,7 @@ else
     [[ "$NXF_JVM_ARGS" ]] && launcher+=($NXF_JVM_ARGS)
     [[ "$remote_debug" ]] && launcher+=(-agentlib:jdwp=transport=dt_socket,server=y,suspend=y,address=$NXF_REMOTE_DEBUG_PORT)
 
-    if [[ "$JAVA_VER" =~ ^(9|10|11|12|13|14|15|16|17|18|19|20) ]]; then
+    if [[ "$JAVA_VER" =~ ^(9|10|11|12|13|14|15|16|17|18|19|20|21) ]]; then
       launcher+=(--add-opens=java.base/java.lang=ALL-UNNAMED)
       launcher+=(--add-opens=java.base/java.io=ALL-UNNAMED)
       launcher+=(--add-opens=java.base/java.nio=ALL-UNNAMED)
@@ -428,7 +430,9 @@ else
       launcher+=(--add-opens=java.base/jdk.internal.vm=ALL-UNNAMED)
       launcher+=(--add-opens=java.base/java.util.regex=ALL-UNNAMED)
       if [[ "$NXF_ENABLE_VIRTUAL_THREADS" == 'true' ]]; then
-        [[ "$JAVA_VER" =~ ^(19|20) ]] && launcher+=(--enable-preview) || die "Virtual threads requires Java 19 or later - current version $JAVA_VER"
+        if [[ "$JAVA_VER" =~ ^(19|20) ]]; then launcher+=(--enable-preview)
+        elif [[ ! "$JAVA_VER" =~ ^(21) ]]; then die "Virtual threads require Java 19 or later - current version $JAVA_VER"
+        fi
       fi
       launcher+=("${cmd_tail[@]}")
     else

From afe3dc4f0c72a26d0eceff3f3ecb4e8e998818be Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sun, 24 Sep 2023 17:00:00 +0200
Subject: [PATCH 170/350] Fix use of GITHUB_TOKEN variable to access GitHub
 repo

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../nextflow/scm/RepositoryProvider.groovy    |  4 ++--
 .../scm/GithubRepositoryProviderTest.groovy   | 21 +++++++++++++++++
 .../scm/RepositoryProviderTest.groovy         | 23 +++++++++++++++++++
 3 files changed, 46 insertions(+), 2 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/scm/RepositoryProvider.groovy b/modules/nextflow/src/main/groovy/nextflow/scm/RepositoryProvider.groovy
index ae1fe3490d..4c83a22e1f 100644
--- a/modules/nextflow/src/main/groovy/nextflow/scm/RepositoryProvider.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/scm/RepositoryProvider.groovy
@@ -79,7 +79,7 @@ abstract class RepositoryProvider {
     }
 
     boolean hasCredentials() {
-        config ? config.user && config.password : false
+        getUser() && getPassword()
     }
 
     String getUser() { config?.user }
@@ -205,7 +205,7 @@ abstract class RepositoryProvider {
      */
     protected void auth( URLConnection connection ) {
         if( hasCredentials() ) {
-            String authString = "${config.user}:${config.password}".bytes.encodeBase64().toString()
+            String authString = "${getUser()}:${getPassword()}".bytes.encodeBase64().toString()
             connection.setRequestProperty("Authorization","Basic " + authString)
         }
     }
diff --git a/modules/nextflow/src/test/groovy/nextflow/scm/GithubRepositoryProviderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/scm/GithubRepositoryProviderTest.groovy
index 789ce7b3fd..50f90c4dca 100644
--- a/modules/nextflow/src/test/groovy/nextflow/scm/GithubRepositoryProviderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/scm/GithubRepositoryProviderTest.groovy
@@ -120,5 +120,26 @@ class GithubRepositoryProviderTest extends Specification {
         cleanup:
         SysEnv.pop()
     }
+
+    def 'should auth using github token' () {
+        given:
+        SysEnv.push(['GITHUB_TOKEN': '1234567890'])
+        and:
+        def provider = Spy(new GithubRepositoryProvider('foo',Mock(ProviderConfig)))
+        and:
+        def conn = Mock(HttpURLConnection)
+
+        when:
+        provider.auth(conn)
+        then:
+        _ * provider.getUser() 
+        _ * provider.getPassword()
+        1 * provider.hasCredentials()
+        and:
+        1 * conn.setRequestProperty('Authorization', "Basic ${'1234567890:x-oauth-basic'.bytes.encodeBase64()}".toString())
+
+        cleanup:
+        SysEnv.pop()
+    }
 }
 
diff --git a/modules/nextflow/src/test/groovy/nextflow/scm/RepositoryProviderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/scm/RepositoryProviderTest.groovy
index 56faf8ae23..e8637294a0 100644
--- a/modules/nextflow/src/test/groovy/nextflow/scm/RepositoryProviderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/scm/RepositoryProviderTest.groovy
@@ -85,4 +85,27 @@ class RepositoryProviderTest extends Specification {
         result == 'foo****:bar****'
 
     }
+
+    def 'should auth using credentials' () {
+        given:
+        def provider = Spy(RepositoryProvider)
+        and:
+        def conn = Mock(HttpURLConnection)
+
+        when:
+        provider.auth(conn)
+        then:
+        1 * provider.getUser() >> null
+        1 * provider.hasCredentials()
+        0 * conn.setRequestProperty('Authorization', _)
+
+        when:
+        provider.auth(conn)
+        then:
+        _ * provider.getUser() >> 'foo'
+        _ * provider.getPassword() >> 'bar'
+        1 * provider.hasCredentials()
+        and:
+        1 * conn.setRequestProperty('Authorization', "Basic ${'foo:bar'.bytes.encodeBase64()}")
+    }
 }

From 79248355799bec1a8f427f42a6fdd1472a764ecb Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Mon, 25 Sep 2023 10:09:42 -0500
Subject: [PATCH 171/350] Retry TimeoutException in azure file system (#4295)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 .../src/main/nextflow/cloud/azure/nio/AzFileSystem.groovy      | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/plugins/nf-azure/src/main/nextflow/cloud/azure/nio/AzFileSystem.groovy b/plugins/nf-azure/src/main/nextflow/cloud/azure/nio/AzFileSystem.groovy
index 26cc521209..2e8b0fd5e9 100644
--- a/plugins/nf-azure/src/main/nextflow/cloud/azure/nio/AzFileSystem.groovy
+++ b/plugins/nf-azure/src/main/nextflow/cloud/azure/nio/AzFileSystem.groovy
@@ -28,6 +28,7 @@ import java.nio.file.WatchService
 import java.nio.file.attribute.UserPrincipalLookupService
 import java.time.Duration
 import java.time.temporal.ChronoUnit
+import java.util.concurrent.TimeoutException
 import java.util.function.Predicate
 
 import com.azure.core.util.polling.SyncPoller
@@ -552,7 +553,7 @@ class AzFileSystem extends FileSystem {
      * @return The result of the supplied action
      */
     protected <T> T apply(CheckedSupplier<T> action) {
-        final policy = retryPolicy((Throwable t) -> t instanceof IOException || t.cause instanceof IOException)
+        final policy = retryPolicy((Throwable t) -> t instanceof IOException || t.cause instanceof IOException || t instanceof TimeoutException || t.cause instanceof TimeoutException)
         return Failsafe.with(policy).get(action)
     }
 }

From 0f3e263feae9cd9e2394f19ceaa53ce7eae0a58f Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Tue, 26 Sep 2023 04:36:22 -0500
Subject: [PATCH 172/350] Use Mermaid diagram in HTML DAG (#4337)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/cli.md                                   |   5 +-
 docs/config.md                                |  18 ++-
 docs/images/dag.mmd                           |   2 +-
 docs/images/dag.png                           | Bin 38622 -> 0 bytes
 docs/tracing.md                               |  69 ++++++----
 .../nextflow/dag/CytoscapeJsRenderer.groovy   |  74 -----------
 ...erer.groovy => MermaidHtmlRenderer.groovy} |  25 ++--
 .../nextflow/dag/MermaidRenderer.groovy       |  25 ++--
 .../nextflow/trace/GraphObserver.groovy       |   8 +-
 .../dag/cytoscape.js.dag.template.html        | 119 ------------------
 .../nextflow/dag/mermaid.dag.template.html    |  29 +++++
 .../nextflow/config/ConfigBuilderTest.groovy  |   2 +-
 .../nextflow/dag/MermaidRendererTest.groovy   |   2 +-
 .../nextflow/trace/GraphObserverTest.groovy   |  41 +++---
 tests/checks/hello.nf/.checks                 |   2 +-
 15 files changed, 147 insertions(+), 274 deletions(-)
 delete mode 100644 docs/images/dag.png
 delete mode 100644 modules/nextflow/src/main/groovy/nextflow/dag/CytoscapeJsRenderer.groovy
 rename modules/nextflow/src/main/groovy/nextflow/dag/{CytoscapeHtmlRenderer.groovy => MermaidHtmlRenderer.groovy} (55%)
 delete mode 100644 modules/nextflow/src/main/resources/nextflow/dag/cytoscape.js.dag.template.html
 create mode 100644 modules/nextflow/src/main/resources/nextflow/dag/mermaid.dag.template.html

diff --git a/docs/cli.md b/docs/cli.md
index 89b274d881..3fe270f7e1 100644
--- a/docs/cli.md
+++ b/docs/cli.md
@@ -1226,8 +1226,11 @@ The `run` command is used to execute a local pipeline script or remote pipeline
 `-with-conda`
 : Use the specified Conda environment package or file (must end with `.yml` or `.yaml`)
 
-`-with-dag` (`dag-<timestamp>.dot`)
+`-with-dag` (`dag-<timestamp>.html`)
 : Create pipeline DAG file.
+: :::{versionchanged} 23.10.0
+  The default format was changed from `dot` to `html`.
+  :::
 
 `-with-docker`
 : Enable process execution in a Docker container.
diff --git a/docs/config.md b/docs/config.md
index c013547aaf..2c51b40ddf 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -511,15 +511,22 @@ The `dag` scope controls the workflow diagram generated by Nextflow.
 The following settings are available:
 
 `dag.enabled`
-: When `true` turns on the generation of the DAG file (default: `false`).
+: When `true` enables the generation of the DAG file (default: `false`).
 
 `dag.depth`
 : :::{versionadded} 23.10.0
   :::
-: Controls the maximum depth at which to render sub-workflows (default: no limit; only supported by the Mermaid render).
+: *Only supported by the HTML and Mermaid renderers.*
+: Controls the maximum depth at which to render sub-workflows (default: no limit).
+
+`dag.direction`
+: :::{versionadded} 23.10.0
+:::
+: *Only supported by the HTML and Mermaid renderers.*
+: Controls the direction of the DAG, can be `'LR'` (left-to-right) or `'TB'` (top-to-bottom) (default: `'TB'`).
 
 `dag.file`
-: Graph file name (default: `dag-<timestamp>.dot`).
+: Graph file name (default: `dag-<timestamp>.html`).
 
 `dag.overwrite`
 : When `true` overwrites any existing DAG file with the same name (default: `false`).
@@ -527,9 +534,10 @@ The following settings are available:
 `dag.verbose`
 : :::{versionadded} 23.10.0
   :::
-: When `false`, channel names are omitted, operators are collapsed, and empty workflow inputs are removed (default: `false`; only supported by the Mermaid render).
+: *Only supported by the HTML and Mermaid renderers.*
+: When `false`, channel names are omitted, operators are collapsed, and empty workflow inputs are removed (default: `false`).
 
-Read the {ref}`dag-visualisation` page to learn more about the execution graph that can be generated by Nextflow.
+Read the {ref}`dag-visualisation` page to learn more about the workflow graph that can be generated by Nextflow.
 
 (config-docker)=
 
diff --git a/docs/images/dag.mmd b/docs/images/dag.mmd
index 388eaf306b..0963e2c106 100644
--- a/docs/images/dag.mmd
+++ b/docs/images/dag.mmd
@@ -1,4 +1,4 @@
-flowchart TD
+flowchart TB
     subgraph " "
     v0["Channel.fromFilePairs"]
     v1["transcriptome"]
diff --git a/docs/images/dag.png b/docs/images/dag.png
deleted file mode 100644
index 33ca19f459af3a693250f6e8af54262abffb4077..0000000000000000000000000000000000000000
GIT binary patch
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diff --git a/docs/tracing.md b/docs/tracing.md
index 6d7647bbd1..32326098a5 100644
--- a/docs/tracing.md
+++ b/docs/tracing.md
@@ -100,7 +100,7 @@ Nextflow can create an HTML execution report: a single document which includes m
 To enable the creation of this report add the `-with-report` command line option when launching the pipeline execution. For example:
 
 ```bash
-nextflow run <pipeline name> -with-report [file name]
+nextflow run <pipeline> -with-report [file name]
 ```
 
 The report file name can be specified as an optional parameter following the report option.
@@ -151,7 +151,7 @@ Nextflow creates an execution tracing file that contains some useful information
 In order to create the execution trace file add the `-with-trace` command line option when launching the pipeline execution. For example:
 
 ```bash
-nextflow run <pipeline name> -with-trace
+nextflow run <pipeline> -with-trace
 ```
 
 It will create a file named `trace.txt` in the current directory. The content looks like the above example:
@@ -338,7 +338,7 @@ As each process can spawn many tasks, colors are used to identify those tasks be
 To enable the creation of the timeline report add the `-with-timeline` command line option when launching the pipeline execution. For example:
 
 ```bash
-nextflow run <pipeline name> -with-timeline [file name]
+nextflow run <pipeline> -with-timeline [file name]
 ```
 
 The report file name can be specified as an optional parameter following the timeline option.
@@ -347,45 +347,60 @@ The report file name can be specified as an optional parameter following the tim
 
 ## DAG visualisation
 
-A Nextflow pipeline is implicitly modelled by a direct acyclic graph (DAG). The vertices in the graph represent the pipeline's processes and operators, while the edges represent the data connections (i.e. channels) between them.
+A Nextflow pipeline can be represented as a direct acyclic graph (DAG). The vertices in the graph represent the pipeline's processes and operators, while the edges represent the data dependencies (i.e. channels) between them.
 
-The pipeline execution DAG can be outputted by adding the `-with-dag` option to the run command line. It creates a file named `dag.dot` containing a textual representation of the pipeline execution graph in the [DOT format](http://www.graphviz.org/content/dot-language).
+To render the workflow DAG, run your pipeline with the `-with-dag` option. By default, it creates a file named `dag-<timestamp>.html` with the workflow DAG rendered as a [Mermaid](https://mermaid.js.org/) diagram.
 
-The execution DAG can be rendered in a different format by specifying an output file name which has an extension corresponding to the required format. For example:
+The workflow DAG can be rendered in a different format by specifying an output file name with a different extension based on the desired format. For example:
 
 ```bash
-nextflow run <script-name> -with-dag flowchart.png
+nextflow run <pipeline> -with-dag flowchart.png
 ```
 
-List of supported file formats:
-
-| Extension | File format                     |
-| --------- | ------------------------------- |
-| dot       | Graphviz DOT file               |
-| html      | HTML file                       |
-| mmd       | Mermaid diagram                 |
-| pdf       | PDF file (\*)                   |
-| png       | PNG file (\*)                   |
-| svg       | SVG file (\*)                   |
-| gexf      | Graph Exchange XML file (Gephi) |
+:::{versionadded} 22.06.0-edge
+You can use the `-preview` option with `-with-dag` to render the workflow DAG without executing any tasks.
+:::
 
-:::{note}
-File formats marked with "\*" require the [Graphviz](http://www.graphviz.org) tool to be installed.
+:::{versionchanged} 23.10.0
+The default output format was changed from DOT to HTML.
 :::
 
-The DAG produced by Nextflow for the [Unistrap](https://github.com/cbcrg/unistrap/) pipeline:
+The following file formats are supported:
 
-```{image} images/dag.png
-```
+`dot`
+: Graphviz [DOT](http://www.graphviz.org/content/dot-language) file
 
-### Mermaid diagram
+`gexf`
+: Graph Exchange XML file (Gephi)
 
-:::{versionadded} 22.04.0
-:::
+`html`
+: HTML file with Mermaid diagram
+: :::{versionchanged} 23.10.0
+  The HTML format was changed to render a Mermaid diagram instead of a Cytoscape diagram.
+  :::
 
-Nextflow can render the DAG as a [Mermaid](https://mermaid-js.github.io/) diagram. Mermaid diagrams are particularly useful because they can be embedded in [GitHub Flavored Markdown](https://github.blog/2022-02-14-include-diagrams-markdown-files-mermaid/) without having to render them yourself. You can customize the diagram with CSS, and you can even add links! Visit the [Mermaid documentation](https://mermaid-js.github.io/mermaid/#/flowchart?id=styling-and-classes) for details.
+`mmd`
+: :::{versionadded} 22.04.0
+  :::
+: Mermaid diagram
+
+`pdf`
+: *Requires [Graphviz](http://www.graphviz.org) to be installed*
+: Graphviz PDF file
+
+`png`
+: *Requires [Graphviz](http://www.graphviz.org) to be installed*
+: Graphviz PNG file
+
+`svg`
+: *Requires [Graphviz](http://www.graphviz.org) to be installed*
+: Graphviz SVG file
 
 Here is the Mermaid diagram produced by Nextflow for the [rnaseq-nf](https://github.com/nextflow-io/rnaseq-nf) pipeline (using the [Mermaid Live Editor](https://mermaid-js.github.io/mermaid-live-editor/edit) with the `default` theme):
 
+```bash
+nextflow run rnaseq-nf -preview -with-dag
+```
+
 ```{mermaid} images/dag.mmd
 ```
diff --git a/modules/nextflow/src/main/groovy/nextflow/dag/CytoscapeJsRenderer.groovy b/modules/nextflow/src/main/groovy/nextflow/dag/CytoscapeJsRenderer.groovy
deleted file mode 100644
index dfcb8246df..0000000000
--- a/modules/nextflow/src/main/groovy/nextflow/dag/CytoscapeJsRenderer.groovy
+++ /dev/null
@@ -1,74 +0,0 @@
-/*
- * Copyright 2013-2023, Seqera Labs
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package nextflow.dag
-import java.nio.file.Path
-
-/**
- * Render the DAG in Cytoscape.js compatible
- * JSON to the specified file.
- * See http://js.cytoscape.org for more info.
- *
- * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
- * @author Mike Smoot <mes@aescon.com>
- */
-class CytoscapeJsRenderer implements DagRenderer {
-
-    @Override
-    void renderDocument(DAG dag, Path file) {
-        file.text = renderNetwork(dag)
-    }
-
-    static String renderNetwork(DAG dag) {
-        def result = []
-        result << "elements: {"
-
-        result << "nodes: ["
-        dag.vertices.each { vertex -> result << renderVertex( vertex ) }
-        result << "],"
-
-        result << "edges: ["
-        dag.edges.each { edge -> result << renderEdge( edge ) }
-        result << "],"
-
-        result << "},"
-
-        return result.join('\n')
-    }
-
-    private static String renderVertex(vertex) {
-        String pre = "{ data: { id: '${vertex.getName()}'"
-        String post = "}, classes: '${vertex.type.name()}' },"
-        if (vertex.label) {
-            return pre + ", label: '${vertex.label}'" + post
-        } else {
-            return pre + post
-        }
-    }
-
-
-    private static String renderEdge(edge) {
-        assert edge.from != null && edge.to != null
-        String dat = "{ data: { source: '${edge.from.name}', target: '${edge.to.name}'"
-        if ( edge.label ) {
-            return dat + ", label: '${edge.label}' } },"
-        }
-        else {
-            return dat + "} },"
-        }
-    }
-
-}
diff --git a/modules/nextflow/src/main/groovy/nextflow/dag/CytoscapeHtmlRenderer.groovy b/modules/nextflow/src/main/groovy/nextflow/dag/MermaidHtmlRenderer.groovy
similarity index 55%
rename from modules/nextflow/src/main/groovy/nextflow/dag/CytoscapeHtmlRenderer.groovy
rename to modules/nextflow/src/main/groovy/nextflow/dag/MermaidHtmlRenderer.groovy
index 5aff50ffe3..f2d175b89b 100644
--- a/modules/nextflow/src/main/groovy/nextflow/dag/CytoscapeHtmlRenderer.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/dag/MermaidHtmlRenderer.groovy
@@ -15,32 +15,31 @@
  */
 
 package nextflow.dag
+
 import java.nio.file.Path
 
 /**
- * Render the DAG in HTML using Cytoscape.js
- * to the specified file.
- * See http://js.cytoscape.org for more info.
+ * Render the DAG as a Mermaid diagram embedded in an HTML document.
+ * See https://mermaid.js.org/ for more info.
  *
- *  @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
- * @author Mike Smoot <mes@aescon.com>
+ * @author Ben Sherman <bentshermann@gmail.com>
  */
-class CytoscapeHtmlRenderer implements DagRenderer {
+class MermaidHtmlRenderer implements DagRenderer {
 
     @Override
     void renderDocument(DAG dag, Path file) {
-        String tmplPage = readTemplate()
-        String network = CytoscapeJsRenderer.renderNetwork(dag)
-        file.text = tmplPage.replaceAll(~/\/\* REPLACE_WITH_NETWORK_DATA \*\//, network)
+        final template = readTemplate()
+        final network = new MermaidRenderer().renderNetwork(dag)
+        file.text = template.replace('REPLACE_WITH_NETWORK_DATA', network)
     }
 
     private String readTemplate() {
-        StringWriter writer = new StringWriter();
-        def res = CytoscapeHtmlRenderer.class.getResourceAsStream('cytoscape.js.dag.template.html')
+        final writer = new StringWriter()
+        final res = MermaidHtmlRenderer.class.getResourceAsStream('mermaid.dag.template.html')
         int ch
         while( (ch=res.read()) != -1 ) {
-            writer.append(ch as char);
+            writer.append(ch as char)
         }
-        writer.toString();
+        writer.toString()
     }
 }
diff --git a/modules/nextflow/src/main/groovy/nextflow/dag/MermaidRenderer.groovy b/modules/nextflow/src/main/groovy/nextflow/dag/MermaidRenderer.groovy
index 76507c4ab4..5538dfed8a 100644
--- a/modules/nextflow/src/main/groovy/nextflow/dag/MermaidRenderer.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/dag/MermaidRenderer.groovy
@@ -42,7 +42,16 @@ class MermaidRenderer implements DagRenderer {
 
     private int depth = session.config.navigate('dag.depth', -1) as int
 
-    private boolean verbose = session.config.navigate('dag.verbose', false)
+    private String direction = session.config.navigate('dag.direction', 'TB')
+
+    private boolean verbose = session.config.navigate('dag.verbose', false);
+
+    {
+        if( direction !in ['TB','LR'] ) {
+            log.warn "Invalid configuration property `dag.direction = '$direction'` - use either: 'TB' (top-bottom) or 'LR' (left-right)"
+            this.direction = 'TB'
+        }
+    }
 
     @Override
     void renderDocument(DAG dag, Path file) {
@@ -70,7 +79,7 @@ class MermaidRenderer implements DagRenderer {
 
         // render diagram
         def lines = [] as List<String>
-        lines << "flowchart TD"
+        lines << "flowchart ${direction}".toString()
 
         // render nodes
         renderNodeTree(lines, null, nodeTree)
@@ -254,23 +263,23 @@ class MermaidRenderer implements DagRenderer {
      *
      * @param nodeLookup
      */
-    private Map getNodeTree(Map<DAG.Vertex,Node> nodeLookup) {
+    private Map<String,Object> getNodeTree(Map<DAG.Vertex,Node> nodeLookup) {
         // infer subgraphs of operator nodes
         final inferredKeys = inferSubgraphKeys(nodeLookup)
 
         // construct node tree
-        def nodeTree = [:]
+        def nodeTree = [:] as Map<String,Object>
 
         for( def node : nodeLookup.values() ) {
             final vertex = node.vertex
 
             // determine the vertex subgraph
-            def keys = []
+            def keys = [] as List<String>
 
             if( vertex.type == DAG.Type.PROCESS ) {
                 // extract keys from fully qualified name
                 final result = getSubgraphKeys(vertex.label)
-                keys = (List)result[0]
+                keys = (List<String>)result[0]
                 node.label = (String)result[1]
             }
             else if( vertex.type == DAG.Type.OPERATOR ) {
@@ -306,7 +315,7 @@ class MermaidRenderer implements DagRenderer {
      * @param nodeLookup
      */
     private Map<Node,List> inferSubgraphKeys(Map<DAG.Vertex,Node> nodeLookup) {
-        def inferredKeys = [:]
+        def inferredKeys = [:] as Map<Node,List>
         def queue = nodeLookup
                 .values()
                 .findAll( n -> n.vertex.type == DAG.Type.OPERATOR ) as List<Node>
@@ -332,7 +341,7 @@ class MermaidRenderer implements DagRenderer {
 
             // extract keys from fully qualified process name
             final keys = process
-                ? getSubgraphKeys(process.vertex.label)[0]
+                ? getSubgraphKeys(process.vertex.label)[0] as List
                 : []
 
             // save inferred keys
diff --git a/modules/nextflow/src/main/groovy/nextflow/trace/GraphObserver.groovy b/modules/nextflow/src/main/groovy/nextflow/trace/GraphObserver.groovy
index a07f611f16..ccadaf9597 100644
--- a/modules/nextflow/src/main/groovy/nextflow/trace/GraphObserver.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/trace/GraphObserver.groovy
@@ -21,13 +21,13 @@ import java.nio.file.Path
 import groovy.transform.PackageScope
 import groovy.util.logging.Slf4j
 import nextflow.Session
-import nextflow.dag.CytoscapeHtmlRenderer
 import nextflow.dag.DAG
 import nextflow.dag.DagRenderer
 import nextflow.dag.DotRenderer
 import nextflow.dag.GexfRenderer
 import nextflow.dag.GraphvizRenderer
 import nextflow.dag.MermaidRenderer
+import nextflow.dag.MermaidHtmlRenderer
 import nextflow.exception.AbortOperationException
 import nextflow.file.FileHelper
 import nextflow.processor.TaskHandler
@@ -41,7 +41,7 @@ import nextflow.processor.TaskProcessor
 @Slf4j
 class GraphObserver implements TraceObserver {
 
-    static public final String DEF_FILE_NAME = "dag-${TraceHelper.launchTimestampFmt()}.dot"
+    static public final String DEF_FILE_NAME = "dag-${TraceHelper.launchTimestampFmt()}.html"
 
     private Path file
 
@@ -61,7 +61,7 @@ class GraphObserver implements TraceObserver {
         assert file
         this.file = file
         this.name = file.baseName
-        this.format = file.getExtension().toLowerCase() ?: 'dot'
+        this.format = file.getExtension().toLowerCase() ?: 'html'
     }
 
     @Override
@@ -91,7 +91,7 @@ class GraphObserver implements TraceObserver {
             new DotRenderer(name)
 
         else if( format == 'html' )
-            new CytoscapeHtmlRenderer()
+            new MermaidHtmlRenderer()
 
         else if( format == 'gexf' )
             new GexfRenderer(name)
diff --git a/modules/nextflow/src/main/resources/nextflow/dag/cytoscape.js.dag.template.html b/modules/nextflow/src/main/resources/nextflow/dag/cytoscape.js.dag.template.html
deleted file mode 100644
index 15258529a2..0000000000
--- a/modules/nextflow/src/main/resources/nextflow/dag/cytoscape.js.dag.template.html
+++ /dev/null
@@ -1,119 +0,0 @@
-<!--
-  ~ Copyright 2013-2023, Seqera Labs
-  ~
-  ~ Licensed under the Apache License, Version 2.0 (the "License");
-  ~ you may not use this file except in compliance with the License.
-  ~ You may obtain a copy of the License at
-  ~
-  ~     http://www.apache.org/licenses/LICENSE-2.0
-  ~
-  ~ Unless required by applicable law or agreed to in writing, software
-  ~ distributed under the License is distributed on an "AS IS" BASIS,
-  ~ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-  ~ See the License for the specific language governing permissions and
-  ~ limitations under the License.
-  -->
-
-<html>
-
-    <head>
-        <title>Nextflow Cytoscape.js with Dagre</title>
-
-        <meta name="viewport" content="width=device-width, user-scalable=no, initial-scale=1, maximum-scale=1">
-
-        <script type="text/javascript">
-        var prot = (("https:" == document.location.protocol) ? "https://" : "http://");
-        document.write(unescape("%3Cscript src='" + prot + "code.jquery.com/jquery-2.0.3.min.js' type='text/javascript' %3E%3C/script%3E"));
-        document.write(unescape("%3Cscript src='" + prot + "cdnjs.cloudflare.com/ajax/libs/cytoscape/2.6.12/cytoscape.min.js' type='text/javascript' %3E%3C/script%3E"));
-        document.write(unescape("%3Cscript src='" + prot + "cdn.rawgit.com/cpettitt/dagre/v0.7.4/dist/dagre.min.js' type='text/javascript' %3E%3C/script%3E"));
-        document.write(unescape("%3Cscript src='" + prot + "cdn.rawgit.com/cytoscape/cytoscape.js-dagre/1.1.2/cytoscape-dagre.js' type='text/javascript' %3E%3C/script%3E"));
-        </script>
-
-        <style>
-            body {
-                font-family: helvetica;
-                font-size: 14px;
-            }
-
-            #cy {
-                width: 100%;
-                height: 100%;
-                position: absolute;
-                left: 0;
-                top: 0;
-                z-index: 999;
-            }
-
-            h1 {
-                opacity: 0.5;
-                font-size: 1em;
-            }
-        </style>
-
-        <script>
-            $(function(){
-                var cy = window.cy = cytoscape({
-                    container: document.getElementById('cy'),
-                    boxSelectionEnabled: false,
-                    autounselectify: true,
-
-                    layout: {
-                        name: 'dagre'
-                    },
-
-                    style: cytoscape.stylesheet()
-                        .selector( 'node')
-                            .css({
-                                'width': 10,
-                                'height': 10,
-                                'content': 'data(label)',
-                                'text-valign': 'center',
-                                'text-halign': 'center',
-                                'text-opacity': 0.5,
-                            })
-                        .selector('node.PROCESS')
-                            .css({
-                                'width': 100,
-                                'height': 50,
-                                'text-opacity': 0.9,
-                                'background-color': '#009911'
-                            })
-                        .selector('node.OPERATOR')
-                            .css({
-                                'background-color': '#11479e',
-                                'text-halign': 'right',
-                            })
-                        .selector('node.ORIGIN')
-                            .css({
-                                'background-color': '#999999',
-                                'text-halign': 'right',
-                            })
-                        .selector('node.TERMINATION')
-                            .css({
-                                'background-color': '#999999',
-                                'text-halign': 'right',
-                            })
-                        .selector('edge')
-                            .css({
-                                'content': 'data(label)',
-                                'text-opacity': 0.5,
-                                'width': 4,
-                                'target-arrow-shape': 'triangle',
-                                'line-color': '#9dbaea',
-                                'target-arrow-color': '#9dbaea'
-                            }),
-
-/* REPLACE_WITH_NETWORK_DATA */
-
-                });
-
-            });
-        </script>
-    </head>
-
-    <body>
-        <h1>Nextflow Cytoscape.js with Dagre</h1>
-        <div id="cy"></div>
-    </body>
-
-</html>
diff --git a/modules/nextflow/src/main/resources/nextflow/dag/mermaid.dag.template.html b/modules/nextflow/src/main/resources/nextflow/dag/mermaid.dag.template.html
new file mode 100644
index 0000000000..2c2a22cc7b
--- /dev/null
+++ b/modules/nextflow/src/main/resources/nextflow/dag/mermaid.dag.template.html
@@ -0,0 +1,29 @@
+<!--
+  ~ Copyright 2013-2023, Seqera Labs
+  ~
+  ~ Licensed under the Apache License, Version 2.0 (the "License");
+  ~ you may not use this file except in compliance with the License.
+  ~ You may obtain a copy of the License at
+  ~
+  ~     http://www.apache.org/licenses/LICENSE-2.0
+  ~
+  ~ Unless required by applicable law or agreed to in writing, software
+  ~ distributed under the License is distributed on an "AS IS" BASIS,
+  ~ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+  ~ See the License for the specific language governing permissions and
+  ~ limitations under the License.
+  -->
+<html>
+<head>
+<meta name="viewport" content="width=device-width, user-scalable=no, initial-scale=1, maximum-scale=1">
+</head>
+<body>
+<pre class="mermaid" style="text-align: center;">
+REPLACE_WITH_NETWORK_DATA
+</pre>
+<script type="module">
+  import mermaid from 'https://cdn.jsdelivr.net/npm/mermaid@10/dist/mermaid.esm.min.mjs';
+  mermaid.initialize({ startOnLoad: true });
+</script>
+</body>
+</html>
diff --git a/modules/nextflow/src/test/groovy/nextflow/config/ConfigBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/config/ConfigBuilderTest.groovy
index 420fe7b54a..de690f0d40 100644
--- a/modules/nextflow/src/test/groovy/nextflow/config/ConfigBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/config/ConfigBuilderTest.groovy
@@ -941,7 +941,7 @@ class ConfigBuilderTest extends Specification {
         then:
         config.dag instanceof Map
         config.dag.enabled
-        config.dag.file == 'dag-20221001.dot'
+        config.dag.file == 'dag-20221001.html'
     }
 
     def 'should set session weblog options' () {
diff --git a/modules/nextflow/src/test/groovy/nextflow/dag/MermaidRendererTest.groovy b/modules/nextflow/src/test/groovy/nextflow/dag/MermaidRendererTest.groovy
index 0c61713b77..57821b8c55 100644
--- a/modules/nextflow/src/test/groovy/nextflow/dag/MermaidRendererTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/dag/MermaidRendererTest.groovy
@@ -46,7 +46,7 @@ class MermaidRendererTest extends Specification {
         then:
         file.text ==
             '''
-            flowchart TD
+            flowchart TB
                 subgraph " "
                 v0[" "]
                 end
diff --git a/modules/nextflow/src/test/groovy/nextflow/trace/GraphObserverTest.groovy b/modules/nextflow/src/test/groovy/nextflow/trace/GraphObserverTest.groovy
index f3d13bc507..7f9fed32be 100644
--- a/modules/nextflow/src/test/groovy/nextflow/trace/GraphObserverTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/trace/GraphObserverTest.groovy
@@ -20,7 +20,7 @@ import java.nio.file.Paths
 
 import groovyx.gpars.dataflow.DataflowQueue
 import nextflow.Session
-import nextflow.dag.CytoscapeHtmlRenderer
+import nextflow.dag.MermaidHtmlRenderer
 import nextflow.dag.DAG
 import nextflow.dag.DotRenderer
 import nextflow.dag.GraphvizRenderer
@@ -112,16 +112,17 @@ class GraphObserverTest extends Specification {
 
         then:
         def result = file.text
-
         // is html
         result.contains('<html>')
         result.contains('</html>')
-
-        // contains some of the expected json
-        result.contains("label: 'Source'")
-        result.contains("label: 'Process 1'")
-        result.contains("label: 'Filter'")
-        result.contains("label: 'Process 2'")
+        // is mermaid
+        result.contains('flowchart')
+        // contains expected nodes
+        result.contains('Source')
+        result.contains('Process 1')
+        result.contains('Process 2')
+        // contains at least one edge
+        result.contains('-->')
 
         cleanup:
         file.delete()
@@ -180,7 +181,7 @@ class GraphObserverTest extends Specification {
         file.delete()
     }
 
-    def 'should output a dot file when no extension is specified' () {
+    def 'should output an html file when no extension is specified' () {
         given:
         def folder = Files.createTempDirectory('test')
         def file = folder.resolve('nope')
@@ -192,15 +193,17 @@ class GraphObserverTest extends Specification {
 
         then:
         def result = file.text
-        // is dot
-        result.contains("digraph \"${file.baseName}\" {")
+        // is html
+        result.contains('<html>')
+        result.contains('</html>')
+        // is mermaid
+        result.contains('flowchart')
         // contains expected nodes
-        result.contains('label="Source"')
-        result.contains('label="Process 1"')
-        result.contains('label="Filter"')
-        result.contains('label="Process 2"')
+        result.contains('Source')
+        result.contains('Process 1')
+        result.contains('Process 2')
         // contains at least one edge
-        result.contains('->')
+        result.contains('-->')
 
         cleanup:
         folder.deleteDir()
@@ -223,7 +226,7 @@ class GraphObserverTest extends Specification {
         then:
         observer.name == 'TheGraph'
         observer.format == 'html'
-        observer.createRender() instanceof CytoscapeHtmlRenderer
+        observer.createRender() instanceof MermaidHtmlRenderer
 
         when:
         observer = new GraphObserver(Paths.get('/path/to/TheGraph.mmd'))
@@ -243,7 +246,7 @@ class GraphObserverTest extends Specification {
         observer = new GraphObserver(Paths.get('/path/to/anonymous'))
         then:
         observer.name == 'anonymous'
-        observer.format == 'dot'
-        observer.createRender() instanceof DotRenderer
+        observer.format == 'html'
+        observer.createRender() instanceof MermaidHtmlRenderer
     }
 }
diff --git a/tests/checks/hello.nf/.checks b/tests/checks/hello.nf/.checks
index e0126df30d..64ff280dd7 100644
--- a/tests/checks/hello.nf/.checks
+++ b/tests/checks/hello.nf/.checks
@@ -28,4 +28,4 @@ $NXF_RUN -with-report -with-timeline -with-trace -with-dag | tee stdout
 [ -s report-*.html ] || false
 [ -s timeline-*.html ] || false
 [ -s trace-*.txt ] || false
-[ -s dag-*.dot ] || false
+[ -s dag-*.html ] || false

From df41e54a7eb6f784bd31fb215826d1aed1a9055d Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Tue, 26 Sep 2023 13:47:40 -0500
Subject: [PATCH 173/350] Remove line endings from container box id (#4334)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 .../src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
index 24b6cbe256..4049eebbe2 100644
--- a/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
@@ -250,7 +250,7 @@ class BashWrapperBuilder {
         binding.helpers_script = getHelpersScript()
 
         if( runWithContainer ) {
-            binding.container_boxid = 'export NXF_BOXID="nxf-$(dd bs=18 count=1 if=/dev/urandom 2>/dev/null | base64 | tr +/ 0A)"'
+            binding.container_boxid = 'export NXF_BOXID="nxf-$(dd bs=18 count=1 if=/dev/urandom 2>/dev/null | base64 | tr +/ 0A | tr -d \'\\r\\n\')"'
             binding.container_helpers = containerBuilder.getScriptHelpers()
             binding.kill_cmd = containerBuilder.getKillCommand()
         }

From 731a29a25030c406c161b800d195d5db2940fb21 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Tue, 26 Sep 2023 14:14:38 -0500
Subject: [PATCH 174/350] Document when process directives are evaluated
 (#4217)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 docs/process.md | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/docs/process.md b/docs/process.md
index 183b0c7f08..d541a94f2a 100644
--- a/docs/process.md
+++ b/docs/process.md
@@ -1211,9 +1211,21 @@ Directives are optional settings that affect the execution of the current proces
 
 They must be entered at the top of the process body, before any other declaration blocks (`input`, `output`, etc), and have the following syntax:
 
+```groovy
+// directive with simple value
+name value
+
+// directive with list value
+name arg1, arg2, arg3
+
+// directive with map value
+name key1: val1, key2: val2
+
+// directive with value and options
+name arg, opt1: val1, opt2: val2
 ```
-name value [, value2 [,..]]
-```
+
+By default, directives are evaluated when the process is defined. However, if the value is a dynamic string or closure, it will be evaluated separately for each task, which allows task-specific variables like `task` and `val` inputs to be used.
 
 Some directives are generally available to all processes, while others depend on the `executor` currently defined.
 

From da7a1942f639467b82b314e8357518026d13035c Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Tue, 26 Sep 2023 21:24:40 +0200
Subject: [PATCH 175/350] Add more tests to container name [ci fast]

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../groovy/nextflow/container/ContainerNameValidatorTest.groovy | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/modules/nextflow/src/test/groovy/nextflow/container/ContainerNameValidatorTest.groovy b/modules/nextflow/src/test/groovy/nextflow/container/ContainerNameValidatorTest.groovy
index 5904b35d5e..5c156f821c 100644
--- a/modules/nextflow/src/test/groovy/nextflow/container/ContainerNameValidatorTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/container/ContainerNameValidatorTest.groovy
@@ -49,7 +49,9 @@ class ContainerNameValidatorTest extends Specification {
         true        | 'image-name:version'
         true        | 'image-name:VERSION'
         true        | 'image-name@sha256:c0e9560cda118f9ec63ddefb4a173a2b2a0347082d7dff7dc14272e7841a5b5a'
+        true        | 'wave.seqera.io/wt/b3f144027b00/biocontainers/control-freec:11.6b--hdbdd923_0'
         and:
+        false       | 'image-name:version '
         false       | 'IMAGE-NAME:123'
         false       | '/some/image'
         false       | 'http://registry/image-name:version'

From 367af52fd901f624ea43ad72fe8a710370b4b0e2 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Tue, 26 Sep 2023 23:35:51 +0200
Subject: [PATCH 176/350] Default Conda basePackages to
 "conda-forge::procps-ng"

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/wave.md                                                  | 2 +-
 plugins/nf-wave/build.gradle                                  | 2 +-
 .../nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy  | 4 ++--
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/docs/wave.md b/docs/wave.md
index 2a7b1a1c86..2d821803de 100644
--- a/docs/wave.md
+++ b/docs/wave.md
@@ -204,7 +204,7 @@ container freeze mode, the container repository authentication needs to be manag
 : The container repository used to cache image layers built by the Wave service (note: the corresponding credentials must be provided in your Nextflow Tower account).
 
 `wave.build.conda.basePackages`
-: One or more Conda packages to be always added in the resulting container e.g. `conda-forge::procps-ng`.
+: One or more Conda packages to be always added in the resulting container (default: `conda-forge::procps-ng`).
 
 `wave.build.conda.commands`
 : One or more commands to be added to the Dockerfile used to build a Conda based image.
diff --git a/plugins/nf-wave/build.gradle b/plugins/nf-wave/build.gradle
index 521a0a335f..4d1c1b47cb 100644
--- a/plugins/nf-wave/build.gradle
+++ b/plugins/nf-wave/build.gradle
@@ -36,7 +36,7 @@ dependencies {
     api 'org.apache.commons:commons-lang3:3.12.0'
     api 'com.google.code.gson:gson:2.10.1'
     api 'org.yaml:snakeyaml:2.0'
-    api 'io.seqera:wave-utils:0.7.5'
+    api 'io.seqera:wave-utils:0.7.7'
 
     testImplementation(testFixtures(project(":nextflow")))
     testImplementation "org.codehaus.groovy:groovy:3.0.19"
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
index f2e3aa475b..264ec33d01 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
@@ -430,11 +430,11 @@ class WaveClient {
                 if( isCondaLocalFile(attrs.conda) ) {
                     // 'conda' attribute is the path to the local conda environment
                     // note: ignore the 'channels' attribute because they are supposed to be provided by the conda file
-                    condaFile = condaFileFromPath(attrs.conda, null, config.condaOpts())
+                    condaFile = condaFileFromPath(attrs.conda, null)
                 }
                 else {
                     // 'conda' attributes is resolved as the conda packages to be used
-                    condaFile = condaFileFromPackages(attrs.conda, condaChannels, config.condaOpts())
+                    condaFile = condaFileFromPackages(attrs.conda, condaChannels)
                 }
                 // create the container file to build the container
                 containerScript = singularity

From d0c47d49d4067cb00f197b72a93ca3a2d2dec772 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Wed, 27 Sep 2023 12:52:12 +0200
Subject: [PATCH 177/350] Bump wave-utils@0.7.8

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-wave/build.gradle                         |  2 +-
 .../test/io/seqera/wave/plugin/WaveClientTest.groovy | 12 ++++++------
 .../seqera/wave/plugin/config/WaveConfigTest.groovy  |  2 +-
 3 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/plugins/nf-wave/build.gradle b/plugins/nf-wave/build.gradle
index 4d1c1b47cb..a65cbd5ab9 100644
--- a/plugins/nf-wave/build.gradle
+++ b/plugins/nf-wave/build.gradle
@@ -36,7 +36,7 @@ dependencies {
     api 'org.apache.commons:commons-lang3:3.12.0'
     api 'com.google.code.gson:gson:2.10.1'
     api 'org.yaml:snakeyaml:2.0'
-    api 'io.seqera:wave-utils:0.7.7'
+    api 'io.seqera:wave-utils:0.7.8'
 
     testImplementation(testFixtures(project(":nextflow")))
     testImplementation "org.codehaus.groovy:groovy:3.0.19"
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
index 755ff11c67..7bcc9fd1da 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
@@ -521,7 +521,7 @@ class WaveClientTest extends Specification {
         def assets = client.resolveAssets(task, null, false)
         then:
         assets.containerFile == '''\
-                FROM mambaorg/micromamba:1.4.9
+                FROM mambaorg/micromamba:1.5.1
                 COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml
                 RUN micromamba install -y -n base -f /tmp/conda.yml \\
                     && micromamba install -y -n base conda-forge::procps-ng \\
@@ -557,7 +557,7 @@ class WaveClientTest extends Specification {
         def assets = client.resolveAssets(task, null, false)
         then:
         assets.containerFile == '''\
-                FROM mambaorg/micromamba:1.4.9
+                FROM mambaorg/micromamba:1.5.1
                 RUN \\
                     micromamba install -y -n base -c conda-forge -c defaults -f https://host.com/conda-lock.yml \\
                     && micromamba install -y -n base conda-forge::procps-ng \\
@@ -632,7 +632,7 @@ class WaveClientTest extends Specification {
         def assets = client.resolveAssets(task, null, false)
         then:
         assets.containerFile == '''\
-                FROM mambaorg/micromamba:1.4.9
+                FROM mambaorg/micromamba:1.5.1
                 COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml
                 RUN micromamba install -y -n base -f /tmp/conda.yml \\
                     && micromamba install -y -n base conda-forge::procps-ng \\
@@ -712,7 +712,7 @@ class WaveClientTest extends Specification {
         then:
         assets.containerFile == '''\
                 BootStrap: docker
-                From: mambaorg/micromamba:1.4.9
+                From: mambaorg/micromamba:1.5.1
                 %files
                     {{wave_context_dir}}/conda.yml /scratch/conda.yml
                 %post
@@ -753,7 +753,7 @@ class WaveClientTest extends Specification {
         then:
         assets.containerFile == '''\
                 BootStrap: docker
-                From: mambaorg/micromamba:1.4.9
+                From: mambaorg/micromamba:1.5.1
                 %post
                     micromamba install -y -n base -c conda-forge -c defaults -f https://host.com/lock-file.yaml
                     micromamba install -y -n base conda-forge::procps-ng
@@ -787,7 +787,7 @@ class WaveClientTest extends Specification {
         then:
         assets.containerFile == '''\
                 BootStrap: docker
-                From: mambaorg/micromamba:1.4.9
+                From: mambaorg/micromamba:1.5.1
                 %files
                     {{wave_context_dir}}/conda.yml /scratch/conda.yml
                 %post
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy
index d7fcc47d2d..2653f5d609 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy
@@ -86,7 +86,7 @@ class WaveConfigTest extends Specification {
         when:
         def opts = new WaveConfig([:])
         then:
-        opts.condaOpts().mambaImage == 'mambaorg/micromamba:1.4.9'
+        opts.condaOpts().mambaImage == 'mambaorg/micromamba:1.5.1'
         opts.condaOpts().commands == null
 
         when:

From e4a878b6ce6d62bfd809fbbb88a6d4f2639e214f Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Wed, 27 Sep 2023 12:53:20 +0200
Subject: [PATCH 178/350] Bump Apache 2.0 license to tower client

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../io/seqera/tower/plugin/TowerClient.groovy  | 16 +++++++++++-----
 .../io/seqera/tower/plugin/TowerFactory.groovy | 16 +++++++++++-----
 .../tower/plugin/TowerJsonGenerator.groovy     | 16 +++++++++++-----
 .../io/seqera/tower/plugin/TowerPlugin.groovy  | 16 +++++++++++-----
 .../io/seqera/tower/plugin/TowerReports.groovy | 16 +++++++++++-----
 .../tower/plugin/WorkflowProgress.groovy       | 16 +++++++++++-----
 .../nextflow.trace.TraceObserverFactory        | 18 ++++++++++++------
 .../src/resources/tower-schema.properties      | 18 ++++++++++++------
 .../tower/plugin/CacheManagerTest.groovy       | 14 ++++++++++++--
 .../seqera/tower/plugin/LogsHandlerTest.groovy | 14 ++++++++++++--
 .../seqera/tower/plugin/TowerClientTest.groovy | 18 ++++++++++++------
 .../tower/plugin/TowerFactoryTest.groovy       | 18 ++++++++++++------
 .../tower/plugin/TowerJsonGeneratorTest.groovy |  1 +
 .../tower/plugin/TowerReportsTest.groovy       | 17 +++++++++++++++++
 14 files changed, 156 insertions(+), 58 deletions(-)

diff --git a/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerClient.groovy b/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerClient.groovy
index b494e8a30b..e723ca939b 100644
--- a/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerClient.groovy
+++ b/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerClient.groovy
@@ -1,12 +1,18 @@
 /*
  * Copyright 2013-2023, Seqera Labs
  *
- * This Source Code Form is subject to the terms of the Mozilla Public
- * License, v. 2.0. If a copy of the MPL was not distributed with this
- * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
  *
- * This Source Code Form is "Incompatible With Secondary Licenses", as
- * defined by the Mozilla Public License, v. 2.0.
  */
 
 package io.seqera.tower.plugin
diff --git a/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerFactory.groovy b/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerFactory.groovy
index d3e93df3bb..e3e7f67aa2 100644
--- a/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerFactory.groovy
+++ b/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerFactory.groovy
@@ -1,12 +1,18 @@
 /*
  * Copyright 2013-2023, Seqera Labs
  *
- * This Source Code Form is subject to the terms of the Mozilla Public
- * License, v. 2.0. If a copy of the MPL was not distributed with this
- * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
  *
- * This Source Code Form is "Incompatible With Secondary Licenses", as
- * defined by the Mozilla Public License, v. 2.0.
  */
 
 package io.seqera.tower.plugin
diff --git a/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerJsonGenerator.groovy b/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerJsonGenerator.groovy
index d7ccc86302..46d3a99881 100644
--- a/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerJsonGenerator.groovy
+++ b/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerJsonGenerator.groovy
@@ -1,12 +1,18 @@
 /*
  * Copyright 2013-2023, Seqera Labs
  *
- * This Source Code Form is subject to the terms of the Mozilla Public
- * License, v. 2.0. If a copy of the MPL was not distributed with this
- * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
  *
- * This Source Code Form is "Incompatible With Secondary Licenses", as
- * defined by the Mozilla Public License, v. 2.0.
  */
 
 package io.seqera.tower.plugin
diff --git a/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerPlugin.groovy b/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerPlugin.groovy
index 03778b9529..72d6e6fd34 100644
--- a/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerPlugin.groovy
+++ b/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerPlugin.groovy
@@ -1,12 +1,18 @@
 /*
  * Copyright 2013-2023, Seqera Labs
  *
- * This Source Code Form is subject to the terms of the Mozilla Public
- * License, v. 2.0. If a copy of the MPL was not distributed with this
- * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
  *
- * This Source Code Form is "Incompatible With Secondary Licenses", as
- * defined by the Mozilla Public License, v. 2.0.
  */
 
 package io.seqera.tower.plugin
diff --git a/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerReports.groovy b/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerReports.groovy
index a48f9bb15d..80fea24635 100644
--- a/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerReports.groovy
+++ b/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerReports.groovy
@@ -1,12 +1,18 @@
 /*
  * Copyright 2013-2023, Seqera Labs
  *
- * This Source Code Form is subject to the terms of the Mozilla Public
- * License, v. 2.0. If a copy of the MPL was not distributed with this
- * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
  *
- * This Source Code Form is "Incompatible With Secondary Licenses", as
- * defined by the Mozilla Public License, v. 2.0.
  */
 package io.seqera.tower.plugin
 
diff --git a/plugins/nf-tower/src/main/io/seqera/tower/plugin/WorkflowProgress.groovy b/plugins/nf-tower/src/main/io/seqera/tower/plugin/WorkflowProgress.groovy
index e2d1a89554..4ee2bc3cea 100644
--- a/plugins/nf-tower/src/main/io/seqera/tower/plugin/WorkflowProgress.groovy
+++ b/plugins/nf-tower/src/main/io/seqera/tower/plugin/WorkflowProgress.groovy
@@ -1,12 +1,18 @@
 /*
  * Copyright 2013-2023, Seqera Labs
  *
- * This Source Code Form is subject to the terms of the Mozilla Public
- * License, v. 2.0. If a copy of the MPL was not distributed with this
- * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
  *
- * This Source Code Form is "Incompatible With Secondary Licenses", as
- * defined by the Mozilla Public License, v. 2.0.
  */
 
 package io.seqera.tower.plugin
diff --git a/plugins/nf-tower/src/resources/META-INF/services/nextflow.trace.TraceObserverFactory b/plugins/nf-tower/src/resources/META-INF/services/nextflow.trace.TraceObserverFactory
index ac8ab3c67a..67af041cb8 100644
--- a/plugins/nf-tower/src/resources/META-INF/services/nextflow.trace.TraceObserverFactory
+++ b/plugins/nf-tower/src/resources/META-INF/services/nextflow.trace.TraceObserverFactory
@@ -1,12 +1,18 @@
 #
-# Copyright (c) 2019-2022, Seqera Labs.
+# Copyright 2013-2023, Seqera Labs
 #
-# This Source Code Form is subject to the terms of the Mozilla Public
-# License, v. 2.0. If a copy of the MPL was not distributed with this
-# file, You can obtain one at http://mozilla.org/MPL/2.0/.
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
 #
-# This Source Code Form is "Incompatible With Secondary Licenses", as
-# defined by the Mozilla Public License, v. 2.0.
 #
 
 
diff --git a/plugins/nf-tower/src/resources/tower-schema.properties b/plugins/nf-tower/src/resources/tower-schema.properties
index 77d9c34146..a0df9fe9d1 100644
--- a/plugins/nf-tower/src/resources/tower-schema.properties
+++ b/plugins/nf-tower/src/resources/tower-schema.properties
@@ -1,12 +1,18 @@
 #
-# Copyright (c) 2019, Seqera Labs.
+# Copyright 2013-2023, Seqera Labs
 #
-# This Source Code Form is subject to the terms of the Mozilla Public
-# License, v. 2.0. If a copy of the MPL was not distributed with this
-# file, You can obtain one at http://mozilla.org/MPL/2.0/.
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
 #
-# This Source Code Form is "Incompatible With Secondary Licenses", as
-# defined by the Mozilla Public License, v. 2.0.
 #
 
 # workflow
diff --git a/plugins/nf-tower/src/test/io/seqera/tower/plugin/CacheManagerTest.groovy b/plugins/nf-tower/src/test/io/seqera/tower/plugin/CacheManagerTest.groovy
index 70e4579a19..6eae285dd1 100644
--- a/plugins/nf-tower/src/test/io/seqera/tower/plugin/CacheManagerTest.groovy
+++ b/plugins/nf-tower/src/test/io/seqera/tower/plugin/CacheManagerTest.groovy
@@ -1,7 +1,17 @@
 /*
- * Copyright (c) 2020-2021. Seqera Labs, S.L.
+ * Copyright 2013-2023, Seqera Labs
  *
- * All Rights reserved
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
  *
  */
 
diff --git a/plugins/nf-tower/src/test/io/seqera/tower/plugin/LogsHandlerTest.groovy b/plugins/nf-tower/src/test/io/seqera/tower/plugin/LogsHandlerTest.groovy
index 5ff927a077..3b51a17bdc 100644
--- a/plugins/nf-tower/src/test/io/seqera/tower/plugin/LogsHandlerTest.groovy
+++ b/plugins/nf-tower/src/test/io/seqera/tower/plugin/LogsHandlerTest.groovy
@@ -1,7 +1,17 @@
 /*
- * Copyright (c) 2020-2021. Seqera Labs, S.L.
+ * Copyright 2013-2023, Seqera Labs
  *
- * All Rights reserved
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
  *
  */
 
diff --git a/plugins/nf-tower/src/test/io/seqera/tower/plugin/TowerClientTest.groovy b/plugins/nf-tower/src/test/io/seqera/tower/plugin/TowerClientTest.groovy
index 49d0d64b2b..fcb62ea9e2 100644
--- a/plugins/nf-tower/src/test/io/seqera/tower/plugin/TowerClientTest.groovy
+++ b/plugins/nf-tower/src/test/io/seqera/tower/plugin/TowerClientTest.groovy
@@ -1,12 +1,18 @@
 /*
- * Copyright (c) 2019, Seqera Labs.
+ * Copyright 2013-2023, Seqera Labs
  *
- * This Source Code Form is subject to the terms of the Mozilla Public
- * License, v. 2.0. If a copy of the MPL was not distributed with this
- * file, You can obtain one at http://mozilla.org/MPL/2.0/. 
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
  *
- * This Source Code Form is "Incompatible With Secondary Licenses", as
- * defined by the Mozilla Public License, v. 2.0.
  */
 
 package io.seqera.tower.plugin
diff --git a/plugins/nf-tower/src/test/io/seqera/tower/plugin/TowerFactoryTest.groovy b/plugins/nf-tower/src/test/io/seqera/tower/plugin/TowerFactoryTest.groovy
index 8faed8cacd..f762924d31 100644
--- a/plugins/nf-tower/src/test/io/seqera/tower/plugin/TowerFactoryTest.groovy
+++ b/plugins/nf-tower/src/test/io/seqera/tower/plugin/TowerFactoryTest.groovy
@@ -1,12 +1,18 @@
 /*
- * Copyright (c) 2019, Seqera Labs.
+ * Copyright 2013-2023, Seqera Labs
  *
- * This Source Code Form is subject to the terms of the Mozilla Public
- * License, v. 2.0. If a copy of the MPL was not distributed with this
- * file, You can obtain one at http://mozilla.org/MPL/2.0/. 
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
  *
- * This Source Code Form is "Incompatible With Secondary Licenses", as
- * defined by the Mozilla Public License, v. 2.0.
  */
 
 package io.seqera.tower.plugin
diff --git a/plugins/nf-tower/src/test/io/seqera/tower/plugin/TowerJsonGeneratorTest.groovy b/plugins/nf-tower/src/test/io/seqera/tower/plugin/TowerJsonGeneratorTest.groovy
index cf09a5856e..a610d0ff28 100644
--- a/plugins/nf-tower/src/test/io/seqera/tower/plugin/TowerJsonGeneratorTest.groovy
+++ b/plugins/nf-tower/src/test/io/seqera/tower/plugin/TowerJsonGeneratorTest.groovy
@@ -12,6 +12,7 @@
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  * See the License for the specific language governing permissions and
  * limitations under the License.
+ *
  */
 
 package io.seqera.tower.plugin
diff --git a/plugins/nf-tower/src/test/io/seqera/tower/plugin/TowerReportsTest.groovy b/plugins/nf-tower/src/test/io/seqera/tower/plugin/TowerReportsTest.groovy
index 8d3832d1f2..5ff5ee1fc0 100644
--- a/plugins/nf-tower/src/test/io/seqera/tower/plugin/TowerReportsTest.groovy
+++ b/plugins/nf-tower/src/test/io/seqera/tower/plugin/TowerReportsTest.groovy
@@ -1,3 +1,20 @@
+/*
+ * Copyright 2013-2023, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
 package io.seqera.tower.plugin
 
 import nextflow.Session

From f3eba3d71d2f6c632f57bd80b68c224210a13098 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Wed, 27 Sep 2023 23:45:26 +0200
Subject: [PATCH 179/350] Wave does not support 'null' container engine

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../src/main/groovy/nextflow/Session.groovy     | 17 ++++++++++++-----
 .../nextflow/script/WorkflowMetadata.groovy     |  9 +++++++--
 .../resolver/WaveContainerResolver.groovy       | 12 +++++++++++-
 3 files changed, 30 insertions(+), 8 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/Session.groovy b/modules/nextflow/src/main/groovy/nextflow/Session.groovy
index 9109d503ea..f8e2cffbd5 100644
--- a/modules/nextflow/src/main/groovy/nextflow/Session.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/Session.groovy
@@ -1201,13 +1201,18 @@ class Session implements ISession {
             return new ContainerConfig(result)
         }
 
-        final enabled = allEngines.findAll { it.enabled?.toString() == 'true' }
+        final enabled = allEngines.findAll(it -> it.enabled?.toString() == 'true')
         if( enabled.size() > 1 ) {
-            def names = enabled.collect { it.engine }
+            final names = enabled.collect(it -> it.engine)
             throw new IllegalConfigException("Cannot enable more than one container engine -- Choose either one of: ${names.join(', ')}")
         }
-
-        (enabled ? enabled.get(0) : ( allEngines ? allEngines.get(0) : [engine:'docker'] )) as ContainerConfig
+        if( enabled ) {
+            return new ContainerConfig(enabled.get(0))
+        }
+        if( allEngines ) {
+            return new ContainerConfig(allEngines.get(0))
+        }
+        return new ContainerConfig(engine:'docker')
     }
 
     ContainerConfig getContainerConfig() {
@@ -1215,9 +1220,11 @@ class Session implements ISession {
     }
 
     private void getContainerConfig0(String engine, List<Map> drivers) {
+        assert engine
         final entry = this.config?.get(engine)
         if( entry instanceof Map ) {
-            final config0 = new LinkedHashMap((Map)entry)
+            final config0 = new LinkedHashMap()
+            config0.putAll((Map)entry)
             config0.put('engine', engine)
             drivers.add(config0)
         }
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/WorkflowMetadata.groovy b/modules/nextflow/src/main/groovy/nextflow/script/WorkflowMetadata.groovy
index 65a1d1cacb..e8c066cea0 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/WorkflowMetadata.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/WorkflowMetadata.groovy
@@ -234,12 +234,12 @@ class WorkflowMetadata {
         this.nextflow = NextflowMeta.instance
         this.workDir = session.workDir
         this.launchDir = Paths.get('.').complete()
-        this.profile = session.profile ?:  ConfigBuilder.DEFAULT_PROFILE
+        this.profile = session.profile ?: ConfigBuilder.DEFAULT_PROFILE
         this.sessionId = session.uniqueId
         this.resume = session.resumeMode
         this.stubRun = session.stubRun
         this.runName = session.runName
-        this.containerEngine = session.containerConfig.with { isEnabled() ? getEngine() : null }
+        this.containerEngine = containerEngine0(session)
         this.configFiles = session.configFiles?.collect { it.toAbsolutePath() }
         this.stats = new WorkflowStats()
         this.userName = System.getProperty('user.name')
@@ -252,6 +252,11 @@ class WorkflowMetadata {
         session.onError( this.&invokeOnError )
     }
 
+    private String containerEngine0(Session session) {
+       final config = session.getContainerConfig()
+       return config.isEnabled() ? config.getEngine() : null
+    }
+
     /**
      * Only for testing purpose -- do not use
      */
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/resolver/WaveContainerResolver.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/resolver/WaveContainerResolver.groovy
index 44cae4f476..a79d169b2f 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/resolver/WaveContainerResolver.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/resolver/WaveContainerResolver.groovy
@@ -52,13 +52,23 @@ class WaveContainerResolver implements ContainerResolver {
         return client0 = new WaveClient( Global.session as Session )
     }
 
+    private String getContainerEngine0(TaskRun task) {
+        final config = task.getContainerConfig()
+        final result = config.getEngine()
+        if( result )
+            return result
+        // fallback to docker by default
+        log.warn "Missing engine in container config - offending value: $config"
+        return 'docker'
+    }
+
     @Override
     ContainerInfo resolveImage(TaskRun task, String imageName) {
         if( !client().enabled() )
             return defaultResolver.resolveImage(task, imageName)
 
         final freeze = client().config().freezeMode()
-        final engine= task.getContainerConfig().getEngine()
+        final engine = getContainerEngine0(task)
         final nativeSingularityBuild = freeze && engine in SINGULARITY_LIKE
         if( !imageName ) {
             // when no image name is provided the module bundle should include a

From b53936b084fc4d412668ddc98047e29ef16f0dc4 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Thu, 28 Sep 2023 00:01:52 +0200
Subject: [PATCH 180/350] Disable Tower container field for multiple images [ci
 fast]

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../src/main/io/seqera/tower/plugin/TowerClient.groovy      | 4 ++--
 .../src/test/io/seqera/tower/plugin/TowerClientTest.groovy  | 6 +++---
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerClient.groovy b/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerClient.groovy
index e723ca939b..541a746696 100644
--- a/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerClient.groovy
+++ b/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerClient.groovy
@@ -655,8 +655,8 @@ class TowerClient implements TraceObserver {
         if( obj instanceof CharSequence )
             return obj.toString()
         if( obj instanceof Map ) {
-            def map = obj as Map
-            return map.collect { k,v -> "$k:$v" }.join(',')
+            // turn this off for multiple containers because the string representation is broken
+            return null
         }
         throw new IllegalArgumentException("Illegal container attribute type: ${obj.getClass().getName()} = ${obj}" )
     }
diff --git a/plugins/nf-tower/src/test/io/seqera/tower/plugin/TowerClientTest.groovy b/plugins/nf-tower/src/test/io/seqera/tower/plugin/TowerClientTest.groovy
index fcb62ea9e2..871492cd46 100644
--- a/plugins/nf-tower/src/test/io/seqera/tower/plugin/TowerClientTest.groovy
+++ b/plugins/nf-tower/src/test/io/seqera/tower/plugin/TowerClientTest.groovy
@@ -91,7 +91,7 @@ class TowerClientTest extends Specification {
         map.workflow.bar == 2
         map.workflow.id == '12ef'
         map.workflow.params == [x: 'hello']
-        map.workflow.container == 'p1:c1,p2:c2'
+        map.workflow.container == null
         map.metrics == [[process:'foo', cpu: [min: 1, max:5], time: [min: 6, max: 9]]]
         map.progress == new WorkflowProgress()
         and:
@@ -331,8 +331,8 @@ class TowerClientTest extends Specification {
         expect:
         tower.mapToString(null)  == null
         tower.mapToString('ciao') == 'ciao'
-        tower.mapToString([:]) == ''
-        tower.mapToString([p:'foo', q:'bar']) == 'p:foo,q:bar'
+        tower.mapToString([:]) == null
+        tower.mapToString([p:'foo', q:'bar']) == null
     }
 
 

From 3311172f53672088b11ad7c9e20cd8a9b9908b84 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Thu, 28 Sep 2023 00:12:28 +0200
Subject: [PATCH 181/350] Bump nf-amazon@2.1.3

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-amazon/changelog.txt                      | 8 +++++++-
 plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF | 2 +-
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/plugins/nf-amazon/changelog.txt b/plugins/nf-amazon/changelog.txt
index 7e783ff79f..4dbd3bac90 100644
--- a/plugins/nf-amazon/changelog.txt
+++ b/plugins/nf-amazon/changelog.txt
@@ -1,6 +1,12 @@
 nf-amazon changelog
 ===================
-2.1.2 - 10 Sep
+2.1.3 - 28 Sep 2023
+- Fix minor typos in changelogs/source code (#4319) [4ce9f1df]
+- Fix List of S3 bucket for custom endpoint [4327fa58]
+- Fix support for S3 custom endpoint with anonymous access [03752815]
+- Fix Prevent multi attempts to retrive AWS creds [b30efe36]
+
+2.1.2 - 10 Sep 2023
 - Disable staging script for remote work dir (#4282) [80f7cd46]
 - Allow setting shell directive when using the trace file. (#4210) [7d6ad624]
 - Bump groovy 3.0.19 [cb411208]
diff --git a/plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF b/plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF
index 6ae09958e7..74871f9a06 100644
--- a/plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: nextflow.cloud.aws.AmazonPlugin
 Plugin-Id: nf-amazon
-Plugin-Version: 2.1.2
+Plugin-Version: 2.1.3
 Plugin-Provider: Seqera Labs
 Plugin-Requires: >=23.05.0-edge

From a9b735cebc62e4f5d953322bf564ec657a8fc6f1 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Thu, 28 Sep 2023 00:12:44 +0200
Subject: [PATCH 182/350] Bump nf-azure@1.3.2

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-azure/changelog.txt                      | 3 +++
 plugins/nf-azure/src/resources/META-INF/MANIFEST.MF | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/plugins/nf-azure/changelog.txt b/plugins/nf-azure/changelog.txt
index 73e9ea7cc8..cc42b1938b 100644
--- a/plugins/nf-azure/changelog.txt
+++ b/plugins/nf-azure/changelog.txt
@@ -1,5 +1,8 @@
 nf-azure changelog
 ===================
+1.3.2 - 28 Sep 2023
+- Retry TimeoutException in azure file system (#4295) [79248355]
+
 1.3.1 - 10 Sep 2023
 - Disable staging script for remote work dir (#4282) [80f7cd46]
 - Fix IOException should be thrown when failing to create Azure directory [b0bdfd79]
diff --git a/plugins/nf-azure/src/resources/META-INF/MANIFEST.MF b/plugins/nf-azure/src/resources/META-INF/MANIFEST.MF
index 73da661c8f..d9273f2629 100644
--- a/plugins/nf-azure/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-azure/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: nextflow.cloud.azure.AzurePlugin
 Plugin-Id: nf-azure
-Plugin-Version: 1.3.1
+Plugin-Version: 1.3.2
 Plugin-Provider: Seqera Labs
 Plugin-Requires: >=23.01.0-edge

From 7219d7f2ac504fd92772d9263b071268e00fc097 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Thu, 28 Sep 2023 00:12:56 +0200
Subject: [PATCH 183/350] Bump nf-google@1.8.2

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-google/changelog.txt                      | 3 +++
 plugins/nf-google/src/resources/META-INF/MANIFEST.MF | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/plugins/nf-google/changelog.txt b/plugins/nf-google/changelog.txt
index ff439bc729..492c2fa1de 100644
--- a/plugins/nf-google/changelog.txt
+++ b/plugins/nf-google/changelog.txt
@@ -1,5 +1,8 @@
 nf-google changelog
 ===================
+1.8.2 - 28 Sep 2023
+- Fix allow_other vulnerability preventing google-batch submissions (#4332) [9b3741e3]
+
 1.8.1 - 22 Jul 2023
 - Wait for all child processes in nxf_parallel (#4050) [60a5f1a7]
 - Bump Groovy 3.0.18 [207eb535]
diff --git a/plugins/nf-google/src/resources/META-INF/MANIFEST.MF b/plugins/nf-google/src/resources/META-INF/MANIFEST.MF
index 92e475ff8d..e5c62ccecd 100644
--- a/plugins/nf-google/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-google/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: nextflow.cloud.google.GoogleCloudPlugin
 Plugin-Id: nf-google
-Plugin-Version: 1.8.1
+Plugin-Version: 1.8.2
 Plugin-Provider: Seqera Labs
 Plugin-Requires: >=23.02.0-edge

From 91a935f9996efd2e0d65dbc8cc9c949b9462e2c4 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Thu, 28 Sep 2023 00:13:14 +0200
Subject: [PATCH 184/350] Bump nf-tower@1.6.2

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-tower/changelog.txt                      | 6 +++++-
 plugins/nf-tower/src/resources/META-INF/MANIFEST.MF | 2 +-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/plugins/nf-tower/changelog.txt b/plugins/nf-tower/changelog.txt
index ee8b075f69..83b7acbb04 100644
--- a/plugins/nf-tower/changelog.txt
+++ b/plugins/nf-tower/changelog.txt
@@ -1,6 +1,10 @@
 nf-tower changelog
 ===================
-1.6.1 -17 Aug 2023
+1.6.2 - 28 Sep 2023
+- Disable Tower container field for multiple images [ci fast] [b53936b0]
+- Bump Apache 2.0 license to tower client [e4a878b6]
+
+1.6.1 - 17 Aug 2023
 - Fix checkpoint thread termination (#4166) [2b449daa]
 - Fix typos in source code comments (#4173) [ci fast] [e78bc37e]
 
diff --git a/plugins/nf-tower/src/resources/META-INF/MANIFEST.MF b/plugins/nf-tower/src/resources/META-INF/MANIFEST.MF
index 2708dd3558..4080672d8b 100644
--- a/plugins/nf-tower/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-tower/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: io.seqera.tower.plugin.TowerPlugin
 Plugin-Id: nf-tower
-Plugin-Version: 1.6.1
+Plugin-Version: 1.6.2
 Plugin-Provider: Seqera Labs
 Plugin-Requires: >=23.05.0-edge

From 0cf2476c19f00ff9dbea5f777a47beb59bbe8de7 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Thu, 28 Sep 2023 00:13:38 +0200
Subject: [PATCH 185/350] Bump nf-wave@0.13.0

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-wave/changelog.txt                      | 7 +++++++
 plugins/nf-wave/src/resources/META-INF/MANIFEST.MF | 2 +-
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/plugins/nf-wave/changelog.txt b/plugins/nf-wave/changelog.txt
index 10992dcad5..1aa7811a29 100644
--- a/plugins/nf-wave/changelog.txt
+++ b/plugins/nf-wave/changelog.txt
@@ -1,5 +1,12 @@
 nf-wave changelog
 ==================
+0.13.0 - 28 Sep 2023
+- Wave does not support 'null' container engine [f3eba3d7]
+- Default Conda basePackages to "conda-forge::procps-ng" [367af52f]
+- Add procps by default to Conda-based Wave builds [66b2d2d2]
+- Improve wave container name validation [73eb5a02]
+- Bump wave-utils@0.7.8 [d0c47d49]
+
 0.12.0 - 10 Sep 2023
 - Add support for Spack to Singularity builds [23c4ec1d]
 - Add inspect command (#4069) [090c31ce]
diff --git a/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF b/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF
index 1ac36f6aac..77d03acf57 100644
--- a/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: io.seqera.wave.plugin.WavePlugin
 Plugin-Id: nf-wave
-Plugin-Version: 0.12.0
+Plugin-Version: 0.13.0
 Plugin-Provider: Seqera Labs
 Plugin-Requires: >=23.05.0-edge

From 564fe06c6aba62642a8a91b2f3806fd48278ce1b Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Thu, 28 Sep 2023 00:15:41 +0200
Subject: [PATCH 186/350] Update changelog

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 changelog.txt | 39 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

diff --git a/changelog.txt b/changelog.txt
index 2b75169a91..2a5b9e3868 100644
--- a/changelog.txt
+++ b/changelog.txt
@@ -1,5 +1,44 @@
 NEXTFLOW CHANGE-LOG
 ===================
+23.09.2-edge - 28 Sep 2023
+- Add conda.enabled to conda config scope docs (#4320) [0b74c4e2]
+- Add developer docs (#4065) [06843d87]
+- Add fs stat command [a79056b7]
+- Add more tests to container name [da7a1942]
+- Add procps by default to Conda-based Wave builds [66b2d2d2]
+- Add support for Java 21 (#4338) [ac1fc9ee]
+- Add Mermaid diagram in HTML DAG (#4337) [0f3e263f]
+- Default Conda basePackages to "conda-forge::procps-ng" [367af52f]
+- Disable Tower container field for multiple images [b53936b0]
+- Document `NXF_DISABLE_CHECK_LATEST` environment var (#4327) [4e3e9aca]
+- Document `fs` CLI command (#4328) [1a680495]
+- Document source of `vol_ctxt` and `inv_ctxt` trace metrics (#4333) [6525b0a1]
+- Document when process directives are evaluated (#4217) [731a29a2]
+- Fix List of S3 bucket for custom endpoint [4327fa58]
+- Fix Prevent false positive resumable task [144e0a8a]
+- Fix Prevent multi attempts to retrive AWS creds [b30efe36]
+- Fix allow_other vulnerability preventing google-batch submissions (#4332) [9b3741e3]
+- Fix fs list command [29ab2f24]
+- Fix minor typos in changelogs/source code (#4319) [4ce9f1df]
+- Fix support for S3 custom endpoint with anonymous access [03752815]
+- Fix use of GITHUB_TOKEN variable to access GitHub repo [afe3dc4f]
+- Fix Wave does not support 'null' container engine [f3eba3d7]
+- Fix Retry TimeoutException in azure file system (#4295) [79248355]
+- Improve K8s unit tests (#4196) [5a43a32b]
+- Improve Mermaid DAG rendering (#4070) [19587f40]
+- Improve error report when exception is thrown in operator ctx [16f54a9c]
+- Improve wave container name validation [73eb5a02]
+- Minor improvements [fff3d7bd]
+- Prevent cache invalidation for task directives (#4339) [aabb6c19]
+- Remove line endings from container box id (#4334) [df41e54a]
+- Bump Apache 2.0 license to tower client [e4a878b6]
+- Bump nf-amazon@2.1.3 [3311172f]
+- Bump nf-azure@1.3.2 [a9b735ce]
+- Bump nf-google@1.8.2 [7219d7f2]
+- Bump nf-tower@1.6.2 [91a935f9]
+- Bump nf-wave@0.13.0 [0cf2476c]
+- Bump wave-utils@0.7.8 [d0c47d49]
+
 23.09.1-edge - 11 Sep 2023
 - Revert "Allow setting shell directive when using the trace file (#4210)" [9f9edcdc]
 

From 46afba88f93714995357b47655cc664051cfc27a Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Thu, 28 Sep 2023 00:16:54 +0200
Subject: [PATCH 187/350] [release 23.09.2-edge] [ci fast] Update timestamp and
 build number

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 VERSION                                                |  2 +-
 docs/conf.py                                           |  2 +-
 .../src/main/resources/META-INF/plugins-info.txt       | 10 +++++-----
 modules/nf-commons/src/main/nextflow/Const.groovy      |  6 +++---
 nextflow                                               |  2 +-
 nextflow.md5                                           |  2 +-
 nextflow.sha1                                          |  2 +-
 nextflow.sha256                                        |  2 +-
 8 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/VERSION b/VERSION
index 4a719b97aa..31d596a086 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-23.09.1-edge
+23.09.2-edge
diff --git a/docs/conf.py b/docs/conf.py
index 6ef95e6b15..6cf81c8dcc 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -61,7 +61,7 @@
 # The short X.Y version.
 version = '23.09'
 # The full version, including alpha/beta/rc tags.
-release = '23.09.1-edge'
+release = '23.09.2-edge'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
diff --git a/modules/nextflow/src/main/resources/META-INF/plugins-info.txt b/modules/nextflow/src/main/resources/META-INF/plugins-info.txt
index eaad0fec0b..923df8f700 100644
--- a/modules/nextflow/src/main/resources/META-INF/plugins-info.txt
+++ b/modules/nextflow/src/main/resources/META-INF/plugins-info.txt
@@ -1,9 +1,9 @@
-nf-amazon@2.1.2
-nf-azure@1.3.1
+nf-amazon@2.1.3
+nf-azure@1.3.2
 nf-cloudcache@0.2.0
 nf-codecommit@0.1.5
 nf-console@1.0.6
 nf-ga4gh@1.1.0
-nf-google@1.8.1
-nf-tower@1.6.1
-nf-wave@0.12.0
\ No newline at end of file
+nf-google@1.8.2
+nf-tower@1.6.2
+nf-wave@0.13.0
\ No newline at end of file
diff --git a/modules/nf-commons/src/main/nextflow/Const.groovy b/modules/nf-commons/src/main/nextflow/Const.groovy
index 2fc8eec099..28444210c5 100644
--- a/modules/nf-commons/src/main/nextflow/Const.groovy
+++ b/modules/nf-commons/src/main/nextflow/Const.groovy
@@ -52,17 +52,17 @@ class Const {
     /**
      * The application version
      */
-    static public final String APP_VER = "23.09.1-edge"
+    static public final String APP_VER = "23.09.2-edge"
 
     /**
      * The app build time as linux/unix timestamp
      */
-    static public final long APP_TIMESTAMP = 1694426936712
+    static public final long APP_TIMESTAMP = 1695852467160
 
     /**
      * The app build number
      */
-    static public final int APP_BUILDNUM = 5882
+    static public final int APP_BUILDNUM = 5884
 
     /**
      * The app build time string relative to UTC timezone
diff --git a/nextflow b/nextflow
index b6983744eb..93342c3697 100755
--- a/nextflow
+++ b/nextflow
@@ -15,7 +15,7 @@
 #  limitations under the License.
 
 [[ "$NXF_DEBUG" == 'x' ]] && set -x
-NXF_VER=${NXF_VER:-'23.09.1-edge'}
+NXF_VER=${NXF_VER:-'23.09.2-edge'}
 NXF_ORG=${NXF_ORG:-'nextflow-io'}
 NXF_HOME=${NXF_HOME:-$HOME/.nextflow}
 NXF_PROT=${NXF_PROT:-'https'}
diff --git a/nextflow.md5 b/nextflow.md5
index 4046935306..a13b13c2e5 100644
--- a/nextflow.md5
+++ b/nextflow.md5
@@ -1 +1 @@
-c6690f184ec1e95646b6a4d60bb5442a
+0daca43a243bc69bbda98d5beae89127
diff --git a/nextflow.sha1 b/nextflow.sha1
index bc00d398a1..f4db5f3041 100644
--- a/nextflow.sha1
+++ b/nextflow.sha1
@@ -1 +1 @@
-31e0a8e79b45d605459781fe3d31e70590e3f2e1
+bc2ca43dea392a6bdfc0c5d41541523b8f80c537
diff --git a/nextflow.sha256 b/nextflow.sha256
index 75fc2abc39..952907fbee 100644
--- a/nextflow.sha256
+++ b/nextflow.sha256
@@ -1 +1 @@
-dd82066091517be8562f0fa9af26c272db00b14ce07145d202f1d6619d3e3a7f
+2f1e00d05581db1d4677185c82b3f2a65ef484d526f8a32b0d3855baa63f9406

From 2b9ae6aa6a7830963da2321fbaf2d2d9e7778846 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Thu, 28 Sep 2023 10:16:28 +0200
Subject: [PATCH 188/350] Improve S3 endpoint validation

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../nextflow/cloud/aws/config/AwsS3Config.groovy  |  5 ++++-
 .../cloud/aws/config/AwsS3ConfigTest.groovy       | 15 +++++++++++++++
 2 files changed, 19 insertions(+), 1 deletion(-)

diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/config/AwsS3Config.groovy b/plugins/nf-amazon/src/main/nextflow/cloud/aws/config/AwsS3Config.groovy
index 6f052d6cb7..16e5a85ee3 100644
--- a/plugins/nf-amazon/src/main/nextflow/cloud/aws/config/AwsS3Config.groovy
+++ b/plugins/nf-amazon/src/main/nextflow/cloud/aws/config/AwsS3Config.groovy
@@ -17,12 +17,13 @@
 
 package nextflow.cloud.aws.config
 
-import static nextflow.cloud.aws.util.AwsHelper.parseS3Acl
+import static nextflow.cloud.aws.util.AwsHelper.*
 
 import com.amazonaws.services.s3.model.CannedAccessControlList
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import nextflow.SysEnv
+import nextflow.file.FileHelper
 /**
  * Model AWS S3 config settings
  *
@@ -51,6 +52,8 @@ class AwsS3Config {
     AwsS3Config(Map opts) {
         this.debug = opts.debug as Boolean
         this.endpoint = opts.endpoint ?: SysEnv.get('AWS_S3_ENDPOINT')
+        if( endpoint && FileHelper.getUrlProtocol(endpoint) !in ['http','https'] )
+            throw new IllegalArgumentException("S3 endpoint must begin with http:// or https:// prefix - offending value: '${endpoint}'")
         this.storageClass = parseStorageClass((opts.storageClass ?: opts.uploadStorageClass) as String)     // 'uploadStorageClass' is kept for legacy purposes
         this.storageEncryption = parseStorageEncryption(opts.storageEncryption as String)
         this.storageKmsKeyId = opts.storageKmsKeyId
diff --git a/plugins/nf-amazon/src/test/nextflow/cloud/aws/config/AwsS3ConfigTest.groovy b/plugins/nf-amazon/src/test/nextflow/cloud/aws/config/AwsS3ConfigTest.groovy
index 96fbda3acb..907e211c14 100644
--- a/plugins/nf-amazon/src/test/nextflow/cloud/aws/config/AwsS3ConfigTest.groovy
+++ b/plugins/nf-amazon/src/test/nextflow/cloud/aws/config/AwsS3ConfigTest.groovy
@@ -98,6 +98,21 @@ class AwsS3ConfigTest extends Specification {
         [AWS_S3_ENDPOINT: 'http://foo'] | [endpoint: 'http://bar']      | 'http://bar'  // <-- config should have priority
     }
 
+    @Unroll
+    def 'should fail with invalid endpoint protocol' () {
+        when:
+        new AwsS3Config(CONFIG)
+        then:
+        def e = thrown(IllegalArgumentException)
+        e.message == EXPECTED
+
+        where:
+        CONFIG                          | EXPECTED
+        [endpoint: 'bar.com']           |  "S3 endpoint must begin with http:// or https:// prefix - offending value: 'bar.com'"
+        [endpoint: 'ftp://bar.com']     |  "S3 endpoint must begin with http:// or https:// prefix - offending value: 'ftp://bar.com'"
+
+    }
+
     def 'should get s3 legacy properties' () {
         given:
         SysEnv.push([:])

From f0d5cc5c674e4e18424e431a5f50930dcd9906c2 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Thu, 28 Sep 2023 21:45:32 +0200
Subject: [PATCH 189/350] Add setting to enable the use of sync command

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/config.md                                     |  5 +++++
 .../nextflow/executor/BashWrapperBuilder.groovy    |  2 +-
 .../executor/BashWrapperBuilderTest.groovy         | 14 ++++++++++++++
 .../executor/test-bash-wrapper-with-trace.txt      |  1 -
 .../nextflow/executor/test-bash-wrapper.txt        |  1 -
 .../GoogleLifeSciencesScriptLauncherTest.groovy    |  2 +-
 .../cloud/google/lifesciences/bash-wrapper-gcp.txt |  1 -
 7 files changed, 21 insertions(+), 5 deletions(-)

diff --git a/docs/config.md b/docs/config.md
index 2c51b40ddf..52d1f70020 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -1588,6 +1588,11 @@ The following environment variables control the configuration of the Nextflow ru
   :::
 : Disables the requirement for Wave service when enabling the Fusion file system.
 
+`NXF_ENABLE_FS_SYNC`
+: :::{versionadded} 23.10.0
+  :::
+: When enabled the job script will execute Linux `sync` command on job completion. This may be useful to synchronize the job state over shared file systems (default: `false`)
+
 `NXF_ENABLE_SECRETS`
 : :::{versionadded} 21.09.0-edge
   :::
diff --git a/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
index 4049eebbe2..bc21186d1a 100644
--- a/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
@@ -527,7 +527,7 @@ class BashWrapperBuilder {
     }
 
     String getSyncCmd() {
-        if ( SysEnv.get( 'NXF_DISABLE_FS_SYNC' ) != "true" ) {
+        if ( SysEnv.get( 'NXF_ENABLE_FS_SYNC' ) == "true" ) {
             return 'sync || true'
         }
         return null
diff --git a/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
index 89a40ca4ea..4a8c012502 100644
--- a/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
@@ -425,6 +425,19 @@ class BashWrapperBuilderTest extends Specification {
         folder?.deleteDir()
     }
 
+    def 'should include sync command' () {
+        given:
+        SysEnv.push([NXF_ENABLE_FS_SYNC: 'true'])
+
+        when:
+        def binding = newBashWrapperBuilder().makeBinding()
+        then:
+        binding.sync_cmd == 'sync || true'
+
+        cleanup:
+        SysEnv.pop()
+    }
+
     def 'should unstage outputs' () {
 
         given:
@@ -486,6 +499,7 @@ class BashWrapperBuilderTest extends Specification {
         binding.containsKey('container_env')
         binding.task_env == null
         binding.container_env == null
+        binding.sync_cmd == null
 
         when:
         binding = newBashWrapperBuilder(environment: [FOO:'aa', BAR:'bb']).makeBinding()
diff --git a/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper-with-trace.txt b/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper-with-trace.txt
index 0aaf49f410..b72d5880ce 100644
--- a/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper-with-trace.txt
+++ b/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper-with-trace.txt
@@ -271,7 +271,6 @@ on_exit() {
     exit_status=${nxf_main_ret:=$?}
     printf -- $exit_status > {{folder}}/.exitcode
     set +u
-    sync || true
     exit $exit_status
 }
 
diff --git a/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper.txt b/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper.txt
index 3c380c4067..5abcf4a511 100644
--- a/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper.txt
+++ b/modules/nextflow/src/test/resources/nextflow/executor/test-bash-wrapper.txt
@@ -82,7 +82,6 @@ on_exit() {
     exit_status=${nxf_main_ret:=$?}
     printf -- $exit_status > {{folder}}/.exitcode
     set +u
-    sync || true
     exit $exit_status
 }
 
diff --git a/plugins/nf-google/src/test/nextflow/cloud/google/lifesciences/GoogleLifeSciencesScriptLauncherTest.groovy b/plugins/nf-google/src/test/nextflow/cloud/google/lifesciences/GoogleLifeSciencesScriptLauncherTest.groovy
index 6b59e3b53e..bc58a13ec6 100644
--- a/plugins/nf-google/src/test/nextflow/cloud/google/lifesciences/GoogleLifeSciencesScriptLauncherTest.groovy
+++ b/plugins/nf-google/src/test/nextflow/cloud/google/lifesciences/GoogleLifeSciencesScriptLauncherTest.groovy
@@ -82,7 +82,7 @@ class GoogleLifeSciencesScriptLauncherTest extends GoogleSpecification {
         def wrapper =  builder.buildNew0()
 
         then:
-        wrapper == load('bash-wrapper-gcp.txt', [folder: WORK_DIR.toString(), sync_cmd: 'sync || true' ])
+        wrapper == load('bash-wrapper-gcp.txt', [folder: WORK_DIR.toString()])
 
         cleanup:
         folder?.deleteDir()
diff --git a/plugins/nf-google/src/test/nextflow/cloud/google/lifesciences/bash-wrapper-gcp.txt b/plugins/nf-google/src/test/nextflow/cloud/google/lifesciences/bash-wrapper-gcp.txt
index f1ac0b4251..ab322a6ef6 100644
--- a/plugins/nf-google/src/test/nextflow/cloud/google/lifesciences/bash-wrapper-gcp.txt
+++ b/plugins/nf-google/src/test/nextflow/cloud/google/lifesciences/bash-wrapper-gcp.txt
@@ -169,7 +169,6 @@ on_exit() {
     exit_status=${nxf_main_ret:=$?}
     printf -- $exit_status > {{folder}}/.exitcode
     set +u
-    {{sync_cmd}}
     exit $exit_status
 }
 

From 7d5a21b0a176d60db4576b88620ddb24de083428 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Mon, 2 Oct 2023 20:56:18 +0200
Subject: [PATCH 190/350] Improve Wave config validation

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-wave/build.gradle                  |  2 +-
 .../io/seqera/wave/plugin/WaveClient.groovy   |  2 +-
 .../io/seqera/wave/plugin/WaveObserver.groovy |  1 +
 .../wave/plugin/config/ReportOpts.groovy      |  1 +
 .../wave/plugin/config/WaveConfig.groovy      | 18 ++++++++--
 .../wave/plugin/config/WaveConfigTest.groovy  | 34 +++++++++++++++++++
 6 files changed, 53 insertions(+), 5 deletions(-)

diff --git a/plugins/nf-wave/build.gradle b/plugins/nf-wave/build.gradle
index a65cbd5ab9..f4deb73c9c 100644
--- a/plugins/nf-wave/build.gradle
+++ b/plugins/nf-wave/build.gradle
@@ -36,7 +36,7 @@ dependencies {
     api 'org.apache.commons:commons-lang3:3.12.0'
     api 'com.google.code.gson:gson:2.10.1'
     api 'org.yaml:snakeyaml:2.0'
-    api 'io.seqera:wave-utils:0.7.8'
+    api 'io.seqera:wave-utils:0.7.9'
 
     testImplementation(testFixtures(project(":nextflow")))
     testImplementation "org.codehaus.groovy:groovy:3.0.19"
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
index 264ec33d01..a5909daf3a 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
@@ -118,7 +118,7 @@ class WaveClient {
         this.tower = new TowerConfig(session.config.tower as Map ?: Collections.emptyMap(), SysEnv.get())
         this.endpoint = config.endpoint()
         this.condaChannels = session.getCondaConfig()?.getChannels() ?: DEFAULT_CONDA_CHANNELS
-        log.debug "Wave endpoint: ${endpoint}; config: $config"
+        log.debug "Wave config: $config"
         this.packer = new Packer()
         this.waveRegistry = new URI(endpoint).getAuthority()
         // create cache
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveObserver.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveObserver.groovy
index 029e034546..7e8a3e6e1d 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveObserver.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveObserver.groovy
@@ -33,6 +33,7 @@ import nextflow.trace.TraceRecord
  */
 @Slf4j
 @CompileStatic
+@Deprecated
 class WaveObserver implements TraceObserver {
 
     private WaveClient client
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/ReportOpts.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/ReportOpts.groovy
index 3f1fb27247..0c15681382 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/ReportOpts.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/ReportOpts.groovy
@@ -27,6 +27,7 @@ import nextflow.trace.TraceHelper
  */
 @ToString(includeNames = true, includePackage = false)
 @CompileStatic
+@Deprecated
 class ReportOpts {
 
     final private Boolean enabled
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/WaveConfig.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/WaveConfig.groovy
index abdd4e2953..6e00733de2 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/WaveConfig.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/WaveConfig.groovy
@@ -22,6 +22,7 @@ import groovy.transform.ToString
 import groovy.util.logging.Slf4j
 import io.seqera.wave.config.CondaOpts
 import io.seqera.wave.config.SpackOpts
+import nextflow.file.FileHelper
 import nextflow.util.Duration
 /**
  * Model Wave client configuration
@@ -29,7 +30,7 @@ import nextflow.util.Duration
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
  */
 @Slf4j
-@ToString(includeNames = true, includePackage = false)
+@ToString(includeNames = true, includePackage = false, includeFields = true, excludes = 'reportOpts')
 @CompileStatic
 class WaveConfig {
     final private static String DEF_ENDPOINT = 'https://wave.seqera.io'
@@ -66,8 +67,8 @@ class WaveConfig {
         this.reportOpts = new ReportOpts(opts.report as Map ?: Map.of())
         this.retryOpts = retryOpts0(opts)
         this.httpClientOpts = new HttpOpts(opts.httpClient as Map ?: Map.of())
-        if( !endpoint.startsWith('http://') && !endpoint.startsWith('https://') )
-            throw new IllegalArgumentException("Endpoint URL should start with 'http:' or 'https:' protocol prefix - offending value: $endpoint")
+        // some validation
+        validateConfig()
     }
 
     Boolean enabled() { this.enabled }
@@ -94,6 +95,16 @@ class WaveConfig {
 
     String cacheRepository() { cacheRepository }
 
+    private void validateConfig() {
+        def scheme= FileHelper.getUrlProtocol(endpoint)
+        if( scheme !in ['http','https'] )
+            throw new IllegalArgumentException("Endpoint URL should start with 'http:' or 'https:' protocol prefix - offending value: '$endpoint'")
+        if( FileHelper.getUrlProtocol(buildRepository) )
+            throw new IllegalArgumentException("Config setting 'wave.build.repository' should not include any protocol prefix - offending value: '$buildRepository'")
+        if( FileHelper.getUrlProtocol(cacheRepository) )
+            throw new IllegalArgumentException("Config setting 'wave.build.cacheRepository' should not include any protocol prefix - offending value: '$cacheRepository'")
+    }
+
     private RetryOpts retryOpts0(Map opts) {
         if( opts.retryPolicy )
             return new RetryOpts(opts.retryPolicy as Map)
@@ -153,5 +164,6 @@ class WaveConfig {
         return tokensCacheMaxDuration 
     }
 
+    @Deprecated
     ReportOpts reportOpts() { reportOpts }
 }
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy
index 2653f5d609..567fd0678d 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy
@@ -194,4 +194,38 @@ class WaveConfigTest extends Specification {
         then:
         opts.httpOpts().connectTimeout() == java.time.Duration.ofSeconds(90)
     }
+
+    def 'should dump config' () {
+        given:
+        def config = new WaveConfig([enabled: true])
+        expect:
+        config.toString() == 'WaveConfig(enabled:true, endpoint:https://wave.seqera.io, containerConfigUrl:[], tokensCacheMaxDuration:30m, condaOpts:CondaOpts(mambaImage=mambaorg/micromamba:1.5.1; basePackages=conda-forge::procps-ng, commands=null), spackOpts:SpackOpts(basePackages=null, commands=null), strategy:[container, dockerfile, conda, spack], bundleProjectResources:null, buildRepository:null, cacheRepository:null, retryOpts:RetryOpts(delay:450ms, maxDelay:1m 30s, maxAttempts:10, jitter:0.25), httpClientOpts:HttpOpts(), freezeMode:null, dryRunMode:false)'
+    }
+
+    def 'should not allow invalid settinga' () {
+        when:
+        new WaveConfig(endpoint: 'foo')
+        then:
+        def e = thrown(IllegalArgumentException)
+        e.message == "Endpoint URL should start with 'http:' or 'https:' protocol prefix - offending value: 'foo'"
+
+        when:
+        new WaveConfig(endpoint: 'ftp://foo.com')
+        then:
+        e = thrown(IllegalArgumentException)
+        e.message == "Endpoint URL should start with 'http:' or 'https:' protocol prefix - offending value: 'ftp://foo.com'"
+
+        when:
+        new WaveConfig(build: [repository: 'http://foo.com'])
+        then:
+        e = thrown(IllegalArgumentException)
+        e.message == "Config setting 'wave.build.repository' should not include any protocol prefix - offending value: 'http://foo.com'"
+
+        when:
+        new WaveConfig(build: [cacheRepository: 'http://foo.com'])
+        then:
+        e = thrown(IllegalArgumentException)
+        e.message == "Config setting 'wave.build.cacheRepository' should not include any protocol prefix - offending value: 'http://foo.com'"
+    }
+
 }

From 5e3f2c0aac33c974c427b1d252acd6f17cbc3ea1 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 3 Oct 2023 10:58:54 +0100
Subject: [PATCH 191/350] Rename Microsoft AAD to Microsoft Entra (#4362)

Signed-off-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
---
 docs/azure.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/azure.md b/docs/azure.md
index ac8ff1a24d..fd68e503de 100644
--- a/docs/azure.md
+++ b/docs/azure.md
@@ -374,7 +374,7 @@ The value of the setting must be the identifier of a subnet available in the vir
 Batch Authentication with Shared Keys does not allow to link external resources (like Virtual Networks) to the pool. Therefore, Active Directory Authentication must be used in conjunction with the `virtualNetwork` setting.
 :::
 
-## Active Directory Authentication
+## Microsoft Entra (formerly Active Directory Authentication)
 
 :::{versionadded} 22.11.0-edge
 :::

From 0bce2be098bfd61bd6d78eb5e5379fd1002fea15 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 3 Oct 2023 18:33:48 +0100
Subject: [PATCH 192/350] Add example of using the transpose operator with
 multiple items in element. (#4364)

Signed-off-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
---
 docs/operator.md | 41 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

diff --git a/docs/operator.md b/docs/operator.md
index 978fbaf85b..a67ebc2047 100644
--- a/docs/operator.md
+++ b/docs/operator.md
@@ -1989,6 +1989,47 @@ The above snippet prints:
 [3, D]
 ```
 
+If each element of the channel has more than 2 items, these will be flattened by the first item in the element and only emit an element when the element is complete:
+
+```groovy
+Channel.of(
+        [1, [1], ['A']],
+        [2, [1, 2], ['B', 'C']],
+        [3, [1, 2, 3], ['D', 'E']]
+    )
+    .transpose()
+    .view()
+```
+
+```
+[1, 1, A]
+[2, 1, B]
+[2, 2, C]
+[3, 1, D]
+[3, 2, E]
+```
+
+To emit all elements, use `remainder: true`:
+
+```groovy
+Channel.of(
+        [1, [1], ['A']],
+        [2, [1, 2], ['B', 'C']],
+        [3, [1, 2, 3], ['D', 'E']]
+    )
+    .transpose(remainder: true)
+    .view()
+```
+
+```
+[1, 1, A]
+[2, 1, B]
+[2, 2, C]
+[3, 1, D]
+[3, 2, E]
+[3, 3, null]
+```
+
 Available options:
 
 ` by`

From 74a0f998e3f7186f8a7233903ae07cb61cdb6250 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Thu, 5 Oct 2023 12:04:34 -0500
Subject: [PATCH 193/350] Incorporate README content into Nextflow docs (#4263)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Phil Ewels <phil.ewels@seqera.io>
Co-authored-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .editorconfig              |   5 +
 CONTRIBUTING.md            |  98 +++----------
 README.md                  | 280 ++++---------------------------------
 docs/config.md             |   6 +
 docs/developer/index.md    |  93 ++++++++++--
 docs/developer/plugins.md  | 157 +++++++++++++++++++++
 docs/index.md              |  27 ++++
 docs/plugins.md            |  60 +++-----
 plugins/README.md          | 161 ---------------------
 plugins/nf-azure/README.md |  67 +++++----
 tests/README.md            |   2 +-
 11 files changed, 376 insertions(+), 580 deletions(-)
 create mode 100644 .editorconfig
 create mode 100644 docs/developer/plugins.md
 delete mode 100644 plugins/README.md

diff --git a/.editorconfig b/.editorconfig
new file mode 100644
index 0000000000..8ed3888e2d
--- /dev/null
+++ b/.editorconfig
@@ -0,0 +1,5 @@
+[*]
+charset = utf-8
+indent_size = 4
+indent_style = space
+tab_width = 4
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 7cb26e6cc7..4259cff330 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -1,73 +1,40 @@
-# CONTRIBUTING TO NEXTFLOW
+# Contributing to Nextflow
 
-This guide documents the best way to make various types of contributions to Nextflow,
-including what is required before submitting a code change.
+This guide documents the various ways to contribute to Nextflow, including what is required before submitting a code change.
 
-Contributing to Nextflow doesn't just mean writing code. Helping new users on the mailing list,
-testing releases and bug fixes, and improving documentation are all essential and valuable contributions. In fact, proposing
-significant code changes usually first requires gaining experience and credibility within the
-community by helping in other ways. This is also a guide to becoming an effective contributor.
+Contributing to Nextflow doesn't just mean writing code. Helping new users in the community, testing releases and bug fixes, and improving documentation are all essential and valuable contributions. Helping in these ways is an excellent way to become an effective contributor and gain credibility within the community, which makes it easier to make larger contributions like code changes and new features.
 
+## Helping Other Users
 
-## Contributing by Helping Other Users
+A great way to contribute to Nextflow is to answer user questions on the [community forum](https://community.seqera.io) and the [Nextflow Slack](https://www.nextflow.io/slack-invite.html). Contributors should ideally be active members here and keep up with the latest developments in the Nextflow community. There are always many new Nextflow users, so taking a few minutes to help answer a question is a valuable community service and a great way to demonstrate your expertise.
 
-A great way to contribute to Nextflow is to help answer user questions on the [discussion forum](https://github.com/nextflow-io/nextflow/discussions), 
-or the [Slack channel](https://www.nextflow.io/slack-invite.html).
-There are always many new Nextflow users; taking a few minutes to help answer a question is a very valuable community service.
+## Documentation Changes
 
-Contributors should ideally subscribe to these channels and follow them in order to keep up to date
-on what's happening in Nextflow. Answering questions is an excellent and visible way to help the
-community and also demonstrates your expertise.
+Propose changes to the [Nextflow documentation](https://nextflow.io/docs/latest/) by editing the source files in the [docs](https://github.com/nextflow-io/nextflow/tree/master/docs) directory. The `README.md` in that directory describes how to build and preview the docs locally. Finally, open a pull request with the proposed changes.
 
+## Bug Reports
 
-## Contributing Documentation Changes
+Submitting a bug report is one of the simplest and most useful ways to contribute, as it helps us to quickly identify and fix issues and thereby make Nextflow more stable.
 
-To propose a change to release documentation (that is, the docs that appear under http://docs.nextflow.io),
-edit the documentation source files in Nextflow's [docs/](https://github.com/nextflow-io/nextflow/tree/master/docs)
-directory, whose README file shows how to build the documentation locally to test your changes.
+Report a bug using the **New issue** button on the [issues page](https://github.com/nextflow-io/nextflow/issues). A good bug report should include a minimal test case that can replicate the reported bug. Please follow the instructions in the issue template when submitting a bug report.
 
-Then open a pull request with the proposed changes.
+## Bug Fixes
 
+Contributing bug fixes is the best way to gain experience with the Nextflow codebase and credibility within the community as a project contributor.
 
-## Contributing Bug Reports
+If you are new to the Nextflow codebase and want to get involved, check out issues marked as [`help wanted`](https://github.com/nextflow-io/nextflow/issues?q=is%3Aissue+is%3Aopen+label%3A%22help+wanted%22) or [`good first issue`](https://github.com/nextflow-io/nextflow/issues?q=is%3Aissue+is%3Aopen+label%3A%22good+first+issue%22+). Feel free to ask for help if you get stuck while trying to implement a fix!
 
-Filling a bug report is likely the simplest and most useful way to contribute to the project.
-It helps us to identify issues and provide patches and therefore to make Nextflow more stable
-and useful.
+## New Features
 
-Report a bug using the "New issue" button in the
-[issues page](https://github.com/nextflow-io/nextflow/issues) of this project.
+Before contributing a new feature, please submit a new feature proposal on the [issues page](https://github.com/nextflow-io/nextflow/issues) and discuss it with the community.
 
-A good bug report should include a minimal executable test case able to replicate the reported bug.
+Submitting a proposal helps identify possible overlaps with other planned features and avoid potential misunderstandings, conflicts, and wasted effort.
 
-Follow the instructions in the bug [report template](https://github.com/nextflow-io/nextflow/blob/master/.github/issue_template.md) that is shown when filling the bug report out.
+## Code Changes
 
-## Contributing Bug Fixes
+When submitting a contribution, you will be required to sign a [Developer Certificate of Origin (DCO)](https://developercertificate.org/) to certify that you are the author of the source code or otherwise have the right to submit it to the project.
 
-Contributing bug fixes is the best way to gain experience and credibility within the community
-and also to become an effective project contributor.
-
-If you are a novice with the Nextflow code base, start by looking at issues marked
-with the [help wanted](https://github.com/nextflow-io/nextflow/issues?q=is%3Aissue+is%3Aopen+label%3A%22help+wanted%22)
-label.
-
-If you have doubts on how to fix an issue, ask for help from senior contributors commenting
-in the issue page.
-
-## Contributing New Features
-
-Before contributing a new feature, submit a new feature proposal in the
-[issues page](https://github.com/nextflow-io/nextflow/issues) of the project and discuss it
-with the community.
-
-This is important to identify possible overlaps with other planned features and avoid misunderstandings and conflicts.
-
-## Contributing Code Changes
-
-When submitting a contribution, you will be required to sign a [Developer Certificate of Origin (DCO)](https://developercertificate.org/) to certify that you are the author of the source code or otherwise you have the right to submit it to the project. 
-
-Contributor signatures are provided by adding a `Signed-off-by` line to the commit message 
-as shown below, or by using the `-s` option for the [git commit command](https://help.github.com/articles/signing-commits/).
+Contributor signatures are provided by adding a `Signed-off-by` line to the commit message as shown below, or by using the `-s` option with [`git commit`](https://help.github.com/articles/signing-commits/). For example:
 
 ```
 This is my commit message
@@ -77,29 +44,4 @@ Signed-off-by: Random J Developer <random@developer.example.org>
 
 The process is automatically managed by the [Probot](https://probot.github.io/apps/dco/) app for GitHub.
 
-
-## IDE settings
-
-The suggested development environment is [IntelliJ IDEA](https://www.jetbrains.com/idea/download/). See the [README](https://github.com/nextflow-io/nextflow/#intellij-idea) for a short primer on how to import
-and configure Nextflow to work with it.
-
-Nextflow does not impose a strict code formatting style, however the following settings should be applied:
-
-* Use spaces for indentation
-* Tab size: 4
-* Indent: 4
-* Use single class import
-* Class count to use import with `*`: 99
-* Names count to use static import with `*`: 99
-* Imports layout:
-    * \<blank line>
-    * `import org.junit.*`
-    * `import spock.lang.*`
-    * \<blank line>
-    * `import java.*`
-    * `import javax.*`
-    * \<blank line>
-    * *all other imports*
-    * *all other static imports*
-
-New files must include the appropriate license header boilerplate and the author name(s) and contact email(s) ([see for example](https://github.com/nextflow-io/nextflow/blob/e8945e8b6fc355d3f2eec793d8f288515db2f409/modules/nextflow/src/main/groovy/nextflow/Const.groovy#L1-L15)).
+For more information about working on the Nextflow source code, visit the [Nextflow docs](https://nextflow.io/docs/latest/developer/).
diff --git a/README.md b/README.md
index b079cf49e8..1f4007fdf4 100644
--- a/README.md
+++ b/README.md
@@ -1,288 +1,66 @@
-![Nextflow logo](https://github.com/nextflow-io/trademark/blob/master/nextflow2014_no-bg.png)
+<picture>
+  <source media="(prefers-color-scheme: dark)" srcset="https://github.com/nextflow-io/trademark/blob/master/nextflow2014_no-bg-bright.png">
+  <source media="(prefers-color-scheme: light)" srcset="https://github.com/nextflow-io/trademark/blob/master/nextflow2014_no-bg.png">
+  <img alt="Nextflow Logo" src="https://github.com/nextflow-io/trademark/blob/master/nextflow2014_no-bg.png">
+</picture>
 
 *"Dataflow variables are spectacularly expressive in concurrent programming"*
 <br>[Henri E. Bal , Jennifer G. Steiner , Andrew S. Tanenbaum](https://dl.acm.org/doi/abs/10.1145/72551.72552)
 
-
-![Nextflow CI](https://github.com/nextflow-io/nextflow/workflows/Nextflow%20CI/badge.svg)
+[![Nextflow CI](https://github.com/nextflow-io/nextflow/workflows/Nextflow%20CI/badge.svg)](https://github.com/nextflow-io/nextflow/actions/workflows/build.yml?query=branch%3Amaster+event%3Apush)
 [![Nextflow version](https://img.shields.io/github/release/nextflow-io/nextflow.svg?colorB=26af64&style=popout)](https://github.com/nextflow-io/nextflow/releases/latest)
 [![Nextflow Twitter](https://img.shields.io/twitter/url/https/nextflowio.svg?colorB=26af64&&label=%40nextflow&style=popout)](https://twitter.com/nextflowio)
 [![Nextflow Publication](https://img.shields.io/badge/Published-Nature%20Biotechnology-26af64.svg?colorB=26af64&style=popout)](https://www.nature.com/articles/nbt.3820)
 [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?colorB=26af64&style=popout)](http://bioconda.github.io/recipes/nextflow/README.html)
 [![Nextflow license](https://img.shields.io/github/license/nextflow-io/nextflow.svg?colorB=26af64&style=popout)](https://github.com/nextflow-io/nextflow/blob/master/COPYING)
 
-Quick overview
-==============
-Nextflow is a bioinformatics workflow manager that enables the development of portable and reproducible workflows.
-It supports deploying workflows on a variety of execution platforms including local, HPC schedulers, AWS Batch,
-Google Cloud Life Sciences, and Kubernetes. Additionally, it provides support for manage your workflow dependencies
-through built-in support for Conda, Spack, Docker, Podman, Singularity, Modules, and more.
-
-## Contents
-- [Rationale](#rationale)
-- [Quick start](#quick-start)
-- [Documentation](#documentation)
-- [Tool Management](#tool-management)
-  - [Conda environments](#conda-environments)
-  - [Spack environments](#spack-environments)
-  - [Docker, Podman and Singularity](#containers)
-  - [Environment Modules](#environment-modules)
-- [HPC Schedulers](#hpc-schedulers)
-  - [SGE](#hpc-schedulers)
-  - [Univa Grid Engine](#hpc-schedulers)
-  - [LSF](#hpc-schedulers)
-  - [SLURM](#hpc-schedulers)
-  - [PBS/Torque](#hpc-schedulers)
-  - [HyperQueue (experimental)](#hpc-schedulers)
-  - [HTCondor (experimental)](#hpc-schedulers)
-  - [Moab](#hpc-schedulers)
-- [Cloud Support](#cloud-support)
-  - [AWS Batch](#cloud-support)
-  - [Google Cloud Batch](#cloud-support)
-  - [Google Life Sciences](#cloud-support)
-  - [Kubernetes](#cloud-support)
-- [Community](#community)
-- [Build from source](#build-from-source)
-- [Contributing](#contributing)
-- [License](#license)
-- [Citations](#citations)
-- [Credits](#credits)
-
-
-Rationale
-=========
-
-With the rise of big data, techniques to analyse and run experiments on large datasets are increasingly necessary.
-
-Parallelization and distributed computing are the best ways to tackle this problem, but the tools commonly available to the bioinformatics community often lack good support for these techniques, or provide a model that fits badly with the specific requirements in the bioinformatics domain and, most of the time, require the knowledge of complex tools or low-level APIs.
-
-Nextflow framework is based on the dataflow programming model, which greatly simplifies writing parallel and distributed pipelines without adding unnecessary complexity and letting you concentrate on the flow of data, i.e. the functional logic of the application/algorithm.
-
-It doesn't aim to be another pipeline scripting language yet, but it is built around the idea that the Linux platform is the *lingua franca* of data science, since it provides many simple command line and scripting tools, which by themselves are powerful, but when chained together facilitate complex data manipulations.
-
-In practice, this means that a Nextflow script is defined by composing many different processes. Each process can execute a given bioinformatics tool or scripting language, to which is added the ability to coordinate and synchronize the processes execution by simply specifying their inputs and outputs.
-
-
-
-Quick start
-============
-
-Download the package
---------------------
-
-Nextflow does not require any installation procedure, just download the distribution package by copying and pasting
-this command in your terminal:
-
-```
-curl -fsSL https://get.nextflow.io | bash
-```
-
-It creates the ``nextflow`` executable file in the current directory. You may want to move it to a folder accessible from your ``$PATH``.
-
-Download from Conda
--------------------
-
-Nextflow can also be installed from Bioconda
-
-```
-conda install -c bioconda nextflow 
-```
-
-Documentation
-=============
-
-Nextflow documentation is available at this link http://docs.nextflow.io
-
-
-HPC Schedulers
-==============
-
-*Nextflow* supports common HPC schedulers, abstracting the submission of jobs from the user. 
-
-Currently the following clusters are supported:
-
-  + [SGE](https://www.nextflow.io/docs/latest/executor.html#sge)
-  + [Univa Grid Engine](https://www.nextflow.io/docs/latest/executor.html#sge)
-  + [LSF](https://www.nextflow.io/docs/latest/executor.html#lsf)
-  + [SLURM](https://www.nextflow.io/docs/latest/executor.html#slurm)
-  + [PBS/Torque](https://www.nextflow.io/docs/latest/executor.html#pbs-torque)
-  + [Flux](https://www.nextflow.io/docs/latest/executor.html#flux)
-  + [HyperQueue (beta)](https://www.nextflow.io/docs/latest/executor.html#hyperqueue)
-  + [HTCondor (beta)](https://www.nextflow.io/docs/latest/executor.html#htcondor)
-  + [Moab](https://www.nextflow.io/docs/latest/executor.html#moab)
-
-For example to submit the execution to a SGE cluster create a file named `nextflow.config`, in the directory
-where the pipeline is going to be launched, with the following content:
-
-```nextflow
-process {
-  executor='sge'
-  queue='<your execution queue>'
-}
-```
-
-In doing that, processes will be executed by Nextflow as SGE jobs using the `qsub` command. Your 
-pipeline will behave like any other SGE job script, with the benefit that *Nextflow* will 
-automatically and transparently manage the processes synchronisation, file(s) staging/un-staging, etc.  
-
-
-Cloud support
-=============
-*Nextflow* also supports running workflows across various clouds and cloud technologies. Managed solutions from major 
-cloud providers are also supported through AWS Batch, Azure Batch and Google Cloud compute services. 
-Additionally, *Nextflow* can run workflows on either on-prem or managed cloud Kubernetes clusters. 
-
-Currently supported cloud platforms:
-  + [AWS Batch](https://www.nextflow.io/docs/latest/awscloud.html#aws-batch)
-  + [Azure Batch](https://azure.microsoft.com/en-us/services/batch/)
-  + [Google Cloud Batch](https://cloud.google.com/batch)
-  + [Google Cloud Life Sciences](https://cloud.google.com/life-sciences)
-  + [Kubernetes](https://www.nextflow.io/docs/latest/kubernetes.html)
-
+Nextflow is a workflow system for creating scalable, portable, and reproducible workflows. It is based on the dataflow programming model, which greatly simplifies the writing of parallel and distributed pipelines, allowing you to focus on the flow of data and computation. Nextflow can deploy workflows on a variety of execution platforms, including your local machine, HPC schedulers, AWS Batch, Azure Batch, Google Cloud Batch, and Kubernetes. Additionally, it supports many ways to manage your software dependencies, including Conda, Spack, Docker, Podman, Singularity, and more.
 
+## Quick start
 
-Tool management
-================
-
-Containers
-----------------
-
-*Nextflow* has first class support for containerization. It supports both [Docker](https://www.nextflow.io/docs/latest/docker.html) and [Singularity](https://www.nextflow.io/docs/latest/singularity.html) container engines. Additionally, *Nextflow* can easily switch between container engines enabling workflow portability. 
-
-```nextflow
-process samtools {
-  container 'biocontainers/samtools:1.3.1'
-
-  """
-  samtools --version 
-  """
-
-}
-```
-
-Conda environments
-------------------
-
-[Conda environments](https://www.nextflow.io/docs/latest/conda.html) provide another option for managing software packages in your workflow. 
-
-
-Spack environments
-------------------
-
-[Spack environments](https://www.nextflow.io/docs/latest/spack.html) provide an option to build software packages from source using Spack, a popular package manager within the HPC community.
-
-
-Environment Modules
--------
-
-[Environment modules](https://www.nextflow.io/docs/latest/process.html#module) commonly found in HPC environments can also be used to manage the tools used in a *Nextflow* workflow. 
-
-
-Community
-=========
-
-You can post questions, or report problems by using the Nextflow [discussions](https://github.com/nextflow-io/nextflow/discussions)
-or the Nextflow [Slack community chat](https://www.nextflow.io/slack-invite.html).
-
-*Nextflow* also hosts a yearly workshop showcasing researcher's workflows and advancements in the language. Talks from the past workshops are available on the [Nextflow YouTube Channel](https://www.youtube.com/channel/UCB-5LCKLdTKVn2F4V4KlPbQ)
-
-The [nf-core](https://nf-co.re/) project is a community effort aggregating high quality *Nextflow* workflows which can be used by the community. 
-
-
-Build from source
-=================
-
-Required dependencies
----------------------
-
-* Compiler Java 11 or later
-* Runtime Java 11 or later
-
-Build from source
------------------
-
-*Nextflow* is written in [Groovy](http://groovy-lang.org) (a scripting language for the JVM). A pre-compiled,
-ready-to-run, package is available at the [Github releases page](https://github.com/nextflow-io/nextflow/releases),
-thus it is not necessary to compile it in order to use it.
-
-If you are interested in modifying the source code, or contributing to the project, it worth knowing that
-the build process is based on the [Gradle](http://www.gradle.org/) build automation system.
-
-You can compile *Nextflow* by typing the following command in the project home directory on your computer:
+Install Nextflow with a single command:
 
 ```bash
-make compile
+curl -fsSL https://get.nextflow.io | bash
 ```
 
-The very first time you run it, it will automatically download all the libraries required by the build process.
-It may take some minutes to complete.
-
-When complete, execute the program by using the `launch.sh` script in the project directory.
+It creates the `nextflow` executable file in the current directory. You can then move it to a directory in your `$PATH` to run it from anywhere.
 
-The self-contained runnable Nextflow packages can be created by using the following command:
+Nextflow can also be installed from Bioconda:
 
 ```bash
-make pack
-```            
-
-Once compiled use the script `./launch.sh` as a replacement for the usual `nextflow` command.
-
-The compiled packages can be locally installed using the following command:
-
-```bash
-make install
+conda install -c bioconda nextflow
 ```
 
-A self-contained distribution can be created with the command: `make pack`.  To include support of GA4GH and its dependencies in the binary, use `make packGA4GH` instead.
-
-
-IntelliJ IDEA
----------------
-
-Nextflow development with [IntelliJ IDEA](https://www.jetbrains.com/idea/) requires a recent version of the IDE (2019.1.2 or later).
-
-If you have it installed in your computer, follow the steps below in order to use it with Nextflow:
-
-1. Clone the Nextflow repository to a directory in your computer.
-2. Open IntelliJ IDEA and choose "New > Project from Existing Sources..." in the "File" menu bar.
-3. Select the Nextflow project root directory in your computer and click "OK".
-4. Then, choose the "Gradle" item in the "Import project from external model" list and click on "Finish" button to finalize the import.
-5. When the import process completes, select the "Project structure" command in the "File" menu bar.
-6. In the showed dialog click on the "Project" item in the list of the left, and make sure that
-   the "Project SDK" choice on the right contains Java 11 (or later, up to 18).
-7. Set the code formatting options with settings provided [here](https://github.com/nextflow-io/nextflow/blob/master/CONTRIBUTING.md#ide-settings).
+## Documentation
 
+The Nextflow documentation is available for the latest [stable](https://nextflow.io/docs/latest/) and [edge](https://nextflow.io/docs/edge/) releases.
 
+## Community
 
-Contributing
-============
+You can post questions and get help in the [Nextflow community forum](https://community.seqera.io) or the [Nextflow Slack](https://www.nextflow.io/slack-invite.html). Bugs and feature requests should be reported as [GitHub issues](https://github.com/nextflow-io/nextflow/issues/new/choose).
 
-Project contribution are more than welcome. See the [CONTRIBUTING](CONTRIBUTING.md) file for details.
+The Nextflow community is highly active with regular community meetings, events, a podcast and more. You can view much of this material on the [Nextflow](https://www.youtube.com/@Nextflow) and [nf-core](https://www.youtube.com/@nf-core) YouTube channels.
 
+The [nf-core](https://nf-co.re/) project is a community effort aggregating high quality Nextflow workflows which can be used by everyone.
 
-Build servers
-=============
+## Contributing
 
-  * [Travis-CI](https://travis-ci.org/nextflow-io/nextflow)
-  * [GitHub Actions](https://github.com/nextflow-io/nextflow/actions)
+Contributions are more than welcome. See the [CONTRIBUTING](CONTRIBUTING.md) file for details.
 
-License
-=======
+## License
 
-The *Nextflow* framework is released under the Apache 2.0 license.
+Nextflow is released under the Apache 2.0 license. Nextflow is a [registered trademark](https://github.com/nextflow-io/trademark).
 
-Citations
-=========
+## Citations
 
-If you use Nextflow in your research, please cite:
+If you use Nextflow in your work, please cite:
 
 P. Di Tommaso, et al. Nextflow enables reproducible computational workflows. Nature Biotechnology 35, 316–319 (2017) doi:[10.1038/nbt.3820](http://www.nature.com/nbt/journal/v35/n4/full/nbt.3820.html)
 
-Credits
-=======
+## Credits
 
-Nextflow is built on two great pieces of open source software, namely <a href='http://groovy-lang.org' target='_blank'>Groovy</a>
-and <a href='http://www.gpars.org/' target='_blank'>Gpars</a>.
+Nextflow is built on two \*great* open-source software projects, <a href='http://groovy-lang.org' target='_blank'>Groovy</a>
+and <a href='http://www.gpars.org/' target='_blank'>GPars</a>.
 
-YourKit is kindly supporting this open source project with its full-featured Java Profiler.
-Read more http://www.yourkit.com
+<a href='http://www.yourkit.com' target='_blank'>YourKit</a> is kindly supporting Nextflow with its fully-featured Java Profiler.
diff --git a/docs/config.md b/docs/config.md
index 52d1f70020..fb3cc8e832 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -1643,6 +1643,12 @@ The following environment variables control the configuration of the Nextflow ru
 `NXF_PID_FILE`
 : Name of the file where the process PID is saved when Nextflow is launched in background.
 
+`NXF_PLUGINS_DEFAULT`
+: Whether to use the default plugins when no plugins are specified in the Nextflow configuration (default: `true`).
+
+`NXF_PLUGINS_DIR`
+: The path where the plugin archives are loaded and stored (default: `$NXF_HOME/plugins`).
+
 `NXF_PLUGINS_TEST_REPOSITORY`
 : :::{versionadded} 23.04.0
   :::
diff --git a/docs/developer/index.md b/docs/developer/index.md
index 6426feaab2..8d2c7d6979 100644
--- a/docs/developer/index.md
+++ b/docs/developer/index.md
@@ -1,8 +1,42 @@
 # Overview
 
-This section is intended to explain the Nextflow source code at a high level for users who want to understand or contribute to it. Rather than a comprehensive API documentation, these docs simply provide a conceptual map to help you understand the key concepts of the Nextflow implementation, and to quickly find code sections of interest for further investigation.
+This section provides a high-level overview of the Nextflow source code for users who want to understand or contribute to it. Rather than a comprehensive API documentation, these docs simply provide a conceptual map to help you understand the key concepts of the Nextflow implementation, and to quickly find code sections of interest for further investigation.
 
-## Programming Languages
+Before you dive into code, be sure to check out the [CONTRIBUTING.md](https://github.com/nextflow-io/nextflow/blob/master/CONTRIBUTING.md) for Nextflow to learn about the many ways to contribute to the project.
+
+## IntelliJ IDEA
+
+The suggested development environment is [IntelliJ IDEA](https://www.jetbrains.com/idea/download/). Nextflow development with IntelliJ IDEA requires a recent version of the IDE (2019.1.2 or later).
+
+After installing IntelliJ IDEA, use the following steps to use it with Nextflow:
+
+1. Clone the Nextflow repository to a directory in your computer.
+
+2. Open IntelliJ IDEA and go to **File > New > Project from Existing Sources...**.
+
+3. Select the Nextflow project root directory in your computer and click **OK**.
+
+4. Select **Import project from external model > Gradle** and click **Finish**.
+
+5. After the import process completes, select **File > Project Structure...**.
+
+6. Select **Project**, and make sure that the **SDK** field contains Java 11 (or later).
+
+7. Go to **File > Settings > Editor > Code Style > Groovy > Imports** and apply the following settings:
+
+   * Use single class import
+   * Class count to use import with '*': `99`
+   * Names count to use static import with '*': `99`
+   * Imports layout:
+      * `import java.*`
+      * `import javax.*`
+      * *blank line*
+      * all other imports
+      * all other static imports
+
+New files must include the appropriate license header boilerplate and the author name(s) and contact email(s) ([see for example](https://github.com/nextflow-io/nextflow/blob/e8945e8b6fc355d3f2eec793d8f288515db2f409/modules/nextflow/src/main/groovy/nextflow/Const.groovy#L1-L15)).
+
+## Groovy
 
 Nextflow is written in [Groovy](http://groovy-lang.org/), which is itself a programming language based on [Java](https://www.java.com/). Groovy is designed to be highly interoperable with Java -- Groovy programs compile to Java bytecode, and nearly any Java program is also a valid Groovy program. However, Groovy adds several language features (e.g. closures, list and map literals, optional typing, optional semicolons, meta-programming) and standard libraries (e.g. JSON and XML parsing) that greatly improve the overall experience of developing for the Java virtual machine.
 
@@ -50,50 +84,83 @@ See {ref}`packages-page` for the list of Nextflow packages.
 Class diagrams are manually curated, so they might not always reflect the latest version of the source code.
 ```
 
-## Building and Testing
+## Building from source
 
-The only dependency that you need to build Nextflow is Java. In other words, if you can run Nextflow, then you can probably build it too!
+If you are interested in modifying the source code, you only need Java 11 or later to build Nextflow from source. Nextflow uses the [Gradle](http://www.gradle.org/) build automation system, but you do not need to install Gradle to build Nextflow. In other words, if you can run Nextflow, then you can probably build it too!
 
-Build and test locally from a branch (useful for testing PRs):
+To build locally from a branch (useful for testing PRs):
 
 ```bash
-# build
 git clone -b <branch> git@github.com:nextflow-io/nextflow.git
 cd nextflow
 make compile
+```
+
+The build system will automatically download all of the necessary dependencies on the first run, which may take several minutes.
 
-# test
+Once complete, you can run your local build of Nextflow using the `launch.sh` script in place of the `nextflow` command:
+
+```bash
 ./launch.sh run <script> ...
 ```
 
-Run tests locally:
+A self-contained executable Nextflow package can be created with the following command:
+
+```bash
+make pack
+```
+
+Again, use `launch.sh` in place of the `nextflow` command to use your local build.
+
+## Testing
+
+To run the unit tests:
 
 ```bash
 # run all tests
 make test
 
 # run individual test
-make test module=<nextflow|plugins:nf-amazon|...> class=<package>.<class>
+make test module=<nextflow|plugins:nf-amazon|...> class=<package>.<class>.<method>
 
-# view the Makefile for all build rules
+# refer to the Makefile for all build rules
 ```
 
-When a test fails, it will give you a report that you can open in your browser to view the stack trace for each failed test. The "Standard output" tab is particularly useful as it shows the console output of each test. You also can view this console output in the terminal by adding `--info` to the `./gradlew` command generated by the Makefile.
+When a test fails, it will give you a report that you can open in your browser to view the reason for each failed test. The **Standard output** tab is particularly useful as it shows the console output of each test.
+
+Refer to the [build.yml](https://github.com/nextflow-io/nextflow/tree/master/.github/workflows/build.yml) configuration to see how to run integration tests locally, if you are interested.
 
 ## Installing from source
 
 The `nextflow` command is just a Bash script that downloads and executes the Nextflow JAR. When you install Nextflow using `get.nextflow.io`, it only downloads this launcher script, while the Nextflow JAR is downloaded on the first Nextflow run.
 
-You can run `make install` to install a local build of the Nextflow JAR to `$NXF_HOME`. Note that it will overwrite any existing JAR with the same version. This approach is useful for testing non-core plugins with a local build of Nextflow.
+You can run `make install` to install a local build of the Nextflow JAR to `$NXF_HOME`. Note that this command will overwrite any existing Nextflow packages with the same version. This approach is useful for testing non-core plugins with a local build of Nextflow.
 
 If you need to test changes to the `nextflow` launcher script, you can run it directly as `./nextflow`, or you can install it using `cp nextflow $(which nextflow)` and then run it as `nextflow`.
 
 ## Debugging
 
+### Groovy REPL
+
 The `groovysh` command provides a command-line REPL that you can use to play around with Groovy code independently of Nextflow. The `groovyConsole` command provides a graphical REPL similar to `nextflow console`. These commands require a standalone Groovy distribution, which can be installed as described for Java in {ref}`Getting started <getstarted-requirement>`.
 
 :::{note}
 If you are using WSL, you must also install an X server for Windows, such as [VcXsrv](https://sourceforge.net/projects/vcxsrv/) or [Xming](http://www.straightrunning.com/XmingNotes/), in order to use these commands.
 :::
 
-For more advanced Groovy debugging capabilities, consider using [IntelliJ IDEA](https://www.jetbrains.com/idea/).
+### IntelliJ IDEA
+
+:::{versionadded} 23.09.0-edge
+:::
+
+You can perform limited breakpoint debugging on a Nextflow script using IntelliJ IDEA.
+
+1. Set a breakpoint in your Nextflow script by clicking on a line number.
+
+2. Run `nextflow -remote-debug run <script>`
+
+3. Select the **Run / Debug Configurations** dropdown, select **Edit Configurations...**, and create a new configuration of type **Remote JVM Debug**. Set the port that appeared in the terminal when you launched your Nextflow script. Click **OK**.
+
+4. Select the green bug icon to begin the remote debug session. The Debug window will appear and allow you to step through and inspect your script as it runs.
+
+Note that this approach can only be used to debug the *script* execution, which does not include the *pipeline* execution.
diff --git a/docs/developer/plugins.md b/docs/developer/plugins.md
new file mode 100644
index 0000000000..99b0c2ee2b
--- /dev/null
+++ b/docs/developer/plugins.md
@@ -0,0 +1,157 @@
+
+# Core plugins
+
+This page describes the build process for Nextflow core plugins. See the {ref}`plugins-page` page to learn how to create your own plugins outside of Nextflow.
+
+## Plugin subprojects
+
+Each plugin subproject has its own `build.gradle` which defines the main build actions and the required dependencies.
+
+The minimal dependencies are as follows:
+
+```groovy
+dependencies {
+    compileOnly project(':nextflow')
+    compileOnly 'org.slf4j:slf4j-api:1.7.10'
+    compileOnly 'org.pf4j:pf4j:3.4.1'
+
+    testImplementation project(':nextflow')
+    testImplementation "org.codehaus.groovy:groovy:3.0.5"
+    testImplementation "org.codehaus.groovy:groovy-nio:3.0.5"
+}
+```
+
+The plugin subproject directory name must begin with the prefix `nf-` and must include a file named `src/resources/META-INF/MANIFEST.MF` which contains the plugin metadata. The manifest content looks like the following:
+
+```
+Manifest-Version: 1.0
+Plugin-Class: the.plugin.ClassName
+Plugin-Id: the-plugin-id
+Plugin-Provider: Your Name or Organization
+Plugin-Version: 0.0.0
+```
+
+## Environment variables
+
+`NXF_PLUGINS_MODE`
+: The plugin execution mode, either `prod` for production or `dev` for development (see below for details).
+
+`NXF_PLUGINS_DIR`
+: The path where the plugin archives are loaded and stored (default: `$NXF_HOME/plugins` in production, `./plugins` in development).
+
+`NXF_PLUGINS_DEFAULT`
+: Whether to use the default plugins when no plugins are specified in the Nextflow configuration (default: `true`).
+
+`NXF_PLUGINS_DEV`
+: Comma-separated list of development plugin root directories.
+
+## Development environment
+
+When running in development mode, the plugin system uses the `DevPluginClasspath` to load plugin classes from each plugin project build path, e.g. `plugins/nf-amazon/build/classes` and `plugins/nf-amazon/build/target/libs` (for deps libraries).
+
+## Plugin registry
+
+The metadata for each plugin is published to the [nextflow-io/plugins](https://github.com/nextflow-io/plugins) GitHub repository, specifically [this file](https://raw.githubusercontent.com/nextflow-io/plugins/main/plugins.json).
+
+The repository index has the following structure:
+
+```json
+[
+  {
+    "id": "nf-amazon",
+    "releases": [
+      {
+        "version": "0.2.0",
+        "url": "https://github.com/nextflow-io/nf-amazon/releases/download/0.2.0/nf-amazon-0.2.0.zip",
+        "date": "2020-10-12T10:05:44.28+02:00",
+        "sha512sum": "9e9e33695c1a7c051271..."
+      }
+    ]
+  },
+  /* ... */
+]
+```
+
+## Plugin releases
+
+A plugin release is a ZIP archive containing the plugin classes and the required dependencies.
+
+Nextflow core plugins are released under a corresponding GitHub project, e.g. `nextflow-io/nf-amazon`. This is not a strict requirement, rather it is done to simplify the build process and provide a consistent download experience.
+
+### Installation
+
+Plugins must be declared in the `nextflow.config` file using the `plugins` scope, for example:
+
+```groovy
+plugins {
+    id 'nf-amazon@0.2.0'
+}
+```
+
+If a plugin is not locally available, Nextflow checks the repository index for the download URL, downloads and extracts the plugin archive, and installs the plugin into the directory specified by `NXF_PLUGINS_DIR` (default: `${NXF_HOME}/plugins`).
+
+Since each Nextflow run can have a different set of plugins (and versions), each run keeps a local plugins directory called `.nextflow/plr/<session-id>` which links the exact set of plugins required for the given run.
+
+Additionally, the "default plugins" (defined in the Nextflow resources file `modules/nextflow/src/main/resources/META-INF/plugins-info.txt`) are always made available for use. To disable the use of default plugins, set the environment variable `NXF_PLUGINS_DEFAULT=false`.
+
+## Gradle Tasks
+
+### `makeZip`
+
+Create the plugin archive and JSON meta file in the subproject `build/libs` directory.
+
+```console
+$ ls -l1 plugins/nf-tower/build/libs/
+nf-tower-0.1.0.jar
+nf-tower-0.1.0.json
+nf-tower-0.1.0.zip
+```
+
+### `copyPluginLibs`
+
+Copy plugin dependencies JAR files into the subproject `build/target/libs` directory. This is needed only when launching the plugin in development mode.
+
+### `copyPluginZip`
+
+Copy the plugin archive to the root project build directory, i.e. `build/plugins`.
+
+### `uploadPlugin`
+
+Upload the plugin archive and meta file to the corresponding GitHub repository. Options:
+
+`release`
+: The plugin version, e.g. `1.0.1`.
+
+`repo`
+: The GitHub repository name, e.g. `nf-amazon`.
+
+`owner`
+: The GitHub owning organization, e.g. `nextflow-io`.
+
+`skipExisting`
+: Do not upload a file if it already exists, i.e. checksum is the same (default: `true`).
+
+`dryRun`
+: Execute the tasks without uploading file (default: `false`).
+
+`overwrite`
+: Prevent to overwrite a remote file already existing (default: `false`).
+
+`userName`
+: The user name used to authenticate GitHub API requests.
+
+`authToken`
+: The personal token used to authenticate GitHub API requests.
+
+### `upload`
+
+Upload the plugin archive and meta file.
+
+### `publishIndex`
+
+Upload the plugins index to the repository hosted at [nextflow-io/plugins](https://github.com/nextflow-io/plugins), which makes them publicly accessible at [this URL](https://raw.githubusercontent.com/nextflow-io/plugins/main/plugins.json).
+
+## Additional Resources
+
+* [PF4J](https://pf4j.org/)
+* [Understanding Gradle: The Build Lifecycle](https://proandroiddev.com/understanding-gradle-the-build-lifecycle-5118c1da613f)
diff --git a/docs/index.md b/docs/index.md
index 6b76b83ca4..b811154c14 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -1,7 +1,27 @@
 
 # Nextflow's documentation!
 
+[![Nextflow CI](https://github.com/nextflow-io/nextflow/workflows/Nextflow%20CI/badge.svg)](https://github.com/nextflow-io/nextflow/actions/workflows/build.yml?query=branch%3Amaster+event%3Apush)
+[![Nextflow version](https://img.shields.io/github/release/nextflow-io/nextflow.svg?colorB=26af64&style=popout)](https://github.com/nextflow-io/nextflow/releases/latest)
+[![Nextflow Twitter](https://img.shields.io/twitter/url/https/nextflowio.svg?colorB=26af64&&label=%40nextflow&style=popout)](https://twitter.com/nextflowio)
+[![Nextflow Publication](https://img.shields.io/badge/Published-Nature%20Biotechnology-26af64.svg?colorB=26af64&style=popout)](https://www.nature.com/articles/nbt.3820)
+[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?colorB=26af64&style=popout)](http://bioconda.github.io/recipes/nextflow/README.html)
+[![Nextflow license](https://img.shields.io/github/license/nextflow-io/nextflow.svg?colorB=26af64&style=popout)](https://github.com/nextflow-io/nextflow/blob/master/COPYING)
+
+Nextflow is a workflow system for creating scalable, portable, and reproducible workflows.
+
+## Rationale
+
+The rise of big data has made it increasingly necessary to be able to analyze and perform experiments on large datasets in a portable and reproducible manner.
+
+Parallelization and distributed computing are the best ways to tackle this challenge, but the tools commonly available to computational scientists often lack good support for these techniques, or they provide a model that fits poorly with the needs of computational scientists and often require knowledge of complex tools and APIs.
+
+The Nextflow language is inspired by [the Unix philosophy](https://en.wikipedia.org/wiki/Unix_philosophy), in which many simple command line tools can be chained together into increasingly complex tasks. Similarly, a Nextflow script consists of composing many simple processes into increasingly complex pipelines. Each process executes a given tool or scripting language, and by specifying the process inputs and outputs, Nextflow coordinates the execution of tasks for you.
+
+The Nextflow runtime integrates with many popular execution platforms (HPC schedulers, cloud providers) and software tools (Git, Docker, Conda), allowing you to fully describe a computational pipeline with all of its dependencies and run it in nearly any environment -- write once, run anywhere.
+
 ```{toctree}
+:hidden:
 :caption: Introduction
 :maxdepth: 1
 
@@ -10,6 +30,7 @@ basic
 ```
 
 ```{toctree}
+:hidden:
 :caption: Language
 :maxdepth: 1
 
@@ -22,6 +43,7 @@ dsl2
 ```
 
 ```{toctree}
+:hidden:
 :caption: Execution
 :maxdepth: 1
 
@@ -37,6 +59,7 @@ secrets
 ```
 
 ```{toctree}
+:hidden:
 :caption: Software dependencies
 :maxdepth: 1
 
@@ -47,6 +70,7 @@ wave
 ```
 
 ```{toctree}
+:hidden:
 :caption: Compute & storage platforms
 :maxdepth: 1
 
@@ -59,6 +83,7 @@ kubernetes
 ```
 
 ```{toctree}
+:hidden:
 :caption: Additional integrations
 :maxdepth: 1
 
@@ -67,9 +92,11 @@ ignite
 ```
 
 ```{toctree}
+:hidden:
 :caption: Contributing
 :maxdepth: 1
 
 developer/index
 developer/packages
+developer/plugins
 ```
diff --git a/docs/plugins.md b/docs/plugins.md
index 66734f5551..cc9b4bfce0 100644
--- a/docs/plugins.md
+++ b/docs/plugins.md
@@ -36,41 +36,31 @@ Or you can use the `-plugins` command line option:
 nextflow run <pipeline> -plugins nf-hello@0.1.0
 ```
 
-The plugin identifier consists of the plugin name and plugin version separated by a `@`. Multiple plugins can be specified 
-in the configuration with multiple `id` declarations, or on the command line as a comma-separated list. When specifying 
-plugins via the command line, any plugin declarations in the configuration file are ignored.
+The plugin identifier consists of the plugin name and plugin version separated by a `@`. Multiple plugins can be specified in the configuration with multiple `id` declarations, or on the command line as a comma-separated list. When specifying plugins via the command line, any plugin declarations in the configuration file are ignored.
 
-The default plugins are documented in this documentation. For all other plugins, please refer to the plugin's code repository 
-for documentation and support.
+The plugin version is optional. If it is not specified, Nextflow will download the latest plugin version that is compatible with your Nextflow version. In general, it recommended that you not specify the plugin version unless you actually want to stick to that version, such as for [offline usage](#offline-usage).
+
+The core plugins are documented in this documentation. For all other plugins, please refer to the plugin's code repository for documentation and support.
 
 ## Writing plugins
 
-To get started with your own plugin, refer to the [nf-hello](https://github.com/nextflow-io/nf-hello) repository, 
-which provides a minimal plugin implementation with several examples of different extension points, as well as instructions 
-for building, testing, and publishing.
+To get started with your own plugin, refer to the [nf-hello](https://github.com/nextflow-io/nf-hello) repository, which provides a minimal plugin implementation with several examples of different extension points, as well as instructions for building, testing, and publishing.
 
-Nextflow's plugin system exposes a variety of extension points for plugins. The following sections describe how to use 
-these extension points when writing a plugin, as well as how they are used in a pipeline.
+Nextflow's plugin system exposes a variety of extension points for plugins. The following sections describe how to use these extension points when writing a plugin, as well as how they are used in a pipeline.
 
 :::{note}
-If you would like to implement something in a plugin that isn't covered by any of the following sections, feel free to 
-create an issue on GitHub and describe your use case. In general, any class in the Nextflow codebase that implements 
-`ExtensionPoint` can be extended by a plugin, and existing plugins are a great source of examples when writing new plugins.
+If you would like to implement something in a plugin that isn't covered by any of the following sections, feel free to create an issue on GitHub and describe your use case. In general, any class in the Nextflow codebase that implements `ExtensionPoint` can be extended by a plugin, and existing plugins are a great source of examples when writing new plugins.
 :::
 
 :::{note}
-Plugin extension points must be added to `extensions.idx` in the plugin repository to make them discoverable. 
-See the `nf-hello` plugin for an example.
+Plugin extension points must be added to `extensions.idx` in the plugin repository to make them discoverable. See the `nf-hello` plugin for an example.
 :::
 
 ### Commands
 
 Plugins can define custom CLI commands that can be executed with the `nextflow plugin` command.
 
-To implement a plugin-specific command, implement the `PluginExecAware` interface in your plugin entrypoint 
-(the class that extends `BasePlugin`). Alternatively, you can implement the `PluginAbstractExec` trait, which 
-provides an abstract implementation with some boilerplate code. This trait requires you to implement two methods, 
-`getCommands()` and `exec()`:
+To implement a plugin-specific command, implement the `PluginExecAware` interface in your plugin entrypoint (the class that extends `BasePlugin`). Alternatively, you can implement the `PluginAbstractExec` trait, which provides an abstract implementation with some boilerplate code. This trait requires you to implement two methods, `getCommands()` and `exec()`:
 
 ```groovy
 import nextflow.cli.PluginAbstractExec
@@ -106,10 +96,7 @@ See the {ref}`cli-plugin` CLI command for usage information.
 
 ### Configuration
 
-Plugins can access the resolved Nextflow configuration through the session object using `session.config.navigate()`. 
-Several extension points provide the session object for this reason. This method allows you to query any configuration 
-option in a safe manner -- if the option isn't defined, it will return `null`. A common practice is to define any 
-configuration for your plugin in a custom config scope.
+Plugins can access the resolved Nextflow configuration through the session object using `session.config.navigate()`. Several extension points provide the session object for this reason. This method allows you to query any configuration option in a safe manner -- if the option isn't defined, it will return `null`. A common practice is to define any configuration for your plugin in a custom config scope.
 
 Here is an example of querying a config option in a trace observer hook:
 
@@ -169,8 +156,7 @@ process foo {
 ```
 
 :::{tip}
-Refer to the source code of Nextflow's built-in executors to see how to implement the various components of an executor. 
-You might be able to implement most of your executor by simply reusing existing code.
+Refer to the source code of Nextflow's built-in executors to see how to implement the various components of an executor. You might be able to implement most of your executor by simply reusing existing code.
 :::
 
 ### Functions
@@ -180,8 +166,7 @@ You might be able to implement most of your executor by simply reusing existing
 
 Plugins can define custom Groovy functions, which can then be included into Nextflow pipelines.
 
-To implement a custom function, create a class in your plugin that extends the `PluginExtensionPoint` class, and implement 
-your function with the `Function` annotation:
+To implement a custom function, create a class in your plugin that extends the `PluginExtensionPoint` class, and implement your function with the `Function` annotation:
 
 ```groovy
 import nextflow.Session
@@ -222,8 +207,7 @@ include { reverseString as anotherReverseMethod } from 'plugin/my-plugin'
 
 Plugins can define custom channel factories and operators, which can then be included into Nextflow pipelines.
 
-To implement a custom factory or operator, create a class in your plugin that extends the `PluginExtensionPoint` class, 
-and implement your function with the `Factory` or `Operator` annotation:
+To implement a custom factory or operator, create a class in your plugin that extends the `PluginExtensionPoint` class, and implement your function with the `Factory` or `Operator` annotation:
 
 ```groovy
 import groovyx.gpars.dataflow.DataflowReadChannel
@@ -267,13 +251,9 @@ is included under the alias `fromTable`.
 
 ### Trace observers
 
-A *trace observer* in Nextflow is an entity that can listen and react to workflow events, such as when a workflow starts, 
-a task completes, a file is published, etc. Several components in Nextflow, such as the execution report and DAG visualization, 
-are implemented as trace observers.
+A *trace observer* in Nextflow is an entity that can listen and react to workflow events, such as when a workflow starts, a task completes, a file is published, etc. Several components in Nextflow, such as the execution report and DAG visualization, are implemented as trace observers.
 
-Plugins can define custom trace observers that react to workflow events with custom behavior. To implement a trace observer, 
-create a class that implements the `TraceObserver` trait and another class that implements the `TraceObserverFactory` interface. 
-Implement any of the hooks defined in `TraceObserver`, and implement the `create()` method in your observer factory:
+Plugins can define custom trace observers that react to workflow events with custom behavior. To implement a trace observer, create a class that implements the `TraceObserver` trait and another class that implements the `TraceObserverFactory` interface. Implement any of the hooks defined in `TraceObserver`, and implement the `create()` method in your observer factory:
 
 ```groovy
 // MyObserverFactory.groovy
@@ -331,8 +311,7 @@ class MyObserver implements TraceObserver {
 }
 ```
 
-You can then use your trace observer by simply enabling the plugin in your pipeline. In the above example, the observer 
-must also be enabled with a config option:
+You can then use your trace observer by simply enabling the plugin in your pipeline. In the above example, the observer must also be enabled with a config option:
 
 ```groovy
 myplugin.enabled = true
@@ -342,8 +321,7 @@ Refer to the `TraceObserver` [source code](https://github.com/nextflow-io/nextfl
 
 ## Plugin registry
 
-Nextflow resolves plugins through a plugin registry, which stores metadata for each plugin version, including the publishing date, 
-checksum, and download URL for the plugin binary. The default registry is located on GitHub at [nextflow-io/plugins](https://github.com/nextflow-io/plugins/).
+Nextflow resolves plugins through a plugin registry, which stores metadata for each plugin version, including the publishing date, checksum, and download URL for the plugin binary. The default registry is located on GitHub at [nextflow-io/plugins](https://github.com/nextflow-io/plugins/).
 
 To publish a plugin release to the main registry, simply create a pull request with the requested plugin metadata.
 
@@ -354,9 +332,7 @@ To publish a plugin release to the main registry, simply create a pull request w
 :::{versionadded} 23.04.0
 :::
 
-You can also use a different plugin registry with the `NXF_PLUGINS_TEST_REPOSITORY` environment variable. This setting 
-is useful for testing a plugin release before publishing it to the main registry. It can refer to the JSON file for a 
-custom registry or a plugin release.
+You can also use a different plugin registry with the `NXF_PLUGINS_TEST_REPOSITORY` environment variable. This setting is useful for testing a plugin release before publishing it to the main registry. It can refer to the JSON file for a custom registry or a plugin release.
 
 For example:
 
diff --git a/plugins/README.md b/plugins/README.md
deleted file mode 100644
index 153eecab26..0000000000
--- a/plugins/README.md
+++ /dev/null
@@ -1,161 +0,0 @@
-# Nextflow plugins
-
-This directory should contain plugin subprojects for Nextflow. 
-
-The `build.gradle` defines the main actions for each plugin.
-
-## Plugin subproject structure 
- 
-### Plugin structure 
-
-The plugin subproject defines its own `build.gradle` and setup the required dependencies. 
-
-Minimal dependencies shown below: 
-
-``` 
-dependencies {
-    compileOnly project(':nextflow')
-    compileOnly 'org.slf4j:slf4j-api:1.7.10'
-    compileOnly 'org.pf4j:pf4j:3.4.1'
-
-    testImplementation project(':nextflow')
-    testImplementation "org.codehaus.groovy:groovy:3.0.5"
-    testImplementation "org.codehaus.groovy:groovy-nio:3.0.5"
-}
-``` 
-
-Each plugin subproject directory name has to begin with the prefix `nf-` and must include 
-a file named `src/resources/META-INF/MANIFEST.MF` which contains the plugin metadata. 
-The manifest content looks like the following:
-
-```
-Manifest-Version: 1.0
-Plugin-Class: the.plugin.ClassName
-Plugin-Id: the-plugin-id
-Plugin-Provider: Some Provider Name
-Plugin-Version: 0.0.0
-```   
-  
-## Environment variables 
-
-* `NXF_PLUGINS_MODE`: Define the plugin system execution mode, either *prod* for production or *dev* for development
-  (see below for details).  
-* `NXF_PLUGINS_DIR`: the path where the plugins archives are stored/loaded. Default is `$NXF_HOME/plugins` for 
-  production mode and `$PWD/plugins` for dev mode. 
-* `NXF_PLUGINS_DEFAULT`: Whenever use the default plugins when no plugin is specified in the config file.   
-* `NXF_PLUGINS_DEV: Comma separate separated list of development plugins root directories
-
-## Development environment
-
-When running in development the plugin system uses the `DevPluginClasspath` to load plugins classes 
-from each plugin project build path e.g. `$PWD/plugins/nf-amazon/build/classes` and 
-`$PWD/plugins/nf-amazon/build/target/libs` (for deps libraries).    
-
-
-## The plugins repository 
-
-The plugins meta-info are published via a GitHub repository at [https://github.com/nextflow-io/plugins]()
-and accessible through the URL [https://raw.githubusercontent.com/nextflow-io/plugins/main/plugins.json]().
-
-The repository index has the following structure: 
-
-```
-[
-  {
-    "id": "nf-amazon",
-    "releases": [
-      {
-        "version": "0.2.0",
-        "url": "https://github.com/nextflow-io/nf-amazon/releases/download/0.2.0/nf-amazon-0.2.0.zip",
-        "date": "2020-10-12T10:05:44.28+02:00",
-        "sha512sum": "9e9e33695c1a7c051271..."
-      }
-    ]
-  },
-  :
-]
-```     
-
-
-## Plugins 
-
-A plugin is a ZIP file holding either the plugin classes and the required dependencies JAR file.  
-
-Nextflow core plugins are stored in the corresponding GitHub project release page. However, this is not a
-strict requirement, it has been chosen to simplify the build deployment process and provide a more consistent 
-download experience keeping all of them with the GitHub [nextflow-io](https://github.com/nextflow-io) organization.   
-
-### The installation process 
-
-Plugins need to be declared in the `nextflow.config` file using the plugins scope, eg. 
-
-```
-plugins {
-    id 'nf-amazon@0.2.0'
-}
-```     
-
-If the plugins is not locally available Nextflow check in the repository index for the download URL, 
-download the ZIP in a temporary file, unzip and store the final plugin in the directory specified by the 
-variable `NXF_PLUGINS_DIR` (default: `$NXF_HOME/plugins`). 
-
-Finally, since each Nextflow run can have a different set of plugins (and version) requirement, each Nextflow 
-instance keep local plugins directory root in directory `$PWD/.nextflow/plr/<unique id>` symlinking the exact list 
-of plugins directory required for the current Nextflow instance.
-
-If no plugins are specified in the nextflow.config file, Nextflow default plugins are automatically added. 
-The default plugins list is defined in the Nextflow resources file included in the distribution runtime 
-`./modules/nextflow/src/main/resources/META-INF/plugins-info.txt`. 
-
-To disable the use of default plugins set the following variable `NXF_PLUGINS_DEFAULT=false`.
-
-## Gradle Tasks 
-
-### makeZip
-    
-Creates the plugin the zip file and the json meta file in the
-subproject `build/libs` directory.
-
-```
-» ls -l1 $PWD/plugins/nf-tower/build/libs/
-nf-tower-0.1.0.jar
-nf-tower-0.1.0.json
-nf-tower-0.1.0.zip
-```               
-
-### copyPluginLibs
-
-Copies plugin dependencies jar files in the plugin build directory ie. `$PWD/plugins/nf-amazon/build/target/libs`. 
-This is only needed when launching the plugin in *development* mode. 
-
-### copyPluginZip
-
-Copies the plugin zip file to the root project build dir ie. `$PWD/build/plugins/`.
-
-### uploadPlugin
-
-Uploads the plugin ZIP and meta (JSON) files to the corresponding GitHub repository. Options: 
-
-* `release`: the plugin version e.g. `1.0.1`
-* `repo`: the GitHub repository name e.g. `nf-amazon`
-* `owner`: the GitHub owning organization e.g. `nextflow-io`
-* `skipExisting`: do not upload a file already existing (only if the checksum is the same, default: `true`). 
-* `dryRun`: execute the tasks without uploading file (default: `false`).
-* `overwrite`: prevent to overwrite a remote file already existing (default: `false`).
-* `userName`: the user name for authenticate GitHub API requests
-* `authToken`: the personal token to authenticate GitHub API requests  
-
-### upload
-
-Uploads the plugin both zip and meat files. 
-
-### publishIndex
-
-Upload the plugins index to the repository hosted at [https://github.com/nextflow-io/plugins](https://github.com/nextflow-io/plugins), which makes 
-them accessible through the URL [https://raw.githubusercontent.com/nextflow-io/plugins/main/plugins.json](https://raw.githubusercontent.com/nextflow-io/plugins/main/plugins.json). 
-
-
-## Links 
-
-* https://pf4j.org/
-* https://proandroiddev.com/understanding-gradle-the-build-lifecycle-5118c1da613f
diff --git a/plugins/nf-azure/README.md b/plugins/nf-azure/README.md
index b3ec360580..512e33b1d6 100644
--- a/plugins/nf-azure/README.md
+++ b/plugins/nf-azure/README.md
@@ -1,20 +1,20 @@
-# Azure plugin for Nextflow 
+# Azure plugin for Nextflow
 
-This plugin implements the support for Azure Blob storage as fie system 
-provider (via JSR203 interface) and Azure Batch executor  for Nextflow 
+This plugin implements the support for Azure Blob storage as file system
+provider (via JSR203 interface) and Azure Batch executor for Nextflow.
 
-## Compile & configuration 
+## Development
 
-Compile nextflow as usual 
+Build Nextflow as usual:
 
-```
+```bash
 make compile
-``` 
+```
 
-Create the `nextflow.config` file with the following content 
+Use the following Nextflow configuration:
 
-```
-plugins { 
+```groovy
+plugins {
   id 'nf-azure'
 }
 
@@ -25,8 +25,8 @@ azure {
   }
 
   batch {
-    endpoint = 'https://<YOUR BATCH ACCOUNT NAME>.westeurope.batch.azure.com' 
-    accountName = '<YOUR BATCH ACCOUNT NAME>' 
+    endpoint = 'https://<YOUR BATCH ACCOUNT NAME>.westeurope.batch.azure.com'
+    accountName = '<YOUR BATCH ACCOUNT NAME>'
     accountKey = '<YOUR BATCH ACCOUNT KEY>'
   }
 }
@@ -35,37 +35,36 @@ process.executor = 'azurebatch'
 workDir = 'az://<YOUR DATA CONTAINER>/work'
 ```
 
-Then run the a pipeline as shown below
+Then test the local build as usual:
 
+```bash
+./launch.sh run -c nextflow.config rnaseq-nf
 ```
-./launch.sh run rnaseq-nf 
-```
-
 
-## Todo 
+## Todo
 
-* Currently, the Blob storage service uses NettyHttpClient and Batch service 
-uses OkHttp client, duplicating the number of required libraries. In principle 
-the Blob service can use OkHttp, adding the following deps, however using that
-Nextflow hangs during the shutdown, apparently because the connection pool used 
-by the blob service is not closed timely. 
+* Currently, the Blob storage service uses NettyHttpClient and Batch service
+  uses OkHttp client, duplicating the number of required libraries. In principle
+  the Blob service can use OkHttp, adding the following deps, however using that
+  Nextflow hangs during the shutdown, apparently because the connection pool used
+  by the blob service is not closed timely.
 
-        compile('com.azure:azure-storage-blob:12.9.0') {
-            exclude group: 'org.slf4j', module: 'slf4j-api'
-            exclude group: 'com.azure', module: 'azure-core-http-netty'
-        }
-        compile('com.azure:azure-core-http-okhttp:1.3.3') {
-            exclude group: 'org.slf4j', module: 'slf4j-api'
-        }
+  ```groovy
+  compile('com.azure:azure-storage-blob:12.9.0') {
+      exclude group: 'org.slf4j', module: 'slf4j-api'
+      exclude group: 'com.azure', module: 'azure-core-http-netty'
+  }
+  compile('com.azure:azure-core-http-okhttp:1.3.3') {
+      exclude group: 'org.slf4j', module: 'slf4j-api'
+  }
+  ```
 
-* Remove invalid directory from .command.run PATH for project having `bin/` folder  
+* Remove invalid directory from .command.run PATH for project having `bin/` folder
 * Add the configuration for the region
-* Make the backend endpoint optional 
+* Make the backend endpoint optional
 
+### Additional Resources
 
-
-### Links
 * https://github.com/Azure/azure-sdk-for-java/wiki
 * https://github.com/Azure/azure-sdk-for-java/tree/master/sdk/storage/azure-storage-blob-nio
 * https://github.com/Azure/azure-sdk-for-java/blob/master/sdk/storage/azure-storage-blob-nio/src/samples/java/com/azure/storage/blob/nio/ReadmeSamples.java
-
diff --git a/tests/README.md b/tests/README.md
index a2aedc2349..2f8c2a56fa 100644
--- a/tests/README.md
+++ b/tests/README.md
@@ -2,4 +2,4 @@
 
 This repository contains a collection of scripts used to validate Nextflow builds 
 
-[![Build Status](https://travis-ci.org/nextflow-io/tests.svg?branch=master)](https://travis-ci.org/nextflow-io/tests)
+![Nextflow CI](https://github.com/nextflow-io/nextflow/workflows/Nextflow%20CI/badge.svg)

From 21190a3c4d8e2783b4ca34a40666dc13f11028b2 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Thu, 5 Oct 2023 13:22:57 -0500
Subject: [PATCH 194/350] Add docs page on caching and resuming (#4371)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 docs/cache-and-resume.md | 198 +++++++++++++++++++++++++++++++++++++++
 docs/cli.md              |   4 +
 docs/getstarted.md       |   2 +
 docs/index.md            |   1 +
 docs/operator.md         |   2 +-
 docs/process.md          |  17 ++--
 docs/script.md           |   2 +-
 docs/sharing.md          |   2 +
 8 files changed, 217 insertions(+), 11 deletions(-)
 create mode 100644 docs/cache-and-resume.md

diff --git a/docs/cache-and-resume.md b/docs/cache-and-resume.md
new file mode 100644
index 0000000000..0fc5ddf4a0
--- /dev/null
+++ b/docs/cache-and-resume.md
@@ -0,0 +1,198 @@
+(cache-resume-page)=
+
+# Caching and resuming
+
+One of the core features of Nextflow is the ability to cache task executions and re-use them in subsequent runs to minimize duplicate work. Resumability is useful both for recovering from errors and for iteratively developing a pipeline. It is similar to [checkpointing](https://en.wikipedia.org/wiki/Application_checkpointing), a common practice used by HPC applications.
+
+You can enable resumability in Nextflow with the `-resume` flag when launching a pipeline with `nextflow run`. In most cases, that is all you need to do and resumability will "just work". This page describes Nextflow's caching behavior in more detail in order to help advanced users understand how the cache works and troubleshoot it when it doesn't work.
+
+## Task cache
+
+All task executions are automatically saved to the task cache, regardless of the `-resume` option (so that you always have the option to resume later). The task cache is a key-value store, where each key-value pair corresponds to a previously-executed task.
+
+The task cache is used in conjunction with the [work directory](#work-directory) to recover cached tasks in a resumed run. It is also used by the {ref}`cli-log` sub-command to query task metadata.
+
+### Task hash
+
+The task hash is computed from the following metadata:
+
+- Session ID (see `workflow.sessionId` in {ref}`metadata-workflow`)
+- Task name (see `name` in {ref}`trace-report`)
+- Task container image (if applicable)
+- Task {ref}`environment modules <process-module>` (if applicable)
+- Task {ref}`Conda environment <process-conda>` (if applicable)
+- Task {ref}`Spack environment <process-spack>` and {ref}`CPU architecture <process-arch>` (if applicable)
+- Task {ref}`process-ext` directive (if applicable)
+- Task {ref}`inputs <process-input>`
+- Task {ref}`script <process-script>`
+- Any global variables referenced in the task script
+- Any {ref}`bundled scripts <bundling-executables>` used in the task script
+- Whether the task is a {ref}`stub run <process-stub>`
+- Task attempt
+
+:::{versionchanged} 23.09.2-edge
+The {ref}`process-ext` directive was added to the task hash.
+:::
+
+Nextflow computes this hash for every task when it is created but before it is executed. If resumability is enabled and there is an entry in the task cache with the same hash, Nextflow tries to recover the previous task execution. A cache hit does not guarantee that the task will be resumed, because it must also recover the task outputs from the [work directory](#work-directory).
+
+Note that files are hashed differently depending on the caching mode. See the {ref}`process-cache` directive for more details.
+
+### Task entry
+
+The task entry is a serialized blob of the task metadata required to resume a task, including the fields used by the {ref}`trace-report` and the task input variables.
+
+### Cache stores
+
+The default cache store uses the `.nextflow/cache` directory, relative to the launch directory (i.e. `workflow.launchDir`), to store the task cache, with a separate subdirectory for each session ID backed by [LevelDB](https://github.com/dain/leveldb).
+
+Due to the limitations of LevelDB, the database for a given session ID can only be accessed by one reader/writer at a time. This means, for example, that you cannot use `nextflow log` to query the task metadata for a pipeline run while it is still running.
+
+:::{versionadded} 23.07.0-edge
+:::
+
+The cloud cache is an alternative cache store that uses cloud storage instead of the local cache directory. You can use it by setting the `NXF_CLOUDCACHE_PATH` environment variable to the desired cache path (e.g. `s3://my-bucket/cache`) and providing the necessary credentials.
+
+The cloud cache is particularly useful when launching Nextflow from within the cloud, where the default cache would be lost once the pipeline completes and the VM instance is terminated. Furthermore, because it is backed by cloud storage, it can support multiple readers and writers.
+
+## Work directory
+
+While the [task cache](#task-cache) stores the task metadata for subsequent runs, the work directory stores various files used during a pipeline run.
+
+Each task uses a unique directory based on its hash. When a task is created, Nextflow stages the task input files, script, and other helper files into the task directory. The task writes any output files to this directory during its execution, and Nextflow uses these output files for downstream tasks and/or publishing.
+
+When a previous task is retrieved from the task cache on a resumed run, Nextflow then checks the corresponding task directory in the work directory. If all the required outputs are present and the exit code is valid, then the task is successfully cached; otherwise, the task is re-executed.
+
+For this reason, it is important to preserve both the task cache (`.nextflow/cache`) and work directories in order to resume runs successfully. You can use the {ref}`cli-clean` command to delete specific runs from the cache.
+
+## Troubleshooting
+
+Cache failures happen when either (1) a task that was supposed to be cached was re-executed, or (2) a task that was supposed to be re-executed was cached.
+
+When this happens, consider the following questions:
+
+- Is resume enabled via `-resume`?
+- Is the {ref}`process-cache` directive set to a non-default value?
+- Is the task still present in the task cache and work directory?
+- Were any of the task inputs changed?
+
+Changing any of the inputs included in the [task hash](#task-hash) will invalidate the cache, for example:
+
+- Resuming from a different session ID
+- Changing the process name
+- Changing the task container image or Conda environment
+- Changing the task script
+- Changing an input file or bundled script used by the task
+
+While the following examples would not invalidate the cache:
+
+- Changing the value of a directive (other than {ref}`process-ext`), even if that directive is used in the task script
+
+In many cases, cache failures happen because of a change to the pipeline script or configuration, or because the pipeline itself has some non-deterministic behavior.
+
+Here are some common reasons for cache failures:
+
+### Modified input files
+
+Make sure that your input files have not been changed. Keep in mind that the default caching mode uses the complete file path, the last modified timestamp, and the file size. If any of these attributes change, the task will be re-executed, even if the file content is unchanged.
+
+### Process that modifies its inputs
+
+If a process modifies its own input files, it cannot be resumed for the reasons described in the previous point. As a result, processes that modify their own input files are considered an anti-pattern and should be avoided.
+
+### Inconsistent file attributes
+
+Some shared file systems, such as NFS, may report inconsistent file timestamps, which can invalidate the cache. If you encounter this problem, you can avoid it by using the `'lenient'` {ref}`caching mode <process-cache>`, which ignores the last modified timestamp and uses only the file path and size.
+
+(cache-global-var-race-condition)=
+
+### Race condition on a global variable
+
+While Nextflow tries to make it easy to write safe concurrent code, it is still possible to create race conditions, which can in turn impact the caching behavior of your pipeline.
+
+Consider the following example:
+
+```groovy
+Channel.of(1,2,3) | map { it -> X=it; X+=2 } | view { "ch1 = $it" }
+Channel.of(1,2,3) | map { it -> X=it; X*=2 } | view { "ch2 = $it" }
+```
+
+The problem here is that `X` is declared in each `map` closure without the `def` keyword (or other type qualifier). Using the `def` keyword makes the variable local to the enclosing scope; omitting the `def` keyword makes the variable global to the entire script.
+
+Because `X` is global, and operators are executed concurrently, there is a *race condition* on `X`, which means that the emitted values will vary depending on the particular order of the concurrent operations. If the values were passed as inputs into a process, the process would execute different tasks on each run due to the race condition.
+
+The solution is to not use a global variable where a local variable is enough (or in this simple example, avoid the variable altogether):
+
+```groovy
+// local variable
+Channel.of(1,2,3) | map { it -> def X=it; X+=2 } | view { "ch1 = $it" }
+
+// no variable
+Channel.of(1,2,3) | map { it -> it * 2 } | view { "ch2 = $it" }
+```
+
+(cache-nondeterministic-inputs)=
+
+### Non-deterministic process inputs
+
+Sometimes a process needs to merge inputs from different sources. Consider the following example:
+
+```groovy
+workflow {
+    ch_foo = Channel.of( ['1', '1.foo'], ['2', '2.foo'] )
+    ch_bar = Channel.of( ['2', '2.bar'], ['1', '1.bar'] )
+    gather(ch_foo, ch_bar)
+}
+
+process gather {
+    input:
+    tuple val(id), file(foo)
+    tuple val(id), file(bar)
+    """
+    merge_command $foo $bar
+    """
+}
+```
+
+It is tempting to assume that the process inputs will be matched by `id` like the {ref}`operator-join` operator. But in reality, they are simply merged like the {ref}`operator-merge` operator. As a result, not only will the process inputs be incorrect, they will also be non-deterministic, thus invalidating the cache.
+
+The solution is to explicitly join the two channels before the process invocation:
+
+```groovy
+workflow {
+    ch_foo = Channel.of( ['1', '1.foo'], ['2', '2.foo'] )
+    ch_bar = Channel.of( ['2', '2.bar'], ['1', '1.bar'] )
+    gather(ch_foo.join(ch_bar))
+}
+
+process gather {
+    input:
+    tuple val(id), file(foo), file(bar)
+    """
+    merge_command $foo $bar
+    """
+}
+```
+
+## Tips
+
+### Resuming from a specific run
+
+Nextflow resumes from the previous run by default. If you want to resume from an earlier run, simply specify the session ID for that run with the `-resume` option:
+
+```bash
+nextflow run rnaseq-nf -resume 4dc656d2-c410-44c8-bc32-7dd0ea87bebf
+```
+
+You can use the {ref}`cli-log` command to view all previous runs as well as the task executions for each run.
+
+### Comparing the hashes of two runs
+
+One way to debug a resumed run is to compare the task hashes of each run using the `-dump-hashes` option.
+
+1. Perform an initial run: `nextflow -log run_initial.log run <pipeline> -dump-hashes`
+2. Perform a resumed run: `nextflow -log run_resumed.log run <pipeline> -dump-hashes -resume`
+3. Extract the task hash lines from each log (search for `cache hash:`)
+4. Compare the runs with a diff viewer
+
+While some manual effort is required, the final diff can often reveal the exact change that caused a task to be re-executed.
diff --git a/docs/cli.md b/docs/cli.md
index 3fe270f7e1..310c97b35d 100644
--- a/docs/cli.md
+++ b/docs/cli.md
@@ -230,6 +230,8 @@ The `-v` option prints out information about Nextflow, such as the version and b
 
 ## Commands
 
+(cli-clean)=
+
 ### clean
 
 Clean up *cache* and *work* directories.
@@ -887,6 +889,8 @@ nextflow-io/hello
 nextflow-hub/fastqc
 ```
 
+(cli-log)=
+
 ### log
 
 Print the execution history and log information.
diff --git a/docs/getstarted.md b/docs/getstarted.md
index 40651b5edb..72aaac0c05 100644
--- a/docs/getstarted.md
+++ b/docs/getstarted.md
@@ -204,6 +204,8 @@ You will see that the execution of the process `splitLetters` is actually skippe
 The pipeline results are cached by default in the directory `$PWD/work`. Depending on your script, this folder can take up a lot of disk space. It's a good idea to clean this folder periodically, as long as you know you won't need to resume any pipeline runs.
 :::
 
+For more information, see the {ref}`cache-resume-page` page.
+
 (getstarted-params)=
 
 ### Pipeline parameters
diff --git a/docs/index.md b/docs/index.md
index b811154c14..40552e7c44 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -49,6 +49,7 @@ dsl2
 
 cli
 executor
+cache-and-resume
 tracing
 metrics
 sharing
diff --git a/docs/operator.md b/docs/operator.md
index a67ebc2047..5d92cdf130 100644
--- a/docs/operator.md
+++ b/docs/operator.md
@@ -1104,7 +1104,7 @@ odds
 ```
 
 :::{danger}
-In general, the use of the `merge` operator is discouraged. Processes and channel operators are not guaranteed to emit items in the order that they were received, due to their parallel and asynchronous nature. Therefore, if you try to merge output channels from different processes, the resulting channel may be different on each run, which will cause resumed runs to not work properly.
+In general, the use of the `merge` operator is discouraged. Processes and channel operators are not guaranteed to emit items in the order that they were received, as they are executed concurrently. Therefore, if you try to merge output channels from different processes, the resulting channel may be different on each run, which will cause resumed runs to {ref}`not work properly <cache-nondeterministic-inputs>`.
 
 You should always use a matching key (e.g. sample ID) to merge multiple channels, so that they are combined in a deterministic way. For this purpose, you can use the [join](#join) operator.
 :::
diff --git a/docs/process.md b/docs/process.md
index d541a94f2a..903b96aabe 100644
--- a/docs/process.md
+++ b/docs/process.md
@@ -824,7 +824,7 @@ The above example executes the `bar` process three times because `x` is a value
 ```
 
 :::{note}
-In general, multiple input channels should be used to process *combinations* of different inputs, using the `each` qualifier or value channels. Having multiple queue channels as inputs is equivalent to using the `merge` operator, which is not recommended as it may lead to inputs being combined in a non-deterministic way.
+In general, multiple input channels should be used to process *combinations* of different inputs, using the `each` qualifier or value channels. Having multiple queue channels as inputs is equivalent to using the {ref}`operator-merge` operator, which is not recommended as it may lead to {ref}`non-deterministic process inputs <cache-nondeterministic-inputs>`.
 :::
 
 See also: {ref}`channel-types`.
@@ -1332,11 +1332,9 @@ When combined with the {ref}`container directive <process-container>`, the `befo
 
 ### cache
 
-The `cache` directive allows you to store the process results to a local cache. When the cache is enabled *and* the pipeline is launched with the {ref}`resume <getstarted-resume>` option, any following attempt to execute the process, along with the same inputs, will cause the process execution to be skipped, producing the stored data as the actual results.
+The `cache` directive allows you to store the process results to a local cache. When the cache is enabled *and* the pipeline is launched with the {ref}`resume <getstarted-resume>` option, any task executions that are already cached will be re-used. See the {ref}`cache-resume-page` page for more information about how the cache works.
 
-The caching feature generates a unique key by indexing the process script and inputs. This key is used to identify univocally the outputs produced by the process execution.
-
-The cache is enabled by default, you can disable it for a specific process by setting the `cache` directive to `false`. For example:
+The cache is enabled by default, but you can disable it for a specific process by setting the `cache` directive to `false`. For example:
 
 ```groovy
 process noCacheThis {
@@ -1347,19 +1345,20 @@ process noCacheThis {
 }
 ```
 
-The following values are available:
+The following options are available:
 
 `false`
 : Disable caching.
 
 `true` (default)
-: Enable caching. Cache keys are created indexing input files meta-data information (name, size and last update timestamp attributes).
+: Enable caching. Input file metadata (name, size, last updated timestamp) are included in the cache keys.
 
 `'deep'`
-: Enable caching. Cache keys are created indexing input files content.
+: Enable caching. Input file content is included in the cache keys.
 
 `'lenient'`
-: Enable caching. Cache keys are created indexing input files path and size attributes (this policy provides a workaround for incorrect caching invalidation observed on shared file systems due to inconsistent files timestamps).
+: Enable caching. Minimal input file metadata (name and size only) are included in the cache keys.
+: This strategy provides a workaround for incorrect caching invalidation observed on shared file systems due to inconsistent file timestamps.
 
 (process-clusteroptions)=
 
diff --git a/docs/script.md b/docs/script.md
index fc1bc761ef..f2ba710a3c 100644
--- a/docs/script.md
+++ b/docs/script.md
@@ -414,7 +414,7 @@ myMap.keySet().each {
 ```
 
 :::{warning}
-Local variables should be declared using a qualifier such as `def` or a type name, otherwise they will be interpreted as global variables, which could lead to a race condition.
+Local variables should be declared using a qualifier such as `def` or a type name, otherwise they will be interpreted as global variables, which could lead to a {ref}`race condition <cache-global-var-race-condition>`.
 :::
 
 Learn more about closures in the [Groovy documentation](http://groovy-lang.org/closures.html)
diff --git a/docs/sharing.md b/docs/sharing.md
index a3f8a5b864..39dde8715f 100644
--- a/docs/sharing.md
+++ b/docs/sharing.md
@@ -461,6 +461,8 @@ This mix of technologies makes it possible to write self-contained and truly rep
 
 [^id2]: BitBucket provides two types of version control system: Git and Mercurial. Nextflow supports only Git repositories.
 
+(bundling-executables)=
+
 ### Bundling executables in the workflow
 
 In most cases, software dependencies should be provided by the execution environment ([container](./container.md), [conda](./conda.md)/[spack](./spack.md) environment, or host-native [modules](./process.md#module)). 

From 4a39542bc6c04acfcbf5155c56608651bf6c2b6a Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Thu, 5 Oct 2023 22:02:58 +0200
Subject: [PATCH 195/350] Never say (nearly) Oops again (#4356)

Signed-off-by: Phil Ewels <phil.ewels@seqera.io>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Ben Sherman <bentshermann@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/metadata.md                                              | 4 ++--
 modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy | 2 +-
 .../src/main/groovy/nextflow/k8s/K8sTaskHandler.groovy        | 2 +-
 .../src/main/groovy/nextflow/processor/StateObj.groovy        | 4 ++--
 .../main/groovy/nextflow/processor/TaskPollingMonitor.groovy  | 4 ++--
 .../src/main/groovy/nextflow/processor/TaskProcessor.groovy   | 2 +-
 .../src/main/groovy/nextflow/util/ClusterConfig.groovy        | 2 +-
 .../src/main/groovy/nextflow/util/LoggerHelper.groovy         | 2 +-
 8 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/docs/metadata.md b/docs/metadata.md
index 7d35375185..529060bb98 100644
--- a/docs/metadata.md
+++ b/docs/metadata.md
@@ -164,7 +164,7 @@ The `onError` event handler is invoked by Nextflow when a runtime or process err
 
 ```groovy
 workflow.onError {
-    println "Oops... Pipeline execution stopped with the following message: ${workflow.errorMessage}"
+    println "Error: Pipeline execution stopped with the following message: ${workflow.errorMessage}"
 }
 ```
 
@@ -186,7 +186,7 @@ workflow.onComplete = {
 }
 
 workflow.onError = {
-    println "Oops .. something when wrong"
+    println "Error: something when wrong"
 }
 ```
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy
index f3f7087cfc..a2deedbb07 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy
@@ -180,7 +180,7 @@ class Launcher {
             colsString.toShort()
         }
         catch( Exception e ) {
-            log.debug "Oops.. not a valid \$COLUMNS value: $colsString"
+            log.debug "Unexpected terminal \$COLUMNS value: $colsString"
             return 0
         }
     }
diff --git a/modules/nextflow/src/main/groovy/nextflow/k8s/K8sTaskHandler.groovy b/modules/nextflow/src/main/groovy/nextflow/k8s/K8sTaskHandler.groovy
index cdbf63411f..8f8b680fc0 100644
--- a/modules/nextflow/src/main/groovy/nextflow/k8s/K8sTaskHandler.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/k8s/K8sTaskHandler.groovy
@@ -473,7 +473,7 @@ class K8sTaskHandler extends TaskHandler implements FusionAwareTask {
                 client.podDelete(podName)
         }
         else {
-            log.debug "[K8s] Oops.. invalid delete action"
+            log.debug "[K8s] Invalid delete action"
         }
     }
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/StateObj.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/StateObj.groovy
index 51aef88b03..069055065b 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/StateObj.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/StateObj.groovy
@@ -48,7 +48,7 @@ class StateObj implements Serializable, Cloneable {
      */
     void incSubmitted() {
         if( poisoned )
-            log.debug "Oops.. Cannot process more messages after Poison-Pill was received"
+            log.debug "Cannot process more messages after Poison-Pill was received"
         else
             submitted++
     }
@@ -58,7 +58,7 @@ class StateObj implements Serializable, Cloneable {
      */
     void incCompleted() {
         if( completed >= submitted ) {
-            log.debug "Oops.. Processed messages ($submitted) should not overcome received messages ($submitted) count"
+            log.debug "Processed messages ($submitted) should not overcome received messages ($submitted) count"
         }
         completed++
     }
diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskPollingMonitor.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskPollingMonitor.groovy
index 6b5d281ba8..86e6792627 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskPollingMonitor.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskPollingMonitor.groovy
@@ -452,7 +452,7 @@ class TaskPollingMonitor implements TaskMonitor {
             log.debug msg.join('\n')
         }
         catch (Throwable e) {
-            log.debug "Oops.. expected exception", e
+            log.debug "Unexpected exception dumping run queue", e
         }
     }
 
@@ -473,7 +473,7 @@ class TaskPollingMonitor implements TaskMonitor {
             log.debug msg.join('\n')
         }
         catch (Throwable e) {
-            log.debug "Oops.. unexpected exception", e
+            log.debug "Unexpected exception dumping submit queue", e
         }
     }
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
index 8e71969661..fbef4b2950 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
@@ -2165,7 +2165,7 @@ class TaskProcessor {
             return CacheHelper.hasher(keys, mode).hash()
         }
         catch (Throwable e) {
-            final msg = "Oops.. something went wrong while creating task '$name' unique id -- Offending keys: ${ keys.collect {"\n - type=${it.getClass().getName()} value=$it"} }"
+            final msg = "Something went wrong while creating task '$name' unique id -- Offending keys: ${ keys.collect {"\n - type=${it.getClass().getName()} value=$it"} }"
             throw new UnexpectedException(msg,e)
         }
     }
diff --git a/modules/nextflow/src/main/groovy/nextflow/util/ClusterConfig.groovy b/modules/nextflow/src/main/groovy/nextflow/util/ClusterConfig.groovy
index 12d9d79189..1611d4af1b 100644
--- a/modules/nextflow/src/main/groovy/nextflow/util/ClusterConfig.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/util/ClusterConfig.groovy
@@ -170,7 +170,7 @@ class ClusterConfig  {
             return getClusterJoin().tokenize(':')[1]
         }
         catch (Throwable e) {
-            log.debug "Oops.. Cannot fetch cloud driver name", e
+            log.debug "Cannot fetch cloud driver name", e
             return null
         }
     }
diff --git a/modules/nextflow/src/main/groovy/nextflow/util/LoggerHelper.groovy b/modules/nextflow/src/main/groovy/nextflow/util/LoggerHelper.groovy
index 33e28bc473..01f4e1af51 100644
--- a/modules/nextflow/src/main/groovy/nextflow/util/LoggerHelper.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/util/LoggerHelper.groovy
@@ -592,7 +592,7 @@ class LoggerHelper {
             return ExceptionUtils.getStackTrace(e).split('\n')
         }
         catch( Throwable t ) {
-            log.warn "Oops.. something went wrong while formatting the error stack trace | ${t.message ?: t}", e
+            log.warn "Something went wrong while formatting the error stack trace | ${t.message ?: t}", e
             return Collections.emptyList() as String[]
         }
     }

From e044b7a51ec95919ceed21c30398c03fbfd9ff06 Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Thu, 5 Oct 2023 13:12:42 -0700
Subject: [PATCH 196/350] Add codespell: config, workflow and have typos fixed
 (#4324)

Signed-off-by: Yaroslav Halchenko <debian@onerussian.com>
---
 .codespellrc                                  |  6 +++++
 .github/workflows/codespell.yml               | 22 +++++++++++++++++++
 changelog.txt                                 |  6 ++---
 docs/conf.py                                  |  2 +-
 docs/sharing.md                               |  2 +-
 .../groovy/nextflow/ast/ASTHelpers.groovy     |  2 +-
 .../nextflow/ast/NextflowDSLImpl.groovy       |  2 +-
 .../main/groovy/nextflow/cli/CmdDrop.groovy   |  2 +-
 .../nextflow/config/ConfigBuilder.groovy      |  2 +-
 .../nextflow/processor/TaskProcessor.groovy   |  2 +-
 .../groovy/nextflow/processor/TaskRun.groovy  |  4 ++--
 .../groovy/nextflow/script/IterableDef.groovy |  2 +-
 .../groovy/nextflow/script/WorkflowDef.groovy |  2 +-
 .../nextflow/script/WorkflowNotifier.groovy   |  2 +-
 .../groovy/nextflow/trace/TraceRecord.groovy  |  2 +-
 .../groovy/nextflow/util/ConfigHelper.groovy  |  2 +-
 .../nextflow/trace/assets/d3-timeline.js      |  2 +-
 .../groovy/nextflow/cli/CmdSecretTest.groovy  |  2 +-
 .../testFixtures/groovy/test/BaseSpec.groovy  |  2 +-
 .../src/main/nextflow/file/FileHelper.groovy  |  2 +-
 .../main/nextflow/file/TagAwareFile.groovy    |  2 +-
 .../cloud/aws/nio/S3FileSystemProvider.java   |  4 ++--
 .../nextflow/cloud/aws/nio/S3Iterator.java    |  2 +-
 tests/Dockerfile                              |  2 +-
 tests/bin/AMPA.pl                             |  2 +-
 25 files changed, 55 insertions(+), 27 deletions(-)
 create mode 100644 .codespellrc
 create mode 100644 .github/workflows/codespell.yml

diff --git a/.codespellrc b/.codespellrc
new file mode 100644
index 0000000000..61cfca6bd6
--- /dev/null
+++ b/.codespellrc
@@ -0,0 +1,6 @@
+[codespell]
+skip = .git,*.pdf,*.svg,timeline-expected.html,*.fq,*.min.js,ScriptDslTest.groovy
+# some cases where we need to catch using regex
+ignore-regex = \bhel\*|fo\\
+# some variables, names, etc to ignore
+ignore-words-list = splitted,ois,tre,marge,smoot,afile,bams,bais
diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml
new file mode 100644
index 0000000000..7373affc38
--- /dev/null
+++ b/.github/workflows/codespell.yml
@@ -0,0 +1,22 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2
diff --git a/changelog.txt b/changelog.txt
index 2a5b9e3868..bd06cac862 100644
--- a/changelog.txt
+++ b/changelog.txt
@@ -1346,7 +1346,7 @@ NEXTFLOW CHANGE-LOG
 - Fix az path handling curly brackets globs #1969 [c78a1bbf]
 - Fix Missing git credentials when checking last commit id [f101308e]
 - Fix plugins version check against local installation [535c2bb5]
-- Fix local dependant formatting #1962 [2a5cbac1]
+- Fix local dependent formatting #1962 [2a5cbac1]
 - Fix Encode path parameter at GitLab getContentUrl [6f80f651]
 - Fix Only use sudo rm with docker #1956 [f9490423]
 - Prevent AZ NPE when missing vmtype + better logging #1992 [711362ca]
@@ -1414,7 +1414,7 @@ NEXTFLOW CHANGE-LOG
 - Add support for basic auth for http/s file provider [6027fcba]
 - Add User-Agent info to httpfs requests [222637de]
 - Update CPU and RAM for containers (#1833) [ccf5c8ba]
-- Move test containes to quay.io [7db053eb] [773be707] [c10a7f53]
+- Move test contains to quay.io [7db053eb] [773be707] [c10a7f53]
 
 20.12.0-edge - 12 Dec 2020 
 - Add support for charliecloud container engine #1809
@@ -1788,7 +1788,7 @@ NEXTFLOW CHANGE-LOG
 - Add Pbs Pro execution documentation [1d39ab31]
 - Add code of conduct document
 - Fix missing LFS executor register invocation #1234 [b1b7ab1]
-- Fix "invalid pod status" when running scrips with the kubernetes executor #1242 [11caac68]
+- Fix "invalid pod status" when running scripts with the kubernetes executor #1242 [11caac68]
 - Revert Fix Environment activation fails with recent versions of Conda #1195 [98c0d1f8]
 - (includes changes from `19.07.0-edge`, `19.05.0-edge` and `19.05.0-edge`)
 
diff --git a/docs/conf.py b/docs/conf.py
index 6cf81c8dcc..3efe91c293 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -299,7 +299,7 @@
 # The format is a list of tuples containing the path and title.
 #epub_pre_files = []
 
-# HTML files shat should be inserted after the pages created by sphinx.
+# HTML files that should be inserted after the pages created by sphinx.
 # The format is a list of tuples containing the path and title.
 #epub_post_files = []
 
diff --git a/docs/sharing.md b/docs/sharing.md
index 39dde8715f..9cdcd90039 100644
--- a/docs/sharing.md
+++ b/docs/sharing.md
@@ -110,7 +110,7 @@ The `pull` command allows you to download a project from a GitHub repository or
 nextflow pull nextflow-io/examples
 ```
 
-Altenatively, you can use the repository URL as the name of the project to pull:
+Alternatively, you can use the repository URL as the name of the project to pull:
 
 ```bash
 nextflow pull https://github.com/nextflow-io/examples
diff --git a/modules/nextflow/src/main/groovy/nextflow/ast/ASTHelpers.groovy b/modules/nextflow/src/main/groovy/nextflow/ast/ASTHelpers.groovy
index 221a37251c..a03db18790 100644
--- a/modules/nextflow/src/main/groovy/nextflow/ast/ASTHelpers.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/ast/ASTHelpers.groovy
@@ -71,7 +71,7 @@ class ASTHelpers {
 
     /**
      * Creates a new {@code ConstructorCallExpression} for the specified class and arguments
-     * specified using an open array. Te
+     * specified using an open array.
      *
      * @param clazz The {@code Class} for which the create a constructor call expression
      * @param args The arguments to be passed to the constructor, they will be wrapped by in a {@code ArgumentListExpression}
diff --git a/modules/nextflow/src/main/groovy/nextflow/ast/NextflowDSLImpl.groovy b/modules/nextflow/src/main/groovy/nextflow/ast/NextflowDSLImpl.groovy
index 5dc906bc32..ecb11da515 100644
--- a/modules/nextflow/src/main/groovy/nextflow/ast/NextflowDSLImpl.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/ast/NextflowDSLImpl.groovy
@@ -1218,7 +1218,7 @@ class NextflowDSLImpl implements ASTTransformation {
          * @return A tuple in which:
          *      <li>1st item: {@code true} if successful or {@code false} otherwise
          *      <li>2nd item: on error condition the line containing the error in the source script, zero otherwise
-         *      <li>3nd item: on error condition the column containing the error in the source script, zero otherwise
+         *      <li>3rd item: on error condition the column containing the error in the source script, zero otherwise
          *
          */
         protected boolean wrapExpressionWithClosure( BlockStatement block, Expression expr, int len, CharSequence source, SourceUnit unit ) {
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdDrop.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdDrop.groovy
index 8fc20346de..dd36368854 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdDrop.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdDrop.groovy
@@ -60,6 +60,6 @@ class CmdDrop extends CmdBase {
             return
         }
 
-        throw new AbortOperationException("Local project repository contains uncommitted changes -- wont drop it")
+        throw new AbortOperationException("Local project repository contains uncommitted changes -- won't drop it")
     }
 }
diff --git a/modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy
index 03bcf3c3b4..f19a785619 100644
--- a/modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy
@@ -321,7 +321,7 @@ class ConfigBuilder {
     }
 
     protected Map configVars() {
-        // this is needed to make sure to re-use the same
+        // this is needed to make sure to reuse the same
         // instance of the config vars across different instances of the ConfigBuilder
         // and prevent multiple parsing of the same params file (which can even be remote resource)
         return cacheableConfigVars(baseDir)
diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
index fbef4b2950..409550ccb7 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
@@ -662,7 +662,7 @@ class TaskProcessor {
 
     /**
      * @return A string 'she-bang' formatted to the added on top script to be executed.
-     * The interpreter to be used define bu the *taskConfig* property {@code shell}
+     * The interpreter to be used define by the *taskConfig* property {@code shell}
      */
     static String shebangLine(shell) {
         assert shell, "Missing 'shell' property in process configuration"
diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskRun.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskRun.groovy
index d4c8f7da32..205951016e 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskRun.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskRun.groovy
@@ -466,7 +466,7 @@ class TaskRun implements Cloneable {
     /**
      * Get the map of *input* objects by the given {@code InParam} type
      *
-     * @param types One ore more subclass of {@code InParam}
+     * @param types One or more subclass of {@code InParam}
      * @return An associative array containing all the objects for the specified type
      */
     def <T extends InParam> Map<T,Object> getInputsByType( Class<T>... types ) {
@@ -482,7 +482,7 @@ class TaskRun implements Cloneable {
     /**
      * Get the map of *output* objects by the given {@code InParam} type
      *
-     * @param types One ore more subclass of {@code InParam}
+     * @param types One or more subclass of {@code InParam}
      * @return An associative array containing all the objects for the specified type
      */
     def <T extends OutParam> Map<T,Object> getOutputsByType( Class<T>... types ) {
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/IterableDef.groovy b/modules/nextflow/src/main/groovy/nextflow/script/IterableDef.groovy
index ee168d17ad..baff26a993 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/IterableDef.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/IterableDef.groovy
@@ -52,7 +52,7 @@ trait IterableDef {
      * To support component recursion, the feedback channels must be used as the channel instances
      * for the outputs instead of creating new ones
      * 
-     * @return A list of output channels brining the process feedback
+     * @return A list of output channels bringing the process feedback
      */
     List<DataflowWriteChannel> getFeedbackChannels() { outputChannels }
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/WorkflowDef.groovy b/modules/nextflow/src/main/groovy/nextflow/script/WorkflowDef.groovy
index 28bdaae23e..ec54d3043a 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/WorkflowDef.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/WorkflowDef.groovy
@@ -45,7 +45,7 @@ class WorkflowDef extends BindableDef implements ChainableDef, IterableDef, Exec
 
     private BaseScript owner
 
-    // -- following attributes are mutable and instance dependant
+    // -- following attributes are mutable and instance dependent
     // -- therefore should not be cloned
 
     private ChannelOut output
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/WorkflowNotifier.groovy b/modules/nextflow/src/main/groovy/nextflow/script/WorkflowNotifier.groovy
index 028e224dec..b242a3533d 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/WorkflowNotifier.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/WorkflowNotifier.groovy
@@ -39,7 +39,7 @@ class WorkflowNotifier {
     private Map config
 
     /**
-    * A map representing the variables defined in the script golab scope
+    * A map representing the variables defined in the script global scope
      */
     private Map variables
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/trace/TraceRecord.groovy b/modules/nextflow/src/main/groovy/nextflow/trace/TraceRecord.groovy
index 93b5b6856b..34f2072751 100644
--- a/modules/nextflow/src/main/groovy/nextflow/trace/TraceRecord.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/trace/TraceRecord.groovy
@@ -176,7 +176,7 @@ class TraceRecord implements Serializable {
     }
 
     /**
-     * Coverts the value to a duration string.
+     * Converts the value to a duration string.
      *
      * See {@link Duration}
      * @param value
diff --git a/modules/nextflow/src/main/groovy/nextflow/util/ConfigHelper.groovy b/modules/nextflow/src/main/groovy/nextflow/util/ConfigHelper.groovy
index e4891e7391..f70490fdbe 100644
--- a/modules/nextflow/src/main/groovy/nextflow/util/ConfigHelper.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/util/ConfigHelper.groovy
@@ -84,7 +84,7 @@ class ConfigHelper {
     }
 
     /**
-     * Given a list of paths looks for the files ending withe the extension '.jar' and return
+     * Given a list of paths looks for the files ending with the extension '.jar' and return
      * a list containing the original directories, plus the JARs paths
      *
      * @param dirs
diff --git a/modules/nextflow/src/main/resources/nextflow/trace/assets/d3-timeline.js b/modules/nextflow/src/main/resources/nextflow/trace/assets/d3-timeline.js
index e59af8123a..95976c5e27 100644
--- a/modules/nextflow/src/main/resources/nextflow/trace/assets/d3-timeline.js
+++ b/modules/nextflow/src/main/resources/nextflow/trace/assets/d3-timeline.js
@@ -177,7 +177,7 @@
       setWidth();
 
       // check if the user wants relative time
-      // if so, substract the first timestamp from each subsequent timestamps
+      // if so, subtract the first timestamp from each subsequent timestamps
       if(timeIsRelative){
         g.each(function (d, i) {
           d.forEach(function (datum, index) {
diff --git a/modules/nextflow/src/test/groovy/nextflow/cli/CmdSecretTest.groovy b/modules/nextflow/src/test/groovy/nextflow/cli/CmdSecretTest.groovy
index 38b4f9d6d5..86145185d8 100644
--- a/modules/nextflow/src/test/groovy/nextflow/cli/CmdSecretTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/cli/CmdSecretTest.groovy
@@ -60,7 +60,7 @@ class CmdSecretTest extends Specification {
         tempDir?.deleteDir()
     }
 
-    def 'should validate #COMMAND doesnt accept #ARGUMENTS' () {
+    def 'should validate #COMMAND does not accept #ARGUMENTS' () {
         when:
         new CmdSecret(args: [COMMAND] + ARGUMENTS).run()
 
diff --git a/modules/nextflow/src/testFixtures/groovy/test/BaseSpec.groovy b/modules/nextflow/src/testFixtures/groovy/test/BaseSpec.groovy
index 45268e1231..dcebf9e6d9 100644
--- a/modules/nextflow/src/testFixtures/groovy/test/BaseSpec.groovy
+++ b/modules/nextflow/src/testFixtures/groovy/test/BaseSpec.groovy
@@ -21,7 +21,7 @@ import spock.lang.Specification
 import groovy.util.logging.Slf4j
 
 /**
- * Base specification class - It wraps each test into begin-close "test name" strigs
+ * Base specification class - It wraps each test into begin-close "test name" strings
  *
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
  */
diff --git a/modules/nf-commons/src/main/nextflow/file/FileHelper.groovy b/modules/nf-commons/src/main/nextflow/file/FileHelper.groovy
index b0f0acc85f..665829a644 100644
--- a/modules/nf-commons/src/main/nextflow/file/FileHelper.groovy
+++ b/modules/nf-commons/src/main/nextflow/file/FileHelper.groovy
@@ -533,7 +533,7 @@ class FileHelper {
             return true
         }
         catch( IOException e ) {
-            log.trace "Cant read file attributes: $self -- Cause: [${e.class.simpleName}] ${e.message}"
+            log.trace "Can't read file attributes: $self -- Cause: [${e.class.simpleName}] ${e.message}"
             return false
         }
 
diff --git a/modules/nf-commons/src/main/nextflow/file/TagAwareFile.groovy b/modules/nf-commons/src/main/nextflow/file/TagAwareFile.groovy
index 6c5a98eed7..1f1f434590 100644
--- a/modules/nf-commons/src/main/nextflow/file/TagAwareFile.groovy
+++ b/modules/nf-commons/src/main/nextflow/file/TagAwareFile.groovy
@@ -18,7 +18,7 @@
 package nextflow.file
 
 /**
- * Defines the interface for annotate a file with one ore more tags
+ * Defines the interface for annotate a file with one or more tags
  * 
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
  */
diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3FileSystemProvider.java b/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3FileSystemProvider.java
index 2e8f818c33..76bd7d3c87 100644
--- a/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3FileSystemProvider.java
+++ b/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3FileSystemProvider.java
@@ -403,7 +403,7 @@ public void close() throws IOException {
                 if (Files.exists(tempFile)) {
                     ObjectMetadata metadata = new ObjectMetadata();
                     metadata.setContentLength(Files.size(tempFile));
-                    // FIXME: #20 ServiceLoader cant load com.upplication.s3fs.util.FileTypeDetector when this library is used inside a ear :(
+                    // FIXME: #20 ServiceLoader can't load com.upplication.s3fs.util.FileTypeDetector when this library is used inside a ear :(
 					metadata.setContentType(Files.probeContentType(tempFile));
 
                     try (InputStream stream = Files.newInputStream(tempFile)) {
@@ -905,7 +905,7 @@ private boolean exists(S3Path path) {
 
 	/**
 	 * Get the Control List, if the path not exists
-     * (because the path is a directory and this key isnt created at amazon s3)
+     * (because the path is a directory and this key isn't created at amazon s3)
      * then return the ACL of the first child.
      *
 	 * @param path {@link S3Path}
diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3Iterator.java b/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3Iterator.java
index ac1df0d30a..680c444399 100644
--- a/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3Iterator.java
+++ b/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3Iterator.java
@@ -122,7 +122,7 @@ private void parseObjectListing(List<S3Path> listPath, ObjectListing current) {
 
     /**
      * The current #buildRequest() get all subdirectories and her content.
-     * This method filter the keyChild and check if is a inmediate
+     * This method filter the keyChild and check if is a immediate
      * descendant of the keyParent parameter
      * @param keyParent String
      * @param keyChild String
diff --git a/tests/Dockerfile b/tests/Dockerfile
index 3b99872565..241e6b3148 100644
--- a/tests/Dockerfile
+++ b/tests/Dockerfile
@@ -5,7 +5,7 @@ MAINTAINER Paolo Di Tommaso <paolo.ditommaso@gmail.com>
 RUN apt-get update -y && apt-get install -q -y gnuplot python && apt-get clean 
 
 #
-# Required PERL moduls
+# Required PERL modules
 #
 RUN cpanm Math::CDF Math::Round && \
   rm -rf /root/.cpanm/work/
diff --git a/tests/bin/AMPA.pl b/tests/bin/AMPA.pl
index 4aa10bbf9e..2591e5a532 100755
--- a/tests/bin/AMPA.pl
+++ b/tests/bin/AMPA.pl
@@ -322,7 +322,7 @@ sub gnuplot_sld {
     print GP "set grid\n";
     print GP "set data style lines\n";
 
-        # if an outpout has been specified output to it 
+        # if an output has been specified output to it 
     if( $graph_file ne "" ) { 
         print GP "set terminal png large enhanced  size 800 600\n";
         print GP "set output '$graph_file' \n";

From 834c27d4fdc3f0b867885572af70843dcdb48935 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Thu, 5 Oct 2023 22:30:47 +0200
Subject: [PATCH 197/350] Fix typos [ci fast]

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .codespellrc                                                  | 2 +-
 changelog.txt                                                 | 2 +-
 .../src/main/groovy/nextflow/splitter/AbstractSplitter.groovy | 2 +-
 .../src/test/groovy/nextflow/util/LoggerHelperTest.groovy     | 4 ++--
 plugins/nf-amazon/changelog.txt                               | 2 +-
 5 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.codespellrc b/.codespellrc
index 61cfca6bd6..e05919e12b 100644
--- a/.codespellrc
+++ b/.codespellrc
@@ -3,4 +3,4 @@ skip = .git,*.pdf,*.svg,timeline-expected.html,*.fq,*.min.js,ScriptDslTest.groov
 # some cases where we need to catch using regex
 ignore-regex = \bhel\*|fo\\
 # some variables, names, etc to ignore
-ignore-words-list = splitted,ois,tre,marge,smoot,afile,bams,bais
+ignore-words-list = splitted,ois,tre,marge,smoot,afile,bams,bais,pre-pending,re-use
diff --git a/changelog.txt b/changelog.txt
index bd06cac862..680f92d856 100644
--- a/changelog.txt
+++ b/changelog.txt
@@ -16,7 +16,7 @@ NEXTFLOW CHANGE-LOG
 - Document when process directives are evaluated (#4217) [731a29a2]
 - Fix List of S3 bucket for custom endpoint [4327fa58]
 - Fix Prevent false positive resumable task [144e0a8a]
-- Fix Prevent multi attempts to retrive AWS creds [b30efe36]
+- Fix Prevent multi attempts to retrieve AWS creds [b30efe36]
 - Fix allow_other vulnerability preventing google-batch submissions (#4332) [9b3741e3]
 - Fix fs list command [29ab2f24]
 - Fix minor typos in changelogs/source code (#4319) [4ce9f1df]
diff --git a/modules/nextflow/src/main/groovy/nextflow/splitter/AbstractSplitter.groovy b/modules/nextflow/src/main/groovy/nextflow/splitter/AbstractSplitter.groovy
index b699b69687..728bbba4ec 100644
--- a/modules/nextflow/src/main/groovy/nextflow/splitter/AbstractSplitter.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/splitter/AbstractSplitter.groovy
@@ -180,7 +180,7 @@ abstract class AbstractSplitter<T> implements SplitterStrategy {
      *      A non-empty list of objects
      * @return
      *      Returns the item at position defined by the attribute {@code #elem} in the list specified as parameter.
-     *      When {@code #elem} is equal to -1 find find out the first occourence of a file object.
+     *      When {@code #elem} is equal to -1 find find out the first occurrence of a file object.
      *      If no file is available the first item in the list is returned
      */
     @PackageScope
diff --git a/modules/nextflow/src/test/groovy/nextflow/util/LoggerHelperTest.groovy b/modules/nextflow/src/test/groovy/nextflow/util/LoggerHelperTest.groovy
index 8b4a7169db..60368e4246 100644
--- a/modules/nextflow/src/test/groovy/nextflow/util/LoggerHelperTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/util/LoggerHelperTest.groovy
@@ -79,7 +79,7 @@ class LoggerHelperTest extends Specification {
         def message =
                 """
                 startup failed:
-                _nf_script_c9a99616: 3: Unknown process block definition: `outpu` @ line 3, column 4.
+                _nf_script_c9a99616: 3: Unknown process block definition: `output` @ line 3, column 4.
                 stdout() into (A,B,C)
                 """
                 .stripIndent().leftTrim()
@@ -88,7 +88,7 @@ class LoggerHelperTest extends Specification {
         expect:
         LoggerHelper.formatStartupErrorMessage(message) ==
                 """
-                Unknown process block definition: `outpu` @ line 3, column 4.
+                Unknown process block definition: `output` @ line 3, column 4.
                 stdout() into (A,B,C)
                 """
                 .stripIndent().leftTrim()
diff --git a/plugins/nf-amazon/changelog.txt b/plugins/nf-amazon/changelog.txt
index 4dbd3bac90..12d654ba91 100644
--- a/plugins/nf-amazon/changelog.txt
+++ b/plugins/nf-amazon/changelog.txt
@@ -4,7 +4,7 @@ nf-amazon changelog
 - Fix minor typos in changelogs/source code (#4319) [4ce9f1df]
 - Fix List of S3 bucket for custom endpoint [4327fa58]
 - Fix support for S3 custom endpoint with anonymous access [03752815]
-- Fix Prevent multi attempts to retrive AWS creds [b30efe36]
+- Fix Prevent multi attempts to retrieve AWS creds [b30efe36]
 
 2.1.2 - 10 Sep 2023
 - Disable staging script for remote work dir (#4282) [80f7cd46]

From 3d6b73580651b85ad6153d3be579eca9dd0abb32 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Fri, 6 Oct 2023 17:34:25 +0200
Subject: [PATCH 198/350] Fix Google Batch do not stop running jobs (#4381)

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../nextflow/processor/TaskHandler.groovy     |  2 ++
 .../nextflow/processor/TaskHandlerTest.groovy | 21 +++++++++++++++++++
 .../batch/GoogleBatchTaskHandler.groovy       |  7 +++----
 3 files changed, 26 insertions(+), 4 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskHandler.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskHandler.groovy
index 2db1e00470..9efb29925a 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskHandler.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskHandler.groovy
@@ -117,6 +117,8 @@ abstract class TaskHandler {
 
     boolean isCompleted()  { return status == COMPLETED  }
 
+    boolean isActive() { status == SUBMITTED || status == RUNNING }
+
     protected StringBuilder toStringBuilder(StringBuilder builder) {
         builder << "id: ${task.id}; name: ${task.name}; status: $status; exit: ${task.exitStatus != Integer.MAX_VALUE ? task.exitStatus : '-'}; error: ${task.error ?: '-'}; workDir: ${task.workDir?.toUriString()}"
     }
diff --git a/modules/nextflow/src/test/groovy/nextflow/processor/TaskHandlerTest.groovy b/modules/nextflow/src/test/groovy/nextflow/processor/TaskHandlerTest.groovy
index 0225478a21..01847a9d5e 100644
--- a/modules/nextflow/src/test/groovy/nextflow/processor/TaskHandlerTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/processor/TaskHandlerTest.groovy
@@ -228,4 +228,25 @@ class TaskHandlerTest extends Specification {
         timeout
 
     }
+
+    @Unroll
+    def 'should validate status' () {
+        given:
+        def handler = Spy(TaskHandler)
+        handler.status = STATUS
+
+        expect:
+        handler.isNew() == EXPECT_NEW
+        handler.isRunning() == EXPECT_RUNNING
+        handler.isSubmitted() == EXPECT_SUBMITTED
+        handler.isActive() == EXPECTED_ACTIVE
+        handler.isCompleted() == EXPECT_COMPLETE
+        
+        where:
+        STATUS              | EXPECT_NEW  | EXPECT_SUBMITTED | EXPECT_RUNNING | EXPECTED_ACTIVE | EXPECT_COMPLETE
+        TaskStatus.NEW      | true        | false            | false          | false           | false
+        TaskStatus.SUBMITTED| false       | true             | false          | true            | false
+        TaskStatus.RUNNING  | false       | false            | true           | true            | false
+        TaskStatus.COMPLETED| false       | false            | false          | false           | true
+    }
 }
diff --git a/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchTaskHandler.groovy b/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchTaskHandler.groovy
index 4fc9a1290c..5fe5c45548 100644
--- a/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchTaskHandler.groovy
+++ b/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchTaskHandler.groovy
@@ -356,10 +356,9 @@ class GoogleBatchTaskHandler extends TaskHandler implements FusionAwareTask {
         return jobState
     }
 
-    private List<String> RUNNING_AND_TERMINATED = ['RUNNING', 'SUCCEEDED', 'FAILED', 'DELETION_IN_PROGRESS']
-
-    private List<String> TERMINATED = ['SUCCEEDED', 'FAILED', 'DELETION_IN_PROGRESS']
+    static private List<String> RUNNING_AND_TERMINATED = ['RUNNING', 'SUCCEEDED', 'FAILED', 'DELETION_IN_PROGRESS']
 
+    static private List<String> TERMINATED = ['SUCCEEDED', 'FAILED', 'DELETION_IN_PROGRESS']
 
     @Override
     boolean checkIfRunning() {
@@ -408,7 +407,7 @@ class GoogleBatchTaskHandler extends TaskHandler implements FusionAwareTask {
 
     @Override
     void kill() {
-        if( isSubmitted() ) {
+        if( isActive() ) {
             log.trace "[GOOGLE BATCH] Process `${task.lazyName()}` - deleting job name=$jobId"
             client.deleteJob(jobId)
         }

From d47e8b0768befe37190a0dac4db4bcd4119afa76 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 7 Oct 2023 10:53:56 +0200
Subject: [PATCH 199/350] Improve Wave error handling

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../io/seqera/wave/plugin/WaveClient.groovy   | 40 ++++++++++--------
 .../seqera/wave/plugin/WaveClientTest.groovy  | 42 +++++++++++++++++++
 2 files changed, 64 insertions(+), 18 deletions(-)

diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
index a5909daf3a..891b4f5a0f 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
@@ -306,8 +306,9 @@ class WaveClient {
 
         final resp = httpSend(req)
         final code = resp.statusCode()
+        final body = resp.body()
         if( code>=200 && code<400 ) {
-            log.debug "Wave container config response: [$code] ${resp.body()}"
+            log.debug "Wave container config response: [$code] ${body}"
             return jsonToContainerConfig(resp.body())
         }
         throw new BadResponseException("Unexpected response for containerContainerConfigUrl \'$configUrl\': [${resp.statusCode()}] ${resp.body()}")
@@ -551,12 +552,13 @@ class WaveClient {
                 .build()
         final begin = System.currentTimeMillis()
         final resp = httpSend(req)
+        final body = resp.body()
         final code = resp.statusCode()
         if( code>=200 && code<400 ) {
-            log.debug "Wave container available in ${nextflow.util.Duration.of(System.currentTimeMillis()-begin)}: [$code] ${resp.body()}"
+            log.debug "Wave container available in ${nextflow.util.Duration.of(System.currentTimeMillis()-begin)}: [$code] ${body}"
         }
         else
-            throw new BadResponseException("Unexpected response for \'$manifest\': [${resp.statusCode()}] ${resp.body()}")
+            throw new BadResponseException("Unexpected response for \'$manifest\': [${code}] ${body}")
     }
 
     static protected boolean isCondaLocalFile(String value) {
@@ -587,7 +589,9 @@ class WaveClient {
                 .build()
 
         final resp = httpSend(req)
-        log.debug "Refresh cookie response: [${resp.statusCode()}] ${resp.body()}"
+        final code = resp.statusCode()
+        final body = resp.body()
+        log.debug "Refresh cookie response: [${code}] ${body}"
         if( resp.statusCode() != 200 )
             return false
 
@@ -623,16 +627,22 @@ class WaveClient {
         return null
     }
 
-    protected <T> RetryPolicy<T> retryPolicy(Predicate<? extends Throwable> cond) {
+    protected <T> RetryPolicy<T> retryPolicy(Predicate<? extends Throwable> cond, Predicate<T> handle) {
         final cfg = config.retryOpts()
         final listener = new EventListener<ExecutionAttemptedEvent<T>>() {
             @Override
             void accept(ExecutionAttemptedEvent<T> event) throws Throwable {
-                log.debug("Wave connection failure - attempt: ${event.attemptCount}", event.lastFailure)
+                def msg = "Wave connection failure - attempt: ${event.attemptCount}"
+                if( event.lastResult!=null )
+                    msg += "; response: ${event.lastResult}"
+                if( event.lastFailure != null )
+                    msg += "; exception: [${event.lastFailure.class.name}] ${event.lastFailure.message}"
+                log.debug(msg)
             }
         }
         return RetryPolicy.<T>builder()
                 .handleIf(cond)
+                .handleResultIf(handle)
                 .withBackoff(cfg.delay.toMillis(), cfg.maxDelay.toMillis(), ChronoUnit.MILLIS)
                 .withMaxAttempts(cfg.maxAttempts)
                 .withJitter(cfg.jitter)
@@ -640,22 +650,16 @@ class WaveClient {
                 .build()
     }
 
-    protected <T> T safeApply(CheckedSupplier<T> action) {
-        final cond = (e -> e instanceof IOException)  as Predicate<? extends Throwable>
-        final policy = retryPolicy(cond)
+    protected <T> HttpResponse<T> safeApply(CheckedSupplier action) {
+        final retryOnException = (e -> e instanceof IOException) as Predicate<? extends Throwable>
+        final retryOnStatusCode = ((HttpResponse<T> resp) -> resp.statusCode() in SERVER_ERRORS) as Predicate<HttpResponse<T>>
+        final policy = retryPolicy(retryOnException, retryOnStatusCode)
         return Failsafe.with(policy).get(action)
     }
 
-    static private final List<Integer> SERVER_ERRORS = [429,502,503,504]
+    static private final List<Integer> SERVER_ERRORS = [429,500,502,503,504]
 
     protected HttpResponse<String> httpSend(HttpRequest req)  {
-        return safeApply(() -> {
-            final resp=httpClient.send(req, HttpResponse.BodyHandlers.ofString())
-            if( resp.statusCode() in SERVER_ERRORS) {
-                // throws an IOException so that the condition is handled by the retry policy
-                throw new IOException("Unexpected server response code ${resp.statusCode()} - message: ${resp.body()}")
-            }
-            return resp
-        })
+        return safeApply(() -> httpClient.send(req, HttpResponse.BodyHandlers.ofString()))
     }
 }
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
index 7bcc9fd1da..36108f236f 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
@@ -19,6 +19,7 @@ package io.seqera.wave.plugin
 
 import static java.nio.file.StandardOpenOption.*
 
+import java.net.http.HttpRequest
 import java.nio.file.Files
 import java.nio.file.Path
 import java.nio.file.attribute.FileTime
@@ -1219,4 +1220,45 @@ class WaveClientTest extends Specification {
         'https://foo.com'   | true
     }
 
+    def 'should retry http request' () {
+
+        given:
+        int requestCount=0
+        HttpHandler handler = { HttpExchange exchange ->
+            if( ++requestCount<3 ) {
+                exchange.getResponseHeaders().add("Content-Type", "text/plain")
+                exchange.sendResponseHeaders(503, 0)
+                exchange.getResponseBody().close()
+            }
+            else {
+                def body = 'Hello world!'
+                exchange.getResponseHeaders().add("Content-Type", "text/plain")
+                exchange.sendResponseHeaders(200, body.size())
+                exchange.getResponseBody().write(body.bytes)
+                exchange.getResponseBody().close()
+            }
+        }
+
+        HttpServer server = HttpServer.create(new InetSocketAddress(9901), 0);
+        server.createContext("/", handler);
+        server.start()
+
+        def session = Mock(Session) {getConfig() >> [:] }
+        def client = new WaveClient(session)
+
+        when:
+        def request = HttpRequest.newBuilder().uri(new URI('http://localhost:9901/foo.txt')).build()
+        def response = client.httpSend(request)
+        then:
+        response.statusCode() == 200
+        response.body() == 'Hello world!'
+        and:
+        requestCount == 3
+        
+        cleanup:
+        server?.stop(0)
+
+    }
+
+
 }

From 11c3aac5b9958f104d10cc5d9e428cdf9651a7c9 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sun, 8 Oct 2023 18:32:46 +0200
Subject: [PATCH 200/350] Use HistoryFile.Record instead of Record type conflic
 [ci fast]

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../src/main/groovy/nextflow/cli/CacheBase.groovy         | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CacheBase.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CacheBase.groovy
index 363fdb969a..a6f7847b47 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CacheBase.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CacheBase.groovy
@@ -24,8 +24,6 @@ import nextflow.cache.CacheFactory
 import nextflow.exception.AbortOperationException
 import nextflow.util.HistoryFile
 
-import static nextflow.util.HistoryFile.Record
-
 /**
  * Common cache operations shared by {@link CmdLog} and {@link CmdClean}
  *
@@ -68,11 +66,11 @@ trait CacheBase {
 
     }
 
-    CacheDB cacheFor(Record entry) {
+    CacheDB cacheFor(HistoryFile.Record entry) {
         CacheFactory.create(entry.sessionId, entry.runName, basePath)
     }
 
-    List<Record> listIds() {
+    List<HistoryFile.Record> listIds() {
 
         if( but ) {
             return history.findBut(but)
@@ -90,7 +88,7 @@ trait CacheBase {
         if( !args )
             return history.findByIdOrName('last')
 
-        List<Record> result = []
+        List<HistoryFile.Record> result = []
         for( String name : args ) {
             result.addAll(history.findByIdOrName(name))
         }

From 3cb91a15d424ce4ef2b57a6570a60f1a09f16df7 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sun, 8 Oct 2023 19:22:30 +0200
Subject: [PATCH 201/350] Remove unused -dsl2 option [ci fast]

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy | 4 ----
 .../nextflow/src/test/groovy/nextflow/cli/LauncherTest.groovy | 2 --
 2 files changed, 6 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy
index a2deedbb07..b41c57a5dc 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy
@@ -296,10 +296,6 @@ class Launcher {
                 normalized << 'true'
             }
 
-            else if( (current == '-dsl2') && (i==args.size() || args[i].startsWith('-'))) {
-                normalized << 'true'
-            }
-
             else if( current == '-syslog' && (i==args.size() || args[i].startsWith('-') || allCommands.find { it.name == args[i] } )) {
                 normalized << 'localhost'
             }
diff --git a/modules/nextflow/src/test/groovy/nextflow/cli/LauncherTest.groovy b/modules/nextflow/src/test/groovy/nextflow/cli/LauncherTest.groovy
index 7f97273e42..5a4594dfe2 100644
--- a/modules/nextflow/src/test/groovy/nextflow/cli/LauncherTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/cli/LauncherTest.groovy
@@ -259,8 +259,6 @@ class LauncherTest extends Specification {
         launcher.normalizeArgs('run','-ansi-log', 'true', '-x') == ['run', '-ansi-log','true', '-x']
         launcher.normalizeArgs('run','-ansi-log', 'false', '-x') == ['run', '-ansi-log','false', '-x']
 
-        launcher.normalizeArgs('run','-dsl2', '-x') == ['run', '-dsl2','true', '-x']
-
         launcher.normalizeArgs('run','-stub', '-x') == ['run', '-stub','true', '-x']
         launcher.normalizeArgs('run','-stub-run', '-x') == ['run', '-stub-run','true', '-x']
         launcher.normalizeArgs('run','-stub-run', 'true', '-x') == ['run', '-stub-run', 'true', '-x']

From d26c42be0be01be25350f73ce377a424945dee11 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Mon, 9 Oct 2023 20:29:00 +0200
Subject: [PATCH 202/350] Return -1 when exitcode file is empty (#4354)

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../src/main/groovy/nextflow/executor/GridTaskHandler.groovy | 4 ++--
 .../test/groovy/nextflow/executor/GridExecutorTest.groovy    | 5 +++--
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/executor/GridTaskHandler.groovy b/modules/nextflow/src/main/groovy/nextflow/executor/GridTaskHandler.groovy
index 503b679d6a..143703b551 100644
--- a/modules/nextflow/src/main/groovy/nextflow/executor/GridTaskHandler.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/executor/GridTaskHandler.groovy
@@ -375,6 +375,7 @@ class GridTaskHandler extends TaskHandler implements FusionAwareTask {
             }
             catch( Exception e ) {
                 log.warn "Unable to parse process exit file: ${exitFile.toUriString()} -- bad value: '$status'"
+                return Integer.MAX_VALUE
             }
         }
 
@@ -400,9 +401,8 @@ class GridTaskHandler extends TaskHandler implements FusionAwareTask {
                 return null
             }
             log.warn "Unable to read command status from: ${exitFile.toUriString()} after $delta ms"
+            return -1
         }
-
-        return Integer.MAX_VALUE
     }
 
     @Override
diff --git a/modules/nextflow/src/test/groovy/nextflow/executor/GridExecutorTest.groovy b/modules/nextflow/src/test/groovy/nextflow/executor/GridExecutorTest.groovy
index d1fee19c4d..478d1f53bf 100644
--- a/modules/nextflow/src/test/groovy/nextflow/executor/GridExecutorTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/executor/GridExecutorTest.groovy
@@ -129,8 +129,9 @@ class GridExecutorTest extends Specification {
         // now 'checkIfCompleted' returns true
         handler.checkIfCompleted()
         handler.status == TaskStatus.COMPLETED
-        // but the 'exitStatus' not ZERO
-        handler.task.exitStatus == Integer.MAX_VALUE
+        // but the 'exitStatus' is-1 to signal the '.exitcode' file was empty
+        // and allow the task to be retried
+        handler.task.exitStatus == -1
 
     }
 

From 73fda5824df8733600ae56a4d94957a190d806a1 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Mon, 9 Oct 2023 23:31:01 +0200
Subject: [PATCH 203/350] Add -cloudcache CLI option (#4385)

This commit adds the -cloudcache run command line option that
allows storing Nextflow cache metadata into a cloud object storage
bucket instead of storing them in the local .nextflow directory.

The target cloud cache path is specified as command line argument,
e.g. -cloudcache s3://bucket-name/path.

Moreover, this commit allows controlling the cloudcache via the
nextflow.config file as shown below:

```
cloudcache.enabled = true|false
cloudcache.path = '<some object storage path>'
```

Supported object storage are AWS S3, Azure Blob storage and Google Storage.

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/cli.md                                   |  3 +
 .../src/main/groovy/nextflow/Session.groovy   | 19 ++++
 .../main/groovy/nextflow/cli/CmdRun.groovy    |  3 +
 .../main/groovy/nextflow/cli/Launcher.groovy  |  4 +
 .../nextflow/config/ConfigBuilder.groovy      | 13 +++
 .../groovy/nextflow/cli/LauncherTest.groovy   |  4 +
 .../nextflow/config/ConfigBuilderTest.groovy  | 92 +++++++++++++++++++
 .../main/nextflow/plugin/PluginsFacade.groovy |  4 +-
 .../nextflow/plugin/PluginsFacadeTest.groovy  |  4 +-
 .../src/test/nextflow/S3SessionTest.groovy    | 61 ++++++++++++
 .../nextflow/cache/CloudCacheFactory.groovy   |  9 +-
 .../nextflow/cache/CloudCacheStore.groovy     | 16 +---
 .../seqera/tower/plugin/CacheCommand.groovy   |  5 +-
 .../seqera/tower/plugin/TowerFactory.groovy   |  2 +-
 14 files changed, 217 insertions(+), 22 deletions(-)
 create mode 100644 plugins/nf-amazon/src/test/nextflow/S3SessionTest.groovy

diff --git a/docs/cli.md b/docs/cli.md
index 310c97b35d..d9faee429d 100644
--- a/docs/cli.md
+++ b/docs/cli.md
@@ -1134,6 +1134,9 @@ The `run` command is used to execute a local pipeline script or remote pipeline
 `-cache`
 : Enable/disable processes caching.
 
+`-cloudcache`
+: Enable the use of the Cloud cache plugin for storing cache metadata to an object storage bucket.
+
 `-d, -deep`
 : Create a shallow clone of the specified depth.
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/Session.groovy b/modules/nextflow/src/main/groovy/nextflow/Session.groovy
index f8e2cffbd5..7f8d4ecf24 100644
--- a/modules/nextflow/src/main/groovy/nextflow/Session.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/Session.groovy
@@ -188,6 +188,11 @@ class Session implements ISession {
      */
     boolean debug
 
+    /**
+     * Defines the cloud path where store cache meta-data
+     */
+    Path cloudCachePath
+
     /**
      * Local path where script generated classes are saved
      */
@@ -361,11 +366,25 @@ class Session implements ISession {
         this.workDir = ((config.workDir ?: 'work') as Path).complete()
         this.setLibDir( config.libDir as String )
 
+        // -- init cloud cache path
+        this.cloudCachePath = cloudCachePath(config.cloudcache as Map, workDir)
+
         // -- file porter config
         this.filePorter = new FilePorter(this)
 
     }
 
+    protected Path cloudCachePath(Map cloudcache, Path workDir) {
+        if( !cloudcache?.enabled )
+            return null
+        final String path = cloudcache.path
+        final result = path ? FileHelper.asPath(path) : workDir
+        if( result.scheme !in ['s3','az','gs'] ) {
+            throw new IllegalArgumentException("Storage path not supported by Cloud-cache - offending value: '${result}'")
+        }
+        return result
+    }
+
     /**
      * Initialize the session workDir, libDir, baseDir and scriptName variables
      */
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
index 67b4fba639..a44201d35a 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
@@ -111,6 +111,9 @@ class CmdRun extends CmdBase implements HubOptions {
     @Parameter(names=['-bucket-dir'], description = 'Remote bucket where intermediate result files are stored')
     String bucketDir
 
+    @Parameter(names=['-cloudcache'], description = 'Enable the use of object storage bucket as storage for cache meta-data')
+    String cloudCachePath
+
     /**
      * Defines the parameters to be passed to the pipeline script
      */
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy
index b41c57a5dc..ad3a32f844 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy
@@ -224,6 +224,10 @@ class Launcher {
                 normalized << '%all'
             }
 
+            else if( current == '-cloudcache' && (i==args.size() || args[i].startsWith('-'))) {
+                normalized << '-'
+            }
+
             else if( current == '-with-trace' && (i==args.size() || args[i].startsWith('-'))) {
                 normalized << '-'
             }
diff --git a/modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy
index f19a785619..02270c9aa1 100644
--- a/modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy
@@ -709,6 +709,19 @@ class ConfigBuilder {
             config.fusion.enabled = cmdRun.withFusion == 'true'
         }
 
+        // -- set cloudcache options
+        final envCloudPath = env.get('NXF_CLOUDCACHE_PATH')
+        if( cmdRun.cloudCachePath || envCloudPath ) {
+            if( !(config.cloudcache instanceof Map) )
+                config.cloudcache = [:]
+            if( !config.cloudcache.isSet('enabled') )
+                config.cloudcache.enabled = true
+            if( cmdRun.cloudCachePath && cmdRun.cloudCachePath != '-' )
+                config.cloudcache.path = cmdRun.cloudCachePath
+            else if( !config.cloudcache.isSet('path') && envCloudPath )
+                config.cloudcache.path = envCloudPath
+        }
+
         // -- add the command line parameters to the 'taskConfig' object
         if( cmdRun.hasParams() )
             config.params = mergeMaps( (Map)config.params, cmdRun.parsedParams(configVars()), NF.strictMode )
diff --git a/modules/nextflow/src/test/groovy/nextflow/cli/LauncherTest.groovy b/modules/nextflow/src/test/groovy/nextflow/cli/LauncherTest.groovy
index 5a4594dfe2..bb1c82e182 100644
--- a/modules/nextflow/src/test/groovy/nextflow/cli/LauncherTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/cli/LauncherTest.groovy
@@ -187,6 +187,10 @@ class LauncherTest extends Specification {
         launcher.normalizeArgs('run', '-', '-a', '-b') == ['run','-stdin', '-a', '-b']
         launcher.normalizeArgs('run') == ['run']
 
+        launcher.normalizeArgs('run','-cloudcache') == ['run', '-cloudcache', '-']
+        launcher.normalizeArgs('run','-cloudcache', '-x') == ['run', '-cloudcache', '-', '-x']
+        launcher.normalizeArgs('run','-cloudcache', 's3://foo/bar') == ['run', '-cloudcache','s3://foo/bar']
+        
         launcher.normalizeArgs('run','-with-tower') == ['run', '-with-tower', '-']
         launcher.normalizeArgs('run','-with-tower', '-x') == ['run', '-with-tower', '-', '-x']
         launcher.normalizeArgs('run','-with-tower', 'foo.com') == ['run', '-with-tower','foo.com']
diff --git a/modules/nextflow/src/test/groovy/nextflow/config/ConfigBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/config/ConfigBuilderTest.groovy
index de690f0d40..08076f3eca 100644
--- a/modules/nextflow/src/test/groovy/nextflow/config/ConfigBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/config/ConfigBuilderTest.groovy
@@ -1157,6 +1157,98 @@ class ConfigBuilderTest extends Specification {
         config.wave.endpoint == 'https://wave.seqera.io'
     }
 
+    def 'should set cloudcache options' () {
+
+        given:
+        def env = [:]
+        def builder = [:] as ConfigBuilder
+
+        when:
+        def config = new ConfigObject()
+        builder.configRunOptions(config, env, new CmdRun())
+        then:
+        !config.cloudcache
+
+        when:
+        config = new ConfigObject()
+        config.cloudcache.path = 's3://foo/bar'
+        builder.configRunOptions(config, env, new CmdRun())
+        then:
+        config.cloudcache instanceof Map
+        !config.cloudcache.enabled
+        config.cloudcache.path == 's3://foo/bar'
+
+        when:
+        config = new ConfigObject()
+        builder.configRunOptions(config, env, new CmdRun(cloudCachePath: 's3://this/that'))
+        then:
+        config.cloudcache instanceof Map
+        config.cloudcache.enabled
+        config.cloudcache.path == 's3://this/that'
+
+        when:
+        config = new ConfigObject()
+        builder.configRunOptions(config, env, new CmdRun(cloudCachePath: '-'))
+        then:
+        config.cloudcache instanceof Map
+        config.cloudcache.enabled
+        !config.cloudcache.path
+
+        when:
+        config = new ConfigObject()
+        config.cloudcache.path = 's3://alpha/delta'
+        builder.configRunOptions(config, env, new CmdRun(cloudCachePath: '-'))
+        then:
+        config.cloudcache instanceof Map
+        config.cloudcache.enabled
+        config.cloudcache.path == 's3://alpha/delta'
+
+        when:
+        config = new ConfigObject()
+        config.cloudcache.path = 's3://alpha/delta'
+        builder.configRunOptions(config, env, new CmdRun(cloudCachePath: 's3://should/override/config'))
+        then:
+        config.cloudcache instanceof Map
+        config.cloudcache.enabled
+        config.cloudcache.path == 's3://should/override/config'
+
+        when:
+        config = new ConfigObject()
+        config.cloudcache.enabled = false
+        builder.configRunOptions(config, env, new CmdRun(cloudCachePath: 's3://should/override/config'))
+        then:
+        config.cloudcache instanceof Map
+        !config.cloudcache.enabled
+        config.cloudcache.path == 's3://should/override/config'
+
+        when:
+        config = new ConfigObject()
+        builder.configRunOptions(config, [NXF_CLOUDCACHE_PATH:'s3://foo'], new CmdRun(cloudCachePath: 's3://should/override/env'))
+        then:
+        config.cloudcache instanceof Map
+        config.cloudcache.enabled
+        config.cloudcache.path == 's3://should/override/env'
+
+        when:
+        config = new ConfigObject()
+        config.cloudcache.path = 's3://config/path'
+        builder.configRunOptions(config, [NXF_CLOUDCACHE_PATH:'s3://foo'], new CmdRun())
+        then:
+        config.cloudcache instanceof Map
+        config.cloudcache.enabled
+        config.cloudcache.path == 's3://config/path'
+
+        when:
+        config = new ConfigObject()
+        config.cloudcache.path = 's3://config/path'
+        builder.configRunOptions(config, [NXF_CLOUDCACHE_PATH:'s3://foo'], new CmdRun(cloudCachePath: 's3://should/override/config'))
+        then:
+        config.cloudcache instanceof Map
+        config.cloudcache.enabled
+        config.cloudcache.path == 's3://should/override/config'
+
+    }
+
     def 'should enable conda env' () {
 
         given:
diff --git a/modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy b/modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy
index 5800582a40..5af5b2d2a6 100644
--- a/modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy
+++ b/modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy
@@ -371,8 +371,8 @@ class PluginsFacade implements PluginStateListener {
             specs << defaultPlugins.getPlugin('nf-wave')
         }
 
-        // add cloudcache plugin when NXF_CLOUDCACHE_PATH is set
-        if( env.NXF_CLOUDCACHE_PATH ) {
+        // add cloudcache plugin when cloudcache is enabled in the config
+        if( Bolts.navigate(config, 'cloudcache.enabled')==true ) {
             specs << defaultPlugins.getPlugin('nf-cloudcache')
         }
 
diff --git a/modules/nf-commons/src/test/nextflow/plugin/PluginsFacadeTest.groovy b/modules/nf-commons/src/test/nextflow/plugin/PluginsFacadeTest.groovy
index d8a58b637e..20eb74ac32 100644
--- a/modules/nf-commons/src/test/nextflow/plugin/PluginsFacadeTest.groovy
+++ b/modules/nf-commons/src/test/nextflow/plugin/PluginsFacadeTest.groovy
@@ -140,8 +140,8 @@ class PluginsFacadeTest extends Specification {
         result == [ new PluginSpec('nf-google','2.0.0') ]
 
         when:
-        handler = new PluginsFacade(defaultPlugins: defaults, env: [NXF_CLOUDCACHE_PATH:'xyz'])
-        result = handler.pluginsRequirement([:])
+        handler = new PluginsFacade(defaultPlugins: defaults, env: [:])
+        result = handler.pluginsRequirement([cloudcache:[enabled:true]])
         then:
         result == [ new PluginSpec('nf-cloudcache', '0.1.0') ]
 
diff --git a/plugins/nf-amazon/src/test/nextflow/S3SessionTest.groovy b/plugins/nf-amazon/src/test/nextflow/S3SessionTest.groovy
new file mode 100644
index 0000000000..6a3b853e64
--- /dev/null
+++ b/plugins/nf-amazon/src/test/nextflow/S3SessionTest.groovy
@@ -0,0 +1,61 @@
+/*
+ * Copyright 2013-2023, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package nextflow
+
+import java.nio.file.Path
+
+import nextflow.file.FileHelper
+import spock.lang.Specification
+import spock.lang.Unroll
+
+/**
+ *
+ * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
+ */
+class S3SessionTest extends Specification {
+
+    @Unroll
+    def 'should get cloud cache path' () {
+        given:
+        def session = Spy(Session)
+
+        expect:
+        session.cloudCachePath(CONFIG, FileHelper.asPath(WORKDIR)) == EXPECTED
+
+        where:
+        CONFIG                                  | WORKDIR           | EXPECTED
+        null                                    | '/foo'            | null
+        [enabled:true]                          | 's3://foo/work'   | FileHelper.asPath('s3://foo/work')
+        [enabled:true, path:'s3://this/that']   | '/foo'            | FileHelper.asPath('s3://this/that')
+
+    }
+
+
+    def 'should error with non-cloud bucket' () {
+        given:
+        def session = Spy(Session)
+
+        when:
+        session.cloudCachePath([enabled:true], Path.of('/foo/dir'))
+        then:
+        def e = thrown(IllegalArgumentException)
+        e.message == "Storage path not supported by Cloud-cache - offending value: '/foo/dir'"
+
+    }
+
+}
diff --git a/plugins/nf-cloudcache/src/main/nextflow/cache/CloudCacheFactory.groovy b/plugins/nf-cloudcache/src/main/nextflow/cache/CloudCacheFactory.groovy
index 41f00b98fb..bcd2de989f 100644
--- a/plugins/nf-cloudcache/src/main/nextflow/cache/CloudCacheFactory.groovy
+++ b/plugins/nf-cloudcache/src/main/nextflow/cache/CloudCacheFactory.groovy
@@ -20,8 +20,8 @@ package nextflow.cache
 import java.nio.file.Path
 
 import groovy.transform.CompileStatic
-import nextflow.cache.CacheDB
-import nextflow.cache.CacheFactory
+import nextflow.Global
+import nextflow.Session
 import nextflow.exception.AbortOperationException
 import nextflow.plugin.Priority
 /**
@@ -39,7 +39,10 @@ class CloudCacheFactory extends CacheFactory {
     protected CacheDB newInstance(UUID uniqueId, String runName, Path home) {
         if( !uniqueId ) throw new AbortOperationException("Missing cache `uuid`")
         if( !runName ) throw new AbortOperationException("Missing cache `runName`")
-        final store = new CloudCacheStore(uniqueId, runName, home)
+        final path = (Global.session as Session).cloudCachePath
+        if( !path )
+            throw new IllegalArgumentException("Cloud-cache path not defined - use either -cloudcatch run option or NXF_CLOUDCACHE_PATH environment variable")
+        final store = new CloudCacheStore(uniqueId, runName, path)
         return new CacheDB(store)
     }
 
diff --git a/plugins/nf-cloudcache/src/main/nextflow/cache/CloudCacheStore.groovy b/plugins/nf-cloudcache/src/main/nextflow/cache/CloudCacheStore.groovy
index c9f98bdef4..10f8c1712e 100644
--- a/plugins/nf-cloudcache/src/main/nextflow/cache/CloudCacheStore.groovy
+++ b/plugins/nf-cloudcache/src/main/nextflow/cache/CloudCacheStore.groovy
@@ -23,7 +23,6 @@ import java.nio.file.Path
 
 import com.google.common.hash.HashCode
 import groovy.transform.CompileStatic
-import nextflow.SysEnv
 import nextflow.exception.AbortOperationException
 import nextflow.extension.FilesEx
 import nextflow.util.CacheHelper
@@ -58,23 +57,18 @@ class CloudCacheStore implements CacheStore {
     /** Index file output stream */
     private OutputStream indexWriter
 
-    CloudCacheStore(UUID uniqueId, String runName, Path basePath=null) {
+    CloudCacheStore(UUID uniqueId, String runName, Path basePath) {
+        assert uniqueId, "Missing cloudcache 'uniqueId' argument"
+        assert runName, "Missing cloudcache 'runName' argument"
+        assert basePath, "Missing cloudcache 'basePath' argument"
         this.KEY_SIZE = CacheHelper.hasher('x').hash().asBytes().size()
         this.uniqueId = uniqueId
         this.runName = runName
-        this.basePath = basePath ?: defaultBasePath()
+        this.basePath = basePath
         this.dataPath = this.basePath.resolve("$uniqueId")
         this.indexPath = dataPath.resolve("index.$runName")
     }
 
-    private Path defaultBasePath() {
-        final basePath = SysEnv.get('NXF_CLOUDCACHE_PATH')
-        if( !basePath )
-            throw new IllegalArgumentException("NXF_CLOUDCACHE_PATH must be defined when using the cloud cache store")
-
-        return basePath as Path
-    }
-
     @Override
     CloudCacheStore open() {
         indexWriter = new BufferedOutputStream(Files.newOutputStream(indexPath))
diff --git a/plugins/nf-tower/src/main/io/seqera/tower/plugin/CacheCommand.groovy b/plugins/nf-tower/src/main/io/seqera/tower/plugin/CacheCommand.groovy
index 846f35f3b9..bfaf0426cf 100644
--- a/plugins/nf-tower/src/main/io/seqera/tower/plugin/CacheCommand.groovy
+++ b/plugins/nf-tower/src/main/io/seqera/tower/plugin/CacheCommand.groovy
@@ -20,7 +20,6 @@ package io.seqera.tower.plugin
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import nextflow.Session
-import nextflow.SysEnv
 import nextflow.cli.PluginAbstractExec
 /**
  * Implements nextflow cache and restore commands
@@ -47,7 +46,7 @@ class CacheCommand implements PluginAbstractExec {
 
     protected void cacheBackup() {
         log.debug "Running Nextflow cache backup"
-        if( !SysEnv.get('NXF_CLOUDCACHE_PATH')) {
+        if( !getSession().cloudCachePath ) {
             // legacy cache manager
             new CacheManager(System.getenv()).saveCacheFiles()
         }
@@ -69,7 +68,7 @@ class CacheCommand implements PluginAbstractExec {
     }
 
     protected void cacheRestore() {
-        if( !SysEnv.get('NXF_CLOUDCACHE_PATH')) {
+        if( !getSession().cloudCachePath ) {
             log.debug "Running Nextflow cache restore"
             // legacy cache manager
             new CacheManager(System.getenv()).restoreCacheFiles()
diff --git a/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerFactory.groovy b/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerFactory.groovy
index e3e7f67aa2..3133a5270b 100644
--- a/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerFactory.groovy
+++ b/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerFactory.groovy
@@ -54,7 +54,7 @@ class TowerFactory implements TraceObserverFactory {
         final tower = createTowerClient(session, config)
         result.add(tower)
         // create the logs checkpoint
-        if( env.containsKey('NXF_CLOUDCACHE_PATH') )
+        if( session.cloudCachePath )
             result.add( new LogsCheckpoint() )
         return result
     }

From 035e6e7bdd722d1bf5852f63ec017fc658d5f4e2 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Tue, 10 Oct 2023 10:19:59 +0200
Subject: [PATCH 204/350] Support for Fusion unprivileged execution (#4387)

This commit allows disabling the privileged container execution
when using the fusion file system. This can be controlled by using the following
configuration setting:

```
 fusion.privileged = true|false // default true
```

The effective use of this setting depends on the target execution.
Currently, it's only supported by the Kubernetes executor which
requires the use the k8s-fuse-plugin to be installed in the target cluster

More details here https://github.com/nextflow-io/k8s-fuse-plugin



Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/fusion.md                                |  8 +++
 .../nextflow/fusion/FusionAwareTask.groovy    |  4 ++
 .../nextflow/fusion/FusionConfig.groovy       | 17 +++++++
 .../nextflow/fusion/FusionEnvProvider.groovy  |  4 +-
 .../groovy/nextflow/k8s/K8sTaskHandler.groovy |  6 ++-
 .../nextflow/k8s/model/PodSpecBuilder.groovy  | 23 +++++++++
 .../nextflow/fusion/FusionConfigTest.groovy   | 13 +++++
 .../nextflow/k8s/K8sTaskHandlerTest.groovy    | 50 ++++++++++++++++++-
 .../k8s/model/PodSpecBuilderTest.groovy       | 46 +++++++++++++++++
 9 files changed, 165 insertions(+), 6 deletions(-)

diff --git a/docs/fusion.md b/docs/fusion.md
index 8b0c1fbca4..186837e76b 100644
--- a/docs/fusion.md
+++ b/docs/fusion.md
@@ -199,6 +199,14 @@ The following configuration options are available:
 `fusion.logOutput`
 : Where the logging output is written. 
 
+`fusion.privileged`
+: :::{versionadded} 23.10.0
+  :::
+: This allows disabling the privileged container execution when using the Fusion file system.
+  The effective use of this setting depends on the target execution. Currently, it's only supported by the Kubernetes
+  executor which requires the use the [k8s-fuse-plugin](https://github.com/nextflow-io/k8s-fuse-plugin) to be installed
+  in the target cluster (default: `true`).
+
 `fusion.tagsEnabled`
 : Enable/disable the tagging of files created in the underlying object storage via the Fusion client (default: `true`).
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/fusion/FusionAwareTask.groovy b/modules/nextflow/src/main/groovy/nextflow/fusion/FusionAwareTask.groovy
index 8adba584cb..d89c462283 100644
--- a/modules/nextflow/src/main/groovy/nextflow/fusion/FusionAwareTask.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/fusion/FusionAwareTask.groovy
@@ -47,6 +47,10 @@ trait FusionAwareTask {
         return fusionEnabled
     }
 
+    FusionConfig fusionConfig() {
+        return FusionConfig.getConfig()
+    }
+
     FusionScriptLauncher fusionLauncher() {
         if( fusionLauncher==null ) {
             fusionLauncher = fusionEnabled()
diff --git a/modules/nextflow/src/main/groovy/nextflow/fusion/FusionConfig.groovy b/modules/nextflow/src/main/groovy/nextflow/fusion/FusionConfig.groovy
index e392bc41ce..e6b71f0dd0 100644
--- a/modules/nextflow/src/main/groovy/nextflow/fusion/FusionConfig.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/fusion/FusionConfig.groovy
@@ -18,6 +18,9 @@
 package nextflow.fusion
 
 import groovy.transform.CompileStatic
+import groovy.transform.Memoized
+import nextflow.Global
+import nextflow.SysEnv
 /**
  * Model Fusion config options
  *
@@ -40,6 +43,7 @@ class FusionConfig {
     final private String logLevel
     final private boolean tagsEnabled
     final private String tagsPattern
+    final private boolean privileged
 
     boolean enabled() { enabled }
 
@@ -63,6 +67,10 @@ class FusionConfig {
         this.containerConfigUrl ? new URL(this.containerConfigUrl) : null
     }
 
+    boolean privileged() {
+        return privileged
+    }
+
     FusionConfig(Map opts, Map<String,String> env=System.getenv()) {
         this.enabled = opts.enabled
         this.exportAwsAccessKeys = opts.exportAwsAccessKeys
@@ -72,6 +80,7 @@ class FusionConfig {
         this.logOutput = opts.logOutput
         this.tagsEnabled = opts.tags==null || opts.tags.toString()!='false'
         this.tagsPattern = (opts.tags==null || (opts.tags instanceof Boolean && opts.tags)) ? DEFAULT_TAGS : ( opts.tags !instanceof Boolean ? opts.tags as String : null )
+        this.privileged = opts.privileged==null || opts.privileged.toString()=='true'
         if( containerConfigUrl && !validProtocol(containerConfigUrl))
             throw new IllegalArgumentException("Fusion container config URL should start with 'http:' or 'https:' protocol prefix - offending value: $containerConfigUrl")
     }
@@ -80,4 +89,12 @@ class FusionConfig {
         url.startsWith('http://') || url.startsWith('https://') || url.startsWith('file:/')
     }
 
+    static FusionConfig getConfig() {
+        return createConfig0(Global.config?.fusion as Map ?: Collections.emptyMap(), SysEnv.get())
+    }
+
+    @Memoized
+    static private FusionConfig createConfig0(Map config, Map env) {
+        new FusionConfig(config, env)
+    }
 }
diff --git a/modules/nextflow/src/main/groovy/nextflow/fusion/FusionEnvProvider.groovy b/modules/nextflow/src/main/groovy/nextflow/fusion/FusionEnvProvider.groovy
index 914efc09a4..a1c2f6e7e3 100644
--- a/modules/nextflow/src/main/groovy/nextflow/fusion/FusionEnvProvider.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/fusion/FusionEnvProvider.groovy
@@ -18,8 +18,6 @@
 package nextflow.fusion
 
 
-import nextflow.Global
-import nextflow.SysEnv
 import nextflow.plugin.Plugins
 /**
  * Provider strategy for {@link FusionEnv}
@@ -29,7 +27,7 @@ import nextflow.plugin.Plugins
 class FusionEnvProvider {
 
     Map<String,String> getEnvironment(String scheme) {
-        final config = new FusionConfig(Global.config?.fusion as Map ?: Collections.emptyMap(), SysEnv.get())
+        final config = FusionConfig.getConfig()
         final list = Plugins.getExtensions(FusionEnv)
         final result = new HashMap<String,String>()
         for( FusionEnv it : list ) {
diff --git a/modules/nextflow/src/main/groovy/nextflow/k8s/K8sTaskHandler.groovy b/modules/nextflow/src/main/groovy/nextflow/k8s/K8sTaskHandler.groovy
index 8f8b680fc0..f782e423d6 100644
--- a/modules/nextflow/src/main/groovy/nextflow/k8s/K8sTaskHandler.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/k8s/K8sTaskHandler.groovy
@@ -249,7 +249,11 @@ class K8sTaskHandler extends TaskHandler implements FusionAwareTask {
         }
 
         if ( fusionEnabled() ) {
-            builder.withPrivileged(true)
+            if( fusionConfig().privileged() )
+                builder.withPrivileged(true)
+            else {
+                builder.withResourcesLimits(["nextflow.io/fuse": 1])
+            }
 
             final env = fusionLauncher().fusionEnv()
             for( Map.Entry<String,String> it : env )
diff --git a/modules/nextflow/src/main/groovy/nextflow/k8s/model/PodSpecBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/k8s/model/PodSpecBuilder.groovy
index 6a36b27e63..45831207ac 100644
--- a/modules/nextflow/src/main/groovy/nextflow/k8s/model/PodSpecBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/k8s/model/PodSpecBuilder.groovy
@@ -116,6 +116,8 @@ class PodSpecBuilder {
 
     List<String> devices
 
+    Map<String,?> resourcesLimits
+
     /**
      * @return A sequential volume unique identifier
      */
@@ -316,6 +318,11 @@ class PodSpecBuilder {
         return this
     }
 
+    PodSpecBuilder withResourcesLimits(Map<String,?> limits) {
+        this.resourcesLimits = limits
+        return this
+    }
+
     PodSpecBuilder withPodOptions(PodOptions opts) {
         // -- pull policy
         if( opts.imagePullPolicy )
@@ -495,6 +502,10 @@ class PodSpecBuilder {
             container.resources = addDiskResources(this.disk, container.resources as Map)
         }
 
+        if( this.resourcesLimits ) {
+            container.resources = addResourcesLimits(this.resourcesLimits, container.resources as Map)
+        }
+
         // add storage definitions ie. volumes and mounts
         final List<Map> mounts = []
         final List<Map> volumes = []
@@ -578,6 +589,18 @@ class PodSpecBuilder {
         ]
     }
 
+    @PackageScope
+    Map addResourcesLimits(Map limits, Map result) {
+        if( result == null )
+            result = new LinkedHashMap(10)
+
+        final limits0 = result.limits as Map ?: new LinkedHashMap(10)
+        limits0.putAll( limits )
+        result.limits = limits0
+
+        return result
+    }
+
     @PackageScope
     Map addCpuResources(Integer cpus, Map res) {
         if( res == null )
diff --git a/modules/nextflow/src/test/groovy/nextflow/fusion/FusionConfigTest.groovy b/modules/nextflow/src/test/groovy/nextflow/fusion/FusionConfigTest.groovy
index 9262496d4e..b6d176038f 100644
--- a/modules/nextflow/src/test/groovy/nextflow/fusion/FusionConfigTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/fusion/FusionConfigTest.groovy
@@ -101,4 +101,17 @@ class FusionConfigTest extends Specification {
         [tags:'[*.txt](x=1)']   | true      | '[*.txt](x=1)'
 
     }
+
+    def 'should check privileged flag' () {
+        given:
+        def opts = new FusionConfig(OPTS)
+        expect:
+        opts.privileged() == EXPECTED
+
+        where:
+        OPTS                    | EXPECTED
+        [:]                     | true
+        [privileged:true]       | true
+        [privileged:false]      | false
+    }
 }
diff --git a/modules/nextflow/src/test/groovy/nextflow/k8s/K8sTaskHandlerTest.groovy b/modules/nextflow/src/test/groovy/nextflow/k8s/K8sTaskHandlerTest.groovy
index 1433ab5b3f..c0b4146b96 100644
--- a/modules/nextflow/src/test/groovy/nextflow/k8s/K8sTaskHandlerTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/k8s/K8sTaskHandlerTest.groovy
@@ -23,8 +23,9 @@ import java.nio.file.Paths
 import nextflow.Session
 import nextflow.SysEnv
 import nextflow.exception.NodeTerminationException
-import nextflow.fusion.FusionScriptLauncher
 import nextflow.file.http.XPath
+import nextflow.fusion.FusionConfig
+import nextflow.fusion.FusionScriptLauncher
 import nextflow.k8s.client.ClientConfig
 import nextflow.k8s.client.K8sClient
 import nextflow.k8s.client.K8sResponseException
@@ -882,7 +883,7 @@ class K8sTaskHandlerTest extends Specification {
         handler.completeTimeMillis == 20
     }
 
-    def 'should create a fusion pod' () {
+    def 'should create a fusion privileged pod' () {
         given:
         def WORK_DIR = XPath.get('http://some/work/dir')
         def config = Mock(TaskConfig)
@@ -925,6 +926,51 @@ class K8sTaskHandlerTest extends Specification {
         result.spec.containers[0].env == [[name:'FUSION_BUCKETS', value:'this,that']]
      }
 
+    def 'should create a fusion unprivileged pod' () {
+        given:
+        def WORK_DIR = XPath.get('http://some/work/dir')
+        def config = Mock(TaskConfig)
+        def task = Mock(TaskRun)
+        def client = Mock(K8sClient)
+        def builder = Mock(K8sWrapperBuilder)
+        def launcher = Mock(FusionScriptLauncher)
+        def handler = Spy(new K8sTaskHandler(builder:builder, client: client))
+        Map result
+
+        when:
+        result = handler.newSubmitRequest(task)
+        then:
+        launcher.fusionEnv() >> [FUSION_BUCKETS: 'this,that']
+        launcher.toContainerMount(WORK_DIR.resolve('.command.run')) >> Path.of('/fusion/http/work/dir/.command.run')
+        launcher.fusionSubmitCli(task) >> ['/usr/bin/fusion', 'bash', '/fusion/http/work/dir/.command.run']
+        and:
+        handler.getTask() >> task
+        handler.fusionEnabled() >> true
+        handler.fusionLauncher() >> launcher
+        handler.fusionConfig() >> new FusionConfig(privileged: false)
+        and:
+        task.getContainer() >> 'debian:latest'
+        task.getWorkDir() >> WORK_DIR
+        task.getConfig() >> config
+        and:
+        1 * handler.fixOwnership() >> false
+        1 * handler.entrypointOverride() >> false
+        1 * handler.getPodOptions() >> new PodOptions()
+        1 * handler.getSyntheticPodName(task) >> 'nf-123'
+        1 * handler.getLabels(task) >> [:]
+        1 * handler.getAnnotations() >> [:]
+        1 * handler.getContainerMounts() >> []
+        and:
+        1 * config.getCpus() >> 0
+        1 * config.getMemory() >> null
+        1 * client.getConfig() >> new ClientConfig()
+        and:
+        result.spec.containers[0].args == ['/usr/bin/fusion', 'bash', '/fusion/http/work/dir/.command.run']
+        result.spec.containers[0].env == [[name:'FUSION_BUCKETS', value:'this,that']]
+        result.spec.containers[0].resources == [limits:['nextflow.io/fuse':1]]
+        !result.spec.containers[0].securityContext
+    }
+
     def 'get fusion submit command' () {
         given:
         def handler = Spy(K8sTaskHandler) {
diff --git a/modules/nextflow/src/test/groovy/nextflow/k8s/model/PodSpecBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/k8s/model/PodSpecBuilderTest.groovy
index e808d0c08e..c01e385243 100644
--- a/modules/nextflow/src/test/groovy/nextflow/k8s/model/PodSpecBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/k8s/model/PodSpecBuilderTest.groovy
@@ -17,6 +17,7 @@
 package nextflow.k8s.model
 
 import nextflow.executor.res.AcceleratorResource
+import nextflow.util.MemoryUnit
 import spock.lang.Specification
 import spock.lang.Unroll
 /**
@@ -118,6 +119,35 @@ class PodSpecBuilderTest extends Specification {
 
     }
 
+    def 'should create pod with resources limits' () {
+        when:
+        def pod1 = new PodSpecBuilder()
+            .withPodName('foo')
+            .withImageName('busybox')
+            .withCommand('echo foo')
+            .withResourcesLimits('nextflow.io/fuse': 1)
+            .build()
+
+        then:
+        pod1.spec.containers[0].resources == [limits:['nextflow.io/fuse':1]]
+
+
+        when:
+        def pod2 = new PodSpecBuilder()
+            .withPodName('foo')
+            .withImageName('busybox')
+            .withCommand('echo foo')
+            .withCpus(8)
+            .withMemory(MemoryUnit.of('10GB'))
+            .withResourcesLimits('nextflow.io/fuse': 1)
+            .build()
+
+        then:
+        pod2.spec.containers[0].resources == [
+                                                requests: ['cpu':8, 'memory':'10240Mi'],
+                                                limits: [memory:'10240Mi', 'nextflow.io/fuse':1] ]
+    }
+
     def 'should set namespace, labels and annotations' () {
 
         when:
@@ -627,6 +657,22 @@ class PodSpecBuilderTest extends Specification {
         res.limits == ['example.com/fpga': 10]
     }
 
+    def 'should add resources limits' () {
+        given:
+        def builder = new PodSpecBuilder()
+        Map resources
+
+        when:
+        resources = builder.addResourcesLimits(['foo':1], null)
+        then:
+        resources == [limits:[foo:1]]
+
+        when:
+        resources = builder.addResourcesLimits(['foo':1], [requests: ['x':1], limits: ['y': 2]])
+        then:
+        resources == [requests:[x:1], limits:[y:2, foo:1]]
+    }
+
 
     @Unroll
     def 'should sanitize k8s label value: #label' () {

From be0cf0c2ee20e0657e278f7c5e3cbc3a45420864 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Tue, 10 Oct 2023 10:33:46 +0200
Subject: [PATCH 205/350] Remove unsupported K8s device capability [ci fast]

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../nextflow/k8s/model/PodSpecBuilder.groovy    |  8 --------
 .../k8s/model/PodSpecBuilderTest.groovy         | 17 -----------------
 2 files changed, 25 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/k8s/model/PodSpecBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/k8s/model/PodSpecBuilder.groovy
index 45831207ac..47a66132d3 100644
--- a/modules/nextflow/src/main/groovy/nextflow/k8s/model/PodSpecBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/k8s/model/PodSpecBuilder.groovy
@@ -308,11 +308,6 @@ class PodSpecBuilder {
         return this
     }
 
-    PodSpecBuilder withDevices(List<String> dev) {
-        this.devices = dev
-        return this
-    }
-
     PodSpecBuilder withActiveDeadline(int seconds) {
         this.activeDeadlineSeconds = seconds
         return this
@@ -417,9 +412,6 @@ class PodSpecBuilder {
         if( imagePullPolicy )
             container.imagePullPolicy = imagePullPolicy
 
-        if( devices )
-            container.devices = devices
-
         final secContext = new LinkedHashMap(10)
         if( privileged ) {
             // note: privileged flag needs to be defined in the *container* securityContext
diff --git a/modules/nextflow/src/test/groovy/nextflow/k8s/model/PodSpecBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/k8s/model/PodSpecBuilderTest.groovy
index c01e385243..188e72dc81 100644
--- a/modules/nextflow/src/test/groovy/nextflow/k8s/model/PodSpecBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/k8s/model/PodSpecBuilderTest.groovy
@@ -102,23 +102,6 @@ class PodSpecBuilderTest extends Specification {
 
     }
 
-    def 'should create pod spec with device and capabilities' () {
-
-        when:
-        def pod = new PodSpecBuilder()
-                .withPodName('foo')
-                .withImageName('busybox')
-                .withCommand('echo foo')
-                .withDevices(['/dev/fuse'])
-                .withCapabilities(add:['SYS_ADMIN'])
-                .build()
-
-        then:
-        pod.spec.containers[0].devices == ['/dev/fuse']
-        pod.spec.containers[0].securityContext == [capabilities: [add:['SYS_ADMIN']]]
-
-    }
-
     def 'should create pod with resources limits' () {
         when:
         def pod1 = new PodSpecBuilder()

From ff012dcdd5a5a9dcd65883430025af82e64faffc Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Tue, 10 Oct 2023 11:50:34 +0200
Subject: [PATCH 206/350] Add bioconda and seqera Conda default channels
 (#4359)

Signed-off-by: Phil Ewels <phil.ewels@seqera.io>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../src/main/io/seqera/wave/plugin/WaveClient.groovy      | 2 +-
 .../src/test/io/seqera/wave/plugin/WaveClientTest.groovy  | 8 ++++++--
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
index 891b4f5a0f..e5761c29e1 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
@@ -79,7 +79,7 @@ class WaveClient {
                         'Accept','application/vnd.docker.distribution.manifest.v2+json',
                         'Accept','application/vnd.docker.distribution.manifest.list.v2+json' }
 
-    private static final List<String> DEFAULT_CONDA_CHANNELS = ['conda-forge','defaults']
+    private static final List<String> DEFAULT_CONDA_CHANNELS = ['seqera','bioconda','conda-forge','defaults']
 
     private static final String DEFAULT_SPACK_ARCH = 'x86_64'
 
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
index 36108f236f..b4232bc803 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
@@ -538,6 +538,8 @@ class WaveClientTest extends Specification {
         and:
         assets.condaFile.text == '''\
                 channels:
+                - seqera
+                - bioconda
                 - conda-forge
                 - defaults
                 dependencies:
@@ -560,7 +562,7 @@ class WaveClientTest extends Specification {
         assets.containerFile == '''\
                 FROM mambaorg/micromamba:1.5.1
                 RUN \\
-                    micromamba install -y -n base -c conda-forge -c defaults -f https://host.com/conda-lock.yml \\
+                    micromamba install -y -n base -c seqera -c bioconda -c conda-forge -c defaults -f https://host.com/conda-lock.yml \\
                     && micromamba install -y -n base conda-forge::procps-ng \\
                     && micromamba clean -a -y
                 USER root
@@ -734,6 +736,8 @@ class WaveClientTest extends Specification {
         and:
         assets.condaFile.text == '''\
                 channels:
+                - seqera
+                - bioconda
                 - conda-forge
                 - defaults
                 dependencies:
@@ -756,7 +760,7 @@ class WaveClientTest extends Specification {
                 BootStrap: docker
                 From: mambaorg/micromamba:1.5.1
                 %post
-                    micromamba install -y -n base -c conda-forge -c defaults -f https://host.com/lock-file.yaml
+                    micromamba install -y -n base -c seqera -c bioconda -c conda-forge -c defaults -f https://host.com/lock-file.yaml
                     micromamba install -y -n base conda-forge::procps-ng
                     micromamba clean -a -y
                 %environment

From a84208a8f5d3c96d4c664ce42c4b8def059317d9 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Tue, 10 Oct 2023 11:58:42 +0200
Subject: [PATCH 207/350] Bump nf-amazon@2.1.4

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-amazon/changelog.txt                      | 4 ++++
 plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/plugins/nf-amazon/changelog.txt b/plugins/nf-amazon/changelog.txt
index 12d654ba91..8696d88720 100644
--- a/plugins/nf-amazon/changelog.txt
+++ b/plugins/nf-amazon/changelog.txt
@@ -1,5 +1,9 @@
 nf-amazon changelog
 ===================
+2.1.4 - 10 Oct 2023
+- Improve S3 endpoint validation [2b9ae6aa]
+- Add -cloudcache CLI option (#4385) [73fda582]
+
 2.1.3 - 28 Sep 2023
 - Fix minor typos in changelogs/source code (#4319) [4ce9f1df]
 - Fix List of S3 bucket for custom endpoint [4327fa58]
diff --git a/plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF b/plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF
index 74871f9a06..f206656eb2 100644
--- a/plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: nextflow.cloud.aws.AmazonPlugin
 Plugin-Id: nf-amazon
-Plugin-Version: 2.1.3
+Plugin-Version: 2.1.4
 Plugin-Provider: Seqera Labs
 Plugin-Requires: >=23.05.0-edge

From b37b40142f6e97c802a80feaa25d8b39efac7a00 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Tue, 10 Oct 2023 11:58:56 +0200
Subject: [PATCH 208/350] Bump nf-cloudcache@0.3.0

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-cloudcache/changelog.txt                      | 3 +++
 plugins/nf-cloudcache/src/resources/META-INF/MANIFEST.MF | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/plugins/nf-cloudcache/changelog.txt b/plugins/nf-cloudcache/changelog.txt
index 2e9af969f8..05fd5fad8e 100644
--- a/plugins/nf-cloudcache/changelog.txt
+++ b/plugins/nf-cloudcache/changelog.txt
@@ -1,5 +1,8 @@
 nf-cloudcache changelog
 =======================
+0.3.0 - 10 Oct 2023
+- Add -cloudcache CLI option (#4385) [73fda582]
+
 0.2.0 - 17 Aug 2023
 - Remove lock file from cloudcache (#4167) [6e6ea579]
 - Enable cloud cache based on environment variable (#4160) [a66b0e63]
diff --git a/plugins/nf-cloudcache/src/resources/META-INF/MANIFEST.MF b/plugins/nf-cloudcache/src/resources/META-INF/MANIFEST.MF
index 042ea9ff79..b4267c3b61 100644
--- a/plugins/nf-cloudcache/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-cloudcache/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: nextflow.CloudCachePlugin
 Plugin-Id: nf-cloudcache
-Plugin-Version: 0.2.0
+Plugin-Version: 0.3.0
 Plugin-Provider: Seqera Labs
 Plugin-Requires: >=23.04.0

From b4eb8b96a6eb776eebb1faea94c312550cde7479 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Tue, 10 Oct 2023 11:59:14 +0200
Subject: [PATCH 209/350] Bump nf-google@1.8.3

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-google/changelog.txt                      | 4 ++++
 plugins/nf-google/src/resources/META-INF/MANIFEST.MF | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/plugins/nf-google/changelog.txt b/plugins/nf-google/changelog.txt
index 492c2fa1de..1637822ae4 100644
--- a/plugins/nf-google/changelog.txt
+++ b/plugins/nf-google/changelog.txt
@@ -1,5 +1,9 @@
 nf-google changelog
 ===================
+1.8.3 - 10 Oct 2023
+- Add setting to enable the use of sync command [f0d5cc5c]
+- Fix Google Batch do not stop running jobs (#4381) [3d6b7358]
+
 1.8.2 - 28 Sep 2023
 - Fix allow_other vulnerability preventing google-batch submissions (#4332) [9b3741e3]
 
diff --git a/plugins/nf-google/src/resources/META-INF/MANIFEST.MF b/plugins/nf-google/src/resources/META-INF/MANIFEST.MF
index e5c62ccecd..8522585c8e 100644
--- a/plugins/nf-google/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-google/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: nextflow.cloud.google.GoogleCloudPlugin
 Plugin-Id: nf-google
-Plugin-Version: 1.8.2
+Plugin-Version: 1.8.3
 Plugin-Provider: Seqera Labs
 Plugin-Requires: >=23.02.0-edge

From 5681ab137d638af8e8948e1211c33133700a0a68 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Tue, 10 Oct 2023 11:59:29 +0200
Subject: [PATCH 210/350] Bump nf-tower@1.6.3

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-tower/changelog.txt                      | 3 +++
 plugins/nf-tower/src/resources/META-INF/MANIFEST.MF | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/plugins/nf-tower/changelog.txt b/plugins/nf-tower/changelog.txt
index 83b7acbb04..897aa3f12a 100644
--- a/plugins/nf-tower/changelog.txt
+++ b/plugins/nf-tower/changelog.txt
@@ -1,5 +1,8 @@
 nf-tower changelog
 ===================
+1.6.3 - 10 Oct 2023
+- Add -cloudcache CLI option (#4385) [73fda582]
+
 1.6.2 - 28 Sep 2023
 - Disable Tower container field for multiple images [ci fast] [b53936b0]
 - Bump Apache 2.0 license to tower client [e4a878b6]
diff --git a/plugins/nf-tower/src/resources/META-INF/MANIFEST.MF b/plugins/nf-tower/src/resources/META-INF/MANIFEST.MF
index 4080672d8b..58bd2aa7d9 100644
--- a/plugins/nf-tower/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-tower/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: io.seqera.tower.plugin.TowerPlugin
 Plugin-Id: nf-tower
-Plugin-Version: 1.6.2
+Plugin-Version: 1.6.3
 Plugin-Provider: Seqera Labs
 Plugin-Requires: >=23.05.0-edge

From de1de6c72736456a629a354f9a46d0766b613e08 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Tue, 10 Oct 2023 11:59:40 +0200
Subject: [PATCH 211/350] Bump nf-wave@0.14.0

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-wave/changelog.txt                      | 5 +++++
 plugins/nf-wave/src/resources/META-INF/MANIFEST.MF | 2 +-
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/plugins/nf-wave/changelog.txt b/plugins/nf-wave/changelog.txt
index 1aa7811a29..8fc6fe8039 100644
--- a/plugins/nf-wave/changelog.txt
+++ b/plugins/nf-wave/changelog.txt
@@ -1,5 +1,10 @@
 nf-wave changelog
 ==================
+0.14.0 - 10 Oct 2023
+- Add bioconda and seqera Conda default channels (#4359) [ff012dcd]
+- Improve Wave error handling [d47e8b07]
+- Improve Wave config validation [7d5a21b0]
+
 0.13.0 - 28 Sep 2023
 - Wave does not support 'null' container engine [f3eba3d7]
 - Default Conda basePackages to "conda-forge::procps-ng" [367af52f]
diff --git a/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF b/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF
index 77d03acf57..b6fdf2ec2b 100644
--- a/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: io.seqera.wave.plugin.WavePlugin
 Plugin-Id: nf-wave
-Plugin-Version: 0.13.0
+Plugin-Version: 0.14.0
 Plugin-Provider: Seqera Labs
 Plugin-Requires: >=23.05.0-edge

From 4f86bed999f2a5f98340e87a88cc0274c6a83487 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Tue, 10 Oct 2023 12:03:43 +0200
Subject: [PATCH 212/350] Update changelog

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 changelog.txt | 27 ++++++++++++++++++++++++++-
 1 file changed, 26 insertions(+), 1 deletion(-)

diff --git a/changelog.txt b/changelog.txt
index 680f92d856..98dddebdf6 100644
--- a/changelog.txt
+++ b/changelog.txt
@@ -1,5 +1,30 @@
 NEXTFLOW CHANGE-LOG
 ===================
+23.09.3-edge - 10 Oct 2023
+- Add -cloudcache CLI option (#4385) [73fda582]
+- Add bioconda and seqera Conda default channels (#4359) [ff012dcd]
+- Add codespell: config, workflow and have typos fixed (#4324) [e044b7a5]
+- Add docs page on caching and resuming (#4371) [21190a3c]
+- Add example of using the transpose operator with multiple items in element (#4364) [0bce2be0]
+- Add setting to enable the use of sync command [f0d5cc5c]
+- Improve S3 endpoint validation [2b9ae6aa]
+- Improve Wave config validation [7d5a21b0]
+- Improve Wave error handling [d47e8b07]
+- Fix Google Batch do not stop running jobs (#4381) [3d6b7358]
+- Incorporate README content into Nextflow docs (#4263) [74a0f998]
+- Never say (nearly) Oops again (#4356) [4a39542b]
+- Remove unsupported K8s device capability [ci fast] [be0cf0c2]
+- Remove unused -dsl2 option [ci fast] [3cb91a15]
+- Rename Microsoft AAD to Microsoft Entra (#4362) [5e3f2c0a]
+- Return -1 when exitcode file is empty (#4354) [d26c42be]
+- Support for Fusion unprivileged execution (#4387) [035e6e7b]
+- Use HistoryFile.Record instead of Record type conflic [ci fast] [11c3aac5]
+- Bump nf-amazon@2.1.4 [a84208a8]
+- Bump nf-cloudcache@0.3.0 [b37b4014]
+- Bump nf-google@1.8.3 [b4eb8b96]
+- Bump nf-tower@1.6.3 [5681ab13]
+- Bump nf-wave@0.14.0 [de1de6c7]
+
 23.09.2-edge - 28 Sep 2023
 - Add conda.enabled to conda config scope docs (#4320) [0b74c4e2]
 - Add developer docs (#4065) [06843d87]
@@ -445,7 +470,7 @@ NEXTFLOW CHANGE-LOG
 - Fix serialization of S3 paths with spaces (#3565) [ce487624]
 - Fix string literal method names with parens (#3604) [8278078a]
 - Fix submit command in error message for grid executors that pipe wrapper script (#3548) [40ebd308]
-- Fix typos in the documentation [skip ci] (#3640) [eccc1130]
+- Fix typos in the documentation (#3640) [eccc1130]
 - Fix unique fingerprint for Wave bundle resources [b59fa728]
 - Log exception when an unexpected  occurs (#3603) [9aeca99f]
 - Minor change on container resolution [23d47ded]

From 1bfb8b14ee5158d8041528d7aeccd7805a0dda5a Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Tue, 10 Oct 2023 12:04:10 +0200
Subject: [PATCH 213/350] [release 23.09.3-edge] [ci fast] Update timestamp and
 build number

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 VERSION                                                |  2 +-
 docs/conf.py                                           |  2 +-
 .../src/main/resources/META-INF/plugins-info.txt       | 10 +++++-----
 modules/nf-commons/src/main/nextflow/Const.groovy      |  6 +++---
 nextflow                                               |  2 +-
 nextflow.md5                                           |  2 +-
 nextflow.sha1                                          |  2 +-
 nextflow.sha256                                        |  2 +-
 8 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/VERSION b/VERSION
index 31d596a086..bc02edad74 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-23.09.2-edge
+23.09.3-edge
diff --git a/docs/conf.py b/docs/conf.py
index 3efe91c293..142e2f76ba 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -61,7 +61,7 @@
 # The short X.Y version.
 version = '23.09'
 # The full version, including alpha/beta/rc tags.
-release = '23.09.2-edge'
+release = '23.09.3-edge'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
diff --git a/modules/nextflow/src/main/resources/META-INF/plugins-info.txt b/modules/nextflow/src/main/resources/META-INF/plugins-info.txt
index 923df8f700..bb727d9a50 100644
--- a/modules/nextflow/src/main/resources/META-INF/plugins-info.txt
+++ b/modules/nextflow/src/main/resources/META-INF/plugins-info.txt
@@ -1,9 +1,9 @@
-nf-amazon@2.1.3
+nf-amazon@2.1.4
 nf-azure@1.3.2
-nf-cloudcache@0.2.0
+nf-cloudcache@0.3.0
 nf-codecommit@0.1.5
 nf-console@1.0.6
 nf-ga4gh@1.1.0
-nf-google@1.8.2
-nf-tower@1.6.2
-nf-wave@0.13.0
\ No newline at end of file
+nf-google@1.8.3
+nf-tower@1.6.3
+nf-wave@0.14.0
\ No newline at end of file
diff --git a/modules/nf-commons/src/main/nextflow/Const.groovy b/modules/nf-commons/src/main/nextflow/Const.groovy
index 28444210c5..726c2ada21 100644
--- a/modules/nf-commons/src/main/nextflow/Const.groovy
+++ b/modules/nf-commons/src/main/nextflow/Const.groovy
@@ -52,17 +52,17 @@ class Const {
     /**
      * The application version
      */
-    static public final String APP_VER = "23.09.2-edge"
+    static public final String APP_VER = "23.09.3-edge"
 
     /**
      * The app build time as linux/unix timestamp
      */
-    static public final long APP_TIMESTAMP = 1695852467160
+    static public final long APP_TIMESTAMP = 1696931920194
 
     /**
      * The app build number
      */
-    static public final int APP_BUILDNUM = 5884
+    static public final int APP_BUILDNUM = 5888
 
     /**
      * The app build time string relative to UTC timezone
diff --git a/nextflow b/nextflow
index 93342c3697..65c4379239 100755
--- a/nextflow
+++ b/nextflow
@@ -15,7 +15,7 @@
 #  limitations under the License.
 
 [[ "$NXF_DEBUG" == 'x' ]] && set -x
-NXF_VER=${NXF_VER:-'23.09.2-edge'}
+NXF_VER=${NXF_VER:-'23.09.3-edge'}
 NXF_ORG=${NXF_ORG:-'nextflow-io'}
 NXF_HOME=${NXF_HOME:-$HOME/.nextflow}
 NXF_PROT=${NXF_PROT:-'https'}
diff --git a/nextflow.md5 b/nextflow.md5
index a13b13c2e5..87c82b6bc7 100644
--- a/nextflow.md5
+++ b/nextflow.md5
@@ -1 +1 @@
-0daca43a243bc69bbda98d5beae89127
+f4597acee862538b6a1beda1c5b07855
diff --git a/nextflow.sha1 b/nextflow.sha1
index f4db5f3041..6a4acbe394 100644
--- a/nextflow.sha1
+++ b/nextflow.sha1
@@ -1 +1 @@
-bc2ca43dea392a6bdfc0c5d41541523b8f80c537
+cb9e8a01275e511f792aa11ecce411f92e7e4625
diff --git a/nextflow.sha256 b/nextflow.sha256
index 952907fbee..1d0470b3d0 100644
--- a/nextflow.sha256
+++ b/nextflow.sha256
@@ -1 +1 @@
-2f1e00d05581db1d4677185c82b3f2a65ef484d526f8a32b0d3855baa63f9406
+7aff41f4a15382c78c06053ee4648ae784e7b4363b248d6ee22a1f05ef27480c

From dfb5bf092066ea5ac81f3c17ed14e1a42a126366 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Tue, 10 Oct 2023 15:10:39 +0200
Subject: [PATCH 214/350] Changelog minor changes [ci skip]

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 changelog.txt | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/changelog.txt b/changelog.txt
index 98dddebdf6..b268d3615b 100644
--- a/changelog.txt
+++ b/changelog.txt
@@ -13,12 +13,12 @@ NEXTFLOW CHANGE-LOG
 - Fix Google Batch do not stop running jobs (#4381) [3d6b7358]
 - Incorporate README content into Nextflow docs (#4263) [74a0f998]
 - Never say (nearly) Oops again (#4356) [4a39542b]
-- Remove unsupported K8s device capability [ci fast] [be0cf0c2]
-- Remove unused -dsl2 option [ci fast] [3cb91a15]
+- Remove unsupported K8s device capability [be0cf0c2]
+- Remove unused -dsl2 option [3cb91a15]
 - Rename Microsoft AAD to Microsoft Entra (#4362) [5e3f2c0a]
 - Return -1 when exitcode file is empty (#4354) [d26c42be]
 - Support for Fusion unprivileged execution (#4387) [035e6e7b]
-- Use HistoryFile.Record instead of Record type conflic [ci fast] [11c3aac5]
+- Use HistoryFile.Record instead of Record type conflic [11c3aac5]
 - Bump nf-amazon@2.1.4 [a84208a8]
 - Bump nf-cloudcache@0.3.0 [b37b4014]
 - Bump nf-google@1.8.3 [b4eb8b96]

From 882f369ebf54c821ea1306f7bb1069a7d0f63e60 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Tue, 10 Oct 2023 23:19:09 +0200
Subject: [PATCH 215/350] Add inspect command validation tests

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../groovy/nextflow/cli/CmdInspect.groovy     | 10 +++++
 .../groovy/nextflow/cli/CmdInspectTest.groovy | 39 ++++++++++++++++++-
 2 files changed, 48 insertions(+), 1 deletion(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdInspect.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdInspect.groovy
index f1f192d031..00c943e83b 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdInspect.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdInspect.groovy
@@ -24,6 +24,7 @@ import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import nextflow.Session
 import nextflow.container.inspect.ContainersInspector
+import nextflow.exception.AbortOperationException
 import nextflow.util.LoggerHelper
 /**
  * Implement `inspect` command
@@ -88,6 +89,8 @@ class CmdInspect extends CmdBase {
     }
 
     protected void applyInspect(Session session) {
+        // disallow singularity w/o wave and freeze
+        checkSingularityConfig(session.config)
         // disable wave await mode when running
         if( session.config.wave instanceof Map )
             checkWaveConfig(session.config.wave as Map)
@@ -103,4 +106,11 @@ class CmdInspect extends CmdBase {
             wave.dryRun = !concretize
     }
 
+    protected void checkSingularityConfig(Map config) {
+        final sing = config.navigate('singularity.enabled',false)
+        final wave = config.navigate('wave.enabled',false)
+        final freeze = config.navigate('wave.freeze',false)
+        if( sing && (!wave || !freeze) )
+            throw new AbortOperationException("Inspect command with Singularity requires enabling 'wave' and 'freeze' settings")
+    }
 }
diff --git a/modules/nextflow/src/test/groovy/nextflow/cli/CmdInspectTest.groovy b/modules/nextflow/src/test/groovy/nextflow/cli/CmdInspectTest.groovy
index c6ed93ca74..2e45bae5c8 100644
--- a/modules/nextflow/src/test/groovy/nextflow/cli/CmdInspectTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/cli/CmdInspectTest.groovy
@@ -17,7 +17,7 @@
 
 package nextflow.cli
 
-
+import nextflow.exception.AbortOperationException
 import spock.lang.Specification
 import spock.lang.Unroll
 /**
@@ -51,4 +51,41 @@ class CmdInspectTest extends Specification {
 
     }
 
+    def 'should allow singularity only with wave and freeze' () {
+        given:
+        def cmd = Spy(new CmdInspect())
+
+        when:
+        cmd.checkSingularityConfig([:])
+        then:
+        noExceptionThrown()
+
+        when:
+        cmd.checkSingularityConfig([singularity:[enabled:false]])
+        then:
+        noExceptionThrown()
+
+        when:
+        cmd.checkSingularityConfig([wave:[enabled:true, freeze:true]])
+        then:
+        noExceptionThrown()
+
+        when:
+        cmd.checkSingularityConfig([singularity:[enabled:true], wave:[enabled:true, freeze:true]])
+        then:
+        noExceptionThrown()
+
+        // singularity w/o wave and freeze is not allowed
+        when:
+        cmd.checkSingularityConfig([singularity:[enabled:true]])
+        then:
+        thrown(AbortOperationException)
+
+        when:
+        cmd.checkSingularityConfig([singularity:[enabled:true], wave:[enabled:true]])
+        then:
+        thrown(AbortOperationException)
+
+    }
+
 }

From 6672c6d7bdee62b1088a14278acc2b45b5cf5297 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Wed, 11 Oct 2023 23:28:05 +0200
Subject: [PATCH 216/350] Fix conda channels order [ci fast]

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../src/main/io/seqera/wave/plugin/WaveClient.groovy      | 2 +-
 .../src/test/io/seqera/wave/plugin/WaveClientTest.groovy  | 8 ++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
index e5761c29e1..c913ef99fb 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
@@ -79,7 +79,7 @@ class WaveClient {
                         'Accept','application/vnd.docker.distribution.manifest.v2+json',
                         'Accept','application/vnd.docker.distribution.manifest.list.v2+json' }
 
-    private static final List<String> DEFAULT_CONDA_CHANNELS = ['seqera','bioconda','conda-forge','defaults']
+    private static final List<String> DEFAULT_CONDA_CHANNELS = ['seqera','conda-forge','bioconda','defaults']
 
     private static final String DEFAULT_SPACK_ARCH = 'x86_64'
 
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
index b4232bc803..3885ce2cf1 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
@@ -539,8 +539,8 @@ class WaveClientTest extends Specification {
         assets.condaFile.text == '''\
                 channels:
                 - seqera
-                - bioconda
                 - conda-forge
+                - bioconda
                 - defaults
                 dependencies:
                 - bioconda::rseqc=3.0.1
@@ -562,7 +562,7 @@ class WaveClientTest extends Specification {
         assets.containerFile == '''\
                 FROM mambaorg/micromamba:1.5.1
                 RUN \\
-                    micromamba install -y -n base -c seqera -c bioconda -c conda-forge -c defaults -f https://host.com/conda-lock.yml \\
+                    micromamba install -y -n base -c seqera -c conda-forge -c bioconda -c defaults -f https://host.com/conda-lock.yml \\
                     && micromamba install -y -n base conda-forge::procps-ng \\
                     && micromamba clean -a -y
                 USER root
@@ -737,8 +737,8 @@ class WaveClientTest extends Specification {
         assets.condaFile.text == '''\
                 channels:
                 - seqera
-                - bioconda
                 - conda-forge
+                - bioconda
                 - defaults
                 dependencies:
                 - salmon=1.2.3
@@ -760,7 +760,7 @@ class WaveClientTest extends Specification {
                 BootStrap: docker
                 From: mambaorg/micromamba:1.5.1
                 %post
-                    micromamba install -y -n base -c seqera -c bioconda -c conda-forge -c defaults -f https://host.com/lock-file.yaml
+                    micromamba install -y -n base -c seqera -c conda-forge -c bioconda -c defaults -f https://host.com/lock-file.yaml
                     micromamba install -y -n base conda-forge::procps-ng
                     micromamba clean -a -y
                 %environment

From 82a3f405edddb40ee31747a693681e6f1c86cad4 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Fri, 13 Oct 2023 08:44:59 +0200
Subject: [PATCH 217/350] Improve error message on invalid file url prefix

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../src/main/nextflow/file/FileHelper.groovy  |  6 ++++
 .../test/nextflow/file/FileHelperTest.groovy  | 29 +++++++++++++++++++
 2 files changed, 35 insertions(+)

diff --git a/modules/nf-commons/src/main/nextflow/file/FileHelper.groovy b/modules/nf-commons/src/main/nextflow/file/FileHelper.groovy
index 665829a644..47d5a72841 100644
--- a/modules/nf-commons/src/main/nextflow/file/FileHelper.groovy
+++ b/modules/nf-commons/src/main/nextflow/file/FileHelper.groovy
@@ -60,6 +60,8 @@ class FileHelper {
 
     static final public Pattern URL_PROTOCOL = ~/^([a-zA-Z][a-zA-Z0-9]*):\\/\\/.+/
 
+    static final public Pattern INVALID_URL_PREFIX = ~/^(?!file)([a-zA-Z][a-zA-Z0-9]*):\\/[^\\/].+/
+
     static final private Pattern BASE_URL = ~/(?i)((?:[a-z][a-zA-Z0-9]*)?:\/\/[^:|\/]+(?::\d*)?)(?:$|\/.*)/
 
     static final private Path localTempBasePath
@@ -288,6 +290,10 @@ class FileHelper {
             return Paths.get(str)
         }
 
+        // check for valid the url scheme
+        if( INVALID_URL_PREFIX.matcher(str).matches() )
+            throw new IllegalArgumentException("File path is prefixed with an invalid URL scheme - Offending path: '${Escape.blanks(str)}'")
+
         return asPath0(str)
     }
 
diff --git a/modules/nf-commons/src/test/nextflow/file/FileHelperTest.groovy b/modules/nf-commons/src/test/nextflow/file/FileHelperTest.groovy
index a6a2542d0c..72aeee017d 100644
--- a/modules/nf-commons/src/test/nextflow/file/FileHelperTest.groovy
+++ b/modules/nf-commons/src/test/nextflow/file/FileHelperTest.groovy
@@ -47,6 +47,29 @@ class FileHelperTest extends Specification {
         Files.createTempDirectory(tmp, 'test')
     }
 
+    def 'should match invalid url prefix' (){
+        expect:
+        FileHelper.INVALID_URL_PREFIX.matcher(STR).matches() == EXPECTED
+
+        where:
+        EXPECTED| STR
+        true    | 's3:/foo'
+        true    | 'az:/foo'
+        true    | 'gs:/foo'
+        true    | 'xyz:/foo'
+        and:
+        false   | 'file:/foo'   // <- this is ok
+        and:
+        false   | 's3://foo'
+        false   | 'az://foo'
+        false   | 'gs://foo'
+        false   | 'http://foo'
+        false   | 'https://foo'
+        false   | 'ftp://foo'
+        false   | 'xyz://foo'
+
+    }
+
     def 'should return a Path object' () {
 
         expect:
@@ -79,6 +102,12 @@ class FileHelperTest extends Specification {
         then:
         e = thrown(IllegalArgumentException)
         e.message == "Path string cannot ends with a blank or special characters -- Offending path: '/some/file.txt\\n'"
+
+        when:
+        FileHelper.asPath('s3:/some/broken/url')
+        then:
+        e = thrown(IllegalArgumentException)
+        e.message == "File path is prefixed with an invalid URL scheme - Offending path: 's3:/some/broken/url'"
     }
 
     def 'should strip query params from http files' () {

From ef5302635565c2e07d0de2e3df446ab63ab41691 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Fri, 13 Oct 2023 09:39:55 +0200
Subject: [PATCH 218/350] Add -with-cloudcache instead of -cloudcache

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/cli.md                                                 | 6 +++---
 modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy | 2 +-
 .../nextflow/src/main/groovy/nextflow/cli/Launcher.groovy   | 2 +-
 .../src/test/groovy/nextflow/cli/LauncherTest.groovy        | 6 +++---
 4 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/docs/cli.md b/docs/cli.md
index d9faee429d..5fd19d7aaa 100644
--- a/docs/cli.md
+++ b/docs/cli.md
@@ -1134,9 +1134,6 @@ The `run` command is used to execute a local pipeline script or remote pipeline
 `-cache`
 : Enable/disable processes caching.
 
-`-cloudcache`
-: Enable the use of the Cloud cache plugin for storing cache metadata to an object storage bucket.
-
 `-d, -deep`
 : Create a shallow clone of the specified depth.
 
@@ -1230,6 +1227,9 @@ The `run` command is used to execute a local pipeline script or remote pipeline
 `-with-charliecloud`
 : Enable process execution in a Charliecloud container.
 
+`-with-cloudcache`
+: Enable the use of the Cloud cache plugin for storing cache metadata to an object storage bucket.
+
 `-with-conda`
 : Use the specified Conda environment package or file (must end with `.yml` or `.yaml`)
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
index a44201d35a..ec233778c9 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
@@ -111,7 +111,7 @@ class CmdRun extends CmdBase implements HubOptions {
     @Parameter(names=['-bucket-dir'], description = 'Remote bucket where intermediate result files are stored')
     String bucketDir
 
-    @Parameter(names=['-cloudcache'], description = 'Enable the use of object storage bucket as storage for cache meta-data')
+    @Parameter(names=['-with-cloudcache'], description = 'Enable the use of object storage bucket as storage for cache meta-data')
     String cloudCachePath
 
     /**
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy
index ad3a32f844..eabdb84bf0 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy
@@ -224,7 +224,7 @@ class Launcher {
                 normalized << '%all'
             }
 
-            else if( current == '-cloudcache' && (i==args.size() || args[i].startsWith('-'))) {
+            else if( current == '-with-cloudcache' && (i==args.size() || args[i].startsWith('-'))) {
                 normalized << '-'
             }
 
diff --git a/modules/nextflow/src/test/groovy/nextflow/cli/LauncherTest.groovy b/modules/nextflow/src/test/groovy/nextflow/cli/LauncherTest.groovy
index bb1c82e182..b0898f48dd 100644
--- a/modules/nextflow/src/test/groovy/nextflow/cli/LauncherTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/cli/LauncherTest.groovy
@@ -187,9 +187,9 @@ class LauncherTest extends Specification {
         launcher.normalizeArgs('run', '-', '-a', '-b') == ['run','-stdin', '-a', '-b']
         launcher.normalizeArgs('run') == ['run']
 
-        launcher.normalizeArgs('run','-cloudcache') == ['run', '-cloudcache', '-']
-        launcher.normalizeArgs('run','-cloudcache', '-x') == ['run', '-cloudcache', '-', '-x']
-        launcher.normalizeArgs('run','-cloudcache', 's3://foo/bar') == ['run', '-cloudcache','s3://foo/bar']
+        launcher.normalizeArgs('run','-with-cloudcache') == ['run', '-with-cloudcache', '-']
+        launcher.normalizeArgs('run','-with-cloudcache', '-x') == ['run', '-with-cloudcache', '-', '-x']
+        launcher.normalizeArgs('run','-with-cloudcache', 's3://foo/bar') == ['run', '-with-cloudcache','s3://foo/bar']
         
         launcher.normalizeArgs('run','-with-tower') == ['run', '-with-tower', '-']
         launcher.normalizeArgs('run','-with-tower', '-x') == ['run', '-with-tower', '-', '-x']

From b83e71488f1f06e65db445bdc95873ca1a58e391 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Fri, 13 Oct 2023 11:16:18 +0200
Subject: [PATCH 219/350] Add AWS SES docs

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/config.md |  6 ++++++
 docs/mail.md   | 17 +++++++++++++++++
 2 files changed, 23 insertions(+)

diff --git a/docs/config.md b/docs/config.md
index fb3cc8e832..7cbed7b6c4 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -1588,6 +1588,12 @@ The following environment variables control the configuration of the Nextflow ru
   :::
 : Disables the requirement for Wave service when enabling the Fusion file system.
 
+`NXF_ENABLE_AWS_SES`
+: :::{versionadded} 23.06.0-edge
+  :::
+: Enable to use of AWS SES native API for sending emails in place of legacy SMTP settings (default: `false`)
+
+
 `NXF_ENABLE_FS_SYNC`
 : :::{versionadded} 23.10.0
   :::
diff --git a/docs/mail.md b/docs/mail.md
index 5396077a51..4ada1916f5 100644
--- a/docs/mail.md
+++ b/docs/mail.md
@@ -130,6 +130,23 @@ mail {
 
 See the {ref}`mail scope <config-mail>` section to learn more the mail server configuration options.
 
+### AWS SES configuration
+
+As of version `23.06.0-edge` Nextflow supports [AWS SES](https://aws.amazon.com/ses/) native API as an alternative
+provider to send emails in place of SMTP server.
+
+To enable this feature add the following environment variable in the launching environment:
+
+```
+export NXF_ENABLE_AWS_SES=true
+```
+
+Make also sure to add the following AWS IAM permission to the AWS user (or role) used to launch the pipeline execution:
+
+```
+ses:SendRawEmail
+```
+
 ## Mail notification
 
 You can use the `sendMail` function with a {ref}`workflow completion handler <metadata-completion-handler>` to notify the completion of a workflow completion. For example:

From 7814822c98f86690e8d239280bbb8457fa7053b7 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Sun, 15 Oct 2023 04:47:47 -0500
Subject: [PATCH 220/350] Update logos, fonts, and colors (#4407)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 README.md                                     |   6 +-
 docs/{images => _static}/dag.mmd              |   0
 docs/_static/degular/Degular-Bold.woff        | Bin 0 -> 45156 bytes
 docs/_static/degular/Degular-Bold.woff2       | Bin 0 -> 36412 bytes
 docs/_static/degular/Degular-BoldItalic.woff  | Bin 0 -> 47284 bytes
 docs/_static/degular/Degular-BoldItalic.woff2 | Bin 0 -> 38192 bytes
 docs/_static/degular/Degular-Italic.woff      | Bin 0 -> 46844 bytes
 docs/_static/degular/Degular-Italic.woff2     | Bin 0 -> 37804 bytes
 docs/_static/degular/Degular-Regular.woff     | Bin 0 -> 45152 bytes
 docs/_static/degular/Degular-Regular.woff2    | Bin 0 -> 36556 bytes
 docs/_static/favicon.ico                      | Bin 0 -> 9662 bytes
 docs/{images => _static}/nextflow-k8s-min.png | Bin
 docs/_static/nextflow-logo-bg-dark.png        | Bin 0 -> 21289 bytes
 docs/_static/nextflow-logo-bg-light.png       | Bin 0 -> 25861 bytes
 docs/_static/nextflow-logo.png                | Bin 0 -> 25285 bytes
 .../report-resource-cpu.png                   | Bin
 .../report-resource-io-read.png               | Bin
 .../report-resource-io-write.png              | Bin
 .../report-resource-job-duration.png          | Bin
 .../report-resource-memory-pctram.png         | Bin
 .../report-resource-memory-ram.png            | Bin
 .../report-resource-memory-vmem.png           | Bin
 .../report-resource-memory.png                | Bin
 .../report-resources-min.png                  | Bin
 .../report-summary-min.png                    | Bin
 docs/{images => _static}/report-tasks-min.png | Bin
 docs/_static/seqera-logo.png                  | Bin 9675 -> 0 bytes
 docs/_static/seqera-logo.svg                  |  19 ++
 docs/_static/theme.css                        | 188 ++++++++++++++++--
 docs/{images => _static}/timeline-min.png     | Bin
 .../workflow-notification-min.png             | Bin
 docs/_templates/layout.html                   |   2 +-
 docs/conf.py                                  |   8 +-
 docs/images/favicon.ico                       | Bin 4286 -> 0 bytes
 docs/images/nextflow-logo.png                 | Bin 23874 -> 0 bytes
 docs/images/yourkit.png                       | Bin 6510 -> 0 bytes
 docs/kubernetes.md                            |   2 +-
 docs/mail.md                                  |   2 +-
 docs/metrics.md                               |  14 +-
 docs/tracing.md                               |  10 +-
 .../nextflow/script/WorkflowNotifier.groovy   |   2 +-
 .../nextflow/mail/nextflow-logo-v2-min.png    | Bin 0 -> 5014 bytes
 .../nextflow/mail/nextflow200x40.png          | Bin 9787 -> 0 bytes
 .../resources/nextflow/mail/notification.html |   2 +-
 .../nextflow/trace/ReportTemplate.html        |   2 +-
 .../nextflow/trace/TimelineTemplate.html      |   1 +
 .../nextflow/trace/timeline-expected.html     |   1 +
 47 files changed, 218 insertions(+), 41 deletions(-)
 rename docs/{images => _static}/dag.mmd (100%)
 create mode 100644 docs/_static/degular/Degular-Bold.woff
 create mode 100644 docs/_static/degular/Degular-Bold.woff2
 create mode 100644 docs/_static/degular/Degular-BoldItalic.woff
 create mode 100644 docs/_static/degular/Degular-BoldItalic.woff2
 create mode 100644 docs/_static/degular/Degular-Italic.woff
 create mode 100644 docs/_static/degular/Degular-Italic.woff2
 create mode 100644 docs/_static/degular/Degular-Regular.woff
 create mode 100644 docs/_static/degular/Degular-Regular.woff2
 create mode 100644 docs/_static/favicon.ico
 rename docs/{images => _static}/nextflow-k8s-min.png (100%)
 create mode 100644 docs/_static/nextflow-logo-bg-dark.png
 create mode 100644 docs/_static/nextflow-logo-bg-light.png
 create mode 100644 docs/_static/nextflow-logo.png
 rename docs/{images => _static}/report-resource-cpu.png (100%)
 rename docs/{images => _static}/report-resource-io-read.png (100%)
 rename docs/{images => _static}/report-resource-io-write.png (100%)
 rename docs/{images => _static}/report-resource-job-duration.png (100%)
 rename docs/{images => _static}/report-resource-memory-pctram.png (100%)
 rename docs/{images => _static}/report-resource-memory-ram.png (100%)
 rename docs/{images => _static}/report-resource-memory-vmem.png (100%)
 rename docs/{images => _static}/report-resource-memory.png (100%)
 rename docs/{images => _static}/report-resources-min.png (100%)
 rename docs/{images => _static}/report-summary-min.png (100%)
 rename docs/{images => _static}/report-tasks-min.png (100%)
 delete mode 100644 docs/_static/seqera-logo.png
 create mode 100644 docs/_static/seqera-logo.svg
 rename docs/{images => _static}/timeline-min.png (100%)
 rename docs/{images => _static}/workflow-notification-min.png (100%)
 delete mode 100644 docs/images/favicon.ico
 delete mode 100644 docs/images/nextflow-logo.png
 delete mode 100644 docs/images/yourkit.png
 create mode 100644 modules/nextflow/src/main/resources/nextflow/mail/nextflow-logo-v2-min.png
 delete mode 100644 modules/nextflow/src/main/resources/nextflow/mail/nextflow200x40.png

diff --git a/README.md b/README.md
index 1f4007fdf4..5c4e42b2d6 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
 <picture>
-  <source media="(prefers-color-scheme: dark)" srcset="https://github.com/nextflow-io/trademark/blob/master/nextflow2014_no-bg-bright.png">
-  <source media="(prefers-color-scheme: light)" srcset="https://github.com/nextflow-io/trademark/blob/master/nextflow2014_no-bg.png">
-  <img alt="Nextflow Logo" src="https://github.com/nextflow-io/trademark/blob/master/nextflow2014_no-bg.png">
+  <source media="(prefers-color-scheme: dark)" srcset="docs/_static/nextflow-logo-bg-dark.png">
+  <source media="(prefers-color-scheme: light)" srcset="docs/_static/nextflow-logo-bg-light.png">
+  <img alt="Nextflow Logo" src="docs/_static/nextflow-logo-bg-light.png">
 </picture>
 
 *"Dataflow variables are spectacularly expressive in concurrent programming"*
diff --git a/docs/images/dag.mmd b/docs/_static/dag.mmd
similarity index 100%
rename from docs/images/dag.mmd
rename to docs/_static/dag.mmd
diff --git a/docs/_static/degular/Degular-Bold.woff b/docs/_static/degular/Degular-Bold.woff
new file mode 100644
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+<defs>
+<clipPath id="clip0_933_7627">
+<rect width="250" height="250" fill="white"/>
+</clipPath>
+</defs>
+</svg>
diff --git a/docs/_static/theme.css b/docs/_static/theme.css
index 27d788d7e8..f4fc4528b3 100644
--- a/docs/_static/theme.css
+++ b/docs/_static/theme.css
@@ -1,22 +1,172 @@
+/* Inter font */
+@import url('https://fonts.googleapis.com/css2?family=Inter:wght@400;700&display=swap');
 
-/* navbar -- Seqera logo */
+/* Degular font */
+@font-face {
+    font-family: "Degular";
+    src: url('degular/Degular-Regular.woff2');
+    src: url('degular/Degular-Regular.woff2') format('woff2'),
+         url('degular/Degular-Regular.woff') format('woff');
+    font-weight: normal;
+    font-style: normal;
+}
+@font-face {
+    font-family: "Degular";
+    src: url('degular/Degular-Italic.woff2');
+    src: url('degular/Degular-Italic.woff2') format('woff2'),
+         url('degular/Degular-Italic.woff') format('woff');
+    font-weight: normal;
+    font-style: italic;
+}
+@font-face {
+    font-family: "Degular";
+    src: url('degular/Degular-Bold.woff2');
+    src: url('degular/Degular-Bold.woff2') format('woff2'),
+         url('degular/Degular-Bold.woff') format('woff');
+    font-weight: bold;
+    font-style: normal;
+}
+@font-face {
+    font-family: "Degular";
+    src: url('degular/Degular-BoldItalic.woff2');
+    src: url('degular/Degular-BoldItalic.woff2') format('woff2'),
+         url('degular/Degular-BoldItalic.woff') format('woff');
+    font-weight: bold;
+    font-style: italic;
+}
 
-.wy-side-nav-search {
-    background-color: #27ae60;
+/* fonts */
+body {
+    font-family: 'Inter', sans-serif;
+}
+
+.btn {
+    font-family: 'Inter', sans-serif;
+}
+
+.rst-content .toctree-wrapper>p.caption,
+h1,
+h2,
+h3,
+h4,
+h5,
+h6,
+legend {
+    font-family: 'Degular', sans-serif;
+}
+
+/* colors */
+.rst-content .danger {
+    background: #FEEDEC;
+}
+
+.rst-content .danger .admonition-title {
+    background: #C3514D;
+}
+
+.rst-content .warning {
+    background: #FDF0E9;
+}
+
+.rst-content .warning .admonition-title {
+    background: #BC6437;
+}
+
+.rst-content .note {
+    background: #E8F2FF;
+}
+
+.rst-content .note .admonition-title {
+    background: #3787E5;
+}
+
+.rst-content .tip {
+    background: #E2F7F3;
+}
+
+.rst-content .tip .admonition-title {
+    background: #0CAE8E;
+}
+
+a, a:visited {
+    color: #3787E5;
 }
 
+a:hover {
+    color: #77B5FE;
+}
+
+.rst-content code,
+.rst-content tt,
+code {
+    color: #C3514D;
+}
+
+.wy-menu-vertical header,
 .wy-menu-vertical p.caption {
-    color: #27ae60;
+    color: #0DC09D;
+}
+
+.wy-menu-vertical a {
+    color: #EAEBEB;
+}
+
+.wy-menu-vertical a:hover {
+    background-color: #7B7B7B;
 }
 
 .wy-menu-vertical a:active {
-    background-color: #27ae60;
+    background-color: #0DC09D;
+}
+
+.wy-side-nav-search {
+    background-color: #0DC09D;
+}
+
+.wy-side-nav-search input[type=text] {
+    border-color: #0DC09D;
+}
+
+.wy-side-nav-search img {
+    background-color: #0DC09D;
+}
+
+.wy-nav-side {
+    background: #160F26;
+}
+
+.wy-nav-top {
+    background: #0DC09D;
+}
+
+.wy-nav-top a {
+    color: #fff;
+}
+
+.wy-nav-top img {
+    width: auto;
+    background-color: inherit;
+    border-radius: unset;
+}
+
+footer {
+    color: #7B7B7B;
+}
+
+#search-results .context {
+    color: #7B7B7B;
+}
+
+.rst-content code.literal,
+.rst-content tt.literal {
+    color: #C3514D;
 }
 
+/* Custom footer with logo */
 .nav-footer-logo {
     width: 300px;
     margin-top: 2rem;
-    border-top: 1px solid #666666;
+    border-top: 1px solid #7B7B7B;
     text-align: center;
     font-size: 80%;
 }
@@ -24,7 +174,7 @@
 .nav-footer-logo a {
     display: block;
     padding: 2rem 0 0.5rem;
-    color: #666666;
+    color: #7B7B7B;
 }
 
 .nav-footer-logo a img {
@@ -33,7 +183,9 @@
 }
 
 /* Version change admonitions */
-div.deprecated, div.versionadded, div.versionchanged {
+div.deprecated,
+div.versionadded,
+div.versionchanged {
     border-left: 0.2rem solid;
     border-radius: 0.25rem;
     box-shadow: 0 0.2rem 0.5rem var(--pst-color-shadow),0 0 0.0625rem var(--pst-color-shadow)!important;
@@ -45,11 +197,15 @@ div.deprecated, div.versionadded, div.versionchanged {
     transition: color .25s,background-color .25s,border-color .25s;
     vertical-align: middle;
 }
-div.deprecated>p, div.versionadded>p, div.versionchanged>p {
+div.deprecated>p,
+div.versionadded>p,
+div.versionchanged>p {
     margin-top: 0.5rem;
     margin-bottom: 0.5rem;
 }
-div.deprecated>p:first-child::before, div.versionadded>p:first-child::before, div.versionchanged>p:first-child::before {
+div.deprecated>p:first-child::before,
+div.versionadded>p:first-child::before,
+div.versionchanged>p:first-child::before {
     font-family: FontAwesome;
     display: inline-block;
     font-style: normal;
@@ -62,9 +218,9 @@ div.deprecated>p:first-child::before, div.versionadded>p:first-child::before, di
     padding: 0.4rem 0.6rem;
     margin: -0.2rem 0rem -0.2rem -0.6rem;
 }
-div.versionadded                         { border-color: #1abc9c; background-color: #dbfaf4; }
-div.versionadded p:first-child::before   { color: #1abc9c; }
-div.versionchanged                       { border-color: #f0b37e; background-color: #ffedcc; }
-div.versionchanged p:first-child::before { color: #f0b37e; }
-div.deprecated                           { border-color: #f29f97; background-color: #fdf3f2; }
-div.deprecated p:first-child::before     { color: #f29f97; }
+div.versionadded                         { border-color: #0CAE8E; background-color: #E2F7F3; }
+div.versionadded p:first-child::before   { color: #0CAE8E; }
+div.versionchanged                       { border-color: #BC6437; background-color: #FDF0E9; }
+div.versionchanged p:first-child::before { color: #BC6437; }
+div.deprecated                           { border-color: #C3514D; background-color: #FEEDEC; }
+div.deprecated p:first-child::before     { color: #C3514D; }
diff --git a/docs/images/timeline-min.png b/docs/_static/timeline-min.png
similarity index 100%
rename from docs/images/timeline-min.png
rename to docs/_static/timeline-min.png
diff --git a/docs/images/workflow-notification-min.png b/docs/_static/workflow-notification-min.png
similarity index 100%
rename from docs/images/workflow-notification-min.png
rename to docs/_static/workflow-notification-min.png
diff --git a/docs/_templates/layout.html b/docs/_templates/layout.html
index b08dd9ff4e..af1d87ad40 100644
--- a/docs/_templates/layout.html
+++ b/docs/_templates/layout.html
@@ -5,7 +5,7 @@
     <div class="nav-footer-logo">
         <a href="https://seqera.io/" target="_blank" title="Developed by Seqera Labs">
             Nextflow is developed by:<br>
-            <img src="_static/seqera-logo.png" alt="Seqera Labs">
+            <img src="_static/seqera-logo.svg" alt="Seqera Labs">
         </a>
     </div>
 {% endblock %}
diff --git a/docs/conf.py b/docs/conf.py
index 142e2f76ba..4591e86d00 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -92,7 +92,7 @@
 #show_authors = False
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = 'default'
 
 # A list of ignored prefixes for module index sorting.
 #modindex_common_prefix = []
@@ -136,12 +136,12 @@
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-html_logo = 'images/nextflow-logo.png'
+html_logo = '_static/nextflow-logo.png'
 
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
 # pixels large.
-html_favicon = 'images/favicon.ico'
+html_favicon = '_static/favicon.ico'
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
@@ -217,7 +217,7 @@
 
 # The name of an image file (relative to this directory) to place at the top of
 # the title page.
-latex_logo = 'images/nextflow-logo.png'
+latex_logo = '_static/nextflow-logo.png'
 
 # For "manual" documents, if this is true, then toplevel headings are parts,
 # not chapters.
diff --git a/docs/images/favicon.ico b/docs/images/favicon.ico
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diff --git a/docs/kubernetes.md b/docs/kubernetes.md
index 06c954d55f..e6f38a9542 100644
--- a/docs/kubernetes.md
+++ b/docs/kubernetes.md
@@ -16,7 +16,7 @@ Kubernetes abstracts also the storage provisioning through the definition of one
 
 When using the `k8s` executor Nextflow deploys the workflow execution as a Kubernetes pod. This pod orchestrates the workflow execution and submits a separate pod execution for each job that need to be carried out by the workflow application.
 
-```{image} /images/nextflow-k8s-min.png
+```{image} _static/nextflow-k8s-min.png
 ```
 
 ## Requirements
diff --git a/docs/mail.md b/docs/mail.md
index 4ada1916f5..59ce19890a 100644
--- a/docs/mail.md
+++ b/docs/mail.md
@@ -183,7 +183,7 @@ nextflow run <pipeline name> -N <recipient address>
 
 It will send a notification mail when the execution completes similar to the one shown below:
 
-```{image} images/workflow-notification-min.png
+```{image} _static/workflow-notification-min.png
 ```
 
 :::{warning}
diff --git a/docs/metrics.md b/docs/metrics.md
index 694d68cd05..0681328ab6 100644
--- a/docs/metrics.md
+++ b/docs/metrics.md
@@ -8,7 +8,7 @@ This section details how the resource usage metrics from the {ref}`Execution rep
 
 The plot reports how much CPU resources were used by each process.
 
-```{image} images/report-resource-cpu.png
+```{image} _static/report-resource-cpu.png
 ```
 
 Let's illustrate how this plot behaves with several examples.
@@ -248,17 +248,17 @@ process bar {
 
 The `Virtual (RAM + Disk swap)` tab shows that both `foo` and `bar` processes use the same amount of virtual memory (~1 GiB):
 
-```{image} images/report-resource-memory-vmem.png
+```{image} _static/report-resource-memory-vmem.png
 ```
 
 However, the `Physical (RAM)` tab shows that only the `bar` process uses ~1 GiB of RAM while `foo` process uses ~0 GiB:
 
-```{image} images/report-resource-memory-ram.png
+```{image} _static/report-resource-memory-ram.png
 ```
 
 As expected, the `% RAM Allocated` tab shows that 0% of the resource set in the `memory` directive was used for `foo` process while 67% (= 1 / 1.5) of the resource were used for `bar` process:
 
-```{image} images/report-resource-memory-pctram.png
+```{image} _static/report-resource-memory-pctram.png
 ```
 
 :::{warning}
@@ -269,7 +269,7 @@ Memory and storage metrics are reported in bytes. This means that 1KB = $1024$ b
 
 The plot has two tabs the job duration (a.k.a. elapsed real time, real time or wall time ) in the `Raw Usage` tag and the percentage of requested time used in the `% Allocated` tab with respect to the duration set in the `time` directive of the process.
 
-```{image} images/report-resource-job-duration.png
+```{image} _static/report-resource-job-duration.png
 ```
 
 ## I/O Usage
@@ -294,10 +294,10 @@ process io_read_write_256M {
 
 `Read` tab:
 
-```{image} images/report-resource-io-read.png
+```{image} _static/report-resource-io-read.png
 ```
 
 `Write` tab:
 
-```{image} images/report-resource-io-write.png
+```{image} _static/report-resource-io-write.png
 ```
diff --git a/docs/tracing.md b/docs/tracing.md
index 32326098a5..0a2a2911a7 100644
--- a/docs/tracing.md
+++ b/docs/tracing.md
@@ -109,7 +109,7 @@ The report file name can be specified as an optional parameter following the rep
 
 The `Summary` section reports the execution status, the launch command, overall execution time and some other workflow metadata. You can see an example below:
 
-```{image} images/report-summary-min.png
+```{image} _static/report-summary-min.png
 ```
 
 ### Resource Usage
@@ -118,7 +118,7 @@ The `Resources` section plots the distribution of resource usage for each workfl
 
 Plots are shown for CPU, memory, job duration and disk I/O. They have two (or three) tabs with the raw values and a percentage representation showing what proportion of the requested resources were used. These plots are very helpful to check that task resources are used efficiently.
 
-```{image} images/report-resource-cpu.png
+```{image} _static/report-resource-cpu.png
 ```
 
 Learn more about how resource usage is computed in the {ref}`Metrics documentation <metrics-page>`.
@@ -129,7 +129,7 @@ Learn more about how resource usage is computed in the {ref}`Metrics documentati
 
 The `Tasks` section lists all executed tasks, reporting for each of them the status, the actual command script, and many other metrics. You can see an example below:
 
-```{image} images/report-tasks-min.png
+```{image} _static/report-tasks-min.png
 ```
 
 :::{note}
@@ -326,7 +326,7 @@ Please read {ref}`Trace scope <config-trace>` section to learn more about it.
 
 Nextflow can render an HTML timeline for all processes executed in your pipeline. An example of the timeline report is shown below:
 
-```{image} images/timeline-min.png
+```{image} _static/timeline-min.png
 ```
 
 Each bar represents a process run in the pipeline execution. The bar length represents the task duration time (wall-time). The colored area in each bar represents the real execution time. The grey area to the *left* of the colored area represents the task scheduling wait time. The grey area to the *right* of the colored area represents the task termination time (clean-up and file un-staging). The numbers on the x-axis represent the time in absolute units e.g. minutes, hours, etc.
@@ -402,5 +402,5 @@ Here is the Mermaid diagram produced by Nextflow for the [rnaseq-nf](https://git
 nextflow run rnaseq-nf -preview -with-dag
 ```
 
-```{mermaid} images/dag.mmd
+```{mermaid} _static/dag.mmd
 ```
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/WorkflowNotifier.groovy b/modules/nextflow/src/main/groovy/nextflow/script/WorkflowNotifier.groovy
index b242a3533d..7cc351048f 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/WorkflowNotifier.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/WorkflowNotifier.groovy
@@ -206,7 +206,7 @@ class WorkflowNotifier {
      * @return A {@link Attachment} object representing the image logo to be included in the HTML email
      */
     protected Attachment loadDefaultLogo() {
-        Attachment.resource('/nextflow/mail/nextflow200x40.png', contentId: '<nxf-logo>', disposition: 'inline')
+        Attachment.resource('/nextflow/mail/nextflow-logo-v2-min.png', contentId: '<nxf-logo>', disposition: 'inline')
     }
 
     private String loadDefaultTemplate0(String classpathResource) {
diff --git a/modules/nextflow/src/main/resources/nextflow/mail/nextflow-logo-v2-min.png b/modules/nextflow/src/main/resources/nextflow/mail/nextflow-logo-v2-min.png
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znB=Gw^wwj}3CcdKtm={EWz72E_ZSD1T*$^v&!H8q_Oh5%zHbDVTE}_`0knfdlh`*U
zy&XQhtB3O|Ul&-K$xb%^;KYtg#6@6UWzA3to~=vhdg#Tr!`#6EIL(`kuqTeDi|eYp
zmAzm(RI+1d7L&zG?gCwAextTWEC^KjexOX9inDgpa`wYolW0WJak%*a+C*1Tazc|k
zKM`_Wb)-&_cVMZ~{4k<A86&WIrB|Hj%~t&-*}3M5+OflPeLM&*Hq{7~miFHIpBr7u
M^6GL`G8V!A3($G6e*gdg

diff --git a/modules/nextflow/src/main/resources/nextflow/mail/notification.html b/modules/nextflow/src/main/resources/nextflow/mail/notification.html
index 96eadfea4b..736630e248 100644
--- a/modules/nextflow/src/main/resources/nextflow/mail/notification.html
+++ b/modules/nextflow/src/main/resources/nextflow/mail/notification.html
@@ -139,7 +139,7 @@ <h2>Execution summary</h2>
     </table>
 
     <hr style="height: 3px; padding: 0; margin: 24px 0; background-color: #e1e4e8; border: 0;">
-    <img style="float:right" src="cid:nxf-logo">
+    <img style="float:right; height: 35px" src="cid:nxf-logo">
     This email was sent by Nextflow<br>
     cite <a href="https://doi.org/10.1038/nbt.3820">doi:10.1038/nbt.3820</a><br>
     <a href="http://nextflow.io">http://nextflow.io</a> <br>
diff --git a/modules/nextflow/src/main/resources/nextflow/trace/ReportTemplate.html b/modules/nextflow/src/main/resources/nextflow/trace/ReportTemplate.html
index 7232373fdd..9d3fe8cf96 100644
--- a/modules/nextflow/src/main/resources/nextflow/trace/ReportTemplate.html
+++ b/modules/nextflow/src/main/resources/nextflow/trace/ReportTemplate.html
@@ -93,7 +93,7 @@
 <body>
   <nav id="nf-report-navbar" class="navbar navbar-expand-md navbar-dark fixed-top bg-dark">
     <a class="navbar-brand" href="#">
-      <img src="data:image/png;base64,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">
+      <img src="data:image/png;base64,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">
       Nextflow Report
     </a>
     <button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarCollapse" aria-controls="navbarCollapse" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/modules/nextflow/src/main/resources/nextflow/trace/TimelineTemplate.html b/modules/nextflow/src/main/resources/nextflow/trace/TimelineTemplate.html
index fb9768c320..e4a1af01cf 100644
--- a/modules/nextflow/src/main/resources/nextflow/trace/TimelineTemplate.html
+++ b/modules/nextflow/src/main/resources/nextflow/trace/TimelineTemplate.html
@@ -19,6 +19,7 @@
 <head>
 <meta charset="utf-8">
 <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+<link rel="icon" type="image/png" href="https://www.nextflow.io/img/favicon.png" />
 <style type="text/css">
 * {
   font-family: 'Lato', 'Helvetica Neue', Arial, Helvetica, sans-serif;
diff --git a/modules/nextflow/src/test/resources/nextflow/trace/timeline-expected.html b/modules/nextflow/src/test/resources/nextflow/trace/timeline-expected.html
index 2e725ee979..fde5b1eefe 100644
--- a/modules/nextflow/src/test/resources/nextflow/trace/timeline-expected.html
+++ b/modules/nextflow/src/test/resources/nextflow/trace/timeline-expected.html
@@ -19,6 +19,7 @@
 <head>
 <meta charset="utf-8">
 <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+<link rel="icon" type="image/png" href="https://www.nextflow.io/img/favicon.png" />
 <style type="text/css">
 * {
   font-family: 'Lato', 'Helvetica Neue', Arial, Helvetica, sans-serif;

From 10c3232536f7c2cf9763b84383d6feab7c59e245 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sun, 15 Oct 2023 15:31:23 +0200
Subject: [PATCH 221/350] Add support for K8s hostPath

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/process.md                               |  6 +++
 .../nextflow/k8s/model/PodOptions.groovy      | 12 ++++++
 .../nextflow/k8s/model/PodSpecBuilder.groovy  |  3 ++
 .../nextflow/k8s/K8sTaskHandlerTest.groovy    |  8 +++-
 .../nextflow/k8s/model/PodOptionsTest.groovy  | 41 +++++++++++++++++++
 5 files changed, 68 insertions(+), 2 deletions(-)

diff --git a/docs/process.md b/docs/process.md
index 903b96aabe..8da1f5376d 100644
--- a/docs/process.md
+++ b/docs/process.md
@@ -2033,6 +2033,12 @@ The following options are available:
 : *Can be specified multiple times*
 : Defines an environment variable with the given name and value.
 
+`hostPath: '/host/absolute/path', mountPath: '</pod/absolute/path>'`
+: :::{versionadded} 23.10.0
+  :::
+: *Can be specified multiple times*
+: Allows creating [hostPath](https://kubernetes.io/docs/concepts/storage/volumes/#hostpath) volume and access it with the specified `mountPath` in the pod.
+
 `imagePullPolicy: 'IfNotPresent' | 'Always' | 'Never'`
 : Specifies the [image pull policy](https://kubernetes.io/docs/concepts/containers/images/#image-pull-policy) used by the pod to pull the container image.
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/k8s/model/PodOptions.groovy b/modules/nextflow/src/main/groovy/nextflow/k8s/model/PodOptions.groovy
index 1438fad21c..19ddc6d8d2 100644
--- a/modules/nextflow/src/main/groovy/nextflow/k8s/model/PodOptions.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/k8s/model/PodOptions.groovy
@@ -48,6 +48,8 @@ class PodOptions {
 
     private Collection<PodVolumeClaim> mountClaims
 
+    private Collection<PodHostMount> mountHostPaths
+
     private Map<String,String> labels = [:]
 
     private Map<String,String> annotations = [:]
@@ -74,6 +76,7 @@ class PodOptions {
         mountEmptyDirs = new HashSet<>(size)
         mountSecrets = new HashSet<>(size)
         mountClaims = new HashSet<>(size)
+        mountHostPaths = new HashSet<>(10)
         automountServiceAccountToken = true
         tolerations = new ArrayList<Map>(size)
         init(options)
@@ -114,6 +117,9 @@ class PodOptions {
         else if( entry.mountPath && entry.volumeClaim ) {
             mountClaims << new PodVolumeClaim(entry)
         }
+        else if( entry.mountPath && entry.hostPath instanceof CharSequence ) {
+            mountHostPaths << new PodHostMount(entry.hostPath, entry.mountPath)
+        }
         else if( entry.pullPolicy || entry.imagePullPolicy ) {
             this.imagePullPolicy = entry.pullPolicy ?: entry.imagePullPolicy as String
         }
@@ -165,6 +171,8 @@ class PodOptions {
 
     Collection<PodMountSecret> getMountSecrets() { mountSecrets }
 
+    Collection<PodHostMount> getMountHostPaths() { mountHostPaths }
+
     Collection<PodVolumeClaim> getVolumeClaims() { mountClaims }
 
     Map<String,String> getLabels() { labels }
@@ -233,6 +241,10 @@ class PodOptions {
         result.mountEmptyDirs.addAll( mountEmptyDirs )
         result.mountEmptyDirs.addAll( other.mountEmptyDirs )
 
+        // host paths
+        result.mountHostPaths.addAll( mountHostPaths )
+        result.mountHostPaths.addAll( other.mountHostPaths )
+
         // secrets
         result.mountSecrets.addAll( mountSecrets )
         result.mountSecrets.addAll( other.mountSecrets )
diff --git a/modules/nextflow/src/main/groovy/nextflow/k8s/model/PodSpecBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/k8s/model/PodSpecBuilder.groovy
index 47a66132d3..e87c0abeb2 100644
--- a/modules/nextflow/src/main/groovy/nextflow/k8s/model/PodSpecBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/k8s/model/PodSpecBuilder.groovy
@@ -336,6 +336,9 @@ class PodSpecBuilder {
         // -- emptyDirs
         if( opts.getMountEmptyDirs() )
             emptyDirs.addAll( opts.getMountEmptyDirs() )
+        // -- host paths
+        if( opts.getMountHostPaths() )
+            hostMounts.addAll( opts.getMountHostPaths() )
         // -- secrets
         if( opts.getMountSecrets() )
             secrets.addAll( opts.getMountSecrets() )
diff --git a/modules/nextflow/src/test/groovy/nextflow/k8s/K8sTaskHandlerTest.groovy b/modules/nextflow/src/test/groovy/nextflow/k8s/K8sTaskHandlerTest.groovy
index c0b4146b96..8ac5093294 100644
--- a/modules/nextflow/src/test/groovy/nextflow/k8s/K8sTaskHandlerTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/k8s/K8sTaskHandlerTest.groovy
@@ -32,6 +32,7 @@ import nextflow.k8s.client.K8sResponseException
 import nextflow.k8s.client.K8sResponseJson
 import nextflow.k8s.client.PodUnschedulableException
 import nextflow.k8s.model.PodEnv
+import nextflow.k8s.model.PodHostMount
 import nextflow.k8s.model.PodMountConfig
 import nextflow.k8s.model.PodMountSecret
 import nextflow.k8s.model.PodOptions
@@ -249,15 +250,18 @@ class K8sTaskHandlerTest extends Specification {
         2 * podOptions.getEnvVars() >> [ PodEnv.value('FOO','bar') ]
         2 * podOptions.getMountSecrets() >> [ new PodMountSecret('my-secret/key-z', '/data/secret.txt') ]
         2 * podOptions.getMountConfigMaps() >> [ new PodMountConfig('my-data/key-x', '/etc/file.txt') ]
+        2 * podOptions.getMountHostPaths() >> [ new PodHostMount('/host/x', '/mnt/x') ]
         and:
         result.spec.containers[0].env == [[name:'FOO', value:'bar']]
         result.spec.containers[0].volumeMounts == [
             [name:'vol-1', mountPath:'/etc'],
-            [name:'vol-2', mountPath:'/data']
+            [name:'vol-2', mountPath:'/data'],
+            [name:'vol-3', mountPath:'/mnt/x']
         ]
         result.spec.volumes == [
             [name:'vol-1', configMap:[name:'my-data', items:[[key:'key-x', path:'file.txt']]]],
-            [name:'vol-2', secret:[secretName:'my-secret', items:[[key:'key-z', path:'secret.txt']]]]
+            [name:'vol-2', secret:[secretName:'my-secret', items:[[key:'key-z', path:'secret.txt']]]],
+            [name:'vol-3', 'hostPath':[path:'/host/x']]
         ]
 
     }
diff --git a/modules/nextflow/src/test/groovy/nextflow/k8s/model/PodOptionsTest.groovy b/modules/nextflow/src/test/groovy/nextflow/k8s/model/PodOptionsTest.groovy
index 269e3ddb8a..9070458eef 100644
--- a/modules/nextflow/src/test/groovy/nextflow/k8s/model/PodOptionsTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/k8s/model/PodOptionsTest.groovy
@@ -206,6 +206,22 @@ class PodOptionsTest extends Specification {
 
     }
 
+    def 'should create host path' () {
+        given:
+        def options = [
+            [hostPath: '/host/one', mountPath: '/pod/1'],
+            [hostPath: '/host/two', mountPath: '/pod/2']
+        ]
+        when:
+        def mounts = new PodOptions(options).getMountHostPaths()
+
+        then:
+        mounts == [
+            new PodHostMount('/host/one', '/pod/1'),
+            new PodHostMount('/host/two', '/pod/2')
+        ] as Set
+
+    }
 
     def 'should not create env' () {
         when:
@@ -398,6 +414,31 @@ class PodOptionsTest extends Specification {
         opts.labels == [FOO: 'one', BAR: 'two']
     }
 
+    def 'should copy host paths' (){
+        given:
+        def data = [
+            [hostPath: "/foo", mountPath: '/one']
+        ]
+
+        when:
+        def opts = new PodOptions() + new PodOptions(data)
+        then:
+        opts.getMountHostPaths() == [new PodHostMount('/foo', '/one')] as Set
+
+        when:
+        opts = new PodOptions(data) + new PodOptions()
+        then:
+        opts.getMountHostPaths() == [new PodHostMount('/foo', '/one')] as Set
+
+        when:
+        opts = new PodOptions([[hostPath:"/foo", mountPath: '/one']]) + new PodOptions([[hostPath:"/bar", mountPath: '/two']])
+        then:
+        opts.getMountHostPaths() == [
+            new PodHostMount('/foo','/one'),
+            new PodHostMount('/bar','/two')
+        ] as Set
+    }
+
     def 'should create pod labels' () {
 
         given:

From 0ef487359422be8f332eee9c2cb08839b66b6ebc Mon Sep 17 00:00:00 2001
From: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
Date: Sun, 15 Oct 2023 10:32:43 -0300
Subject: [PATCH 222/350] Update warning complaining about tuple but mentioning
 set (#4400) [ci fast]

Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
---
 .../src/main/groovy/nextflow/processor/TaskProcessor.groovy   | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
index 409550ccb7..c31597e1a3 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
@@ -420,12 +420,12 @@ class TaskProcessor {
         // -- check that input set defines at least two elements
         def invalidInputSet = config.getInputs().find { it instanceof TupleInParam && it.inner.size()<2 }
         if( invalidInputSet )
-            checkWarn "Input `set` must define at least two component -- Check process `$name`"
+            checkWarn "Input `tuple` must define at least two component -- Check process `$name`"
 
         // -- check that output set defines at least two elements
         def invalidOutputSet = config.getOutputs().find { it instanceof TupleOutParam && it.inner.size()<2 }
         if( invalidOutputSet )
-            checkWarn "Output `set` must define at least two component -- Check process `$name`"
+            checkWarn "Output `tuple` must define at least two component -- Check process `$name`"
 
         /**
          * Verify if this process run only one time

From d5a8098f56008979574fbe69e6aa3b2293dfc1eb Mon Sep 17 00:00:00 2001
From: Rory Nolan <rorynoolan@gmail.com>
Date: Sun, 15 Oct 2023 07:06:12 -0700
Subject: [PATCH 223/350] Document aws.batch.retrymode = 'built-in'. (#4229)

Co-authored-by: Rory Nolan <rory@mirvie.com>
---
 docs/config.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/config.md b/docs/config.md
index 7cbed7b6c4..9af6de89f2 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -189,7 +189,7 @@ The following settings are available:
 : Max number of downloads attempts from S3 (default: `1`).
 
 `aws.batch.retryMode`
-: The retry mode configuration setting, to accommodate rate-limiting on [AWS services](https://docs.aws.amazon.com/cli/latest/userguide/cli-configure-retries.html) (default: `standard`)
+: The retry mode configuration setting, to accommodate rate-limiting on [AWS services](https://docs.aws.amazon.com/cli/latest/userguide/cli-configure-retries.html) (default: `standard`, other options: `legacy`, `adaptive`); this handling is delegated to AWS. To have Nextflow handle retries instead, use `built-in`.
 
 `aws.batch.schedulingPriority`
 : :::{versionadded} 23.01.0-edge

From 5bdaac9447a989f6a12d2507a3eee78ddec70d60 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Sun, 15 Oct 2023 09:19:45 -0500
Subject: [PATCH 224/350] Improve `-dump-hashes` output adding json format
 (#4369)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/cache-and-resume.md                      | 27 +++++++++++++++++++
 docs/cli.md                                   |  5 +++-
 .../src/main/groovy/nextflow/Session.groovy   |  4 +--
 .../main/groovy/nextflow/cli/CmdRun.groovy    |  2 +-
 .../main/groovy/nextflow/cli/Launcher.groovy  |  4 +++
 .../nextflow/config/ConfigBuilder.groovy      |  7 ++---
 .../nextflow/processor/TaskProcessor.groovy   | 15 ++++++++++-
 7 files changed, 56 insertions(+), 8 deletions(-)

diff --git a/docs/cache-and-resume.md b/docs/cache-and-resume.md
index 0fc5ddf4a0..55b890ef43 100644
--- a/docs/cache-and-resume.md
+++ b/docs/cache-and-resume.md
@@ -186,6 +186,8 @@ nextflow run rnaseq-nf -resume 4dc656d2-c410-44c8-bc32-7dd0ea87bebf
 
 You can use the {ref}`cli-log` command to view all previous runs as well as the task executions for each run.
 
+(cache-compare-hashes)=
+
 ### Comparing the hashes of two runs
 
 One way to debug a resumed run is to compare the task hashes of each run using the `-dump-hashes` option.
@@ -196,3 +198,28 @@ One way to debug a resumed run is to compare the task hashes of each run using t
 4. Compare the runs with a diff viewer
 
 While some manual effort is required, the final diff can often reveal the exact change that caused a task to be re-executed.
+
+:::{versionadded} 23.10.0
+:::
+
+When using `-dump-hashes json`, the task hashes can be more easily extracted into a diff. Here is an example Bash script to perform two runs and produce a diff:
+
+```bash
+nextflow -log run_1.log run $pipeline -dump-hashes json
+nextflow -log run_2.log run $pipeline -dump-hashes json -resume
+
+get_hashes() {
+    cat $1 \
+    | grep 'cache hash:' \
+    | cut -d ' ' -f 10- \
+    | sort \
+    | awk '{ print; print ""; }'
+}
+
+get_hashes run_1.log > run_1.tasks.log
+get_hashes run_2.log > run_2.tasks.log
+
+diff run_1.tasks.log run_2.tasks.log
+```
+
+You can then view the `diff` output or use a graphical diff viewer to compare `run_1.tasks.log` and `run_2.tasks.log`.
diff --git a/docs/cli.md b/docs/cli.md
index 5fd19d7aaa..dbe54312b2 100644
--- a/docs/cli.md
+++ b/docs/cli.md
@@ -1154,7 +1154,10 @@ The `run` command is used to execute a local pipeline script or remote pipeline
 : Dump channels for debugging purpose.
 
 `-dump-hashes`
-: Dump task hash keys for debugging purpose.
+: Dump task hash keys for debugging purposes.
+: :::{versionadded} 23.10.0
+  You can use `-dump-hashes json` to dump the task hash keys as JSON for easier post-processing. See the {ref}`caching and resuming tips <cache-compare-hashes>` for more details.
+  :::
 
 `-e.<key>=<value>`
 : Add the specified variable to execution environment.
diff --git a/modules/nextflow/src/main/groovy/nextflow/Session.groovy b/modules/nextflow/src/main/groovy/nextflow/Session.groovy
index 7f8d4ecf24..668b1166ad 100644
--- a/modules/nextflow/src/main/groovy/nextflow/Session.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/Session.groovy
@@ -247,11 +247,11 @@ class Session implements ISession {
 
     boolean getStatsEnabled() { statsEnabled }
 
-    private boolean dumpHashes
+    private String dumpHashes
 
     private List<String> dumpChannels
 
-    boolean getDumpHashes() { dumpHashes }
+    String getDumpHashes() { dumpHashes }
 
     List<String> getDumpChannels() { dumpChannels }
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
index ec233778c9..7fa7d65298 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
@@ -223,7 +223,7 @@ class CmdRun extends CmdBase implements HubOptions {
     String profile
 
     @Parameter(names=['-dump-hashes'], description = 'Dump task hash keys for debugging purpose')
-    boolean dumpHashes
+    String dumpHashes
 
     @Parameter(names=['-dump-channels'], description = 'Dump channels for debugging purpose')
     String dumpChannels
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy
index eabdb84bf0..50e9d8df2a 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy
@@ -224,6 +224,10 @@ class Launcher {
                 normalized << '%all'
             }
 
+            else if( current == '-dump-hashes' && (i==args.size() || args[i].startsWith('-'))) {
+                normalized << '-'
+            }
+
             else if( current == '-with-cloudcache' && (i==args.size() || args[i].startsWith('-'))) {
                 normalized << '-'
             }
diff --git a/modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy
index 02270c9aa1..d30ad9e0dd 100644
--- a/modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy
@@ -595,9 +595,10 @@ class ConfigBuilder {
         if( config.isSet('resume') )
             config.resume = normalizeResumeId(config.resume as String)
 
-        // -- sets `dumpKeys` option
-        if( cmdRun.dumpHashes )
-            config.dumpHashes = cmdRun.dumpHashes
+        // -- sets `dumpHashes` option
+        if( cmdRun.dumpHashes ) {
+            config.dumpHashes = cmdRun.dumpHashes != '-' ? cmdRun.dumpHashes : 'default'
+        }
 
         if( cmdRun.dumpChannels )
             config.dumpChannels = cmdRun.dumpChannels.tokenize(',')
diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
index c31597e1a3..bfcb34d4da 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
@@ -32,6 +32,7 @@ import java.util.regex.Pattern
 
 import ch.artecat.grengine.Grengine
 import com.google.common.hash.HashCode
+import groovy.json.JsonOutput
 import groovy.transform.CompileStatic
 import groovy.transform.Memoized
 import groovy.transform.PackageScope
@@ -2155,7 +2156,9 @@ class TaskProcessor {
         final mode = config.getHashMode()
         final hash = computeHash(keys, mode)
         if( session.dumpHashes ) {
-            traceInputsHashes(task, keys, mode, hash)
+            session.dumpHashes=='json'
+                ? traceInputsHashesJson(task, keys, mode, hash)
+                : traceInputsHashes(task, keys, mode, hash)
         }
         return hash
     }
@@ -2191,6 +2194,16 @@ class TaskProcessor {
         return result
     }
 
+    private void traceInputsHashesJson( TaskRun task, List entries, CacheHelper.HashMode mode, hash ) {
+        final collector = (item) -> [
+            hash: CacheHelper.hasher(item, mode).hash().toString(),
+            type: item?.getClass()?.getName(),
+            value: item?.toString()
+        ]
+        final json = JsonOutput.toJson(entries.collect(collector))
+        log.info "[${safeTaskName(task)}] cache hash: ${hash}; mode: ${mode}; entries: ${JsonOutput.prettyPrint(json)}"
+    }
+
     private void traceInputsHashes( TaskRun task, List entries, CacheHelper.HashMode mode, hash ) {
 
         def buffer = new StringBuilder()

From efd041cb1080b65deb3119bfaac378e1e682c764 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Sun, 15 Oct 2023 09:46:24 -0500
Subject: [PATCH 225/350] Incorporate DSL2 features into docs (#3793)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Phil Ewels <phil@seqera.io>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/azure.md                      |   2 +-
 docs/cli.md                        |   8 +-
 docs/conf.py                       |   7 +-
 docs/container.md                  |   4 +-
 docs/dsl1.md                       | 187 +++++++
 docs/dsl2.md                       | 789 -----------------------------
 docs/getstarted.md                 |  28 +-
 docs/index.md                      |   4 +-
 docs/make-html.sh                  |   2 +-
 docs/module.md                     | 272 ++++++++++
 docs/process.md                    |   2 +-
 docs/requirements.txt              |   3 +-
 docs/script.md                     |  35 ++
 docs/snippets/your-first-script.nf |  26 +
 docs/wave.md                       |   2 +-
 docs/workflow.md                   | 405 +++++++++++++++
 16 files changed, 945 insertions(+), 831 deletions(-)
 create mode 100644 docs/dsl1.md
 delete mode 100644 docs/dsl2.md
 create mode 100644 docs/module.md
 create mode 100644 docs/snippets/your-first-script.nf
 create mode 100644 docs/workflow.md

diff --git a/docs/azure.md b/docs/azure.md
index fd68e503de..406aa2c751 100644
--- a/docs/azure.md
+++ b/docs/azure.md
@@ -221,7 +221,7 @@ The pool name can only contain alphanumeric, hyphen and underscore characters.
 :::
 
 :::{warning}
-If the pool name includes a hyphen, make sure to wrap it with single quotes. For example::
+If the pool name includes a hyphen, make sure to wrap it with single quotes. For example:
 
 ```groovy
 azure {
diff --git a/docs/cli.md b/docs/cli.md
index dbe54312b2..988a1d5586 100644
--- a/docs/cli.md
+++ b/docs/cli.md
@@ -1322,13 +1322,7 @@ The `run` command is used to execute a local pipeline script or remote pipeline
   $ nextflow run nextflow-io/hello -qs 4
   ```
 
-- Execute the pipeline with DSL-2 syntax.
-
-  ```console
-  $ nextflow run nextflow-io/hello -dsl2
-  ```
-
-- Execute a pipeline with a specific workflow as the entry-point, this option is meant to be used with DSL-2. For more information on DSL-2, please refer to {ref}`dsl2-page`
+- Invoke the pipeline with a specific workflow as the entry-point.
 
   ```console
   $ nextflow run main.nf -entry workflow_A
diff --git a/docs/conf.py b/docs/conf.py
index 4591e86d00..db55afb734 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -30,6 +30,7 @@
 extensions = [
   'sphinx.ext.mathjax',
   'sphinxcontrib.mermaid',
+  'sphinxext.rediraffe',
   'sphinx_rtd_theme',
   'myst_parser'
 ]
@@ -38,6 +39,10 @@
 
 myst_heading_anchors = 3
 
+rediraffe_redirects = {
+    'dsl2.md': 'dsl1.md'
+}
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 
@@ -75,7 +80,7 @@
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns = ['_build']
+exclude_patterns = ['_build', '**README.md']
 
 # The reST default role (used for this markup: `text`) to use for all documents.
 #default_role = None
diff --git a/docs/container.md b/docs/container.md
index 39281700f7..a1f3799693 100644
--- a/docs/container.md
+++ b/docs/container.md
@@ -35,7 +35,7 @@ If your Apptainer installation support the "user bind control" feature, enable t
 
 ### How it works
 
-The integration for Apptainer follows the same execution model implemented for Docker. You won't need to modify your Nextflow script in order to run it with Apptainer. Simply specify the Apptainer image file from where the containers are started by using the `-with-apptainer` command line option. For example::
+The integration for Apptainer follows the same execution model implemented for Docker. You won't need to modify your Nextflow script in order to run it with Apptainer. Simply specify the Apptainer image file from where the containers are started by using the `-with-apptainer` command line option. For example:
 
 ```bash
 nextflow run <your script> -with-apptainer [apptainer image file]
@@ -72,7 +72,7 @@ Nextflow no longer mounts the home directory when launching an Apptainer contain
 
 ### Multiple containers
 
-It is possible to specify a different Apptainer image for each process definition in your pipeline script. For example, let's suppose you have two processes named `foo` and `bar`. You can specify two different Apptainer images specifying them in the `nextflow.config` file as shown below::
+It is possible to specify a different Apptainer image for each process definition in your pipeline script. For example, let's suppose you have two processes named `foo` and `bar`. You can specify two different Apptainer images specifying them in the `nextflow.config` file as shown below:
 
 ```groovy
 process {
diff --git a/docs/dsl1.md b/docs/dsl1.md
new file mode 100644
index 0000000000..5635590b3d
--- /dev/null
+++ b/docs/dsl1.md
@@ -0,0 +1,187 @@
+(dsl1-page)=
+
+# Migrating from DSL 1
+
+In Nextflow version `22.03.0-edge`, DSL2 became the default DSL version. In version `22.12.0-edge`, DSL1 support was removed, and the Nextflow documentation was updated to use DSL2 by default. Users who are still using DSL1 should migrate their pipelines to DSL2 in order to use the latest versions of Nextflow. This page describes the differences between DSL1 and DSL2, and how to migrate to DSL2.
+
+In Nextflow versions prior to `22.03.0-edge`, you must enable DSL2 explicitly in order to use it. You can either set the feature flag in your pipeline script:
+
+```groovy
+nextflow.enable.dsl=2
+```
+
+Or set the environment variable where you launch Nextflow:
+
+```bash
+export NXF_DEFAULT_DSL=2
+```
+
+## Processes and workflows
+
+In DSL1, a process definition is also the process invocation. Process inputs and outputs are connected to channels using `from` and `into`. Here is the {ref}`getstarted-first` example written in DSL1:
+
+```groovy
+nextflow.enable.dsl=1
+
+params.str = 'Hello world!'
+
+process splitLetters {
+    output:
+    file 'chunk_*' into letters
+
+    """
+    printf '${params.str}' | split -b 6 - chunk_
+    """
+}
+
+process convertToUpper {
+    input:
+    file x from letters.flatten()
+
+    output:
+    stdout result
+
+    """
+    cat $x | tr '[a-z]' '[A-Z]'
+    """
+}
+
+result.view { it.trim() }
+```
+
+To migrate this code to DSL2, you need to move all of your channel logic throughout the script into a `workflow` definition. Additionally, you must call each process explicitly, passing any input channels as arguments (instead of `from ...`) and receiving any output channels as return values (instead of `into ...`).
+
+Refer to the {ref}`workflow-page` page to learn how to define a workflow. The DSL2 version of the above script is duplicated here for your convenience:
+
+```{literalinclude} snippets/your-first-script.nf
+:language: groovy
+```
+
+## Channel forking
+
+In DSL1, a channel can be used as an input only once; to use a channel multiple times, the channel must be forked using the `into` operator.
+
+In DSL2, channels are automatically forked when connecting two or more consumers.
+
+For example, this would not work in DSL1 but is not a problem in DSL2:
+
+```groovy
+Channel
+    .from('Hello','Hola','Ciao')
+    .set{ cheers }
+
+cheers
+    .map{ it.toUpperCase() }
+    .view()
+
+cheers
+    .map{ it.reverse() }
+    .view()
+```
+
+Similarly, process outputs can be consumed by multiple consumers automatically, which makes workflow scripts much easier to read and write.
+
+## Modules
+
+In DSL1, the entire Nextflow pipeline must be defined in a single file (e.g. `main.nf`). This restriction becomes quite cumbersome as a pipeline becomes larger, and it hinders the sharing and reuse of pipeline components.
+
+DSL2 introduces the concept of "module scripts" (or "modules" for short), which are Nextflow scripts that can be "included" by other scripts. While modules are not essential to migrating to DSL2, nor are they mandatory in DSL2 by any means, modules can help you organize a large pipeline into multiple smaller files, and take advantage of modules created by others. Check out the {ref}`module-page` to get started.
+
+:::{note}
+With DSL2, the Groovy shell used by Nextflow also imposes a 64KB size limit on pipeline scripts, so if your DSL1 script is very large, you may need to split your script into modules anyway to avoid this limit.
+:::
+
+## Deprecations
+
+### Processes
+
+- The `set` process input type is no longer supported, use {ref}`tuple <process-input-tuple>` instead.
+
+- The `set` process output type is no longer supported, use {ref}`tuple <process-out-tuple>` instead.
+
+- The `mode flatten` option for process outputs is no longer available. Use the {ref}`operator-flatten` operator on the corresponding output channel instead.
+
+- Unqualified value and file elements in a tuple declaration are no longer allowed. Use an explicit `val` or `path` qualifier.
+
+  For example:
+
+  ```groovy
+  process foo {
+      input:
+      tuple X, 'some-file.sam'
+      output:
+      tuple X, 'some-file.bam'
+
+      script:
+      """
+      your_command --in $X some-file.sam > some-file.bam
+      """
+  }
+  ```
+
+  Use:
+
+  ```groovy
+  process foo {
+      input:
+      tuple val(X), path('some-file.sam')
+      output:
+      tuple val(X), path('some-file.bam')
+
+      script:
+      """
+      your_command --in $X some-file.sam > some-file.bam
+      """
+  }
+  ```
+
+### Channels
+
+- Channel method `bind` has been deprecated in DSL2.
+- Channel method `<<` has been deprecated in DSL2.
+- Channel factory `create` has been deprecated in DSL2.
+
+### Operators
+
+- Operator `choice` has been deprecated in DSL2. Use {ref}`operator-branch` instead.
+- Operator `close` has been deprecated in DSL2.
+- Operator `countBy` has been deprecated in DSL2.
+- Operator `into` has been deprecated in DSL2, as it is no longer needed.
+- Operator `fork` has been renamed to {ref}`operator-multimap`.
+- Operator `groupBy` has been deprecated in DSL2. Use {ref}`operator-grouptuple` instead.
+- Operators `print` and `println` have been deprecated in DSL2. Use {ref}`operator-view` instead.
+- Operator `route` has been deprecated in DSL2.
+- Operator `separate` has been deprecated in DSL2.
+- Operator `spread` has been deprecated in DSL2. Use {ref}`operator-combine` instead.
+
+### DSL2 Preview
+
+An early preview of DSL2 was available in 2020. Note that some of that early DSL2 syntax has since changed.
+
+- The `nextflow.preview.dsl=2` (and `nextflow.enable.dsl=1`) feature flags are no longer needed.
+
+- Anonymous and unwrapped includes are no longer supported. Use an explicit module inclusion instead.
+
+  For example:
+
+  ```groovy
+  include './some/library'
+  include bar from './other/library'
+
+  workflow {
+      foo()
+      bar()
+  }
+  ```
+
+  Should be replaced with:
+
+  ```groovy
+  include { foo } from './some/library'
+  include { bar } from './other/library'
+
+  workflow {
+      foo()
+      bar()
+  }
+  ```
diff --git a/docs/dsl2.md b/docs/dsl2.md
deleted file mode 100644
index 036c5d8ecf..0000000000
--- a/docs/dsl2.md
+++ /dev/null
@@ -1,789 +0,0 @@
-(dsl2-page)=
-
-# DSL 2
-
-Nextflow provides a syntax extension that allows the definition of module libraries and simplifies the writing of complex data analysis pipelines.
-
-To enable this feature you need to define the following directive at the beginning of your workflow script:
-
-```groovy
-nextflow.enable.dsl=2
-```
-
-:::{versionchanged} 22.03.0-edge
-Nextflow uses DSL2 if no version is specified explicitly. You can restore the previous behavior by setting the following environment variable:
-
-```bash
-export NXF_DEFAULT_DSL=1
-```
-:::
-
-:::{versionchanged} 22.03.0-edge
-The DSL version specification (either 1 or 2) can also be specified in the Nextflow configuration file using the same notation shown above.
-:::
-
-:::{versionchanged} 22.11.0-edge
-Support for DSL1 was removed from Nextflow.
-:::
-
-## Function
-
-Nextflow allows the definition of custom functions in the workflow script using the following syntax:
-
-```groovy
-def <function name> ( arg1, arg, .. ) {
-    <function body>
-}
-```
-
-For example:
-
-```groovy
-def foo() {
-    'Hello world'
-}
-
-def bar(alpha, omega) {
-    alpha + omega
-}
-```
-
-The above snippet defines two simple functions, that can be invoked in the workflow script as `foo()` which returns the `Hello world` string and `bar(10,20)` which returns the sum of two parameters (`30` in this case).
-
-:::{note}
-Functions implicitly return the result of the last evaluated statement.
-:::
-
-The keyword `return` can be used to explicitly exit from a function and return the specified value. For example:
-
-```groovy
-def fib( x ) {
-    if( x <= 1 )
-        return x
-    else
-        fib(x-1) + fib(x-2)
-}
-```
-
-## Process
-
-### Process definition
-
-The new DSL separates the definition of a process from its invocation. The process definition follows the usual syntax as described in the {ref}`process documentation <process-page>`. The only difference is that the `from` and `into` channel declarations have to be omitted.
-
-Then a process can be invoked as a function in the `workflow` scope, passing the expected input channels as parameters as if it were a custom function. For example:
-
-```groovy
-nextflow.enable.dsl=2
-
-process foo {
-    output:
-      path 'foo.txt'
-
-    script:
-      """
-      your_command > foo.txt
-      """
-}
-
-process bar {
-    input:
-      path x
-
-    output:
-      path 'bar.txt'
-
-    script:
-      """
-      another_command $x > bar.txt
-      """
-}
-
-workflow {
-    data = channel.fromPath('/some/path/*.txt')
-    foo()
-    bar(data)
-}
-```
-
-:::{warning}
-A process component can be invoked only once in the same workflow context.
-:::
-
-### Process composition
-
-Processes having matching *input-output* declaration can be composed so that the output of the first process is passed as input to the next process. Taking in consideration the previous example, it's possible to write the following:
-
-```groovy
-workflow {
-    bar(foo())
-}
-```
-
-### Process output
-
-A process output can also be accessed using the `out` attribute on the corresponding process object. For example:
-
-```groovy
-workflow {
-    foo()
-    bar(foo.out)
-    bar.out.view()
-}
-```
-
-When a process defines two or more output channels, each of them can be accessed using the array element operator e.g. `out[0]`, `out[1]`, etc. or using *named outputs* (see below).
-
-### Process named output
-
-The `emit` option can be added to the process output definition to assign a name identifier. This name can be used to reference the channel within the caller scope. For example:
-
-```groovy
-process foo {
-  output:
-    path '*.bam', emit: samples_bam
-
-  '''
-  your_command --here
-  '''
-}
-
-workflow {
-    foo()
-    foo.out.samples_bam.view()
-}
-```
-
-### Process named stdout
-
-The `emit` option can be used also to name the stdout:
-
-```groovy
-process sayHello {
-    input:
-        val cheers
-
-    output:
-        stdout emit: verbiage
-
-    script:
-    """
-    echo -n $cheers
-    """
-}
-
-workflow {
-    things = channel.of('Hello world!', 'Yo, dude!', 'Duck!')
-    sayHello(things)
-    sayHello.out.verbiage.view()
-}
-```
-
-:::{note}
-Optional params for a process input/output are always prefixed with a comma, except for `stdout`. Because `stdout` does not have an associated name or value like other types, the first param should not be prefixed.
-:::
-
-## Workflow
-
-### Workflow definition
-
-The `workflow` keyword allows the definition of sub-workflow components that enclose the invocation of one or more processes and operators:
-
-```groovy
-workflow my_pipeline {
-    foo()
-    bar( foo.out.collect() )
-}
-```
-
-For example, the above snippet defines a workflow component, named `my_pipeline`, that can be invoked from another workflow component definition as any other function or process with `my_pipeline()`.
-
-### Workflow parameters
-
-A workflow component can access any variable and parameter defined in the outer scope:
-
-```groovy
-params.data = '/some/data/file'
-
-workflow my_pipeline {
-    if( params.data )
-        bar(params.data)
-    else
-        bar(foo())
-}
-```
-
-### Workflow input
-
-A workflow component can declare one or more input channels using the `take` keyword. For example:
-
-```groovy
-workflow my_pipeline {
-    take: data
-    main:
-        foo(data)
-        bar(foo.out)
-}
-```
-
-:::{warning}
-When the `take` keyword is used, the beginning of the workflow body must be identified with the `main` keyword.
-:::
-
-Then, the input can be specified as an argument in the workflow invocation statement:
-
-```groovy
-workflow {
-    my_pipeline( channel.from('/some/data') )
-}
-```
-
-:::{note}
-Workflow inputs are always channels by definition. If a basic data type is provided instead, such as a number, string, list, etc, it is implicitly converted to a {ref}`value channel <channel-type-value>`.
-:::
-
-### Workflow output
-
-A workflow component can declare one or more output channels using the `emit` keyword. For example:
-
-```groovy
-workflow my_pipeline {
-    main:
-      foo(data)
-      bar(foo.out)
-    emit:
-      bar.out
-}
-```
-
-Then, the result of the `my_pipeline` execution can be accessed using the `out` property, i.e. `my_pipeline.out`. When multiple output channels are declared, use the array bracket notation to access each output channel as described for the [Process output](#process-output) definition.
-
-### Workflow named output
-
-If the output channel is assigned to an identifier in the `emit` declaration, such identifier can be used to reference the channel within the caller scope. For example:
-
-```groovy
-workflow my_pipeline {
-   main:
-     foo(data)
-     bar(foo.out)
-   emit:
-     my_data = bar.out
-}
-```
-
-Then, the result of the above snippet can accessed using `my_pipeline.out.my_data`.
-
-### Workflow entrypoint
-
-A workflow definition which does not declare any name (also known as *implicit workflow*) is the entry point of execution for the workflow application.
-
-:::{note}
-Implicit workflow definition is ignored when a script is included as a module. This allows the writing of a workflow script that can be used either as a library module or as an application script.
-:::
-
-:::{tip}
-A different workflow entrypoint can be specified using the `-entry` command line option.
-:::
-
-### Workflow composition
-
-Workflows defined in your script or imported with [Module inclusion](#module-inclusion) can be invoked and composed as any other process in your application.
-
-```groovy
-workflow flow1 {
-    take: data
-    main:
-        foo(data)
-        bar(foo.out)
-    emit:
-        bar.out
-}
-
-workflow flow2 {
-    take: data
-    main:
-        foo(data)
-        baz(foo.out)
-    emit:
-        baz.out
-}
-
-workflow {
-    take: data
-    main:
-        flow1(data)
-        flow2(flow1.out)
-}
-```
-
-:::{note}
-Nested workflow execution determines an implicit scope. Therefore the same process can be invoked in two different workflow scopes, like for example `foo` in the above snippet that is used both in `flow1` and `flow2`. The workflow execution path, along with the process names, determines the *fully qualified process name* that is used to distinguish the two different process invocations, i.e. `flow1:foo` and `flow2:foo` in the above example.
-:::
-
-:::{tip}
-The fully qualified process name can be used as a valid {ref}`process selector <config-process-selectors>` in the `nextflow.config` file and it has priority over the simple process name.
-:::
-
-## Modules
-
-The new DSL allows the definition of *module scripts* that can be included and shared across workflow applications.
-
-A module script (or simply, module) can contain the definition of functions, processes and workflows as described in the previous sections.
-
-:::{note}
-Functions, processes and workflows are globally referred to as *components*.
-:::
-
-### Module inclusion
-
-A component defined in a module script can be imported into another Nextflow script using the `include` keyword.
-
-For example:
-
-```groovy
-include { foo } from './some/module'
-
-workflow {
-    data = channel.fromPath('/some/data/*.txt')
-    foo(data)
-}
-```
-
-The above snippet includes a process with name `foo` defined in the module script in the main execution context. This way, `foo` can be invoked in the `workflow` scope.
-
-Nextflow implicitly looks for the script file `./some/module.nf` resolving the path against the *including* script location.
-
-:::{note}
-Relative paths must begin with the `./` prefix. Also, the `include` statement must be defined **outside** of the workflow definition.
-:::
-
-(dsl2-module-directory)=
-
-### Module directory
-
-:::{versionadded} 22.10.0
-:::
-
-The module can be defined as a directory whose name matches the module name and contains a script named `main.nf`. For example:
-
-```
-some
-└-module
-  └-main.nf
-```
-
-When defined as a directory the module needs to be included specifying the module directory path:
-
-```groovy
-include { foo } from './some/module'
-```
-
-Module directories allows the use of module scoped binaries scripts. See [Module binaries](#module-binaries) for details.
-
-### Multiple inclusions
-
-A Nextflow script allows the inclusion of an arbitrary number of modules and components. When multiple components need to be included from the same module script, the component names can be specified in the same inclusion using the curly brackets notation as shown below:
-
-```groovy
-include { foo; bar } from './some/module'
-
-workflow {
-    data = channel.fromPath('/some/data/*.txt')
-    foo(data)
-    bar(data)
-}
-```
-
-### Module aliases
-
-When including a module component, it's possible to specify an *alias* with the `as` keyword. This allows the inclusion and the invocation of components with the same name in your script using different names. For example:
-
-```groovy
-include { foo } from './some/module'
-include { foo as bar } from './other/module'
-
-workflow {
-    foo(some_data)
-    bar(other_data)
-}
-```
-
-The same is possible when including the same component multiple times from the same module script as shown below:
-
-```groovy
-include { foo; foo as bar } from './some/module'
-
-workflow {
-    foo(some_data)
-    bar(other_data)
-}
-```
-
-### Module parameters
-
-A module script can define one or more parameters using the same syntax of a Nextflow workflow script:
-
-```groovy
-params.foo = 'Hello'
-params.bar = 'world!'
-
-def sayHello() {
-    println "$params.foo $params.bar"
-}
-```
-
-Then, parameters are inherited from the including context. For example:
-
-```groovy
-params.foo = 'Hola'
-params.bar = 'Mundo'
-
-include {sayHello} from './some/module'
-
-workflow {
-    sayHello()
-}
-```
-
-The above snippet prints:
-
-```
-Hola Mundo
-```
-
-:::{note}
-The module inherits the parameters defined *before* the `include` statement, therefore any further parameter set later is ignored.
-:::
-
-:::{tip}
-Define all pipeline parameters at the beginning of the script *before* any `include` declaration.
-:::
-
-The option `addParams` can be used to extend the module parameters without affecting the external scope. For example:
-
-```groovy
-include {sayHello} from './some/module' addParams(foo: 'Ciao')
-
-workflow {
-    sayHello()
-}
-```
-
-The above snippet prints:
-
-```
-Ciao world!
-```
-
-Finally, the include option `params` allows the specification of one or more parameters without inheriting any value from the external environment.
-
-(module-templates)=
-
-### Module templates
-
-The module script can be defined in an external {ref}`template <process-template>` file. With DSL2 the template file can be placed under the `templates` directory where the module script is located.
-
-For example, let's suppose to have a project L with a module script defining 2 processes (P1 and P2) and both use templates. The template files can be made available under the local `templates` directory:
-
-```
-Project L
-|─myModules.nf
-└─templates
-  |─P1-template.sh
-  └─P2-template.sh
-```
-
-Then, we have a second project A with a workflow that includes P1 and P2:
-
-```
-Pipeline A
-└-main.nf
-```
-
-Finally, we have a third project B with a workflow that includes again P1 and P2:
-
-```
-Pipeline B
-└-main.nf
-```
-
-With the possibility to keep the template files inside the project L, A and B can use the modules defined in L without any changes. A future project C would do the same, just cloning L (if not available on the system) and including its module script.
-
-Beside promoting sharing modules across pipelines, there are several advantages in keeping the module template under the script path:
-
-1. module components are *self-contained*,
-2. module components can be tested independently from the pipeline(s) importing them,
-3. it is possible to create libraries of module components.
-
-Ultimately, having multiple template locations allows a more structured organization within the same project. If a project has several module components, and all them use templates, the project could group module scripts and their templates as needed. For example:
-
-```
-baseDir
-|─main.nf
-|─Phase0-Modules
-  |─mymodules1.nf
-  |─mymodules2.nf
-  └─templates
-    |─P1-template.sh
-    └─P2-template.sh
-|─Phase1-Modules
-  |─mymodules3.nf
-  |─mymodules4.nf
-  └─templates
-    |─P3-template.sh
-    └─P4-template.sh
-└─Phase2-Modules
-  |─mymodules5.nf
-  |─mymodules6.nf
-  └─templates
-    |─P5-template.sh
-    |─P6-template.sh
-    └─P7-template.sh
-```
-
-(module-binaries)=
-
-### Module binaries
-
-:::{versionadded} 22.10.0
-:::
-
-Modules can define binary scripts that are locally scoped to the processes defined by the tasks.
-
-To enable this feature add the following setting in pipeline configuration file:
-
-```groovy
-nextflow.enable.moduleBinaries = true
-```
-
-The binary scripts must be placed in the module directory names `<module-dir>/resources/usr/bin`:
-
-```
-<module-dir>
-|─main.nf
-└─resources
-  └─usr
-    └─bin
-      |─your-module-script1.sh
-      └─another-module-script2.py
-```
-
-Those scripts will be accessible as any other command in the tasks environment, provided they have been granted the Linux execute permissions.
-
-:::{note}
-This feature requires the use of a local or shared file system as the pipeline work directory or {ref}`wave-page` when using cloud based executors.
-:::
-
-## Channel forking
-
-Using the new DSL, Nextflow channels are automatically forked when connecting two or more consumers.
-
-For example:
-
-```groovy
-channel
-    .from('Hello','Hola','Ciao')
-    .set{ cheers }
-
-cheers
-    .map{ it.toUpperCase() }
-    .view()
-
-cheers
-    .map{ it.reverse() }
-    .view()
-```
-
-The same is valid for the result (channel) of a process execution. Therefore a process output can be consumed by two or more processes without the need to fork it using the `into` operator, making the writing of workflow scripts more fluent and readable.
-
-## Pipes
-
-### The *pipe* operator
-
-Nextflow processes and operators can be composed using the `|` *pipe* operator. For example:
-
-```groovy
-process foo {
-    input:
-    val data
-
-    output:
-    val result
-
-    exec:
-    result = "$data world"
-}
-
-workflow {
-   channel.from('Hello','Hola','Ciao') | foo | map { it.toUpperCase() } | view
-}
-```
-
-The above snippet defines a process named `foo` and invokes it passing the content of the `data` channel. The result is then piped to the {ref}`operator-map` operator which converts each string to uppercase and finally, the last {ref}`operator-view` operator prints it.
-
-### The *and* operator
-
-The `&` *and* operator allows feeding of two or more processes with the content of the same channel(s). For example:
-
-```groovy
-process foo {
-    input:
-    val data
-
-    output:
-    val result
-
-    exec:
-    result = "$data world"
-}
-
-process bar {
-    input:
-    val data
-
-    output:
-    val result
-
-    exec:
-    result = data.toUpperCase()
-}
-
-workflow {
-    channel.from('Hello') | map { it.reverse() } | (foo & bar) | mix | view
-}
-```
-
-In the above snippet the channel emitting the `Hello` string is piped with the {ref}`operator-map` which reverses the string value. Then, the result is passed to both `foo` and `bar` processes which are executed in parallel. Each process outputs a channel, and the two channels are merged into a single channel using the {ref}`operator-mix` operator. Finally the result is printed using the {ref}`operator-view` operator.
-
-:::{tip}
-The break-line operator `\` can be used to split long statements over multiple lines. The above snippet can also be written as:
-
-```groovy
-workflow {
-    channel.from('Hello') \
-      | map { it.reverse() } \
-      | (foo & bar) \
-      | mix \
-      | view
-}
-```
-:::
-
-## DSL2 migration notes
-
-- DSL2 final version is activated using the declaration `nextflow.enable.dsl=2` in place of `nextflow.preview.dsl=2`.
-
-- Process inputs of type `set` have to be replaced with {ref}`tuple <process-input-tuple>`.
-
-- Process outputs of type `set` have to be replaced with {ref}`tuple <process-out-tuple>`.
-
-- Process output option `mode flatten` is no longer available. Replace it using the {ref}`operator-flatten` operator on the corresponding output channel.
-
-- Anonymous and unwrapped includes are not supported anymore. Replace them with an explicit module inclusion. For example:
-
-  ```groovy
-  include './some/library'
-  include bar from './other/library'
-
-  workflow {
-    foo()
-    bar()
-  }
-  ```
-
-  Should be replaced with:
-
-  ```groovy
-  include { foo } from './some/library'
-  include { bar } from './other/library'
-
-  workflow {
-    foo()
-    bar()
-  }
-  ```
-
-- The use of unqualified value and file elements into input tuples is not allowed anymore. Replace them with a corresponding
-  `val` or `path` qualifier:
-
-  ```groovy
-  process foo {
-  input:
-    tuple X, 'some-file.bam'
-
-  script:
-    '''
-    your_command --in $X some-file.bam
-    '''
-  }
-  ```
-
-  Use:
-
-  ```groovy
-  process foo {
-  input:
-    tuple val(X), path('some-file.bam')
-
-  script:
-    '''
-    your_command --in $X some-file.bam
-    '''
-  }
-  ```
-
-- The use of unqualified value and file elements into output tuples is not allowed anymore. Replace them with a corresponding
-  `val` or `path` qualifier:
-
-  ```groovy
-  process foo {
-  output:
-    tuple X, 'some-file.bam'
-
-  script:
-    X = 'some value'
-    '''
-    your_command > some-file.bam
-    '''
-  }
-  ```
-
-  Use:
-
-  ```groovy
-  process foo {
-  output:
-    tuple val(X), path('some-file.bam')
-
-  script:
-    X = 'some value'
-    '''
-    your_command > some-file.bam
-    '''
-  }
-  ```
-
-- The `bind` channel method (and corresponding `<<` operator) has been deprecated in DSL2.
-
-- The `choice` operator has been deprecated in DSL2. Use {ref}`operator-branch` instead.
-
-- The `close` operator has been deprecated in DSL2.
-
-- The `countBy` operator has been deprecated in DSL2.
-
-- The `create` channel factory has been deprecated in DSL2.
-
-- The `fork` operator has been renamed to {ref}`operator-multimap`.
-
-- The `groupBy` operator has been deprecated in DSL2. Replace it with {ref}`operator-grouptuple`
-
-- The `into` operator has been deprecated in DSL2 since it's not needed anymore.
-
-- The `print` and `println` operators have been deprecated in DSL2. Use {ref}`operator-view` instead.
-
-- The `route` operator has been deprecated in DSL2.
-
-- The `separate` operator has been deprecated in DSL2.
-
-- The `spread` operator has been deprecated in DSL2. Replace it with {ref}`operator-combine`.
diff --git a/docs/getstarted.md b/docs/getstarted.md
index 72aaac0c05..0501317e81 100644
--- a/docs/getstarted.md
+++ b/docs/getstarted.md
@@ -96,32 +96,8 @@ nextflow self-update
 
 Copy the following example into your favorite text editor and save it to a file named `tutorial.nf`:
 
-```groovy
-params.str = 'Hello world!'
-
-process splitLetters {
-  output:
-    path 'chunk_*'
-
-  """
-  printf '${params.str}' | split -b 6 - chunk_
-  """
-}
-
-process convertToUpper {
-  input:
-    path x
-  output:
-    stdout
-
-  """
-  cat $x | tr '[a-z]' '[A-Z]'
-  """
-}
-
-workflow {
-  splitLetters | flatten | convertToUpper | view { it.trim() }
-}
+```{literalinclude} snippets/your-first-script.nf
+:language: groovy
 ```
 
 :::{note}
diff --git a/docs/index.md b/docs/index.md
index 40552e7c44..44cde1ed59 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -38,8 +38,10 @@ script
 process
 channel
 operator
+workflow
+module
 config
-dsl2
+dsl1
 ```
 
 ```{toctree}
diff --git a/docs/make-html.sh b/docs/make-html.sh
index ebf3378c75..da26d88bf2 100755
--- a/docs/make-html.sh
+++ b/docs/make-html.sh
@@ -1,4 +1,4 @@
 #!/bin/bash
 
-docker run -v $(pwd):/tmp nextflow/sphinx:5.3.0 -- make html
+docker run -v $(pwd):/tmp $(wave -f Dockerfile --context .) -- make html
 echo "Done. See _build/html/index.html"
diff --git a/docs/module.md b/docs/module.md
new file mode 100644
index 0000000000..11298699dc
--- /dev/null
+++ b/docs/module.md
@@ -0,0 +1,272 @@
+(module-page)=
+
+# Modules
+
+In Nextflow, a **module** is a script that may contain functions, processes, and workflows (collectively referred to as *components*). A module can be included in other modules or pipeline scripts and even shared across workflows.
+
+:::{note}
+Modules were introduced in DSL2. If you are still using DSL1, see the {ref}`dsl1-page` page to learn how to migrate your Nextflow pipelines to DSL2.
+:::
+
+## Module inclusion
+
+A component defined in a module script can be imported into another Nextflow script using the `include` keyword.
+
+For example:
+
+```groovy
+include { foo } from './some/module'
+
+workflow {
+    data = channel.fromPath('/some/data/*.txt')
+    foo(data)
+}
+```
+
+The above snippet imports a process named `foo`, defined in the module script, into the main execution context. This way, `foo` can be invoked in the `workflow` scope.
+
+Nextflow implicitly looks for the script file `./some/module.nf`, resolving the path against the *including* script location.
+
+Module includes are subject to the following rules:
+
+- Relative paths must begin with the `./` prefix.
+- Include statements are not allowed from within a workflow. They must occur at the script level.
+
+(module-directory)=
+
+## Module directory
+
+:::{versionadded} 22.10.0
+:::
+
+A module can be defined as a directory with the same name as the module and with a script named `main.nf`. For example:
+
+```
+some
+└── module
+    └── main.nf
+```
+
+When defined as a directory, the module must be included by specifying the module directory path:
+
+```groovy
+include { foo } from './some/module'
+```
+
+Module directories allow the use of module scoped binaries scripts. See [Module binaries] for details.
+
+## Multiple inclusions
+
+A Nextflow script can include any number of modules, and an `include` statement can import any number of components from a module. Multiple components can be included from the same module by using the syntax shown below:
+
+```groovy
+include { foo; bar } from './some/module'
+
+workflow {
+    data = channel.fromPath('/some/data/*.txt')
+    foo(data)
+    bar(data)
+}
+```
+
+(module-aliases)=
+
+## Module aliases
+
+When including a module component, it's possible to specify an *alias* with the `as` keyword. Aliasing allows you to avoid module name clashes, by assigning them different names in the including context. For example:
+
+```groovy
+include { foo } from './some/module'
+include { foo as bar } from './other/module'
+
+workflow {
+    foo(some_data)
+    bar(other_data)
+}
+```
+
+You can even include the same component multiple times under different names:
+
+```groovy
+include { foo; foo as bar } from './some/module'
+
+workflow {
+    foo(some_data)
+    bar(other_data)
+}
+```
+
+## Module parameters
+
+A module script can define parameters using the same syntax as a Nextflow workflow script:
+
+```groovy
+params.foo = 'Hello'
+params.bar = 'world!'
+
+def sayHello() {
+    println "$params.foo $params.bar"
+}
+```
+
+When including a module, the module will first use parameters from the including context. For example:
+
+```groovy
+params.foo = 'Hola'
+params.bar = 'Mundo'
+
+include { sayHello } from './some/module'
+
+workflow {
+    sayHello()
+}
+```
+
+The above snippet prints:
+
+```
+Hola Mundo
+```
+
+:::{note}
+The module inherits the parameters defined *before* the `include` statement, therefore any parameters set afterwards will not be used by the module.
+:::
+
+:::{tip}
+It is best to define all pipeline parameters *before* any `include` statements.
+:::
+
+The `addParams` option can be used to pass parameters to the module without adding them to the including scope.
+
+```groovy
+params.foo = 'Hola'
+params.bar = 'Mundo'
+
+include { sayHello } from './some/module' addParams(foo: 'Ciao')
+
+workflow {
+    sayHello()
+}
+```
+
+The above snippet prints:
+
+```
+Ciao Mundo
+```
+
+Alternatively, the `params` option can be used to pass parameters to module without adding them to the including scope, *and* without inheriting any parameters from the including scope.
+
+```groovy
+params.foo = 'Hola'
+params.bar = 'Mundo'
+
+include { sayHello } from './some/module' params(foo: 'Ciao')
+
+workflow {
+    sayHello()
+}
+```
+
+The above snippet prints:
+
+```
+Ciao world!
+```
+
+(module-templates)=
+
+## Module templates
+
+The module script can be defined in an external {ref}`template <process-template>` file. The template file can be placed in the `templates` directory where the module script is located.
+
+For example, suppose we have a project L with a module script that defines two processes, P1 and P2, both of which use templates. The template files can be made available in the local `templates` directory:
+
+```
+Project L
+|── myModules.nf
+└── templates
+    |── P1-template.sh
+    └── P2-template.sh
+```
+
+Then, we have a second project A with a workflow that includes P1 and P2:
+
+```
+Pipeline A
+└── main.nf
+```
+
+Finally, we have a third project B with a workflow that also includes P1 and P2:
+
+```
+Pipeline B
+└── main.nf
+```
+
+With the possibility to keep the template files inside the project L, A and B can use the modules defined in L without any changes. A future project C would do the same, just cloning L (if not available on the system) and including its module script.
+
+Beside promoting the sharing of modules across pipelines, there are several advantages to keeping the module template under the script path:
+
+1. module components are *self-contained*,
+2. module components can be tested independently from the pipeline(s) that import them,
+3. it is possible to create libraries of module components.
+
+Ultimately, having multiple template locations allows a more structured organization within the same project. If a project has several module components, and all of them use templates, the project could group module scripts and their templates as needed. For example:
+
+```
+baseDir
+|── main.nf
+|── Phase0-Modules
+    |── mymodules1.nf
+    |── mymodules2.nf
+    └── templates
+        |── P1-template.sh
+        |── P2-template.sh
+|── Phase1-Modules
+    |── mymodules3.nf
+    |── mymodules4.nf
+    └── templates
+        |── P3-template.sh
+        └── P4-template.sh
+└── Phase2-Modules
+    |── mymodules5.nf
+    |── mymodules6.nf
+    └── templates
+        |── P5-template.sh
+        |── P6-template.sh
+        └── P7-template.sh
+```
+
+(module-binaries)=
+
+## Module binaries
+
+:::{versionadded} 22.10.0
+:::
+
+Modules can define binary scripts that are locally scoped to the processes defined by the tasks.
+
+To enable this feature, enable the following flag in your pipeline script or configuration file:
+
+```groovy
+nextflow.enable.moduleBinaries = true
+```
+
+The binary scripts must be placed in the module directory names `<module-dir>/resources/usr/bin`:
+
+```
+<module-dir>
+|── main.nf
+└── resources
+    └── usr
+        └── bin
+            |── your-module-script1.sh
+            └── another-module-script2.py
+```
+
+Those scripts will be made accessible like any other command in the task environment, provided they have been granted the Linux execute permissions.
+
+:::{note}
+This feature requires the use of a local or shared file system for the pipeline work directory, or {ref}`wave-page` when using cloud-based executors.
+:::
diff --git a/docs/process.md b/docs/process.md
index 8da1f5376d..7f99670ed5 100644
--- a/docs/process.md
+++ b/docs/process.md
@@ -4,7 +4,7 @@
 
 In Nextflow, a **process** is the basic processing primitive to execute a user script.
 
-The process definition starts with the keyword `process`, followed by process name and finally the process body delimited by curly brackets. The process body must contain a string which represents the command or, more generally, a script that is executed by it. A basic process looks like the following example:
+The process definition starts with the keyword `process`, followed by process name and finally the process body delimited by curly braces. The process body must contain a string which represents the command or, more generally, a script that is executed by it. A basic process looks like the following example:
 
 ```groovy
 process sayHello {
diff --git a/docs/requirements.txt b/docs/requirements.txt
index 6e887390ed..06694e6ca0 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -1,4 +1,5 @@
 myst-parser==0.18.1
 sphinx==5.3.0
 sphinx-rtd-theme==1.1.1
-sphinxcontrib-mermaid==0.9.2
\ No newline at end of file
+sphinxcontrib-mermaid==0.9.2
+sphinxext-rediraffe==0.2.7
\ No newline at end of file
diff --git a/docs/script.md b/docs/script.md
index f2ba710a3c..071675e103 100644
--- a/docs/script.md
+++ b/docs/script.md
@@ -338,6 +338,41 @@ Remove the first number with its trailing whitespace from a string:
 assert ('Line contains 20 characters' - ~/\d+\s+/) == 'Line contains characters'
 ```
 
+### Functions
+
+Functions can be defined using the following syntax:
+
+```groovy
+def <function name> ( arg1, arg, .. ) {
+    <function body>
+}
+```
+
+For example:
+
+```groovy
+def foo() {
+    'Hello world'
+}
+
+def bar(alpha, omega) {
+    alpha + omega
+}
+```
+
+The above snippet defines two simple functions, that can be invoked in the workflow script as `foo()`, which returns `'Hello world'`, and `bar(10, 20)`, which returns the sum of two parameters (`30` in this case).
+
+Functions implicitly return the result of the last statement. Additionally, the `return` keyword can be used to explicitly exit from a function and return the specified value. For example:
+
+```groovy
+def fib( x ) {
+    if( x <= 1 )
+        return x
+
+    fib(x-1) + fib(x-2)
+}
+```
+
 (script-closure)=
 
 ### Closures
diff --git a/docs/snippets/your-first-script.nf b/docs/snippets/your-first-script.nf
new file mode 100644
index 0000000000..f457ff3deb
--- /dev/null
+++ b/docs/snippets/your-first-script.nf
@@ -0,0 +1,26 @@
+params.str = 'Hello world!'
+
+process splitLetters {
+    output:
+    path 'chunk_*'
+
+    """
+    printf '${params.str}' | split -b 6 - chunk_
+    """
+}
+
+process convertToUpper {
+    input:
+    path x
+
+    output:
+    stdout
+
+    """
+    cat $x | tr '[a-z]' '[A-Z]'
+    """
+}
+
+workflow {
+    splitLetters | flatten | convertToUpper | view { it.trim() }
+}
\ No newline at end of file
diff --git a/docs/wave.md b/docs/wave.md
index 2d821803de..426267ffe1 100644
--- a/docs/wave.md
+++ b/docs/wave.md
@@ -62,7 +62,7 @@ tower {
 
 Wave can build and provision container images on-demand for your Nextflow pipelines.
 
-To enable this feature, add the Dockerfile of the container to be built in the {ref}`module directory <dsl2-module-directory>` where the pipeline process is defined. When Wave is enabled, it automatically uses the Dockerfile to build the required container, upload to the registry, and it uses the container to carry out the tasks defined in the module.
+To enable this feature, add the Dockerfile of the container to be built in the {ref}`module directory <module-directory>` where the pipeline process is defined. When Wave is enabled, it automatically uses the Dockerfile to build the required container, upload to the registry, and it uses the container to carry out the tasks defined in the module.
 
 :::{tip}
 Make sure the process does not declare a `container` directive, otherwise it will take precedence over the Dockerfile definition.
diff --git a/docs/workflow.md b/docs/workflow.md
new file mode 100644
index 0000000000..209b3e769b
--- /dev/null
+++ b/docs/workflow.md
@@ -0,0 +1,405 @@
+(workflow-page)=
+
+# Workflows
+
+In Nextflow, a **workflow** is a composition of processes and dataflow logic (i.e. channels and operators).
+
+The workflow definition starts with the keyword `workflow`, followed by an optional name, and finally the workflow body delimited by curly braces. A basic workflow looks like the following example:
+
+```groovy
+workflow {
+    foo()
+}
+```
+
+Where `foo` could be a function, a process, or another workflow.
+
+Workflows are *lazily executed*, which means that Nextflow parses the entire workflow structure first, and then executes the entire workflow at once. The order in which a task is executed is determined only by its dependencies, so a task will be executed as soon as all of its required inputs are available.
+
+The syntax of a workflow is defined as follows:
+
+```groovy
+workflow [ name ] {
+
+    take:
+    < workflow inputs >
+
+    main:
+    < dataflow statements >
+
+    emit:
+    < workflow outputs >
+
+}
+```
+
+:::{tip}
+The `main:` label can be omitted if there are no `take:` or `emit:` blocks.
+:::
+
+:::{note}
+Workflows were introduced in DSL2. If you are still using DSL1, see the {ref}`dsl1-page` page to learn how to migrate your Nextflow pipelines to DSL2.
+:::
+
+## Process invocation
+
+A process can be invoked like a function in a workflow definition, passing the expected input channels like function arguments. For example:
+
+```groovy
+process foo {
+    output:
+    path 'foo.txt'
+
+    script:
+    """
+    your_command > foo.txt
+    """
+}
+
+process bar {
+    input:
+    path x
+
+    output:
+    path 'bar.txt'
+
+    script:
+    """
+    another_command $x > bar.txt
+    """
+}
+
+workflow {
+    data = channel.fromPath('/some/path/*.txt')
+    foo()
+    bar(data)
+}
+```
+
+:::{warning}
+A process can be only be invoked once in a single workflow, however you can get around this restriction by using {ref}`module-aliases`.
+:::
+
+### Process composition
+
+Processes with matching input/output declarations can be composed so that the output of the first process is passed as input to the second process. The previous example can be rewritten as follows:
+
+```groovy
+workflow {
+    bar(foo())
+}
+```
+
+### Process outputs
+
+A process output can be accessed using the `out` attribute on the corresponding process object. For example:
+
+```groovy
+workflow {
+    foo()
+    bar(foo.out)
+    bar.out.view()
+}
+```
+
+When a process defines multiple output channels, each output can be accessed using the array element operator (`out[0]`, `out[1]`, etc.) or using *named outputs* (see below).
+
+The process output(s) can also be accessed like the return value of a function:
+
+```groovy
+workflow {
+    f_out = foo()
+    (b1, b2) = bar(f_out)
+    b1.view()
+}
+```
+
+### Process named outputs
+
+The `emit` option can be added to the process output definition to assign a name identifier. This name can be used to reference the channel from the calling workflow. For example:
+
+```groovy
+process foo {
+    output:
+    path '*.bam', emit: samples_bam
+
+    '''
+    your_command --here
+    '''
+}
+
+workflow {
+    foo()
+    foo.out.samples_bam.view()
+}
+```
+
+When referencing a named output directly from the process invocation, you can use a more concise syntax:
+
+```groovy
+workflow {
+    ch_samples = foo().samples_bam
+}
+```
+
+### Process named stdout
+
+The `emit` option can also be used to name a `stdout` output:
+
+```groovy
+process sayHello {
+    input:
+    val cheers
+
+    output:
+    stdout emit: verbiage
+
+    script:
+    """
+    echo -n $cheers
+    """
+}
+
+workflow {
+    things = channel.of('Hello world!', 'Yo, dude!', 'Duck!')
+    sayHello(things)
+    sayHello.out.verbiage.view()
+}
+```
+
+:::{note}
+Optional params for a process input/output are always prefixed with a comma, except for `stdout`. Because `stdout` does not have an associated name or value like other types, the first param should not be prefixed.
+:::
+
+## Subworkflows
+
+A named workflow is a "subworkflow" that can be invoked from other workflows. For example:
+
+```groovy
+workflow my_pipeline {
+    foo()
+    bar( foo.out.collect() )
+}
+
+workflow {
+    my_pipeline()
+}
+```
+
+The above snippet defines a workflow named `my_pipeline`, that can be invoked from another workflow as `my_pipeline()`, just like any other function or process.
+
+### Workflow parameters
+
+A workflow component can access any variable or parameter defined in the global scope:
+
+```groovy
+params.data = '/some/data/file'
+
+workflow my_pipeline {
+    if( params.data )
+        bar(params.data)
+    else
+        bar(foo())
+}
+```
+
+### Workflow inputs
+
+A workflow can declare one or more input channels using the `take` keyword. For example:
+
+```groovy
+workflow my_pipeline {
+    take: data
+
+    main:
+    foo(data)
+    bar(foo.out)
+}
+```
+
+Multiple inputs must be specified on separate lines:
+
+```groovy
+workflow my_pipeline {
+    take:
+    data1
+    data2
+
+    main:
+    foo(data1, data2)
+    bar(foo.out)
+}
+```
+
+:::{warning}
+When the `take` keyword is used, the beginning of the workflow body must be defined with the `main` keyword.
+:::
+
+Inputs can be specified like arguments when invoking the workflow:
+
+```groovy
+workflow {
+    my_pipeline( channel.from('/some/data') )
+}
+```
+
+:::{note}
+Workflow inputs are always channels by definition. If a basic data type, such as a number, string, list, etc, is provided, it is implicitly converted to a {ref}`value channel <channel-type-value>`.
+:::
+
+### Workflow outputs
+
+A workflow can declare one or more output channels using the `emit` keyword. For example:
+
+```groovy
+workflow my_pipeline {
+    main:
+    foo(data)
+    bar(foo.out)
+
+    emit:
+    bar.out
+}
+```
+
+When invoking the workflow, the output channel(s) can be accessed using the `out` property, i.e. `my_pipeline.out`. When multiple output channels are declared, use the array bracket notation or the assignment syntax to access each output channel as described for [process outputs](#process-outputs).
+
+### Workflow named outputs
+
+If an output channel is assigned to an identifier in the `emit` block, the identifier can be used to reference the channel from the calling workflow. For example:
+
+```groovy
+workflow my_pipeline {
+    main:
+    foo(data)
+    bar(foo.out)
+
+    emit:
+    my_data = bar.out
+}
+```
+
+The result of the above workflow can be accessed using `my_pipeline.out.my_data`.
+
+### Workflow entrypoint
+
+A workflow with no name (also known as the *implicit workflow*) is the default entrypoint of the Nextflow pipeline. A different workflow entrypoint can be specified using the `-entry` command line option.
+
+:::{note}
+Implicit workflow definitions are ignored when a script is included as a module. This way, a workflow script can be written in such a way that it can be used either as a library module or an application script.
+:::
+
+### Workflow composition
+
+Named workflows can be invoked and composed just like any other process or function.
+
+```groovy
+workflow flow1 {
+    take: data
+    main:
+        foo(data)
+        bar(foo.out)
+    emit:
+        bar.out
+}
+
+workflow flow2 {
+    take: data
+    main:
+        foo(data)
+        baz(foo.out)
+    emit:
+        baz.out
+}
+
+workflow {
+    take: data
+    main:
+        flow1(data)
+        flow2(flow1.out)
+}
+```
+
+:::{note}
+Each workflow invocation has its own scope. As a result, the same process can be invoked in two different workflow scopes, like `foo` in the above snippet, which is used in both `flow1` and `flow2`. The workflow execution path, along with the process names, determines the *fully qualified process name* that is used to distinguish the different process invocations, i.e. `flow1:foo` and `flow2:foo` in the above example.
+:::
+
+:::{tip}
+The fully qualified process name can be used as a {ref}`process selector <config-process-selectors>` in a Nextflow configuration file, and it takes priority over the simple process name.
+:::
+
+## Special operators
+
+### Pipe `|`
+
+The `|` *pipe* operator can be used to compose Nextflow processes and operators. For example:
+
+```groovy
+process foo {
+    input:
+    val data
+
+    output:
+    val result
+
+    exec:
+    result = "$data world"
+}
+
+workflow {
+   channel.from('Hello','Hola','Ciao') | foo | map { it.toUpperCase() } | view
+}
+```
+
+The above snippet defines a process named `foo` and invokes it with the `data` channel. The result is then piped to the {ref}`operator-map` operator, which converts each string to uppercase, and finally to the {ref}`operator-view` operator which prints it.
+
+:::{tip}
+Statements can also be split across multiple lines for better readability:
+
+```groovy
+workflow {
+    channel.from('Hello','Hola','Ciao')
+      | foo
+      | map { it.toUpperCase() }
+      | view
+}
+```
+:::
+
+### And `&`
+
+The `&` *and* operator can be used to feed multiple processes with the same channel(s). For example:
+
+```groovy
+process foo {
+    input:
+    val data
+
+    output:
+    val result
+
+    exec:
+    result = "$data world"
+}
+
+process bar {
+    input:
+    val data
+
+    output:
+    val result
+
+    exec:
+    result = data.toUpperCase()
+}
+
+workflow {
+    channel.from('Hello')
+      | map { it.reverse() }
+      | (foo & bar)
+      | mix
+      | view
+}
+```
+
+In the above snippet, the initial channel is piped to the {ref}`operator-map` operator, which reverses the string value. Then, the result is passed to the processes `foo` and `bar`, which are executed in parallel. Each process outputs a channel, and the two channels are combined using the {ref}`operator-mix` operator. Finally, the result is printed using the {ref}`operator-view` operator.

From 795849d7730d6ecb3d89437d7d27580abd855643 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sun, 15 Oct 2023 17:06:25 +0200
Subject: [PATCH 226/350] Bump nf-wave@1.0.0

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-wave/changelog.txt                      | 3 +++
 plugins/nf-wave/src/resources/META-INF/MANIFEST.MF | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/plugins/nf-wave/changelog.txt b/plugins/nf-wave/changelog.txt
index 8fc6fe8039..8d24dc858e 100644
--- a/plugins/nf-wave/changelog.txt
+++ b/plugins/nf-wave/changelog.txt
@@ -1,5 +1,8 @@
 nf-wave changelog
 ==================
+1.0.0 - 15 Oct 2023
+- Fix conda channels order [ci fast] [6672c6d7]
+
 0.14.0 - 10 Oct 2023
 - Add bioconda and seqera Conda default channels (#4359) [ff012dcd]
 - Improve Wave error handling [d47e8b07]
diff --git a/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF b/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF
index b6fdf2ec2b..c45b973508 100644
--- a/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: io.seqera.wave.plugin.WavePlugin
 Plugin-Id: nf-wave
-Plugin-Version: 0.14.0
+Plugin-Version: 1.0.0
 Plugin-Provider: Seqera Labs
 Plugin-Requires: >=23.05.0-edge

From e2c8831837757c689917310c2ec847e41ee68d97 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sun, 15 Oct 2023 17:07:11 +0200
Subject: [PATCH 227/350] Update changelog

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 changelog.txt                 | 15 +++++++++++++++
 plugins/nf-wave/changelog.txt |  1 +
 2 files changed, 16 insertions(+)

diff --git a/changelog.txt b/changelog.txt
index b268d3615b..ac135b9f76 100644
--- a/changelog.txt
+++ b/changelog.txt
@@ -1,5 +1,20 @@
 NEXTFLOW CHANGE-LOG
 ===================
+23.10.0 - 15 Oct 2023
+- Add support for K8s hostPath [10c32325]
+- Add AWS SES docs [b83e7148]
+- Add -with-cloudcache instead of -cloudcache [ef530263]
+- Add inspect command validation tests [882f369e]
+- Improve warning complaining about tuple but mentioning set (#4400) [0ef48735]
+- Improve `-dump-hashes` output adding json format (#4369) [5bdaac94]
+- Improve error message on invalid file url prefix [82a3f405]
+- Fix conda channels order [6672c6d7]
+- Docs: Incorporate DSL2 features (#3793) [efd041cb]
+- Docs: aws.batch.retrymode = 'built-in' (#4229) [d5a8098f]
+- Docs: Update logos, fonts, and colors (#4407) [7814822c]
+- Changelog minor changes [dfb5bf09]
+- Bump nf-wave@1.0.0 [795849d7]
+
 23.09.3-edge - 10 Oct 2023
 - Add -cloudcache CLI option (#4385) [73fda582]
 - Add bioconda and seqera Conda default channels (#4359) [ff012dcd]
diff --git a/plugins/nf-wave/changelog.txt b/plugins/nf-wave/changelog.txt
index 8d24dc858e..5886b9be8a 100644
--- a/plugins/nf-wave/changelog.txt
+++ b/plugins/nf-wave/changelog.txt
@@ -2,6 +2,7 @@ nf-wave changelog
 ==================
 1.0.0 - 15 Oct 2023
 - Fix conda channels order [ci fast] [6672c6d7]
+- Bump nf-wave@1.0.0 [795849d7]
 
 0.14.0 - 10 Oct 2023
 - Add bioconda and seqera Conda default channels (#4359) [ff012dcd]

From 2cce747d77466c049a792bffa258f90869be6c52 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sun, 15 Oct 2023 17:12:07 +0200
Subject: [PATCH 228/350] [release 23.10.0] [ci fast] Update timestamp and
 build number

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 VERSION                                                     | 2 +-
 docs/conf.py                                                | 4 ++--
 .../nextflow/src/main/resources/META-INF/plugins-info.txt   | 2 +-
 modules/nf-commons/src/main/nextflow/Const.groovy           | 6 +++---
 nextflow                                                    | 2 +-
 nextflow.md5                                                | 2 +-
 nextflow.sha1                                               | 2 +-
 nextflow.sha256                                             | 2 +-
 8 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/VERSION b/VERSION
index bc02edad74..7d7a070243 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-23.09.3-edge
+23.10.0
diff --git a/docs/conf.py b/docs/conf.py
index db55afb734..7a9f214174 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -64,9 +64,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '23.09'
+version = '23.10'
 # The full version, including alpha/beta/rc tags.
-release = '23.09.3-edge'
+release = '23.10.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
diff --git a/modules/nextflow/src/main/resources/META-INF/plugins-info.txt b/modules/nextflow/src/main/resources/META-INF/plugins-info.txt
index bb727d9a50..4f2d453db3 100644
--- a/modules/nextflow/src/main/resources/META-INF/plugins-info.txt
+++ b/modules/nextflow/src/main/resources/META-INF/plugins-info.txt
@@ -6,4 +6,4 @@ nf-console@1.0.6
 nf-ga4gh@1.1.0
 nf-google@1.8.3
 nf-tower@1.6.3
-nf-wave@0.14.0
\ No newline at end of file
+nf-wave@1.0.0
\ No newline at end of file
diff --git a/modules/nf-commons/src/main/nextflow/Const.groovy b/modules/nf-commons/src/main/nextflow/Const.groovy
index 726c2ada21..6ad8318823 100644
--- a/modules/nf-commons/src/main/nextflow/Const.groovy
+++ b/modules/nf-commons/src/main/nextflow/Const.groovy
@@ -52,17 +52,17 @@ class Const {
     /**
      * The application version
      */
-    static public final String APP_VER = "23.09.3-edge"
+    static public final String APP_VER = "23.10.0"
 
     /**
      * The app build time as linux/unix timestamp
      */
-    static public final long APP_TIMESTAMP = 1696931920194
+    static public final long APP_TIMESTAMP = 1697382483238
 
     /**
      * The app build number
      */
-    static public final int APP_BUILDNUM = 5888
+    static public final int APP_BUILDNUM = 5890
 
     /**
      * The app build time string relative to UTC timezone
diff --git a/nextflow b/nextflow
index 65c4379239..2a73246ddf 100755
--- a/nextflow
+++ b/nextflow
@@ -15,7 +15,7 @@
 #  limitations under the License.
 
 [[ "$NXF_DEBUG" == 'x' ]] && set -x
-NXF_VER=${NXF_VER:-'23.09.3-edge'}
+NXF_VER=${NXF_VER:-'23.10.0'}
 NXF_ORG=${NXF_ORG:-'nextflow-io'}
 NXF_HOME=${NXF_HOME:-$HOME/.nextflow}
 NXF_PROT=${NXF_PROT:-'https'}
diff --git a/nextflow.md5 b/nextflow.md5
index 87c82b6bc7..ca1fedf1bf 100644
--- a/nextflow.md5
+++ b/nextflow.md5
@@ -1 +1 @@
-f4597acee862538b6a1beda1c5b07855
+72d4fc9e2c3d8cf2d1232690b7ea0121
diff --git a/nextflow.sha1 b/nextflow.sha1
index 6a4acbe394..0e653c427c 100644
--- a/nextflow.sha1
+++ b/nextflow.sha1
@@ -1 +1 @@
-cb9e8a01275e511f792aa11ecce411f92e7e4625
+9ff8060a99bad698d5ad9316ea3a4acfe2ae51c1
diff --git a/nextflow.sha256 b/nextflow.sha256
index 1d0470b3d0..9c595903d8 100644
--- a/nextflow.sha256
+++ b/nextflow.sha256
@@ -1 +1 @@
-7aff41f4a15382c78c06053ee4648ae784e7b4363b248d6ee22a1f05ef27480c
+4b7fba61ecc6d53a6850390bb435455a54ae4d0c3108199f88b16b49e555afdd

From 3cb1c53c18eda3f4afaacd149d65fd2925853042 Mon Sep 17 00:00:00 2001
From: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
Date: Mon, 16 Oct 2023 12:18:21 +0200
Subject: [PATCH 229/350] Update background color of docs status badges (#4411)

Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
---
 docs/index.md | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/docs/index.md b/docs/index.md
index 44cde1ed59..a8a113ad90 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -2,11 +2,11 @@
 # Nextflow's documentation!
 
 [![Nextflow CI](https://github.com/nextflow-io/nextflow/workflows/Nextflow%20CI/badge.svg)](https://github.com/nextflow-io/nextflow/actions/workflows/build.yml?query=branch%3Amaster+event%3Apush)
-[![Nextflow version](https://img.shields.io/github/release/nextflow-io/nextflow.svg?colorB=26af64&style=popout)](https://github.com/nextflow-io/nextflow/releases/latest)
-[![Nextflow Twitter](https://img.shields.io/twitter/url/https/nextflowio.svg?colorB=26af64&&label=%40nextflow&style=popout)](https://twitter.com/nextflowio)
-[![Nextflow Publication](https://img.shields.io/badge/Published-Nature%20Biotechnology-26af64.svg?colorB=26af64&style=popout)](https://www.nature.com/articles/nbt.3820)
-[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?colorB=26af64&style=popout)](http://bioconda.github.io/recipes/nextflow/README.html)
-[![Nextflow license](https://img.shields.io/github/license/nextflow-io/nextflow.svg?colorB=26af64&style=popout)](https://github.com/nextflow-io/nextflow/blob/master/COPYING)
+[![Nextflow version](https://img.shields.io/github/release/nextflow-io/nextflow.svg?colorB=58bd9f&style=popout)](https://github.com/nextflow-io/nextflow/releases/latest)
+[![Nextflow Twitter](https://img.shields.io/twitter/url/https/nextflowio.svg?colorB=58bd9f&&label=%40nextflow&style=popout)](https://twitter.com/nextflowio)
+[![Nextflow Publication](https://img.shields.io/badge/Published-Nature%20Biotechnology-26af64.svg?colorB=58bd9f&style=popout)](https://www.nature.com/articles/nbt.3820)
+[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?colorB=58bd9f&style=popout)](http://bioconda.github.io/recipes/nextflow/README.html)
+[![Nextflow license](https://img.shields.io/github/license/nextflow-io/nextflow.svg?colorB=58bd9f&style=popout)](https://github.com/nextflow-io/nextflow/blob/master/COPYING)
 
 Nextflow is a workflow system for creating scalable, portable, and reproducible workflows.
 

From 7a13b18bd16e71670e5872108b65f6b4fe112c05 Mon Sep 17 00:00:00 2001
From: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
Date: Mon, 16 Oct 2023 13:08:03 +0200
Subject: [PATCH 230/350] Update README.md with new branding color for Nextflow
 (#4412) [ci skip]

Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
---
 README.md | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/README.md b/README.md
index 5c4e42b2d6..ed754aa081 100644
--- a/README.md
+++ b/README.md
@@ -8,11 +8,11 @@
 <br>[Henri E. Bal , Jennifer G. Steiner , Andrew S. Tanenbaum](https://dl.acm.org/doi/abs/10.1145/72551.72552)
 
 [![Nextflow CI](https://github.com/nextflow-io/nextflow/workflows/Nextflow%20CI/badge.svg)](https://github.com/nextflow-io/nextflow/actions/workflows/build.yml?query=branch%3Amaster+event%3Apush)
-[![Nextflow version](https://img.shields.io/github/release/nextflow-io/nextflow.svg?colorB=26af64&style=popout)](https://github.com/nextflow-io/nextflow/releases/latest)
-[![Nextflow Twitter](https://img.shields.io/twitter/url/https/nextflowio.svg?colorB=26af64&&label=%40nextflow&style=popout)](https://twitter.com/nextflowio)
-[![Nextflow Publication](https://img.shields.io/badge/Published-Nature%20Biotechnology-26af64.svg?colorB=26af64&style=popout)](https://www.nature.com/articles/nbt.3820)
-[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?colorB=26af64&style=popout)](http://bioconda.github.io/recipes/nextflow/README.html)
-[![Nextflow license](https://img.shields.io/github/license/nextflow-io/nextflow.svg?colorB=26af64&style=popout)](https://github.com/nextflow-io/nextflow/blob/master/COPYING)
+[![Nextflow version](https://img.shields.io/github/release/nextflow-io/nextflow.svg?colorB=58bd9f&style=popout)](https://github.com/nextflow-io/nextflow/releases/latest)
+[![Nextflow Twitter](https://img.shields.io/twitter/url/https/nextflowio.svg?colorB=58bd9f&&label=%40nextflow&style=popout)](https://twitter.com/nextflowio)
+[![Nextflow Publication](https://img.shields.io/badge/Published-Nature%20Biotechnology-26af64.svg?colorB=58bd9f&style=popout)](https://www.nature.com/articles/nbt.3820)
+[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?colorB=58bd9f&style=popout)](http://bioconda.github.io/recipes/nextflow/README.html)
+[![Nextflow license](https://img.shields.io/github/license/nextflow-io/nextflow.svg?colorB=58bd9f&style=popout)](https://github.com/nextflow-io/nextflow/blob/master/COPYING)
 
 Nextflow is a workflow system for creating scalable, portable, and reproducible workflows. It is based on the dataflow programming model, which greatly simplifies the writing of parallel and distributed pipelines, allowing you to focus on the flow of data and computation. Nextflow can deploy workflows on a variety of execution platforms, including your local machine, HPC schedulers, AWS Batch, Azure Batch, Google Cloud Batch, and Kubernetes. Additionally, it supports many ways to manage your software dependencies, including Conda, Spack, Docker, Podman, Singularity, and more.
 

From b00539a0c6c29989fd8b57700504dcf3103ed6fb Mon Sep 17 00:00:00 2001
From: Harry Hung <4848896+HarryHung@users.noreply.github.com>
Date: Tue, 17 Oct 2023 15:17:20 +0100
Subject: [PATCH 231/350] Reflect current macOS naming convention (#4421)

OS X has been officially known as macOS since 2016.

Signed-off-by: Harry Hung <4848896+HarryHung@users.noreply.github.com>
---
 docs/getstarted.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/getstarted.md b/docs/getstarted.md
index 0501317e81..2b182f28c4 100644
--- a/docs/getstarted.md
+++ b/docs/getstarted.md
@@ -6,7 +6,7 @@
 
 ## Requirements
 
-Nextflow can be used on any POSIX compatible system (Linux, OS X, etc). It requires Bash 3.2 (or later) and [Java 11 (or later, up to 21)](http://www.oracle.com/technetwork/java/javase/downloads/index.html) to be installed.
+Nextflow can be used on any POSIX compatible system (Linux, macOS, etc). It requires Bash 3.2 (or later) and [Java 11 (or later, up to 21)](http://www.oracle.com/technetwork/java/javase/downloads/index.html) to be installed.
 
 For the execution in a cluster of computers, the use of a shared file system is required to allow the sharing of tasks input/output files.
 

From e952299f74aa2d209e408fe91b8dd783f04b64f3 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Fri, 20 Oct 2023 15:02:07 +0200
Subject: [PATCH 232/350] Fix Singularity docs [ci skip]

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/config.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/config.md b/docs/config.md
index 9af6de89f2..6d90a8b121 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -87,7 +87,7 @@ The `apptainer` scope controls how [Apptainer](https://apptainer.org) containers
 The following settings are available:
 
 `apptainer.autoMounts`
-: When `true` Nextflow automatically mounts host paths in the executed container. It requires the `user bind control` feature to be enabled in your Apptainer installation (default: `false`).
+: When `true` Nextflow automatically mounts host paths in the executed container. It requires the `user bind control` feature to be enabled in your Apptainer installation (default: `true`).
 
 `apptainer.cacheDir`
 : The directory where remote Apptainer images are stored. When using a computing cluster it must be a shared folder accessible to all compute nodes.

From 171831eaa1211df641a98564229fa1fcb68838e2 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 21 Oct 2023 16:12:42 +0200
Subject: [PATCH 233/350] Minor test improvements [ci fast]

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../extension/PluginExtensionMethodsTest.groovy  | 16 ++++++----------
 1 file changed, 6 insertions(+), 10 deletions(-)

diff --git a/modules/nf-commons/src/test/nextflow/plugin/extension/PluginExtensionMethodsTest.groovy b/modules/nf-commons/src/test/nextflow/plugin/extension/PluginExtensionMethodsTest.groovy
index 7c9f3107a6..25ec51be4e 100644
--- a/modules/nf-commons/src/test/nextflow/plugin/extension/PluginExtensionMethodsTest.groovy
+++ b/modules/nf-commons/src/test/nextflow/plugin/extension/PluginExtensionMethodsTest.groovy
@@ -17,19 +17,15 @@
 
 package nextflow.plugin.extension
 
-import nextflow.plugin.hello.HelloExtension
-
 import java.nio.file.Path
 
 import nextflow.Channel
 import nextflow.exception.DuplicateModuleFunctionException
 import nextflow.plugin.Plugins
 import nextflow.plugin.TestPluginManager
-import nextflow.plugin.extension.PluginExtensionProvider
 import spock.lang.Shared
 import spock.lang.TempDir
 import test.Dsl2Spec
-import test.MockScriptRunner
 /**
  *
  * @author Jorge Aguilera <jorge.aguilera@seqera.io>
@@ -202,7 +198,7 @@ class PluginExtensionMethodsTest extends Dsl2Spec {
             '''
 
         when:
-        def result = dsl_eval(SCRIPT_TEXT)
+        dsl_eval(SCRIPT_TEXT)
 
         then:
         thrown(IllegalStateException)
@@ -245,7 +241,7 @@ class PluginExtensionMethodsTest extends Dsl2Spec {
         '''
 
         when:
-        def result = dsl_eval(SCRIPT_TEXT)
+        dsl_eval(SCRIPT_TEXT)
 
         then:
         thrown(IllegalStateException)
@@ -338,7 +334,7 @@ class PluginExtensionMethodsTest extends Dsl2Spec {
         '''
 
         when:
-        def result = new MockScriptRunner([:]).setScript(SCRIPT).execute()
+        def result = dsl_eval(SCRIPT)
 
         then:
         result.val == 'hi'
@@ -407,7 +403,7 @@ class PluginExtensionMethodsTest extends Dsl2Spec {
         SCRIPT.text = SCRIPT_TEXT
 
         when:
-        def result = new MockScriptRunner([:]).setScript(SCRIPT).execute()
+        def result = dsl_eval(SCRIPT)
 
         then:
         result.val == EXPECTED
@@ -445,7 +441,7 @@ class PluginExtensionMethodsTest extends Dsl2Spec {
         """.stripIndent()
 
         when:
-        new MockScriptRunner([:]).setScript(SCRIPT).execute()
+        dsl_eval(SCRIPT)
 
         then:
         thrown(DuplicateModuleFunctionException)
@@ -491,7 +487,7 @@ class PluginExtensionMethodsTest extends Dsl2Spec {
         """.stripIndent()
 
         when:
-        new MockScriptRunner([:]).setScript(SCRIPT).execute()
+        dsl_eval(SCRIPT)
 
         then:
         thrown(DuplicateModuleFunctionException)

From f5bb829f5b08d8390870e7cc08643875b8f0821c Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 28 Oct 2023 07:34:24 +0200
Subject: [PATCH 234/350] Fix Inspect command fails with Singularity

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../groovy/nextflow/cli/CmdInspect.groovy     | 12 +-----
 .../container/ContainerHandler.groovy         |  9 ++++-
 .../inspect/ContainerInspectMode.groovy       | 35 +++++++++++++++++
 .../groovy/nextflow/cli/CmdInspectTest.groovy | 39 +------------------
 .../io/seqera/wave/plugin/WaveAssets.groovy   |  4 +-
 .../io/seqera/wave/plugin/WaveClient.groovy   |  9 +++--
 .../wave/plugin/config/WaveConfig.groovy      |  4 --
 .../seqera/wave/plugin/WaveAssetsTest.groovy  |  8 ++--
 .../seqera/wave/plugin/WaveClientTest.groovy  |  8 +++-
 .../wave/plugin/config/WaveConfigTest.groovy  |  2 +-
 10 files changed, 64 insertions(+), 66 deletions(-)
 create mode 100644 modules/nextflow/src/main/groovy/nextflow/container/inspect/ContainerInspectMode.groovy

diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdInspect.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdInspect.groovy
index 00c943e83b..c865c8aee8 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdInspect.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdInspect.groovy
@@ -23,8 +23,8 @@ import com.beust.jcommander.Parameters
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import nextflow.Session
+import nextflow.container.inspect.ContainerInspectMode
 import nextflow.container.inspect.ContainersInspector
-import nextflow.exception.AbortOperationException
 import nextflow.util.LoggerHelper
 /**
  * Implement `inspect` command
@@ -70,6 +70,7 @@ class CmdInspect extends CmdBase {
 
     @Override
     void run() {
+        ContainerInspectMode.activate(true)
         // configure quiet mode
         LoggerHelper.setQuiet(true)
         // setup the target run command
@@ -89,8 +90,6 @@ class CmdInspect extends CmdBase {
     }
 
     protected void applyInspect(Session session) {
-        // disallow singularity w/o wave and freeze
-        checkSingularityConfig(session.config)
         // disable wave await mode when running
         if( session.config.wave instanceof Map )
             checkWaveConfig(session.config.wave as Map)
@@ -106,11 +105,4 @@ class CmdInspect extends CmdBase {
             wave.dryRun = !concretize
     }
 
-    protected void checkSingularityConfig(Map config) {
-        final sing = config.navigate('singularity.enabled',false)
-        final wave = config.navigate('wave.enabled',false)
-        final freeze = config.navigate('wave.freeze',false)
-        if( sing && (!wave || !freeze) )
-            throw new AbortOperationException("Inspect command with Singularity requires enabling 'wave' and 'freeze' settings")
-    }
 }
diff --git a/modules/nextflow/src/main/groovy/nextflow/container/ContainerHandler.groovy b/modules/nextflow/src/main/groovy/nextflow/container/ContainerHandler.groovy
index 2e446fc86c..aafa544913 100644
--- a/modules/nextflow/src/main/groovy/nextflow/container/ContainerHandler.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/container/ContainerHandler.groovy
@@ -23,6 +23,7 @@ import java.util.regex.Pattern
 import groovy.transform.CompileStatic
 import groovy.transform.PackageScope
 import groovy.util.logging.Slf4j
+import nextflow.container.inspect.ContainerInspectMode
 import nextflow.util.Escape
 /**
  * Helper class to normalise a container image name depending
@@ -67,7 +68,8 @@ class ContainerHandler {
             if( !config.isEnabled() || !normalizedImageName )
                 return normalizedImageName
             final requiresCaching = normalizedImageName =~ IMAGE_URL_PREFIX
-
+            if( ContainerInspectMode.active() && requiresCaching )
+                return imageName
             final result = requiresCaching ? createSingularityCache(this.config, normalizedImageName) : normalizedImageName
             return Escape.path(result)
         }
@@ -76,7 +78,8 @@ class ContainerHandler {
             if( !config.isEnabled() || !normalizedImageName )
                 return normalizedImageName
             final requiresCaching = normalizedImageName =~ IMAGE_URL_PREFIX
-
+            if( ContainerInspectMode.active() && requiresCaching )
+                return imageName
             final result = requiresCaching ? createApptainerCache(this.config, normalizedImageName) : normalizedImageName
             return Escape.path(result)
         }
@@ -84,6 +87,8 @@ class ContainerHandler {
             // if the imagename starts with '/' it's an absolute path
             // otherwise we assume it's in a remote registry and pull it from there
             final requiresCaching = !imageName.startsWith('/')
+            if( ContainerInspectMode.active() && requiresCaching )
+                return imageName
             final result = requiresCaching ? createCharliecloudCache(this.config, imageName) : imageName
             return Escape.path(result)
         }
diff --git a/modules/nextflow/src/main/groovy/nextflow/container/inspect/ContainerInspectMode.groovy b/modules/nextflow/src/main/groovy/nextflow/container/inspect/ContainerInspectMode.groovy
new file mode 100644
index 0000000000..593736c62f
--- /dev/null
+++ b/modules/nextflow/src/main/groovy/nextflow/container/inspect/ContainerInspectMode.groovy
@@ -0,0 +1,35 @@
+/*
+ * Copyright 2013-2023, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package nextflow.container.inspect
+
+import groovy.transform.CompileStatic
+/**
+ * Activate the container inspect mode
+ *
+ * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
+ */
+@CompileStatic
+class ContainerInspectMode {
+
+    private static boolean active
+
+    static boolean active() { return active }
+
+    static void activate(boolean value) { active=value }
+
+}
diff --git a/modules/nextflow/src/test/groovy/nextflow/cli/CmdInspectTest.groovy b/modules/nextflow/src/test/groovy/nextflow/cli/CmdInspectTest.groovy
index 2e45bae5c8..c6ed93ca74 100644
--- a/modules/nextflow/src/test/groovy/nextflow/cli/CmdInspectTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/cli/CmdInspectTest.groovy
@@ -17,7 +17,7 @@
 
 package nextflow.cli
 
-import nextflow.exception.AbortOperationException
+
 import spock.lang.Specification
 import spock.lang.Unroll
 /**
@@ -51,41 +51,4 @@ class CmdInspectTest extends Specification {
 
     }
 
-    def 'should allow singularity only with wave and freeze' () {
-        given:
-        def cmd = Spy(new CmdInspect())
-
-        when:
-        cmd.checkSingularityConfig([:])
-        then:
-        noExceptionThrown()
-
-        when:
-        cmd.checkSingularityConfig([singularity:[enabled:false]])
-        then:
-        noExceptionThrown()
-
-        when:
-        cmd.checkSingularityConfig([wave:[enabled:true, freeze:true]])
-        then:
-        noExceptionThrown()
-
-        when:
-        cmd.checkSingularityConfig([singularity:[enabled:true], wave:[enabled:true, freeze:true]])
-        then:
-        noExceptionThrown()
-
-        // singularity w/o wave and freeze is not allowed
-        when:
-        cmd.checkSingularityConfig([singularity:[enabled:true]])
-        then:
-        thrown(AbortOperationException)
-
-        when:
-        cmd.checkSingularityConfig([singularity:[enabled:true], wave:[enabled:true]])
-        then:
-        thrown(AbortOperationException)
-
-    }
-
 }
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveAssets.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveAssets.groovy
index 2b7e6fb6e7..1810791a90 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveAssets.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveAssets.groovy
@@ -85,11 +85,11 @@ class WaveAssets {
     }
 
 
-    static void validateContainerRepo(String name) {
+    static void validateContainerName(String name) {
         if( !name )
             return
         final scheme = StringUtils.getUrlProtocol(name)
         if( scheme )
-            throw new IllegalArgumentException("Container repository should not start with URL like prefix - offending value: $name")
+            throw new IllegalArgumentException("Wave container request image cannot start with URL like prefix - offending value: $name")
     }
 }
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
index c913ef99fb..7e4b4f7487 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
@@ -51,6 +51,7 @@ import io.seqera.wave.plugin.exception.UnauthorizedException
 import io.seqera.wave.plugin.packer.Packer
 import nextflow.Session
 import nextflow.SysEnv
+import nextflow.container.inspect.ContainerInspectMode
 import nextflow.container.resolver.ContainerInfo
 import nextflow.fusion.FusionConfig
 import nextflow.processor.Architecture
@@ -184,7 +185,7 @@ class WaveClient {
                 fingerprint: assets.fingerprint(),
                 freeze: config.freezeMode(),
                 format: assets.singularity ? 'sif' : null,
-                dryRun: config.dryRun()
+                dryRun: ContainerInspectMode.active()
         )
     }
 
@@ -208,7 +209,7 @@ class WaveClient {
                 towerEndpoint: tower.endpoint,
                 workflowId: tower.workflowId,
                 freeze: config.freezeMode(),
-                dryRun: config.dryRun(),
+                dryRun: ContainerInspectMode.active(),
         )
         return sendRequest(request)
     }
@@ -489,7 +490,7 @@ class WaveClient {
         final platform = dockerArch
 
         // check is a valid container image
-        WaveAssets.validateContainerRepo(containerImage)
+        WaveAssets.validateContainerName(containerImage)
         // read the container config and go ahead
         final containerConfig = this.resolveContainerConfig(platform)
         return new WaveAssets(
@@ -521,7 +522,7 @@ class WaveClient {
             // get from cache or submit a new request
             final response = cache.get(key, { sendRequest(assets) } as Callable )
             if( config.freezeMode() )  {
-                if( response.buildId && !config.dryRun() ) {
+                if( response.buildId && !ContainerInspectMode.active() ) {
                     // await the image to be available when a new image is being built
                     awaitImage(response.targetImage)
                 }
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/WaveConfig.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/WaveConfig.groovy
index 6e00733de2..5a47010a78 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/WaveConfig.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/WaveConfig.groovy
@@ -49,13 +49,11 @@ class WaveConfig {
     final private RetryOpts retryOpts
     final private HttpOpts httpClientOpts
     final private Boolean freezeMode
-    final private Boolean dryRunMode
 
     WaveConfig(Map opts, Map<String,String> env=System.getenv()) {
         this.enabled = opts.enabled
         this.endpoint = (opts.endpoint?.toString() ?: env.get('WAVE_API_ENDPOINT') ?: DEF_ENDPOINT)?.stripEnd('/')
         this.freezeMode = opts.freeze as Boolean
-        this.dryRunMode = opts.navigate('dryRun', false)
         this.containerConfigUrl = parseConfig(opts, env)
         this.tokensCacheMaxDuration = opts.navigate('tokens.cache.maxDuration', '30m') as Duration
         this.condaOpts = opts.navigate('build.conda', Collections.emptyMap()) as CondaOpts
@@ -87,8 +85,6 @@ class WaveConfig {
 
     boolean freezeMode() { return this.freezeMode }
 
-    boolean dryRun() { return this.dryRunMode }
-
     boolean bundleProjectResources() { bundleProjectResources }
 
     String buildRepository() { buildRepository }
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveAssetsTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveAssetsTest.groovy
index 8ecf593e61..8844af0328 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveAssetsTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveAssetsTest.groovy
@@ -39,22 +39,22 @@ class WaveAssetsTest extends Specification {
 
     def 'should validate container name' () {
         when:
-        WaveAssets.validateContainerRepo('ubuntu')
+        WaveAssets.validateContainerName('ubuntu')
         then:
         noExceptionThrown()
 
         when:
-        WaveAssets.validateContainerRepo('ubuntu:latest')
+        WaveAssets.validateContainerName('ubuntu:latest')
         then:
         noExceptionThrown()
 
         when:
-        WaveAssets.validateContainerRepo('quay.io/wtsicgp/nanoseq:3.3.0')
+        WaveAssets.validateContainerName('quay.io/wtsicgp/nanoseq:3.3.0')
         then:
         noExceptionThrown()
 
         when:
-        WaveAssets.validateContainerRepo('docker://quay.io/wtsicgp/nanoseq:3.3.0')
+        WaveAssets.validateContainerName('docker://quay.io/wtsicgp/nanoseq:3.3.0')
         then:
         thrown(IllegalArgumentException)
     }
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
index 3885ce2cf1..c0259af468 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
@@ -32,6 +32,8 @@ import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import nextflow.Session
 import nextflow.SysEnv
+import nextflow.container.inspect.ContainerInspectMode
+import nextflow.container.inspect.ContainersInspector
 import nextflow.extension.FilesEx
 import nextflow.file.FileHelper
 import nextflow.processor.TaskRun
@@ -197,7 +199,8 @@ class WaveClientTest extends Specification {
 
     def 'should create request object with dry-run mode' () {
         given:
-        def session = Mock(Session) { getConfig() >> [wave:[dryRun:true]]}
+        ContainerInspectMode.activate(true)
+        def session = Mock(Session) { getConfig() >> [:]}
         def IMAGE =  'foo:latest'
         def wave = new WaveClient(session)
 
@@ -215,6 +218,9 @@ class WaveClientTest extends Specification {
         and:
         req.fingerprint == 'bd2cb4b32df41f2d290ce2366609f2ad'
         req.timestamp instanceof String
+
+        cleanup:
+        ContainerInspectMode.activate(false)
     }
 
     def 'should create request object and platform' () {
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy
index 567fd0678d..a904258b2f 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy
@@ -199,7 +199,7 @@ class WaveConfigTest extends Specification {
         given:
         def config = new WaveConfig([enabled: true])
         expect:
-        config.toString() == 'WaveConfig(enabled:true, endpoint:https://wave.seqera.io, containerConfigUrl:[], tokensCacheMaxDuration:30m, condaOpts:CondaOpts(mambaImage=mambaorg/micromamba:1.5.1; basePackages=conda-forge::procps-ng, commands=null), spackOpts:SpackOpts(basePackages=null, commands=null), strategy:[container, dockerfile, conda, spack], bundleProjectResources:null, buildRepository:null, cacheRepository:null, retryOpts:RetryOpts(delay:450ms, maxDelay:1m 30s, maxAttempts:10, jitter:0.25), httpClientOpts:HttpOpts(), freezeMode:null, dryRunMode:false)'
+        config.toString() == 'WaveConfig(enabled:true, endpoint:https://wave.seqera.io, containerConfigUrl:[], tokensCacheMaxDuration:30m, condaOpts:CondaOpts(mambaImage=mambaorg/micromamba:1.5.1; basePackages=conda-forge::procps-ng, commands=null), spackOpts:SpackOpts(basePackages=null, commands=null), strategy:[container, dockerfile, conda, spack], bundleProjectResources:null, buildRepository:null, cacheRepository:null, retryOpts:RetryOpts(delay:450ms, maxDelay:1m 30s, maxAttempts:10, jitter:0.25), httpClientOpts:HttpOpts(), freezeMode:null)'
     }
 
     def 'should not allow invalid settinga' () {

From 8cb2702c2fc0b9ff0261883ee08157eeefca497e Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sun, 29 Oct 2023 12:43:48 +0100
Subject: [PATCH 235/350] Bump Gradle 8.4 and test vs Java 21 (#4450)

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .github/workflows/build.yml              |  4 ++--
 build.gradle                             |  4 ++--
 buildSrc/build.gradle                    | 19 ++++++-------------
 gradle/wrapper/gradle-wrapper.properties |  2 +-
 packing.gradle                           |  6 +++---
 settings.gradle                          |  7 +++++++
 6 files changed, 21 insertions(+), 21 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index a5e1951c22..d1d2e1025b 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -24,7 +24,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        java_version: [11, 17, 19]
+        java_version: [11, 17, 21]
 
     steps:
       - name: Environment
@@ -98,7 +98,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        java_version: [11, 19]
+        java_version: [11, 21]
         test_mode: ["test_integration", "test_aws", "test_azure", "test_google", "test_wave"]
     steps:
       - name: Checkout
diff --git a/build.gradle b/build.gradle
index d8c9a80f18..fa5df23a8d 100644
--- a/build.gradle
+++ b/build.gradle
@@ -299,12 +299,12 @@ configure(coreProjects) {
     apply plugin: 'signing'
 
     task javadocJar(type: Jar) {
-        classifier = 'javadoc'
+        archiveClassifier = 'javadoc'
         from configurations.groovyDoc
     }
 
     task sourcesJar(type: Jar) {
-        classifier = 'sources'
+        archiveClassifier = 'sources'
         from sourceSets.main.allSource
     }
 
diff --git a/buildSrc/build.gradle b/buildSrc/build.gradle
index c6e9e2491e..fa35d4112b 100644
--- a/buildSrc/build.gradle
+++ b/buildSrc/build.gradle
@@ -1,6 +1,6 @@
 plugins {
     id 'groovy-gradle-plugin'
-    id "com.gradle.plugin-publish" version "0.12.0"
+    id "com.gradle.plugin-publish" version "1.2.1"
 }
 
 repositories {
@@ -16,24 +16,17 @@ dependencies {
 }
 
 gradlePlugin {
-    plugins {
-        nextflowPlugin {
-            id = 'io.nextflow.nf-build-plugin'
-            implementationClass = 'io.nextflow.gradle.NextflowBuildPlugin'
-        }
-    }
-}
-
-pluginBundle {
     website = 'https://www.nextflow.io/'
     vcsUrl = 'https://github.com/nextflow-io/nextflow'
     description = 'Helper plugin for Nextflow project build'
-    tags = ['nextflow']
-
+    
     plugins {
-        nextflowPlugin {
+        create("nextflowPlugin") {
+            id = 'io.nextflow.nf-build-plugin'
+            implementationClass = 'io.nextflow.gradle.NextflowBuildPlugin'
             // id is captured from java-gradle-plugin configuration
             displayName = 'Nextflow Build plugin'
         }
     }
 }
+
diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
index 774fae8767..e411586a54 100644
--- a/gradle/wrapper/gradle-wrapper.properties
+++ b/gradle/wrapper/gradle-wrapper.properties
@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.6.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.4-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
diff --git a/packing.gradle b/packing.gradle
index 9131bd7bbc..05993e0465 100644
--- a/packing.gradle
+++ b/packing.gradle
@@ -98,7 +98,7 @@ protected coordinates( it ) {
  */
 task packOne(type: Jar) {
     dependsOn configurations.capsule, configurations.defaultCfg
-    archiveName = "nextflow-${version}-one.jar"
+    archiveFileName = "nextflow-${version}-one.jar"
 
     from (configurations.capsule.collect { zipTree(it) })
 
@@ -133,7 +133,7 @@ task packOne(type: Jar) {
 
 task packAll(type: Jar) {
     dependsOn configurations.capsule, configurations.defaultCfg
-    archiveName = "nextflow-${version}-all.jar"
+    archiveFileName = "nextflow-${version}-all.jar"
 
     from jar // embed our application jar
     from (configurations.amazon + configurations.google + configurations.tower + configurations.wave)
@@ -175,7 +175,7 @@ task packAll(type: Jar) {
 
 task packCore(type: Jar) {
     dependsOn configurations.capsule, configurations.defaultCfg
-    archiveName = "nextflow-${version}-core.jar"
+    archiveFileName = "nextflow-${version}-core.jar"
 
     from jar // embed our application jar
     from (configurations.defaultCfg)
diff --git a/settings.gradle b/settings.gradle
index ca6ae0164a..a3ac0737c9 100644
--- a/settings.gradle
+++ b/settings.gradle
@@ -14,6 +14,13 @@
  * limitations under the License.
  */
 
+plugins {
+    // required to download the toolchain (jdk) from a remote repository
+    // https://github.com/gradle/foojay-toolchains
+    // https://docs.gradle.org/current/userguide/toolchains.html#sub:download_repositories
+    id("org.gradle.toolchains.foojay-resolver-convention") version "0.7.0"
+}
+
 rootProject.name = 'nextflow-prj'
 
 include 'nextflow'

From b651dd3d92c414e3472dd2bb50e20a4903146610 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Sun, 29 Oct 2023 12:44:52 +0100
Subject: [PATCH 236/350] Docs: Plugins offline, don't recommend -all (#4447)

Signed-off-by: Phil Ewels <phil.ewels@seqera.io>
---
 docs/plugins.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/plugins.md b/docs/plugins.md
index cc9b4bfce0..061207a9b9 100644
--- a/docs/plugins.md
+++ b/docs/plugins.md
@@ -350,7 +350,7 @@ nextflow run <pipeline> -plugins nf-hello
 
 To use Nextflow plugins in an offline environment:
 
-1. Download the {ref}`"all" release <getstarted-install>` of Nextflow, which comes with the following default plugins: `nf-amazon`, `nf-google`, `nf-tower`.
+1. {ref}`Download Nextflow <getstarted-install>` and install it on a system with an internet connection. Do not use the "all" package, as this does not allow the use of custom plugins.
 
 2. Download any additional plugins by running `nextflow plugin install <pluginId,..>`. Alternatively, simply run your pipeline once and Nextflow will download all of the plugins that it needs.
 

From 35609cb0edcbbb232d8d500bf524a097854dbf4a Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Mon, 30 Oct 2023 17:37:03 +0100
Subject: [PATCH 237/350] Improve error details for AbortOperationException

This commit improves the error reporting for error reported
via the AbortOperationException, so the script line location
is added in the error message when available.

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../main/groovy/nextflow/cli/Launcher.groovy   |  6 ++++--
 .../groovy/nextflow/util/LoggerHelper.groovy   | 18 ++++++++++++++++--
 2 files changed, 20 insertions(+), 4 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy
index 50e9d8df2a..be9458eaa2 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy
@@ -441,7 +441,8 @@ class Launcher {
 
         }
         catch ( AbortOperationException e ) {
-            System.err.println (e.message ?: "Unknown abort reason")
+            final msg = e.message ?: "Unknown abort reason"
+            System.err.println(LoggerHelper.formatErrMessage(msg, e))
             System.exit(1)
         }
         catch( Throwable e ) {
@@ -509,7 +510,8 @@ class Launcher {
 
         catch ( AbortOperationException e ) {
             def message = e.getMessage()
-            if( message ) System.err.println(message)
+            if( message )
+                System.err.println(LoggerHelper.formatErrMessage(message,e))
             log.debug ("Operation aborted", e.cause ?: e)
             return(1)
         }
diff --git a/modules/nextflow/src/main/groovy/nextflow/util/LoggerHelper.groovy b/modules/nextflow/src/main/groovy/nextflow/util/LoggerHelper.groovy
index 01f4e1af51..f78e7c8bd6 100644
--- a/modules/nextflow/src/main/groovy/nextflow/util/LoggerHelper.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/util/LoggerHelper.groovy
@@ -55,8 +55,8 @@ import nextflow.Session
 import nextflow.cli.CliOptions
 import nextflow.cli.Launcher
 import nextflow.exception.AbortOperationException
-import nextflow.exception.ProcessException
 import nextflow.exception.PlainExceptionMessage
+import nextflow.exception.ProcessException
 import nextflow.exception.ScriptRuntimeException
 import nextflow.extension.OpCall
 import nextflow.file.FileHelper
@@ -506,12 +506,15 @@ class LoggerHelper {
 
         // extra formatting
         if( error ) {
-            buffer.append(" -- Check script '${error[0]}' at line: ${error[1]} or see '${logFileName}' file for more details")
+            buffer.append(errorDetailsMsg(error))
         }
         else if( logFileName && !quiet ) {
             buffer.append(" -- Check '${logFileName}' file for details")
         }
+    }
 
+    static private String errorDetailsMsg(List<String> error) {
+        return " -- Check script '${error[0]}' at line: ${error[1]} or see '${logFileName}' file for more details"
     }
 
     @PackageScope
@@ -572,6 +575,17 @@ class LoggerHelper {
         return msg
     }
 
+    static String formatErrMessage(String message, Throwable error) {
+        try {
+            final line = findErrorLine(error)
+            return line ? message + errorDetailsMsg(line) : message
+        }
+        catch (Throwable t) {
+            log.debug "Unable to determine script line for error: $error", t
+            return message
+        }
+    }
+
     static List<String> findErrorLine( Throwable e ) {
         return findErrorLine(e, ScriptMeta.allScriptNames())
     }

From ff8e06a3cfe3ae5def9c82e395b8d53b28adc1f6 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Mon, 30 Oct 2023 18:15:07 +0100
Subject: [PATCH 238/350] Remove deprecated TowerArchiver feature

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../seqera/tower/plugin/CacheCommand.groovy   |  14 -
 .../seqera/tower/plugin/TowerArchiver.groovy  | 256 ------------------
 .../io/seqera/tower/plugin/TowerClient.groovy |   9 +-
 .../tower/plugin/TowerArchiverTest.groovy     | 153 -----------
 4 files changed, 1 insertion(+), 431 deletions(-)
 delete mode 100644 plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerArchiver.groovy
 delete mode 100644 plugins/nf-tower/src/test/io/seqera/tower/plugin/TowerArchiverTest.groovy

diff --git a/plugins/nf-tower/src/main/io/seqera/tower/plugin/CacheCommand.groovy b/plugins/nf-tower/src/main/io/seqera/tower/plugin/CacheCommand.groovy
index bfaf0426cf..fd77864476 100644
--- a/plugins/nf-tower/src/main/io/seqera/tower/plugin/CacheCommand.groovy
+++ b/plugins/nf-tower/src/main/io/seqera/tower/plugin/CacheCommand.groovy
@@ -19,7 +19,6 @@ package io.seqera.tower.plugin
 
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
-import nextflow.Session
 import nextflow.cli.PluginAbstractExec
 /**
  * Implements nextflow cache and restore commands
@@ -37,7 +36,6 @@ class CacheCommand implements PluginAbstractExec {
 
         if( cmd == 'cache-backup') {
             cacheBackup()
-            archiveLogs(session)
         }
         if( cmd == 'cache-restore' )
             cacheRestore()
@@ -55,18 +53,6 @@ class CacheCommand implements PluginAbstractExec {
         }
     }
 
-    protected void archiveLogs(Session sess) {
-        // archive logs
-        final archiver = TowerArchiver.create(sess, System.getenv())
-        if( archiver ) try {
-            log.debug "Running Nextflow logs archiver"
-            archiver.archiveLogs()
-        }
-        finally {
-            archiver.shutdown(sess)
-        }
-    }
-
     protected void cacheRestore() {
         if( !getSession().cloudCachePath ) {
             log.debug "Running Nextflow cache restore"
diff --git a/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerArchiver.groovy b/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerArchiver.groovy
deleted file mode 100644
index 6f8d270237..0000000000
--- a/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerArchiver.groovy
+++ /dev/null
@@ -1,256 +0,0 @@
-/*
- * Copyright 2013-2023, Seqera Labs
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package io.seqera.tower.plugin
-
-import java.nio.file.FileAlreadyExistsException
-import java.nio.file.Path
-import java.time.temporal.ChronoUnit
-import java.util.concurrent.ExecutorService
-import java.util.function.Predicate
-import java.util.regex.Pattern
-
-import dev.failsafe.Failsafe
-import dev.failsafe.RetryPolicy
-import dev.failsafe.event.EventListener
-import dev.failsafe.event.ExecutionAttemptedEvent
-import dev.failsafe.function.CheckedSupplier
-import groovy.transform.CompileStatic
-import groovy.transform.Memoized
-import groovy.util.logging.Slf4j
-import nextflow.Session
-import nextflow.file.FileHelper
-import nextflow.util.Duration
-import nextflow.util.ThreadPoolManager
-/**
- * This class stores all nextflow task '.command.*' files and pipeline reports
- *  into a storage path specified via the NXF_ARCHIVE_DIR env variable
- *
- * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
- */
-@Slf4j
-@CompileStatic
-@Deprecated
-class TowerArchiver {
-
-    private static final String RETRY_REASON = 'slowdown|slow down|toomany|too many'
-    private Map<String,String> env = System.getenv()
-
-    private final Path baseDir
-    private final Path targetDir
-
-    private Duration delay
-    private Duration maxDelay
-    private Integer maxAttempts
-    private Double jitter
-    private Duration maxAwait
-    private String retryReason
-    private ExecutorService executor
-    private ThreadPoolManager poolManager = new ThreadPoolManager('TowerArchiver')
-
-    Path getBaseDir() { baseDir }
-
-    Path getTargetDir() { targetDir }
-
-    protected TowerArchiver(Path baseDir, Path targetDir, Session session, Map<String,String> env=null) {
-        log.debug "Creating tower archiver for base-dir: '$baseDir'; target-dir: '$targetDir'"
-        this.baseDir = baseDir
-        this.targetDir = targetDir
-        // retry settings
-        this.delay = session.config.navigate('tower.archiver.delay', '100ms') as Duration
-        this.maxDelay = session.config.navigate('tower.archiver.maxDelay', '1m') as Duration
-        this.maxAttempts = session.config.navigate('tower.archiver.maxAttempts', '2') as Integer
-        this.jitter = session.config.navigate('tower.archiver.jitter', '0.25') as Double
-        this.maxAwait = session.config.navigate('tower.archiver.shutdown.maxAwait', '1h') as Duration
-        this.retryReason = session.config.navigate('tower.archiver.shutdown.retryReason', RETRY_REASON) as String
-        this.executor = poolManager.withConfig(session.config).create()
-        if( env!=null )
-            this.env = env
-    }
-
-    static TowerArchiver create(Session session, Map<String,String> env) {
-        final paths = parse(env.get('NXF_ARCHIVE_DIR'))
-        if( !paths )
-            return null
-        final result = new TowerArchiver(Path.of(paths[0]), FileHelper.asPath(paths[1]), session, env)
-        return result
-    }
-
-    static protected List<String> parse(String archiveDef) {
-        if( !archiveDef )
-            return Collections.<String>emptyList()
-        final paths = splitPaths(archiveDef)
-        if( !paths )
-            return Collections.<String>emptyList()
-
-        if( paths.size()!=2 )
-            throw new IllegalArgumentException("Invalid NXF_ARCHIVE_DIR format - expected exactly two paths separated by a comma - offending value: ${System.getenv('NXF_ARCHIVE_DIR')}")
-        if( !paths[0].startsWith('/') )
-            throw new IllegalArgumentException("Invalid NXF_ARCHIVE_DIR base path — must start with a slash character - offending value: '${paths[0]}'")
-        final scheme = FileHelper.getUrlProtocol(paths[1])
-        if ( !scheme && !paths[1].startsWith('/') )
-            throw new IllegalArgumentException("Invalid NXF_ARCHIVE_DIR target path - must be a remote path - offending value: '${paths[1]}'")
-
-        return paths
-    }
-
-    static List<String> splitPaths(String paths){
-        // multiple paths should be separated by comma
-        // allow to escape the separator using backslash
-        paths.split(/(?<!\\),/).collect( it-> unescapeQuote(it))
-    }
-
-    static protected String unescapeQuote(String uri) {
-        uri.replaceAll(/\\,/,',').trim()
-    }
-
-    Path archivePath(Path source) {
-        if( baseDir==null )
-            return null
-        if( source==null )
-            return null
-        if( !source.startsWith(baseDir) )
-            return null
-        final delta = baseDir.relativize(source)
-        // convert to string to prevent 'ProviderMismatchException'
-        return targetDir.resolve(delta.toString())
-    }
-
-    void archiveLogs() {
-        // Nextflow log file are expected to be found at the working directory
-        // when running from Tower launcher the cache command, if needed, has
-        // copied them before starting the archive process
-
-        final work = env.get('NXF_WORK') ?: env.get('NXF_TEST_WORK')
-        if( !work ) {
-            log.error("Missing target work dir - Tower archive cannot be performed")
-            return
-        }
-        if( !work.startsWith('/') ) {
-            log.error("Invalid NXF_WORK work directory - it must start with a slash character - offending value: '${work}'")
-            return
-        }
-
-        final base = Path.of(work)
-        archiveFile(base, env.get('NXF_OUT_FILE'))
-        archiveFile(base, env.get('NXF_LOG_FILE'))
-        archiveFile(base, env.get('NXF_TML_FILE'))
-        archiveFile(base, env.get('TOWER_CONFIG_FILE'))
-        archiveFile(base, env.get('TOWER_REPORTS_FILE'))
-    }
-
-    void archiveTaskLogs(String workDir) {
-        final base = Path.of(workDir)
-        archiveFile(base, '.command.out')
-        archiveFile(base, '.command.err')
-        archiveFile(base, '.command.log')
-        archiveFile(base, '.command.run')
-        archiveFile(base, '.command.sh')
-        archiveFile(base, '.exitcode')
-    }
-
-    protected void archiveFile(Path base, String name) {
-        if( name )
-            archiveFile(base.resolve(name))
-    }
-
-    protected void archiveFile(Path source) {
-        try {
-            if( !source.exists() ) {
-                log.debug "File does not exist: $source -- skipping archiving"
-                return
-            }
-            // go ahead with archiving
-            final target = archivePath(source)
-            if( target==null )
-                return
-            log.debug "Submit file archive request: ${source.toUriString()}"
-            executor.submit(submitArchive(source,target))
-        }
-        catch (Throwable t) {
-            log.warn("Unable to archive file: $source -- cause: ${t.message ?: t}", t)
-        }
-    }
-
-    protected void copyPath(Path source, Path target) {
-        FileHelper.copyPath(source, target)
-    }
-
-    Runnable submitArchive(Path source, Path target) {
-        new Runnable() {
-            @Override
-            void run() {
-                try {
-                    safeExecute(() -> copyPath(source,target) )
-                    log.trace("Archived file: '$source to: '$target'")
-                }
-                catch (FileAlreadyExistsException e) {
-                    log.debug "Skipping archive of file: $source -- target already exists: $target"
-                }
-                catch (Exception e) {
-                    log.warn("Unable to archive file: $source -- cause: ${e.message ?: e}", e)
-                }
-            }
-        }
-    }
-
-
-    protected <T> RetryPolicy<T> retryPolicy() {
-        final listener = new EventListener<ExecutionAttemptedEvent<T>>() {
-            @Override
-            void accept(ExecutionAttemptedEvent<T> event) throws Throwable {
-                log.debug("Archiver failed to transfer file - attempt: ${event.attemptCount}", event.lastFailure)
-            }
-        }
-        return RetryPolicy.<T>builder()
-                .handleIf(retryCondition())
-                .withBackoff(delay.toMillis(), maxDelay.toMillis(), ChronoUnit.MILLIS)
-                .withMaxAttempts(maxAttempts)
-                .withJitter(jitter)
-                .onRetry(listener)
-                .build()
-    }
-
-    protected Pattern retryPattern() {
-        log.debug "File archiver retry-reason='$retryReason'"
-        return Pattern.compile(retryReason, Pattern.CASE_INSENSITIVE | Pattern.MULTILINE)
-    }
-
-    @Memoized
-    protected Predicate<? extends Throwable> retryCondition() {
-
-        return new Predicate<Throwable>() {
-            @Override
-            boolean test(Throwable failure) {
-                final reason = failure.message ?: failure.toString()
-                log.trace "Testing file archiver failure -- reason for retry: '$reason'"
-                return retryPattern()
-                        .matcher(reason)
-                        .find()
-            }
-        }
-    }
-
-    protected <T> T safeExecute(CheckedSupplier<T> action) {
-        final policy = retryPolicy()
-        return Failsafe.with(policy).get(action)
-    }
-
-    void shutdown(Session session) {
-        poolManager.shutdown(session)
-    }
-}
diff --git a/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerClient.groovy b/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerClient.groovy
index 541a746696..a216fa1a6c 100644
--- a/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerClient.groovy
+++ b/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerClient.groovy
@@ -138,7 +138,6 @@ class TowerClient implements TraceObserver {
 
     private TowerReports reports
 
-    private TowerArchiver archiver
 
     /**
      * Constructor that consumes a URL and creates
@@ -151,7 +150,6 @@ class TowerClient implements TraceObserver {
         this.schema = loadSchema()
         this.generator = TowerJsonGenerator.create(schema)
         this.reports = new TowerReports(session)
-        this.archiver = TowerArchiver.create(session, env)
     }
 
     TowerClient withEnvironment(Map env) {
@@ -401,8 +399,6 @@ class TowerClient implements TraceObserver {
         final req = makeCompleteReq(session)
         final resp = sendHttpMessage(urlTraceComplete, req, 'PUT')
         logHttpResponse(urlTraceComplete, resp)
-        // shutdown file archiver
-        archiver?.shutdown(session)
     }
 
     @Override
@@ -446,7 +442,6 @@ class TowerClient implements TraceObserver {
             aggregator.aggregate(trace)
         }
 
-        archiver?.archiveTaskLogs(trace.workDir)
     }
 
     @Override
@@ -482,9 +477,7 @@ class TowerClient implements TraceObserver {
      */
     @Override
     void onFilePublish(Path destination) {
-        final result = reports.filePublish(destination)
-        if( result && archiver )
-            archiver.archiveFile(destination)
+        reports.filePublish(destination)
     }
 
     protected void refreshToken(String refresh) {
diff --git a/plugins/nf-tower/src/test/io/seqera/tower/plugin/TowerArchiverTest.groovy b/plugins/nf-tower/src/test/io/seqera/tower/plugin/TowerArchiverTest.groovy
deleted file mode 100644
index 014e3249c2..0000000000
--- a/plugins/nf-tower/src/test/io/seqera/tower/plugin/TowerArchiverTest.groovy
+++ /dev/null
@@ -1,153 +0,0 @@
-/*
- * Copyright 2013-2023, Seqera Labs
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package io.seqera.tower.plugin
-
-import java.nio.file.Files
-import java.nio.file.Path
-import java.util.concurrent.Executors
-
-import nextflow.Session
-import nextflow.file.FileHelper
-import spock.lang.Specification
-import spock.lang.Timeout
-import spock.lang.Unroll
-import test.TestHelper
-/**
- *
- * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
- */
-@Timeout(5)
-class TowerArchiverTest extends Specification {
-
-    def 'should empty target path' () {
-        expect:
-        TowerArchiver.create(Mock(Session), [:]) == null
-    }
-
-    @Unroll
-    def 'should final target path' () {
-        given:
-        def sess = Mock(Session) {
-            getConfig() >> [:]
-        }
-        def helper = TowerArchiver.create(sess, [NXF_ARCHIVE_DIR:'/data,http://bucket/data/export'])
-
-        expect:
-        helper.getBaseDir() == Path.of('/data')
-        helper.getTargetDir() == FileHelper.asPath('http://bucket/data/export')
-
-        and:
-        helper.archivePath(Path.of(SOURCE)) == (TARGET ? FileHelper.asPath(TARGET) : null)
-
-        where:
-        SOURCE                      | TARGET
-        '/some/file.txt'            | null
-        '/data/work/some/file.txt'  | 'http://bucket/data/export/work/some/file.txt'
-
-    }
-
-    def 'should parse paths' () {
-        expect:
-        TowerArchiver.parse(null) == []
-        TowerArchiver.parse('/this,http://that') == ['/this','http://that']
-        TowerArchiver.parse('/this,http://that/and/1\\,2\\,3') == ['/this','http://that/and/1,2,3']
-    }
-
-    def 'should failed parsing paths' () {
-        when:
-        TowerArchiver.parse('/this')
-        then:
-        thrown(IllegalArgumentException)
-
-        when:
-        TowerArchiver.parse('this,/that')
-        then:
-        thrown(IllegalArgumentException)
-
-        when:
-        TowerArchiver.parse('/this,that')
-        then:
-        thrown(IllegalArgumentException)
-
-        when:
-        TowerArchiver.parse('/a,/b,/c')
-        then:
-        thrown(IllegalArgumentException)
-    }
-
-    def 'should validate retry policy' () {
-        given:
-        def sess = Mock(Session) { getConfig() >> [:] }
-        def archiver = new TowerArchiver(Path.of('/foo'),Path.of('/bar'), sess, [:])
-
-        expect:
-        !archiver.retryPattern().matcher('hello').find()
-        !archiver.retryPattern().matcher('slow').find()
-        and:
-        archiver.retryPattern().matcher('slowdown').find()
-        archiver.retryPattern().matcher('SlowDown').find()
-        archiver.retryPattern().matcher('Slow Down').find()
-        archiver.retryPattern().matcher('TooMany').find()
-        archiver.retryPattern().matcher('Too Many').find()
-    }
-
-    def 'should archive path' () {
-        given:
-        def folder = TestHelper.createInMemTempDir()
-        def source = folder.resolve('foo.txt'); source.text = 'xya'
-        and:
-        def sess = Mock(Session) { getConfig() >> [:] }
-        def exec = Executors.newSingleThreadExecutor()
-        def archiver = Spy(new TowerArchiver(folder,Path.of('/bar'), sess, [:]))
-        def target = folder.resolve('bar.txt')
-
-        when:
-        archiver.archiveFile(source)
-        then:
-        1 * archiver.archivePath(source) >> target
-        and:sleep 100   // <-- sleep a bit to allow the task to enter in the exec pool
-        exec.shutdown()
-        and:
-        target.exists()
-    }
-
-    def 'should archive Nextflow log file' () {
-        given:
-        def workDir = Files.createTempDirectory('workdir')
-        def targetDir = Files.createTempDirectory('target')
-        def nextflowLog = workDir.resolve('nextflow.log'); nextflowLog.text = 'nextflow logs'
-        def targetLog = targetDir.resolve('nextflow.log')
-        and:
-        def sess = Mock(Session) { getConfig() >> [:] }
-        def exec = Executors.newSingleThreadExecutor()
-        def archiver = new TowerArchiver(workDir,targetDir, sess, ['NXF_WORK': workDir.toString(), 'NXF_LOG_FILE': 'nextflow.log'])
-
-        when:
-        archiver.archiveLogs()
-        sleep 100 // <-- sleep a bit to allow the task to enter in the exec pool
-        exec.shutdown()
-
-        then:
-        targetLog.exists()
-
-        cleanup:
-        workDir?.deleteDir()
-        targetDir?.deleteDir()
-    }
-
-}

From 35a4424b51e9f5df62be9bdc63f644ff3244022d Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Mon, 30 Oct 2023 18:42:09 +0100
Subject: [PATCH 239/350] Allow the use of error build-in function in
 onComplete handler (#4458) [ci fast]

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../nextflow/script/WorkflowMetadata.groovy   |  5 +++++
 .../script/WorkflowMetadataTest.groovy        | 19 +++++++++++++++++++
 2 files changed, 24 insertions(+)

diff --git a/modules/nextflow/src/main/groovy/nextflow/script/WorkflowMetadata.groovy b/modules/nextflow/src/main/groovy/nextflow/script/WorkflowMetadata.groovy
index e8c066cea0..af00db5be0 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/WorkflowMetadata.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/WorkflowMetadata.groovy
@@ -29,6 +29,7 @@ import nextflow.NextflowMeta
 import nextflow.Session
 import nextflow.config.ConfigBuilder
 import nextflow.config.Manifest
+import nextflow.exception.WorkflowScriptErrorException
 import nextflow.trace.WorkflowStats
 import nextflow.util.Duration
 import org.codehaus.groovy.runtime.InvokerHelper
@@ -392,6 +393,10 @@ class WorkflowMetadata {
             try {
                 action.call()
             }
+            catch (WorkflowScriptErrorException e) {
+                // re-throw it to allow `error` function to be invoked by completion handler
+                throw e
+            }
             catch (Exception e) {
                 log.error("Failed to invoke `workflow.onComplete` event handler", e)
             }
diff --git a/modules/nextflow/src/test/groovy/nextflow/script/WorkflowMetadataTest.groovy b/modules/nextflow/src/test/groovy/nextflow/script/WorkflowMetadataTest.groovy
index 5cda717fff..05e370c612 100644
--- a/modules/nextflow/src/test/groovy/nextflow/script/WorkflowMetadataTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/script/WorkflowMetadataTest.groovy
@@ -22,6 +22,7 @@ import java.time.OffsetDateTime
 
 import nextflow.Const
 import nextflow.Session
+import nextflow.exception.WorkflowScriptErrorException
 import nextflow.trace.TraceRecord
 import nextflow.trace.WorkflowStats
 import nextflow.trace.WorkflowStatsObserver
@@ -171,6 +172,24 @@ class WorkflowMetadataTest extends Specification {
 
     }
 
+    def 'should be able to throw an error from onComplete handler' () {
+
+        given:
+        def session = Spy(Session)
+        session.getStatsObserver() >> Mock(WorkflowStatsObserver) { getStats() >> new WorkflowStats() }
+        
+        def metadata = new WorkflowMetadata(session, null)
+
+        when:
+        metadata.onComplete {
+            throw new WorkflowScriptErrorException('You failed!')
+        }
+        metadata.invokeOnComplete()
+
+        then:
+        thrown(WorkflowScriptErrorException)
+    }
+
     def 'should access workflow script variables onError' () {
 
         given:

From 91c1ab15e6572b2492eb85d3d1439a69eb7f6e9e Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Mon, 30 Oct 2023 19:09:30 +0100
Subject: [PATCH 240/350] Minor types improvement for mix operator [ci fast]

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../src/main/groovy/nextflow/extension/MixOp.groovy       | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/extension/MixOp.groovy b/modules/nextflow/src/main/groovy/nextflow/extension/MixOp.groovy
index 2904e5ab6b..f8e0aed304 100644
--- a/modules/nextflow/src/main/groovy/nextflow/extension/MixOp.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/extension/MixOp.groovy
@@ -35,16 +35,16 @@ import nextflow.Channel
 class MixOp {
 
     private DataflowReadChannel source
-    private DataflowReadChannel[] others
+    private List<DataflowReadChannel> others
 
     MixOp(DataflowReadChannel source, DataflowReadChannel other) {
         this.source = source
-        this.others = [other]
+        this.others = List.of(other)
     }
 
     MixOp(DataflowReadChannel source, DataflowReadChannel[] others) {
         this.source = source
-        this.others = others
+        this.others = others.toList()
     }
 
     DataflowWriteChannel apply() {
@@ -60,7 +60,7 @@ class MixOp {
             subscribeImpl(it, handlers)
         }
 
-        def allSources = [source]
+        final allSources = [source]
         allSources.addAll(others)
         return target
     }

From fe5bea992e2c0dd99a2f72388df386975c32c83a Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Tue, 31 Oct 2023 13:54:23 +0100
Subject: [PATCH 241/350] Fix errors when NXF_HOME contains spaces (#4456) [ci
 fast]

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 nextflow | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/nextflow b/nextflow
index 2a73246ddf..fdbdedccd3 100755
--- a/nextflow
+++ b/nextflow
@@ -320,7 +320,7 @@ else
   if [[ ! $JAVA_VER =~ ^(11|12|13|14|15|16|17|18|19|20|21) ]]; then
       echo_yellow "NOTE: Nextflow is not tested with Java $JAVA_VER -- It's recommended the use of version 11 up to 21\n"
   fi
-  mkdir -p $(dirname "$JAVA_KEY")
+  mkdir -p "$(dirname "$JAVA_KEY")"
   [[ -f $JAVA_VER ]] && echo $JAVA_VER > "$JAVA_KEY"
 fi
 
@@ -404,8 +404,8 @@ else
     # we extract first part into `cmd_base`` and remainder into `cmd_tail`` and convert them to array as previous version
     cmd_pattern='"([^"]*)"(.*)'
     [[ "${cli[@]}" =~ $cmd_pattern ]]
-    cmd_base=(${BASH_REMATCH[1]})
-    cmd_tail=(${BASH_REMATCH[2]})
+    declare -a cmd_base="(${BASH_REMATCH[1]})"
+    declare -a cmd_tail="(${BASH_REMATCH[2]})"
 
     launcher="${cmd_base[@]}"
     [[ "$NXF_JVM_ARGS" ]] && launcher+=($NXF_JVM_ARGS)
@@ -443,7 +443,7 @@ else
     if mkdir -p "${NXF_LAUNCHER}" 2>/dev/null; then
         STR=''
         for x in "${launcher[@]}"; do
-        [[ "$x" != "\"-Duser.dir=$PWD\"" ]] && [[ ! "$x" == *"-agentlib:jdwp"* ]] && STR+="$x "
+        [[ "$x" != "\"-Duser.dir=$PWD\"" ]] && [[ ! "$x" == *"-agentlib:jdwp"* ]] && STR+=$(printf '%q ' "$x")
         done
         printf "$STR">"$LAUNCH_FILE"
     else

From 2b433a5219254235dd2c6bd066b0a5892bf49451 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Wed, 1 Nov 2023 21:03:45 +0100
Subject: [PATCH 242/350] Remove dsl1 deprecated code

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../src/main/groovy/nextflow/NF.groovy        |  5 --
 .../src/main/groovy/nextflow/Nextflow.groovy  |  2 -
 .../main/groovy/nextflow/NextflowMeta.groovy  | 16 +-----
 .../nextflow/ast/NextflowDSLImpl.groovy       |  8 ---
 .../groovy/nextflow/ast/OpXformImpl.groovy    | 12 ----
 .../groovy/nextflow/cli/CmdPlugins.groovy     | 43 --------------
 .../main/groovy/nextflow/cli/CmdSecret.groovy | 14 -----
 .../main/groovy/nextflow/cli/Launcher.groovy  |  1 -
 .../main/groovy/nextflow/extension/CH.groovy  |  2 -
 .../nextflow/extension/ChannelEx.groovy       | 15 -----
 .../extension/ChannelExtensionPoint.groovy    | 29 ----------
 .../nextflow/extension/DeprecatedDsl2.groovy  | 40 -------------
 .../groovy/nextflow/extension/OpCall.groovy   |  7 ---
 .../nextflow/extension/OperatorImpl.groovy    |  6 --
 .../extension/PluginExtensionProvider.groovy  |  9 ---
 .../groovy/nextflow/processor/TaskBean.groovy |  3 -
 .../groovy/nextflow/script/BaseScript.groovy  |  9 +--
 .../nextflow/script/ProcessConfig.groovy      | 12 ----
 .../nextflow/script/ScriptBinding.groovy      |  4 +-
 .../script/params/FileOutParam.groovy         | 57 -------------------
 .../script/params/TupleInParam.groovy         | 20 ++-----
 .../script/params/TupleOutParam.groovy        | 12 +---
 .../nextflow/extension/ChannelExTest.groovy   | 41 -------------
 .../nextflow/extension/CombineOpTest.groovy   |  2 +-
 .../extension/DataflowTapExtensionTest.groovy | 51 -----------------
 .../extension/OperatorImplTest.groovy         | 13 +++--
 .../processor/TaskProcessorTest.groovy        | 24 ++++----
 .../nextflow/script/ScriptDslTest.groovy      | 20 -------
 .../script/params/ParamsDsl2Test.groovy       | 16 +++---
 29 files changed, 39 insertions(+), 454 deletions(-)
 delete mode 100644 modules/nextflow/src/main/groovy/nextflow/cli/CmdPlugins.groovy
 delete mode 100644 modules/nextflow/src/main/groovy/nextflow/extension/ChannelExtensionPoint.groovy
 delete mode 100644 modules/nextflow/src/main/groovy/nextflow/extension/DeprecatedDsl2.groovy
 delete mode 100644 modules/nextflow/src/test/groovy/nextflow/extension/ChannelExTest.groovy

diff --git a/modules/nextflow/src/main/groovy/nextflow/NF.groovy b/modules/nextflow/src/main/groovy/nextflow/NF.groovy
index 33836c6c62..df8b592b31 100644
--- a/modules/nextflow/src/main/groovy/nextflow/NF.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/NF.groovy
@@ -50,11 +50,6 @@ class NF {
         NextflowMeta.instance.isDsl2()
     }
 
-    @Deprecated
-    static boolean isDsl2Final() {
-        NextflowMeta.instance.isDsl2Final()
-    }
-
     static Binding getBinding() {
         isDsl2() ? ExecutionStack.binding() : session().getBinding()
     }
diff --git a/modules/nextflow/src/main/groovy/nextflow/Nextflow.groovy b/modules/nextflow/src/main/groovy/nextflow/Nextflow.groovy
index dd1b03f8e8..5976f229e3 100644
--- a/modules/nextflow/src/main/groovy/nextflow/Nextflow.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/Nextflow.groovy
@@ -407,6 +407,4 @@ class Nextflow {
      */
     static Closure<TokenMultiMapDef> multiMapCriteria(Closure<TokenBranchDef> closure) { closure }
 
-    @Deprecated
-    static Closure<TokenMultiMapDef> forkCriteria(Closure<TokenBranchDef> closure) { closure }
 }
diff --git a/modules/nextflow/src/main/groovy/nextflow/NextflowMeta.groovy b/modules/nextflow/src/main/groovy/nextflow/NextflowMeta.groovy
index 73783af860..b9b279fb87 100644
--- a/modules/nextflow/src/main/groovy/nextflow/NextflowMeta.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/NextflowMeta.groovy
@@ -105,12 +105,9 @@ class NextflowMeta {
         result.version = version.toString()
         result.build = build
         result.timestamp = parseDateStr(timestamp)
-        if( isDsl2Final() ) {
+        if( isDsl2() ) {
             result.enable = featuresMap()
         }
-        else if( isDsl2() ) {
-            result.preview = featuresMap()
-        }
         return result
     }
 
@@ -128,17 +125,6 @@ class NextflowMeta {
         enable.dsl == 2f
     }
 
-    /**
-     * As of the removal of DSL2 preview mode, the semantic of this method
-     * is identical to {@link #isDsl2()}.
-     * @return
-     *  {@code true} when the workflow script uses DSL2 syntax, {@code false} otherwise.
-     */
-    @Deprecated
-    boolean isDsl2Final() {
-        enable.dsl == 2f
-    }
-
     void enableDsl2() {
         this.enable.dsl = 2f
     }
diff --git a/modules/nextflow/src/main/groovy/nextflow/ast/NextflowDSLImpl.groovy b/modules/nextflow/src/main/groovy/nextflow/ast/NextflowDSLImpl.groovy
index ecb11da515..112c2ffbb5 100644
--- a/modules/nextflow/src/main/groovy/nextflow/ast/NextflowDSLImpl.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/ast/NextflowDSLImpl.groovy
@@ -79,8 +79,6 @@ import org.codehaus.groovy.transform.GroovyASTTransformation
 @GroovyASTTransformation(phase = CompilePhase.CONVERSION)
 class NextflowDSLImpl implements ASTTransformation {
 
-    @Deprecated final static private String WORKFLOW_GET = 'get'
-    @Deprecated final static private String WORKFLOW_PUBLISH = 'publish'
     final static private String WORKFLOW_TAKE = 'take'
     final static private String WORKFLOW_EMIT = 'emit'
     final static private String WORKFLOW_MAIN = 'main'
@@ -508,12 +506,6 @@ class NextflowDSLImpl implements ASTTransformation {
                 visited[context] = true
 
                 switch (context) {
-                    case WORKFLOW_GET:
-                        syntaxError(stm, "Workflow 'get' is not supported anymore use 'take' instead")
-
-                    case WORKFLOW_PUBLISH:
-                        syntaxError(stm, "Workflow 'publish' is not supported anymore use process 'publishDir' instead")
-
                     case WORKFLOW_TAKE:
                     case WORKFLOW_EMIT:
                         if( !(stm instanceof ExpressionStatement) ) {
diff --git a/modules/nextflow/src/main/groovy/nextflow/ast/OpXformImpl.groovy b/modules/nextflow/src/main/groovy/nextflow/ast/OpXformImpl.groovy
index 039ccfda86..c60a2a341e 100644
--- a/modules/nextflow/src/main/groovy/nextflow/ast/OpXformImpl.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/ast/OpXformImpl.groovy
@@ -79,10 +79,6 @@ class OpXformImpl implements ASTTransformation {
 
     static final public String MULTIMAP_CRITERIA_FUN = 'multiMapCriteria'
 
-    @Deprecated static final public String FORK_METHOD_NAME = 'fork'
-
-    @Deprecated static final public String FORK_CRITERIA_FUN = 'forkCriteria'
-
     SourceUnit unit
 
     static class BranchCondition {
@@ -385,14 +381,6 @@ class OpXformImpl implements ASTTransformation {
                 return ret
             if( name==MULTIMAP_CRITERIA_FUN && args.size()==1 && m.objectExpression.text=='this')
                 return ret
-            if( name==FORK_METHOD_NAME && args.size()==1 ) {
-                log.debug "Operator `fork` has been renamed to `multiMap`"
-                return ret
-            }
-            if( name==FORK_CRITERIA_FUN && args.size()==1 && m.objectExpression.text=='this') {
-                log.warn "Function `forkCriteria` has been renamed to `multiMapCriteria`"
-                return ret
-            }
 
         }
         return null
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdPlugins.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdPlugins.groovy
deleted file mode 100644
index 360d29e2d3..0000000000
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdPlugins.groovy
+++ /dev/null
@@ -1,43 +0,0 @@
-/*
- * Copyright 2013-2023, Seqera Labs
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package nextflow.cli
-
-import groovy.transform.CompileStatic
-import groovy.util.logging.Slf4j
-
-/**
- * Deprecate - see {@link CmdPlugin} instead
- *
- * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
- */
-@Slf4j
-@Deprecated
-@CompileStatic
-class CmdPlugins extends CmdPlugin {
-
-    @Override
-    String getName() {
-        return 'plugins'
-    }
-
-    @Override
-    void run() {
-        log.info "Command 'plugins' has been deprecated - Use 'plugin' instead"
-        super.run()
-    }
-}
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdSecret.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdSecret.groovy
index 3ef3163d86..d7e86278d3 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdSecret.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdSecret.groovy
@@ -56,7 +56,6 @@ class CmdSecret extends CmdBase implements UsageAware {
 
     CmdSecret() {
         commands.add( new GetCmd() )
-        commands.add( new PutCmd() )
         commands.add( new SetCmd() )
         commands.add( new ListCmd() )
         commands.add( new DeleteCmd() )
@@ -146,19 +145,6 @@ class CmdSecret extends CmdBase implements UsageAware {
         }
     }
 
-    /**
-     * Implements the secret `put` sub-command
-     */
-    @Deprecated
-    class PutCmd extends SetCmd {
-        String getName() { 'put' }
-
-        void apply(List<String> result) {
-            log.warn "Put command is deprecated - use 'set' instead'"
-            super.apply(result)
-        }
-    }
-
     class SetCmd implements SubCmd {
 
         @Override
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy
index be9458eaa2..8ed41196c1 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy
@@ -101,7 +101,6 @@ class Launcher {
                 new CmdView(),
                 new CmdHelp(),
                 new CmdSelfUpdate(),
-                new CmdPlugins(),
                 new CmdPlugin(),
                 new CmdInspect()
         ]
diff --git a/modules/nextflow/src/main/groovy/nextflow/extension/CH.groovy b/modules/nextflow/src/main/groovy/nextflow/extension/CH.groovy
index 2ba44edde4..ba8727808e 100644
--- a/modules/nextflow/src/main/groovy/nextflow/extension/CH.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/extension/CH.groovy
@@ -58,8 +58,6 @@ class CH {
     }
 
     static private DataflowReadChannel getRead2(DataflowBroadcast channel) {
-        if( !NF.isDsl2() )
-            throw new IllegalStateException("Broadcast channel are only allowed in a workflow definition scope")
         channel.createReadChannel()
     }
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/extension/ChannelEx.groovy b/modules/nextflow/src/main/groovy/nextflow/extension/ChannelEx.groovy
index 499124ce44..2ebc20ae87 100644
--- a/modules/nextflow/src/main/groovy/nextflow/extension/ChannelEx.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/extension/ChannelEx.groovy
@@ -83,18 +83,6 @@ class ChannelEx {
         return target
     }
 
-    /**
-     * Close a dataflow queue channel binding a {@link Channel#STOP} item
-     *
-     * @param source The source dataflow channel to be closed.
-     */
-    @Deprecated
-    static DataflowWriteChannel close(DataflowWriteChannel source) {
-        if( NF.isDsl2() )
-            throw new DeprecationException("Channel `close` method is not supported anymore")
-        return CH.close0(source)
-    }
-
     /**
      * INTERNAL ONLY API
      * <p>
@@ -113,9 +101,6 @@ class ChannelEx {
     }
 
     static private void checkContext(String method, Object operand) {
-        if( !NF.isDsl2() )
-            throw new MissingMethodException(method, operand.getClass())
-
         if( operand instanceof ComponentDef && !ExecutionStack.withinWorkflow() )
             throw new IllegalArgumentException("Process invocation are only allowed within a workflow context")
     }
diff --git a/modules/nextflow/src/main/groovy/nextflow/extension/ChannelExtensionPoint.groovy b/modules/nextflow/src/main/groovy/nextflow/extension/ChannelExtensionPoint.groovy
deleted file mode 100644
index 9ef47aea60..0000000000
--- a/modules/nextflow/src/main/groovy/nextflow/extension/ChannelExtensionPoint.groovy
+++ /dev/null
@@ -1,29 +0,0 @@
-/*
- * Copyright 2013-2023, Seqera Labs
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package nextflow.extension
-
-import nextflow.plugin.extension.PluginExtensionPoint
-
-/**
- * This class is deprecated, use {@link PluginExtensionPoint} instead
- *
- * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
- */
-@Deprecated
-abstract class ChannelExtensionPoint extends PluginExtensionPoint {
-}
diff --git a/modules/nextflow/src/main/groovy/nextflow/extension/DeprecatedDsl2.groovy b/modules/nextflow/src/main/groovy/nextflow/extension/DeprecatedDsl2.groovy
deleted file mode 100644
index 19eebad424..0000000000
--- a/modules/nextflow/src/main/groovy/nextflow/extension/DeprecatedDsl2.groovy
+++ /dev/null
@@ -1,40 +0,0 @@
-/*
- * Copyright 2013-2023, Seqera Labs
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package nextflow.extension
-
-import static java.lang.annotation.ElementType.CONSTRUCTOR
-import static java.lang.annotation.ElementType.FIELD
-import static java.lang.annotation.ElementType.LOCAL_VARIABLE
-import static java.lang.annotation.ElementType.METHOD
-import static java.lang.annotation.ElementType.PACKAGE
-import static java.lang.annotation.ElementType.PARAMETER
-import static java.lang.annotation.ElementType.TYPE
-
-import java.lang.annotation.Retention
-import java.lang.annotation.RetentionPolicy
-import java.lang.annotation.Target
-
-/**
- * Deprecation introduced by Dsl-2 syntax
- *
- * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
- */
-@Retention(RetentionPolicy.RUNTIME)
-@Target(value=[CONSTRUCTOR, FIELD, LOCAL_VARIABLE, METHOD, PACKAGE, PARAMETER, TYPE])
-@interface DeprecatedDsl2 {
-    String message() default ''
-}
diff --git a/modules/nextflow/src/main/groovy/nextflow/extension/OpCall.groovy b/modules/nextflow/src/main/groovy/nextflow/extension/OpCall.groovy
index 11fd5c6dd5..a18e02dd72 100644
--- a/modules/nextflow/src/main/groovy/nextflow/extension/OpCall.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/extension/OpCall.groovy
@@ -320,13 +320,6 @@ class OpCall implements Callable {
     protected void checkDeprecation(Method method) {
         if( method.getAnnotation(Deprecated) ) {
             def messg = "Operator `$methodName` is deprecated -- it will be removed in a future release"
-            if( NF.isDsl2() )
-                throw new DeprecationException(messg)
-            log.warn messg
-        }
-        else if( method.getAnnotation(DeprecatedDsl2) && NF.isDsl2() ) {
-            def annot = method.getAnnotation(DeprecatedDsl2)
-            def messg = annot.message() ?: "Operator `$methodName` has been deprecated -- it's not available in DSL2 syntax".toString()
             throw new DeprecationException(messg)
         }
     }
diff --git a/modules/nextflow/src/main/groovy/nextflow/extension/OperatorImpl.groovy b/modules/nextflow/src/main/groovy/nextflow/extension/OperatorImpl.groovy
index 16a9b87a45..ceeb26f858 100644
--- a/modules/nextflow/src/main/groovy/nextflow/extension/OperatorImpl.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/extension/OperatorImpl.groovy
@@ -1016,12 +1016,6 @@ class OperatorImpl {
         return tap.result
     }
 
-    @DeprecatedDsl2
-    DataflowWriteChannel tap( final DataflowReadChannel source, final DataflowWriteChannel target ) {
-        def tap = new TapOp(source, target).apply()
-        return tap.result
-    }
-
 
     /**
      * Empty the specified value only if the source channel to which is applied is empty i.e. do not emit
diff --git a/modules/nextflow/src/main/groovy/nextflow/plugin/extension/PluginExtensionProvider.groovy b/modules/nextflow/src/main/groovy/nextflow/plugin/extension/PluginExtensionProvider.groovy
index 2f3f050fb1..f24de108a5 100644
--- a/modules/nextflow/src/main/groovy/nextflow/plugin/extension/PluginExtensionProvider.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/plugin/extension/PluginExtensionProvider.groovy
@@ -290,13 +290,4 @@ class PluginExtensionProvider implements ExtensionProvider {
         }
     }
 
-    @Deprecated
-    static void reloadExtensionPoints() {
-        if( !instance )
-            return
-        instance.channelExtensionPoints=null
-        instance.operatorExtensions.clear()
-        instance.install()
-    }
-
 }
diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskBean.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskBean.groovy
index c20a8ac2eb..441c19795e 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskBean.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskBean.groovy
@@ -77,9 +77,6 @@ class TaskBean implements Serializable, Cloneable {
 
     String afterScript
 
-    @Deprecated
-    boolean containerExecutable
-
     boolean containerNative
 
     boolean containerEnabled
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/BaseScript.groovy b/modules/nextflow/src/main/groovy/nextflow/script/BaseScript.groovy
index 81c7891c6b..28fed0795c 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/BaseScript.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/BaseScript.groovy
@@ -90,13 +90,8 @@ abstract class BaseScript extends Script implements ExecutionContext {
     }
 
     protected process( String name, Closure<BodyDef> body ) {
-        if( NF.isDsl2() ) {
-            def process = new ProcessDef(this,body,name)
-            meta.addDefinition(process)
-        }
-        else {
-            throw new UnsupportedOperationException("DSL1 is not supported anymore")
-        }
+        def process = new ProcessDef(this,body,name)
+        meta.addDefinition(process)
     }
 
     /**
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/ProcessConfig.groovy b/modules/nextflow/src/main/groovy/nextflow/script/ProcessConfig.groovy
index d88a11cf1d..f7df88d2bf 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/ProcessConfig.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/ProcessConfig.groovy
@@ -536,12 +536,6 @@ class ProcessConfig implements Map<String,Object>, Cloneable {
         new EachInParam(this).bind(obj)
     }
 
-    InParam _in_set( Object... obj ) {
-        final msg = "Input of type `set` is deprecated -- Use `tuple` instead"
-        if( NF.isDsl2() ) throw new DeprecationException(msg)
-        new TupleInParam(this).bind(obj)
-    }
-
     InParam _in_tuple( Object... obj ) {
         new TupleInParam(this).bind(obj)
     }
@@ -606,12 +600,6 @@ class ProcessConfig implements Map<String,Object>, Cloneable {
         }
     }
 
-    OutParam _out_set( Object... obj ) {
-        final msg = "Output of type `set` is deprecated -- Use `tuple` instead"
-        if( NF.isDsl2() ) throw new DeprecationException(msg)
-        new TupleOutParam(this) .bind(obj)
-    }
-
     OutParam _out_tuple( Object... obj ) {
         new TupleOutParam(this) .bind(obj)
     }
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/ScriptBinding.groovy b/modules/nextflow/src/main/groovy/nextflow/script/ScriptBinding.groovy
index 7cde04e282..09293c144b 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/ScriptBinding.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/ScriptBinding.groovy
@@ -186,9 +186,7 @@ class ScriptBinding extends WorkflowBinding {
     @Override
     void setVariable( String name, Object value ) {
         if( name == 'channel' ) {
-            final msg = 'The use of the identifier `channel` as variable name is discouraged and will be deprecated in a future version'
-            if( NF.isDsl2() ) throw new DeprecationException(msg)
-            log.warn(msg)
+            throw new IllegalAccessException("The use of the identifier `$name` as variable name is not allowed")
         }
         if( name != 'args' && name != 'params' )
             super.setVariable(name, value)
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/params/FileOutParam.groovy b/modules/nextflow/src/main/groovy/nextflow/script/params/FileOutParam.groovy
index a55cd957c7..97721ea7b2 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/params/FileOutParam.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/params/FileOutParam.groovy
@@ -92,63 +92,6 @@ class FileOutParam extends BaseOutParam implements OutParam, ArityParam, Optiona
      */
     boolean isDynamic() { dynamicObj || gstring != null }
 
-    @Deprecated
-    FileOutParam separatorChar( String value ) {
-        if( NF.dsl2 ) throw new DeprecationException("Option `separatorChar is not supported anymore")
-        this.separatorChar = value
-        return this
-    }
-
-    @Deprecated
-    FileOutParam includeInputs( boolean flag ) {
-        if( NF.dsl2 ) throw new DeprecationException("Deprecated syntax error - replace `includeInputs $flag` with `, includeInputs: $flag` ")
-        this.includeInputs = flag
-        return this
-    }
-
-    @Deprecated
-    FileOutParam includeHidden( boolean flag ) {
-        if( NF.dsl2 ) throw new DeprecationException("Deprecated syntax error - replace `includeHidden $flag` with `, includeHidden: $flag`")
-        this.hidden = flag
-        return this
-    }
-
-    @Deprecated
-    FileOutParam hidden( boolean flag ) {
-        if( NF.dsl2 ) throw new DeprecationException("Deprecated syntax error - replace `hidden $flag` with use `, hidden: $flag`")
-        this.hidden = flag
-        return this
-    }
-
-    @Deprecated
-    FileOutParam type( String value ) {
-        if( NF.dsl2 ) throw new DeprecationException("Deprecated syntax error - replace `type $value` with `, type: $value`")
-        assert value in ['file','dir','any']
-        type = value
-        return this
-    }
-
-    @Deprecated
-    FileOutParam maxDepth( int value ) {
-        if( NF.dsl2 ) throw new DeprecationException("Deprecated syntax error - replace `maxDepth $value` with `, maxDepth: $value`")
-        maxDepth = value
-        return this
-    }
-
-    @Deprecated
-    FileOutParam followLinks( boolean value ) {
-        if( NF.dsl2 ) throw new DeprecationException("Deprecated syntax error - replace `followLinks $value` with `, followLinks: $value`")
-        followLinks = value
-        return this
-    }
-
-    @Deprecated
-    FileOutParam glob( boolean value ) {
-        if( NF.dsl2 ) throw new DeprecationException("Deprecated syntax error - replace `glob $value` with `, glob: $value` ")
-        glob = value
-        return this
-    }
-
     @Override
     BaseOutParam bind( obj ) {
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/params/TupleInParam.groovy b/modules/nextflow/src/main/groovy/nextflow/script/params/TupleInParam.groovy
index 4c2bc3ff69..fadd87cdff 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/params/TupleInParam.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/params/TupleInParam.groovy
@@ -56,11 +56,7 @@ class TupleInParam extends BaseInParam {
         for( def item : obj ) {
 
             if( item instanceof TokenVar ) {
-                if( NF.dsl2 ) {
-                    final msg = "Unqualified input value declaration has been deprecated - replace `tuple ${item.name},..` with `tuple val(${item.name}),..`"
-                    throw new DeprecationException(msg)
-                }
-                newItem(ValueInParam).bind(item)
+                throw new IllegalArgumentException("Unqualified input value declaration is not allowed - replace `tuple ${item.name},..` with `tuple val(${item.name}),..`")
             }
             else if( item instanceof TokenFileCall ) {
                 newItem(FileInParam).bind( item.target )
@@ -72,11 +68,7 @@ class TupleInParam extends BaseInParam {
                         .bind( item.target )
             }
             else if( item instanceof Map ) {
-                if( NF.dsl2 ) {
-                    final msg = "Unqualified input file declaration has been deprecated - replace `tuple $item,..` with `tuple path(${item.key}, stageAs:'${item.value}'),..`"
-                    throw new DeprecationException(msg)
-                }
-                newItem(FileInParam).bind(item)
+                throw new IllegalArgumentException("Unqualified input file declaration is not allowed - replace `tuple $item,..` with `tuple path(${item.key}, stageAs:'${item.value}'),..`")
             }
             else if( item instanceof TokenValCall ) {
                 newItem(ValueInParam).bind(item.val)
@@ -88,17 +80,13 @@ class TupleInParam extends BaseInParam {
                 newItem(StdInParam)
             }
             else if( item instanceof GString ) {
-                if( NF.dsl2 )
-                    throw new DeprecationException("Unqualified input file declaration has been deprecated - replace `tuple \"$item\".. with `tuple path(\"$item\")..`")
-                newItem(FileInParam).bind(item)
+                throw new IllegalArgumentException("Unqualified input file declaration is not allowed - replace `tuple \"$item\".. with `tuple path(\"$item\")..`")
             }
             else if( item == '-' ) {
                 newItem(StdInParam)
             }
             else if( item instanceof String ) {
-                if( NF.dsl2 )
-                    throw new DeprecationException("Unqualified input file declaration has been deprecated - replace `tuple '$item',..` with `tuple path('$item'),..`")
-                newItem(FileInParam).bind(item)
+                throw new IllegalArgumentException("Unqualified input file declaration is not allowed - replace `tuple '$item',..` with `tuple path('$item'),..`")
             }
             else
                 throw new IllegalArgumentException()
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/params/TupleOutParam.groovy b/modules/nextflow/src/main/groovy/nextflow/script/params/TupleOutParam.groovy
index d038eb7331..e0de9e24ed 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/params/TupleOutParam.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/params/TupleOutParam.groovy
@@ -51,9 +51,7 @@ class TupleOutParam extends BaseOutParam implements OptionalParam {
 
         for( def item : obj ) {
             if( item instanceof TokenVar ) {
-                if( NF.dsl2 )
-                    throw new DeprecationException("Unqualified output value declaration has been deprecated - replace `tuple ${item.name},..` with `tuple val(${item.name}),..`")
-                create(ValueOutParam).bind(item)
+                throw new IllegalArgumentException("Unqualified output value declaration is not allowed - replace `tuple ${item.name},..` with `tuple val(${item.name}),..`")
             }
             else if( item instanceof TokenValCall ) {
                 create(ValueOutParam).bind(item.val)
@@ -62,17 +60,13 @@ class TupleOutParam extends BaseOutParam implements OptionalParam {
                 create(EnvOutParam).bind(item.val)
             }
             else if( item instanceof GString ) {
-                if( NF.dsl2 )
-                    throw new DeprecationException("Unqualified output path declaration has been deprecated - replace `tuple \"$item\",..` with `tuple path(\"$item\"),..`")
-                create(FileOutParam).bind(item)
+                throw new IllegalArgumentException("Unqualified output path declaration is not allowed - replace `tuple \"$item\",..` with `tuple path(\"$item\"),..`")
             }
             else if( item instanceof TokenStdoutCall || item == '-'  ) {
                 create(StdOutParam).bind('-')
             }
             else if( item instanceof String ) {
-                if( NF.dsl2 )
-                    throw new DeprecationException("Unqualified output path declaration has been deprecated - replace `tuple '$item',..` with `tuple path('$item'),..`")
-                create(FileOutParam).bind(item)
+                throw new IllegalArgumentException("Unqualified output path declaration is not allowed - replace `tuple '$item',..` with `tuple path('$item'),..`")
             }
             else if( item instanceof TokenFileCall ) {
                 // note that 'filePattern' can be a string or a GString
diff --git a/modules/nextflow/src/test/groovy/nextflow/extension/ChannelExTest.groovy b/modules/nextflow/src/test/groovy/nextflow/extension/ChannelExTest.groovy
deleted file mode 100644
index ca61e44ceb..0000000000
--- a/modules/nextflow/src/test/groovy/nextflow/extension/ChannelExTest.groovy
+++ /dev/null
@@ -1,41 +0,0 @@
-package nextflow.extension
-
-import spock.lang.Specification
-
-import nextflow.Channel
-/**
- *
- * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
- */
-class ChannelExTest extends Specification {
-
-
-    def 'should close the dataflow channel'() {
-
-        when:
-        def source = Channel.create()
-        source << 10
-        source << 20
-        source << 30
-        def result = source.close()
-        then:
-        result.is source
-        result.val == 10
-        result.val == 20
-        result.val == 30
-        result.val == Channel.STOP
-
-        when:
-        source = Channel.value().close()
-        then:
-        source.val == Channel.STOP
-
-        when:
-        source = Channel.value(1).close()
-        then:
-        source.val == 1
-
-    }
-
-
-}
diff --git a/modules/nextflow/src/test/groovy/nextflow/extension/CombineOpTest.groovy b/modules/nextflow/src/test/groovy/nextflow/extension/CombineOpTest.groovy
index 8d0e1b8daa..ae8bce0788 100644
--- a/modules/nextflow/src/test/groovy/nextflow/extension/CombineOpTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/extension/CombineOpTest.groovy
@@ -149,7 +149,7 @@ class CombineOpTest extends Specification {
 
     def 'should combine with empty value' () {
         given:
-        def left = Channel.value().close()
+        def left = Channel.empty()
         def right = Channel.value('z')
         def op = new CombineOp(left, right)
         when:
diff --git a/modules/nextflow/src/test/groovy/nextflow/extension/DataflowTapExtensionTest.groovy b/modules/nextflow/src/test/groovy/nextflow/extension/DataflowTapExtensionTest.groovy
index ea3c65d241..de3c3d67e3 100644
--- a/modules/nextflow/src/test/groovy/nextflow/extension/DataflowTapExtensionTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/extension/DataflowTapExtensionTest.groovy
@@ -79,55 +79,4 @@ class DataflowTapExtensionTest extends Specification {
 
     }
 
-    def 'should `tap` target channel' () {
-
-        when:
-        def target = Channel.create()
-        def result = Channel.of( 8,2,5 ) .tap(target).map { it+1 }
-        then:
-        result instanceof DataflowQueue
-        target instanceof DataflowQueue
-
-        target.val == 8
-        target.val == 2
-        target.val == 5
-        target.val == Channel.STOP
-
-        result.val == 9
-        result.val == 3
-        result.val == 6
-        result.val == Channel.STOP
-
-        !session.dag.isEmpty()
-
-    }
-
-    def 'should `tap` dataflow value' () {
-
-        when:
-        def target = Channel.value()
-        def result = Channel.value(7) .tap(target).map { it+1 }
-        then:
-        result instanceof DataflowVariable
-        target instanceof DataflowVariable
-
-        target.val == 7
-        target.val == 7
-        result.val == 8
-        result.val == 8
-
-        !session.dag.isEmpty()
-
-    }
-
-    def 'should `tap` dataflow value and target as queue' () {
-
-        when:
-        new DataflowVariable() .tap( new DataflowQueue() )
-        then:
-        thrown(IllegalArgumentException)
-        session.dag.isEmpty()
-
-    }
-
 }
diff --git a/modules/nextflow/src/test/groovy/nextflow/extension/OperatorImplTest.groovy b/modules/nextflow/src/test/groovy/nextflow/extension/OperatorImplTest.groovy
index ebb92b1a2e..888b7aa765 100644
--- a/modules/nextflow/src/test/groovy/nextflow/extension/OperatorImplTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/extension/OperatorImplTest.groovy
@@ -18,6 +18,7 @@ package nextflow.extension
 
 import java.nio.file.Paths
 
+import groovyx.gpars.dataflow.DataflowQueue
 import groovyx.gpars.dataflow.DataflowVariable
 import nextflow.Channel
 import nextflow.Session
@@ -225,7 +226,7 @@ class OperatorImplTest extends Specification {
         result.val == Channel.STOP
 
         when:
-        result = Channel.value().close().flatMap()
+        result = Channel.empty().flatMap()
         then:
         result.val == Channel.STOP
 
@@ -443,7 +444,7 @@ class OperatorImplTest extends Specification {
         channel.toList().val == [1]
 
         when:
-        channel = Channel.value().close()
+        channel = Channel.empty()
         then:
         channel.toList().val == []
     }
@@ -472,7 +473,7 @@ class OperatorImplTest extends Specification {
         channel.toSortedList().val == [1]
 
         when:
-        channel = Channel.value().close()
+        channel = Channel.empty()
         then:
         channel.toSortedList().val == []
 
@@ -542,7 +543,7 @@ class OperatorImplTest extends Specification {
         result.val == Channel.STOP
 
         when:
-        result = Channel.value().close().flatten()
+        result = Channel.empty().flatten()
         then:
         result.val ==  Channel.STOP
     }
@@ -1099,9 +1100,9 @@ class OperatorImplTest extends Specification {
         result.val == 1
 
         when:
-        result = Channel.value().close().ifEmpty(100)
+        result = Channel.empty().ifEmpty(100)
         then:
-        result instanceof DataflowVariable
+        result instanceof DataflowQueue
         result.val == 100
 
     }
diff --git a/modules/nextflow/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy b/modules/nextflow/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy
index 4307c7edb4..b616669c2e 100644
--- a/modules/nextflow/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy
@@ -608,14 +608,14 @@ class TaskProcessorTest extends Specification {
 
         when:
         param = new FileOutParam(Mock(Binding), Mock(List))
-        param.type('file')
+        param.setType('file')
         result = fetchResultFiles(processor, param, '*.fa', folder)
         then:
         result  == ['file2.fa']
 
         when:
         param = new FileOutParam(Mock(Binding), Mock(List))
-        param.type('dir')
+        param.setType('dir')
         result = fetchResultFiles(processor, param, '*.fa', folder)
         then:
         result == []
@@ -628,14 +628,14 @@ class TaskProcessorTest extends Specification {
 
         when:
         param = new FileOutParam(Mock(Binding), Mock(List))
-        param.followLinks(false)
+        param.setFollowLinks(false)
         result = fetchResultFiles(processor, param, '**.fa', folder)
         then:
         result == ['dir1/dir2/file4.fa', 'file2.fa']
 
         when:
         param = new FileOutParam(Mock(Binding), Mock(List))
-        param.maxDepth(1)
+        param.setMaxDepth(1)
         result = fetchResultFiles(processor, param, '**.fa', folder)
         then:
         result == ['file2.fa']
@@ -648,22 +648,22 @@ class TaskProcessorTest extends Specification {
 
         when:
         param = new FileOutParam(Mock(Binding), Mock(List))
-        param.type('dir')
+        param.setType('dir')
         result = fetchResultFiles(processor, param, '*', folder)
         then:
         result == ['dir1', 'dir_link']
 
         when:
         param = new FileOutParam(Mock(Binding), Mock(List))
-        param.type('file')
+        param.setType('file')
         result = fetchResultFiles(processor, param, '*', folder)
         then:
         result == ['file1.txt', 'file2.fa']
 
         when:
         param = new FileOutParam(Mock(Binding), Mock(List))
-        param.type('file')
-        param.hidden(true)
+        param.setType('file')
+        param.setHidden(true)
         result = fetchResultFiles(processor, param, '*', folder)
         then:
         result == ['.hidden.fa', 'file1.txt', 'file2.fa']
@@ -700,25 +700,25 @@ class TaskProcessorTest extends Specification {
 
         when:
         param = new FileOutParam(Mock(Binding), Mock(List))
-        param.type('dir')
+        param.setType('dir')
         then:
         processor.visitOptions(param,'dir-name') == [type:'dir', followLinks: true, maxDepth: null, hidden: false, relative: false]
 
         when:
         param = new FileOutParam(Mock(Binding), Mock(List))
-        param.hidden(true)
+        param.setHidden(true)
         then:
         processor.visitOptions(param,'dir-name') == [type:'any', followLinks: true, maxDepth: null, hidden: true, relative: false]
 
         when:
         param = new FileOutParam(Mock(Binding), Mock(List))
-        param.followLinks(false)
+        param.setFollowLinks(false)
         then:
         processor.visitOptions(param,'dir-name') == [type:'any', followLinks: false, maxDepth: null, hidden: false, relative: false]
 
         when:
         param = new FileOutParam(Mock(Binding), Mock(List))
-        param.maxDepth(5)
+        param.setMaxDepth(5)
         then:
         processor.visitOptions(param,'dir-name') == [type:'any', followLinks: true, maxDepth: 5, hidden: false, relative: false]
     }
diff --git a/modules/nextflow/src/test/groovy/nextflow/script/ScriptDslTest.groovy b/modules/nextflow/src/test/groovy/nextflow/script/ScriptDslTest.groovy
index 7f8a69ee5a..9e48c8e55e 100644
--- a/modules/nextflow/src/test/groovy/nextflow/script/ScriptDslTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/script/ScriptDslTest.groovy
@@ -475,26 +475,6 @@ class ScriptDslTest extends Dsl2Spec {
         err.message == "Access to 'flow1.out' is undefined since the workflow 'flow1' has not been invoked before accessing the output attribute"
     }
 
-    def 'should report unsupported error' () {
-        when:
-        dsl_eval('''
-        process foo {
-          /echo foo/
-        }
-        
-        workflow {
-          get: 
-            x
-          main: 
-          flow()
-        }
-        ''')
-
-        then:
-        def err = thrown(ScriptCompilationException)
-        err.message.contains "Workflow 'get' is not supported anymore use 'take' instead"
-    }
-
     def 'should fail with wrong scope'() {
         when:
         dsl_eval('''\
diff --git a/modules/nextflow/src/test/groovy/nextflow/script/params/ParamsDsl2Test.groovy b/modules/nextflow/src/test/groovy/nextflow/script/params/ParamsDsl2Test.groovy
index 2739e73c27..b703b22187 100644
--- a/modules/nextflow/src/test/groovy/nextflow/script/params/ParamsDsl2Test.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/script/params/ParamsDsl2Test.groovy
@@ -35,8 +35,8 @@ class ParamsDsl2Test extends Dsl2Spec {
         when:
         new MockScriptRunner() .setScript(SCRIPT).execute()
         then:
-        def e = thrown(DeprecationException)
-        e.message == "Unqualified input file declaration has been deprecated - replace `tuple 'x',..` with `tuple path('x'),..`"
+        def e = thrown(IllegalArgumentException)
+        e.message == "Unqualified input file declaration is not allowed - replace `tuple 'x',..` with `tuple path('x'),..`"
     }
 
     def 'should not allow unqualified input val' () {
@@ -57,8 +57,8 @@ class ParamsDsl2Test extends Dsl2Spec {
         when:
         new MockScriptRunner() .setScript(SCRIPT).execute()
         then:
-        def e = thrown(DeprecationException)
-        e.message == "Unqualified input value declaration has been deprecated - replace `tuple X,..` with `tuple val(X),..`"
+        def e = thrown(IllegalArgumentException)
+        e.message == "Unqualified input value declaration is not allowed - replace `tuple X,..` with `tuple val(X),..`"
     }
 
 
@@ -80,8 +80,8 @@ class ParamsDsl2Test extends Dsl2Spec {
         when:
         new MockScriptRunner() .setScript(SCRIPT).execute()
         then:
-        def e = thrown(DeprecationException)
-        e.message == "Unqualified output path declaration has been deprecated - replace `tuple 'x',..` with `tuple path('x'),..`"
+        def e = thrown(IllegalArgumentException)
+        e.message == "Unqualified output path declaration is not allowed - replace `tuple 'x',..` with `tuple path('x'),..`"
     }
 
     def 'should not allow unqualified output value' () {
@@ -102,8 +102,8 @@ class ParamsDsl2Test extends Dsl2Spec {
         when:
         new MockScriptRunner() .setScript(SCRIPT).execute()
         then:
-        def e = thrown(DeprecationException)
-        e.message == "Unqualified output value declaration has been deprecated - replace `tuple X,..` with `tuple val(X),..`"
+        def e = thrown(IllegalArgumentException)
+        e.message == "Unqualified output value declaration is not allowed - replace `tuple X,..` with `tuple val(X),..`"
     }
 
 

From 159effb1cf6dfee98ef8647d9bee1ce6df15fcfd Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Wed, 1 Nov 2023 22:24:37 +0100
Subject: [PATCH 243/350] Remove dsl1 deprecated code (part 2)

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../nextflow/ast/NextflowDSLImpl.groovy       | 58 ------------------
 .../nextflow/processor/TaskProcessor.groovy   | 26 ++++----
 .../groovy/nextflow/script/BaseScript.groovy  |  3 +-
 .../groovy/nextflow/script/IncludeDef.groovy  | 11 ----
 .../nextflow/script/ProcessConfig.groovy      |  1 -
 .../groovy/nextflow/script/ScriptMeta.groovy  | 27 ---------
 .../nextflow/script/ScriptTokens.groovy       | 14 ++---
 .../nextflow/script/params/BaseInParam.groovy | 43 +-------------
 .../script/params/BaseOutParam.groovy         | 39 ++----------
 .../nextflow/script/params/FileInParam.groovy |  7 ---
 .../nextflow/script/params/InParam.groovy     |  4 --
 .../nextflow/script/params/OutParam.groovy    | 11 ----
 .../script/params/TupleInParam.groovy         |  2 +-
 .../nextflow/ast/NextflowDSLImplTest.groovy   | 59 +++++++++----------
 .../nextflow/script/IncludeDefTest.groovy     | 15 +++--
 .../nextflow/script/ProcessConfigTest.groovy  |  8 +--
 .../nextflow/script/ProcessDefTest.groovy     | 43 +-------------
 17 files changed, 71 insertions(+), 300 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/ast/NextflowDSLImpl.groovy b/modules/nextflow/src/main/groovy/nextflow/ast/NextflowDSLImpl.groovy
index 112c2ffbb5..a278fdd8f6 100644
--- a/modules/nextflow/src/main/groovy/nextflow/ast/NextflowDSLImpl.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/ast/NextflowDSLImpl.groovy
@@ -38,7 +38,6 @@ import nextflow.script.TokenVar
 import org.codehaus.groovy.ast.ASTNode
 import org.codehaus.groovy.ast.ClassCodeVisitorSupport
 import org.codehaus.groovy.ast.ClassNode
-import org.codehaus.groovy.ast.ConstructorNode
 import org.codehaus.groovy.ast.MethodNode
 import org.codehaus.groovy.ast.Parameter
 import org.codehaus.groovy.ast.VariableScope
@@ -149,63 +148,6 @@ class NextflowDSLImpl implements ASTTransformation {
             super.visitMethod(node)
         }
 
-        protected Statement makeSetProcessNamesStm() {
-            final names = new ListExpression()
-            for( String it: processNames ) {
-                names.addExpression(new ConstantExpression(it.toString()))
-            }
-
-            // the method list argument
-            final args = new ArgumentListExpression()
-            args.addExpression(names)
-
-            // some magic code
-            // this generates the invocation of the method:
-            //   nextflow.script.ScriptMeta.get(this).setProcessNames(<list of process names>)
-            final scriptMeta = new PropertyExpression( new PropertyExpression(new VariableExpression('nextflow'),'script'), 'ScriptMeta')
-            final thiz = new ArgumentListExpression(); thiz.addExpression( new VariableExpression('this') )
-            final meta = new MethodCallExpression( scriptMeta, 'get', thiz )
-            final call = new MethodCallExpression( meta, 'setDsl1ProcessNames', args)
-            final stm = new ExpressionStatement(call)
-            return stm
-        }
-
-        /**
-         * Add to constructor a method call to inject parsed metadata.
-         * Only needed by DSL1.
-         *
-         * @param node The node representing the class to be invoked
-         */
-        protected void injectMetadata(ClassNode node) {
-            for( ConstructorNode constructor : node.getDeclaredConstructors() ) {
-                def code = constructor.getCode()
-                if( code instanceof BlockStatement ) {
-                    code.addStatement(makeSetProcessNamesStm())
-                }
-                else if( code instanceof ExpressionStatement ) {
-                    def expr = code
-                    def block = new BlockStatement()
-                    block.addStatement(expr)
-                    block.addStatement(makeSetProcessNamesStm())
-                    constructor.setCode(block)
-                }
-                else
-                    throw new IllegalStateException("Invalid constructor expression: $code")
-            }
-        }
-
-        /**
-         * Only needed by DSL1 to inject process names declared in the script
-         *
-         * @param node The node representing the class to be invoked
-         */
-        @Override
-        protected void visitObjectInitializerStatements(ClassNode node) {
-            if( node.getSuperClass().getName() == BaseScript.getName() )
-                injectMetadata(node)
-            super.visitObjectInitializerStatements(node)
-        }
-
         @Override
         void visitMethodCallExpression(MethodCallExpression methodCall) {
             // pre-condition to be verified to apply the transformation
diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
index bfcb34d4da..69b95e689a 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
@@ -418,15 +418,15 @@ class TaskProcessor {
         if ( !taskBody )
             throw new IllegalStateException("Missing task body for process `$name`")
 
-        // -- check that input set defines at least two elements
-        def invalidInputSet = config.getInputs().find { it instanceof TupleInParam && it.inner.size()<2 }
-        if( invalidInputSet )
-            checkWarn "Input `tuple` must define at least two component -- Check process `$name`"
+        // -- check that input tuple defines at least two elements
+        def invalidInputTuple = config.getInputs().find { it instanceof TupleInParam && it.inner.size()<2 }
+        if( invalidInputTuple )
+            checkWarn "Input `tuple` must define at least two elements -- Check process `$name`"
 
-        // -- check that output set defines at least two elements
-        def invalidOutputSet = config.getOutputs().find { it instanceof TupleOutParam && it.inner.size()<2 }
-        if( invalidOutputSet )
-            checkWarn "Output `tuple` must define at least two component -- Check process `$name`"
+        // -- check that output tuple defines at least two elements
+        def invalidOutputTuple = config.getOutputs().find { it instanceof TupleOutParam && it.inner.size()<2 }
+        if( invalidOutputTuple )
+            checkWarn "Output `tuple` must define at least two elements -- Check process `$name`"
 
         /**
          * Verify if this process run only one time
@@ -610,7 +610,7 @@ class TaskProcessor {
         currentTask.set(task)
 
         // -- validate input lengths
-        validateInputSets(values)
+        validateInputTuples(values)
 
         // -- map the inputs to a map and use to delegate closure values interpolation
         final secondPass = [:]
@@ -640,13 +640,13 @@ class TaskProcessor {
     }
 
     @Memoized
-    private List<TupleInParam> getDeclaredInputSet() {
+    private List<TupleInParam> getDeclaredInputTuple() {
         getConfig().getInputs().ofType(TupleInParam)
     }
 
-    protected void validateInputSets( List values ) {
+    protected void validateInputTuples( List values ) {
 
-        def declaredSets = getDeclaredInputSet()
+        def declaredSets = getDeclaredInputTuple()
         for( int i=0; i<declaredSets.size(); i++ ) {
             final param = declaredSets[i]
             final entry = values[param.index]
@@ -654,7 +654,7 @@ class TaskProcessor {
             final actual = entry instanceof Collection ? entry.size() : (entry instanceof Map ? entry.size() : 1)
 
             if( actual != expected ) {
-                final msg = "Input tuple does not match input set cardinality declared by process `$name` -- offending value: $entry"
+                final msg = "Input tuple does not match tuple declaration in process `$name` -- offending value: $entry"
                 checkWarn(msg, [firstOnly: true, cacheKey: this])
             }
         }
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/BaseScript.groovy b/modules/nextflow/src/main/groovy/nextflow/script/BaseScript.groovy
index 28fed0795c..58498fec71 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/BaseScript.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/BaseScript.groovy
@@ -20,7 +20,6 @@ import java.lang.reflect.InvocationTargetException
 import java.nio.file.Paths
 
 import groovy.util.logging.Slf4j
-import nextflow.NF
 import nextflow.NextflowMeta
 import nextflow.Session
 import nextflow.exception.AbortOperationException
@@ -90,7 +89,7 @@ abstract class BaseScript extends Script implements ExecutionContext {
     }
 
     protected process( String name, Closure<BodyDef> body ) {
-        def process = new ProcessDef(this,body,name)
+        final process = new ProcessDef(this,body,name)
         meta.addDefinition(process)
     }
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/IncludeDef.groovy b/modules/nextflow/src/main/groovy/nextflow/script/IncludeDef.groovy
index 9ea328347a..3dd0ea1aad 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/IncludeDef.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/IncludeDef.groovy
@@ -56,17 +56,6 @@ class IncludeDef {
     @PackageScope Map addedParams
     private Session session
 
-    @Deprecated
-    IncludeDef( String module ) {
-        final msg = "Anonymous module inclusion is deprecated -- Replace `include '${module}'` with `include { MODULE_NAME } from '${module}'`"
-        if( NF.isDsl2() )
-            throw new DeprecationException(msg)
-        log.warn msg
-        this.path = module
-        this.modules = new ArrayList<>(1)
-        this.modules << new Module(null,null)
-    }
-
     IncludeDef(TokenVar token, String alias=null) {
         def component = token.name; if(alias) component += " as $alias"
         def msg = "Unwrapped module inclusion is deprecated -- Replace `include $component from './MODULE/PATH'` with `include { $component } from './MODULE/PATH'`"
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/ProcessConfig.groovy b/modules/nextflow/src/main/groovy/nextflow/script/ProcessConfig.groovy
index f7df88d2bf..a9c2a86cf9 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/ProcessConfig.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/ProcessConfig.groovy
@@ -82,7 +82,6 @@ class ProcessConfig implements Map<String,Object>, Cloneable {
             'time',
             // input-output qualifiers
             'file',
-            'set',
             'val',
             'each',
             'env',
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/ScriptMeta.groovy b/modules/nextflow/src/main/groovy/nextflow/script/ScriptMeta.groovy
index 726253eafe..784b40d784 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/ScriptMeta.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/ScriptMeta.groovy
@@ -97,8 +97,6 @@ class ScriptMeta {
     /** The module components included in the script */
     private Map<String,ComponentDef> imports = new HashMap<>(10)
 
-    private List<String> dsl1ProcessNames
-
     /** Whenever it's a module script or the main script */
     private boolean module
 
@@ -162,25 +160,6 @@ class ScriptMeta {
         }
     }
 
-    /*
-     * This method invocation is made by the NF AST transformer to pass
-     * the process names declared in the workflow script. This is only required
-     * for DSL1 script.
-     *
-     * When using DSL2 process names can be discovered during
-     * the script execution since, the process declaration is de-coupled by the
-     * process invocations.
-     */
-    @PackageScope
-    void setDsl1ProcessNames(List<String> names) {
-        this.dsl1ProcessNames = names
-    }
-
-    @PackageScope
-    List<String> getDsl1ProcessNames() {
-        dsl1ProcessNames ?: Collections.<String>emptyList()
-    }
-
     @PackageScope
     static ScriptMeta register(BaseScript script) {
         def meta = new ScriptMeta(script)
@@ -277,9 +256,6 @@ class ScriptMeta {
     }
 
     Set<String> getProcessNames() {
-        if( NF.dsl1 )
-            return new HashSet<String>(getDsl1ProcessNames())
-
         def result = new HashSet(definitions.size() + imports.size())
         // local definitions
         for( def item : definitions.values() ) {
@@ -295,9 +271,6 @@ class ScriptMeta {
     }
 
     Set<String> getLocalProcessNames() {
-        if( NF.dsl1 )
-            return new HashSet<String>(getDsl1ProcessNames())
-
         def result = new HashSet(definitions.size() + imports.size())
         // local definitions
         for( def item : definitions.values() ) {
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/ScriptTokens.groovy b/modules/nextflow/src/main/groovy/nextflow/script/ScriptTokens.groovy
index 8edabdacb3..c7d38a1b7c 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/ScriptTokens.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/ScriptTokens.groovy
@@ -36,10 +36,10 @@ class TokenVar {
 }
 
 /**
- *  A token used by the DSL to identify a 'file' declaration in a 'set' parameter, for example:
+ *  A token used by the DSL to identify a 'file' declaration in a 'tuple' parameter, for example:
  *      <pre>
  *      input:
- *      set( file('name'), ... )
+ *      tuple( file('name'), ... )
  *      </pre>
  *
  */
@@ -49,10 +49,10 @@ class TokenFileCall {
 }
 
 /**
- *  A token used by the DSL to identify a 'path' declaration in a 'set' parameter, for example:
+ *  A token used by the DSL to identify a 'path' declaration in a 'tuple' parameter, for example:
  *      <pre>
  *      input:
- *      set( path('name'), ... )
+ *      tuple( path('name'), ... )
  *      </pre>
  *
  */
@@ -99,7 +99,7 @@ class TokenStdoutCall { }
  * Token used by the DSL to identify a environment variable declaration, like this
  *     <pre>
  *     input:
- *     set( env(X), ... )
+ *     tuple( env(X), ... )
  *     <pre>
  */
 @ToString
@@ -114,10 +114,10 @@ class TokenEnvCall {
  * This class is used to identify a 'val' when used like in this example:
  * <pre>
  *  input:
- *  set ( val(x), ...  )
+ *  tuple ( val(x), ...  )
  *
  *  output:
- *  set( val(y), ...  )
+ *  tuple( val(y), ...  )
  *
  * </pre>
  *
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/params/BaseInParam.groovy b/modules/nextflow/src/main/groovy/nextflow/script/params/BaseInParam.groovy
index 12d396414f..efe613805b 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/params/BaseInParam.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/params/BaseInParam.groovy
@@ -80,23 +80,9 @@ abstract class BaseInParam extends BaseParam implements InParam {
             return CH.getReadChannel(value)
         }
 
-        if( NF.isDsl2() ) {
-            final result = CH.value()
-            result.bind(value)
-            return result
-        }
-
-        // wrap any collections with a DataflowQueue
-        if( value instanceof Collection ) {
-            return CH.emitAndClose(CH.queue(), value)
-        }
-
-        // wrap any array with a DataflowQueue
-        if ( value && value.class.isArray() ) {
-            return CH.emitAndClose(CH.queue(), value as Collection)
-        }
-
-        value!=null ? CH.value(value) : CH.value() 
+        final result = CH.value()
+        result.bind(value)
+        return result
     }
 
 
@@ -169,13 +155,6 @@ abstract class BaseInParam extends BaseParam implements InParam {
         throw new IllegalArgumentException(message)
     }
 
-    BaseInParam from( def obj ) {
-        if( NF.isDsl2() )
-            throw new ScriptRuntimeException("Process clause `from` should not be provided when using DSL 2")
-        setFrom(obj)
-        return this
-    }
-
     void setFrom( obj ) {
         checkFromNotNull(obj)
         fromObject = obj
@@ -189,22 +168,6 @@ abstract class BaseInParam extends BaseParam implements InParam {
         throw new IllegalStateException("Missing input channel")
     }
 
-    BaseInParam from( Object... obj ) {
-
-        def normalize = obj.collect {
-            if( it instanceof DataflowReadChannel )
-                throw new IllegalArgumentException("Multiple channels are not allowed on 'from' input declaration")
-
-            if( it instanceof Closure )
-                return it.call()
-            else
-                it
-        }
-
-        fromObject = normalize as List
-        return this
-    }
-
     def decodeInputs( List inputs ) {
         final UNDEF = -1 as short
         def value = inputs[index]
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/params/BaseOutParam.groovy b/modules/nextflow/src/main/groovy/nextflow/script/params/BaseOutParam.groovy
index 686a952755..366110ded4 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/params/BaseOutParam.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/params/BaseOutParam.groovy
@@ -20,12 +20,10 @@ import groovy.transform.PackageScope
 import groovy.util.logging.Slf4j
 import groovyx.gpars.dataflow.DataflowWriteChannel
 import nextflow.NF
-import nextflow.exception.ScriptRuntimeException
 import nextflow.extension.CH
 import nextflow.script.ProcessConfig
 import nextflow.script.TokenVar
 import nextflow.util.ConfigHelper
-
 /**
  * Model a process generic output parameter
  *
@@ -62,10 +60,8 @@ abstract class BaseOutParam extends BaseParam implements OutParam {
 
     void lazyInit() {
 
-        if( intoObj instanceof TokenVar[] ) {
-            if( NF.dsl2 )
-                throw new IllegalArgumentException("Not a valid output channel argument: $intoObj")
-            for( def it : intoObj ) { lazyInitImpl(it) }
+        if( intoObj instanceof TokenVar || intoObj instanceof TokenVar[] ) {
+            throw new IllegalArgumentException("Not a valid output channel argument: $intoObj")
         }
         else if( intoObj != null ) {
             lazyInitImpl(intoObj)
@@ -83,14 +79,9 @@ abstract class BaseOutParam extends BaseParam implements OutParam {
 
     @PackageScope
     void lazyInitImpl( def target ) {
-        def channel = null
-        if( target instanceof TokenVar ) {
-            assert !NF.dsl2
-            channel = outputValToChannel(target.name)
-        }
-        else if( target != null ) {
-            channel = outputValToChannel(target)
-        }
+        final channel = (target != null)
+            ? outputValToChannel(target)
+            : null
 
         if( channel ) {
             outChannels.add(channel)
@@ -156,20 +147,6 @@ abstract class BaseOutParam extends BaseParam implements OutParam {
         return this
     }
 
-    BaseOutParam into( def value ) {
-        if( NF.dsl2 )
-            throw new ScriptRuntimeException("Process clause `into` should not be provided when using DSL 2")
-        this.intoObj = value
-        return this
-    }
-
-    BaseOutParam into( TokenVar... vars ) {
-        if( NF.dsl2 )
-            throw new ScriptRuntimeException("Process clause `into` should not be provided when using DSL 2")
-        intoObj = vars
-        return this
-    }
-
     void setInto( Object obj ) {
         intoObj = obj
     }
@@ -179,12 +156,6 @@ abstract class BaseOutParam extends BaseParam implements OutParam {
         return outChannels ? outChannels.get(0) : null
     }
 
-    @Deprecated
-    List<DataflowWriteChannel> getOutChannels() {
-        init()
-        return outChannels
-    }
-
     String getName() {
         if( nameObj != null )
             return nameObj.toString()
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/params/FileInParam.groovy b/modules/nextflow/src/main/groovy/nextflow/script/params/FileInParam.groovy
index 8bebf83d70..397a759b15 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/params/FileInParam.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/params/FileInParam.groovy
@@ -55,13 +55,6 @@ class FileInParam extends BaseInParam implements ArityParam, PathQualifier {
             return this
         }
 
-        // the ability to pass a closure as file name has been replaced by
-        // lazy gstring -- this should be deprecated
-        if( obj instanceof Closure && !NF.dsl2 ) {
-            filePattern = obj
-            return this
-        }
-
         throw new IllegalArgumentException()
     }
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/params/InParam.groovy b/modules/nextflow/src/main/groovy/nextflow/script/params/InParam.groovy
index 35c95ecac0..d41e3c5c28 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/params/InParam.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/params/InParam.groovy
@@ -31,10 +31,6 @@ interface InParam extends Cloneable {
 
     Object getRawChannel()
 
-    InParam from( Object value )
-
-    InParam from( Object... values )
-
     short index
 
     short mapIndex
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/params/OutParam.groovy b/modules/nextflow/src/main/groovy/nextflow/script/params/OutParam.groovy
index 7f17a5ea3b..3f4977974d 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/params/OutParam.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/params/OutParam.groovy
@@ -31,17 +31,6 @@ interface OutParam extends Cloneable {
      */
     String getName()
 
-    /**
-     * Defines the channel to which bind the output(s) in the script context
-     *
-     * @param value It can be a string representing a channel variable name in the script context. If
-     *      the variable does not exist it creates a {@code DataflowVariable} in the script with that name.
-     *      If the specified {@code value} is a {@code DataflowWriteChannel} object, use this object
-     *      as the output channel
-     * @return
-     */
-    OutParam into( def value )
-
     /**
      * @return The output channel instance
      */
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/params/TupleInParam.groovy b/modules/nextflow/src/main/groovy/nextflow/script/params/TupleInParam.groovy
index fadd87cdff..6255954eec 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/params/TupleInParam.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/params/TupleInParam.groovy
@@ -35,7 +35,7 @@ class TupleInParam extends BaseInParam {
 
     protected List<BaseInParam> inner = []
 
-    @Override String getTypeName() { 'set' }
+    @Override String getTypeName() { 'tuple' }
 
     List<BaseInParam> getInner() { inner }
 
diff --git a/modules/nextflow/src/test/groovy/nextflow/ast/NextflowDSLImplTest.groovy b/modules/nextflow/src/test/groovy/nextflow/ast/NextflowDSLImplTest.groovy
index 3305d23121..a8c89e4266 100644
--- a/modules/nextflow/src/test/groovy/nextflow/ast/NextflowDSLImplTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/ast/NextflowDSLImplTest.groovy
@@ -1,24 +1,34 @@
 package nextflow.ast
 
+import nextflow.Session
 import nextflow.script.BaseScript
 import nextflow.script.ScriptMeta
+import nextflow.script.ScriptParser
 import org.codehaus.groovy.control.CompilerConfiguration
 import org.codehaus.groovy.control.MultipleCompilationErrorsException
 import org.codehaus.groovy.control.customizers.ASTTransformationCustomizer
-import test.BaseSpec
+import test.Dsl2Spec
+import test.MockExecutorFactory
 /**
  *
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
  */
-class NextflowDSLImplTest extends BaseSpec {
+class NextflowDSLImplTest extends Dsl2Spec {
 
-    def 'should fetch method names' () {
-
-        given:
+    def createCompilerConfig() {
         def config = new CompilerConfiguration()
         config.setScriptBaseClass(BaseScript.class.name)
         config.addCompilationCustomizers( new ASTTransformationCustomizer(NextflowDSL))
 
+        return config
+    }
+
+
+    def 'should fetch method names' () {
+
+        given:
+        def config = createCompilerConfig()
+
         def SCRIPT = '''
             def foo() { 
                 return 0 
@@ -35,8 +45,8 @@ class NextflowDSLImplTest extends BaseSpec {
             process alpha {
               /hello/
             }
-
         '''
+
         when:
         new GroovyShell(config).parse(SCRIPT)
         then:
@@ -45,12 +55,9 @@ class NextflowDSLImplTest extends BaseSpec {
 
     def 'should not allow duplicate processes' () {
         given:
-        def config = new CompilerConfiguration()
-        config.setScriptBaseClass(BaseScript.class.name)
-        config.addCompilationCustomizers( new ASTTransformationCustomizer(NextflowDSL))
+        def config = createCompilerConfig()
 
         def SCRIPT = '''
-                    
             process alpha {
               /hello/
             }
@@ -58,7 +65,6 @@ class NextflowDSLImplTest extends BaseSpec {
             process alpha {
               /world/
             }
-
         '''
 
         when:
@@ -71,12 +77,9 @@ class NextflowDSLImplTest extends BaseSpec {
 
     def 'should not allow duplicate workflow' () {
         given:
-        def config = new CompilerConfiguration()
-        config.setScriptBaseClass(BaseScript.class.name)
-        config.addCompilationCustomizers( new ASTTransformationCustomizer(NextflowDSL))
+        def config = createCompilerConfig()
 
         def SCRIPT = '''
-                    
             workflow alpha {
               /hello/
             }
@@ -84,7 +87,6 @@ class NextflowDSLImplTest extends BaseSpec {
             workflow alpha {
               /world/
             }
-
         '''
 
         when:
@@ -97,29 +99,24 @@ class NextflowDSLImplTest extends BaseSpec {
     def 'should throw illegal name exception' () {
 
         given:
-        def config = new CompilerConfiguration()
-        config.setScriptBaseClass(BaseScript.class.name)
-        config.addCompilationCustomizers( new ASTTransformationCustomizer(NextflowDSL))
+        def config = createCompilerConfig()
 
         when:
         def SCRIPT = '''
             workflow 'foo:bar' {
               /hello/
             }
-
         '''
         new GroovyShell(config).parse(SCRIPT)
         then:
         def e = thrown(MultipleCompilationErrorsException)
         e.message.contains 'Process and workflow names cannot contain colon character'
 
-
         when:
         SCRIPT = '''
             process 'foo:bar' {
               /hello/
             }
-
         '''
         new GroovyShell(config).parse(SCRIPT)
         then:
@@ -129,12 +126,12 @@ class NextflowDSLImplTest extends BaseSpec {
 
     def 'should set process name in the script meta' () {
         given:
-        def config = new CompilerConfiguration()
-        config.setScriptBaseClass(BaseScript.class.name)
-        config.addCompilationCustomizers( new ASTTransformationCustomizer(NextflowDSL))
+        def session = new Session()
+        session.executorFactory = new MockExecutorFactory()
+        and:
+        def parser = new ScriptParser(session)
 
         def SCRIPT = '''
-                    
             process alpha {
               /hello/
             }
@@ -142,14 +139,16 @@ class NextflowDSLImplTest extends BaseSpec {
             process beta {
               /world/
             }
-
+            
+            workflow {
+              alpha(); beta()
+            }
         '''
 
         when:
-        def script = new GroovyShell(config).parse(SCRIPT)
+        parser.runScript(SCRIPT)
         then:
-        ScriptMeta.get(script).getDsl1ProcessNames() == ['alpha', 'beta']
-        ScriptMeta.get(script).getProcessNames() == ['alpha', 'beta'] as Set
+        ScriptMeta.get(parser.getScript()).getProcessNames() == ['alpha', 'beta'] as Set
     }
 
 }
diff --git a/modules/nextflow/src/test/groovy/nextflow/script/IncludeDefTest.groovy b/modules/nextflow/src/test/groovy/nextflow/script/IncludeDefTest.groovy
index 510ec22ce7..01b1b83164 100644
--- a/modules/nextflow/src/test/groovy/nextflow/script/IncludeDefTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/script/IncludeDefTest.groovy
@@ -168,6 +168,7 @@ class IncludeDefTest extends Specification {
         }
     }
 
+    @Unroll
     def 'should add includes' () {
         given:
         def binding = new ScriptBinding([params: [foo:1, bar:2]])
@@ -186,14 +187,12 @@ class IncludeDefTest extends Specification {
 
 
         where:
-        INCLUDE                                         | PATH          | NAME      | ALIAS     | PARAMS
-        "include 'some/path'"                           | 'some/path'   | null      | null      | null
-        "include ALPHA from 'modules/path'"             | 'modules/path'| 'ALPHA'   | null      | null
-        "include ALPHA as BRAVO from 'modules/x'"       | 'modules/x'   | 'ALPHA'   | 'BRAVO'   | null
-        "include 'modules/1' params(a:1, b:2)"          | 'modules/1'   | null      | null      | [a:1, b:2]
-        "include DELTA from 'abc' params(x:1)"          | 'abc'         | 'DELTA'   | null      | [x:1]
-        "include GAMMA as FOO from 'm1' params(p:2)"    | 'm1'          | 'GAMMA'   | 'FOO'     | [p:2]
-        "include GAMMA as FOO from 'm1' params([:])"    | 'm1'          | 'GAMMA'   | 'FOO'     | [:]
+        INCLUDE                                          | PATH          | NAME      | ALIAS     | PARAMS
+        "include { ALPHA } from 'modules/path'"          | 'modules/path'| 'ALPHA'   | null      | null
+        "include { ALPHA as BRAVO } from 'modules/x'"    | 'modules/x'   | 'ALPHA'   | 'BRAVO'   | null
+        "include { DELTA } from 'abc' params(x:1)"       | 'abc'         | 'DELTA'   | null      | [x:1]
+        "include { GAMMA as FOO } from 'm1' params(p:2)" | 'm1'          | 'GAMMA'   | 'FOO'     | [p:2]
+        "include { GAMMA as FOO } from 'm1' params([:])" | 'm1'          | 'GAMMA'   | 'FOO'     | [:]
 
     }
 
diff --git a/modules/nextflow/src/test/groovy/nextflow/script/ProcessConfigTest.groovy b/modules/nextflow/src/test/groovy/nextflow/script/ProcessConfigTest.groovy
index 5fc7f31367..a9d8a108d8 100644
--- a/modules/nextflow/src/test/groovy/nextflow/script/ProcessConfigTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/script/ProcessConfigTest.groovy
@@ -179,7 +179,7 @@ class ProcessConfigTest extends Specification {
 
         when:
         config._in_file([infile:'filename.fa'])
-        config._in_val('x') .from(1)
+        config._in_val('x').setFrom(1)
         config._in_stdin()
 
         then:
@@ -208,9 +208,9 @@ class ProcessConfigTest extends Specification {
 
         when:
         config._out_stdout()
-        config._out_file(new TokenVar('file1')).into('ch1')
-        config._out_file(new TokenVar('file2')).into('ch2')
-        config._out_file(new TokenVar('file3')).into('ch3')
+        config._out_file(new TokenVar('file1')).setInto('ch1')
+        config._out_file(new TokenVar('file2')).setInto('ch2')
+        config._out_file(new TokenVar('file3')).setInto('ch3')
 
         then:
         config.outputs.size() == 4
diff --git a/modules/nextflow/src/test/groovy/nextflow/script/ProcessDefTest.groovy b/modules/nextflow/src/test/groovy/nextflow/script/ProcessDefTest.groovy
index d008e29491..6b8fc4805a 100644
--- a/modules/nextflow/src/test/groovy/nextflow/script/ProcessDefTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/script/ProcessDefTest.groovy
@@ -1,54 +1,13 @@
 package nextflow.script
 
-import spock.lang.Specification
-
 import nextflow.Session
-import nextflow.ast.NextflowDSL
-import org.codehaus.groovy.control.CompilerConfiguration
-import org.codehaus.groovy.control.customizers.ASTTransformationCustomizer
-import test.MockSession
+import spock.lang.Specification
 /**
  *
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
  */
 class ProcessDefTest extends Specification {
 
-    def 'should define processes' () {
-
-        given:
-        def session = new MockSession()
-        def binding = new ScriptBinding(session)
-        def config = new CompilerConfiguration()
-        config.setScriptBaseClass(BaseScript.class.name)
-        config.addCompilationCustomizers( new ASTTransformationCustomizer(NextflowDSL))
-
-        def SCRIPT = '''
-            
-            process foo {
-              input: val data 
-              output: val result
-              exec:
-                result = "$data mundo"
-            }     
-            
-            process bar {
-                input: val data 
-                output: val result
-                exec: 
-                  result = data.toUpperCase()
-            }   
-            
-        '''
-
-        when:
-        def script = (BaseScript)new GroovyShell(binding,config).parse(SCRIPT)
-
-        then:
-        ScriptMeta.get(script).getProcessNames() == ['foo','bar'] as Set
-
-    }
-
-
     def 'should clone a process with a new name '() {
 
         given:

From 6a0626f72455dfdef4135a119f48c3950bc6d9c6 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Thu, 2 Nov 2023 05:50:21 +0100
Subject: [PATCH 244/350] Add note about local executor and enforcing resource
 limits (#4468)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 docs/executor.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/docs/executor.md b/docs/executor.md
index a14d867146..0f50eff6ae 100644
--- a/docs/executor.md
+++ b/docs/executor.md
@@ -328,6 +328,10 @@ The `local` executor is used by default. It runs the pipeline processes on the c
 
 The `local` executor is useful for developing and testing a pipeline script on your computer, before switching to a cluster or cloud environment with production data.
 
+:::{note}
+While the `local` executor limits the number of concurrent tasks based on requested vs available resources, it does not enforce task resource requests. In other words, it is possible for a local task to use more CPUs and memory than it requested, in which case it may starve other tasks. An exception to this behavior is when using {ref}`container-docker` or {ref}`container-podman` containers, in which case the resource requests are enforced by the container runtime.
+:::
+
 (lsf-executor)=
 
 ## LSF

From 27d132f3c7ad1af903354819ebb5d657cefbdb0c Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Thu, 2 Nov 2023 18:53:05 +0100
Subject: [PATCH 245/350] Fix google batch network/subnetwork docs (#4475)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 docs/config.md | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/docs/config.md b/docs/config.md
index 6d90a8b121..0486ab7a8e 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -789,7 +789,13 @@ The following settings are available:
 : Set the minimum CPU Platform, e.g. `'Intel Skylake'`. See [Specifying a minimum CPU Platform for VM instances](https://cloud.google.com/compute/docs/instances/specify-min-cpu-platform#specifications) (default: none).
 
 `google.batch.network`
-: Set network name to attach the VM's network interface to. The value will be prefixed with `global/networks/` unless it contains a `/`, in which case it is assumed to be a fully specified network resource URL. If unspecified, the global default network is used.
+: The URL of an existing network resource to which the VM will be attached.
+
+  You can specify the network as a full or partial URL. For example, the following are all valid URLs:
+
+  - https://www.googleapis.com/compute/v1/projects/{project}/global/networks/{network}
+  - projects/{project}/global/networks/{network}
+  - global/networks/{network}
 
 `google.batch.serviceAccountEmail`
 : Define the Google service account email to use for the pipeline execution. If not specified, the default Compute Engine service account for the project will be used.
@@ -798,7 +804,13 @@ The following settings are available:
 : When `true` enables the usage of *spot* virtual machines or `false` otherwise (default: `false`).
 
 `google.batch.subnetwork`
-: Define the name of the subnetwork to attach the instance to must be specified here, when the specified network is configured for custom subnet creation. The value is prefixed with `regions/subnetworks/` unless it contains a `/`, in which case it is assumed to be a fully specified subnetwork resource URL.
+: The URL of an existing subnetwork resource in the network to which the VM will be attached.
+
+  You can specify the subnetwork as a full or partial URL. For example, the following are all valid URLs:
+
+  - https://www.googleapis.com/compute/v1/projects/{project}/regions/{region}/subnetworks/{subnetwork}
+  - projects/{project}/regions/{region}/subnetworks/{subnetwork}
+  - regions/{region}/subnetworks/{subnetwork}
 
 `google.batch.usePrivateAddress`
 : When `true` the VM will NOT be provided with a public IP address, and only contain an internal IP. If this option is enabled, the associated job can only load docker images from Google Container Registry, and the job executable cannot use external services other than Google APIs (default: `false`).

From 8f8b09fa40ed7ef40d2f64ea70e7f695ebb31754 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Fri, 3 Nov 2023 15:32:57 +0100
Subject: [PATCH 246/350] Add support for FUSION_AWS_REGION (#4481)

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../cloud/aws/config/AwsConfig.groovy         |  7 +++
 .../cloud/aws/config/AwsS3Config.groovy       |  4 ++
 .../cloud/aws/fusion/AwsFusionEnv.groovy      |  2 +
 .../cloud/aws/nio/S3FileSystemProvider.java   |  8 +++-
 .../cloud/aws/config/AwsS3ConfigTest.groovy   | 16 +++++++
 .../aws/nio/S3FileSystemProviderTest.groovy   | 47 +++++++++++++++++++
 6 files changed, 83 insertions(+), 1 deletion(-)
 create mode 100644 plugins/nf-amazon/src/test/nextflow/cloud/aws/nio/S3FileSystemProviderTest.groovy

diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/config/AwsConfig.groovy b/plugins/nf-amazon/src/main/nextflow/cloud/aws/config/AwsConfig.groovy
index 1c7da0dd66..d1ae070bda 100644
--- a/plugins/nf-amazon/src/main/nextflow/cloud/aws/config/AwsConfig.groovy
+++ b/plugins/nf-amazon/src/main/nextflow/cloud/aws/config/AwsConfig.groovy
@@ -20,6 +20,7 @@ package nextflow.cloud.aws.config
 import java.nio.file.Path
 import java.nio.file.Paths
 
+import com.amazonaws.regions.Regions
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import nextflow.Global
@@ -80,6 +81,12 @@ class AwsConfig {
         return s3Legacy.getAwsClientConfig()
     }
 
+    String getS3GlobalRegion() {
+        return !region || !s3Config.endpoint || s3Config.endpoint.contains(".amazonaws.com")
+            ? Regions.US_EAST_1.getName()   // always use US_EAST_1 as global region for AWS endpoints
+            : region                        // for custom endpoint use the config provided region
+    }
+
     static protected String getAwsProfile0(Map env, Map<String,Object> config) {
 
         final profile = config?.profile as String
diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/config/AwsS3Config.groovy b/plugins/nf-amazon/src/main/nextflow/cloud/aws/config/AwsS3Config.groovy
index 16e5a85ee3..df6629e889 100644
--- a/plugins/nf-amazon/src/main/nextflow/cloud/aws/config/AwsS3Config.groovy
+++ b/plugins/nf-amazon/src/main/nextflow/cloud/aws/config/AwsS3Config.groovy
@@ -114,4 +114,8 @@ class AwsS3Config {
     Boolean getAnonymous() {
         return anonymous
     }
+
+    boolean isCustomEndpoint() {
+        endpoint && !endpoint.contains(".amazonaws.com")
+    }
 }
diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/fusion/AwsFusionEnv.groovy b/plugins/nf-amazon/src/main/nextflow/cloud/aws/fusion/AwsFusionEnv.groovy
index c999b29e94..4c2bcb82d4 100644
--- a/plugins/nf-amazon/src/main/nextflow/cloud/aws/fusion/AwsFusionEnv.groovy
+++ b/plugins/nf-amazon/src/main/nextflow/cloud/aws/fusion/AwsFusionEnv.groovy
@@ -46,6 +46,8 @@ class AwsFusionEnv implements FusionEnv {
         }
         if( endpoint )
             result.AWS_S3_ENDPOINT = endpoint
+        if( awsConfig.region && awsConfig.s3Config.isCustomEndpoint() )
+            result.FUSION_AWS_REGION = awsConfig.region
         if( awsConfig.s3Config.storageEncryption )
             result.FUSION_AWS_SERVER_SIDE_ENCRYPTION = awsConfig.s3Config.storageEncryption
         if( awsConfig.s3Config.storageKmsKeyId )
diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3FileSystemProvider.java b/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3FileSystemProvider.java
index 76bd7d3c87..b376ba7532 100644
--- a/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3FileSystemProvider.java
+++ b/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3FileSystemProvider.java
@@ -836,7 +836,7 @@ protected S3FileSystem createFileSystem(URI uri, AwsConfig awsConfig) {
 
 		final String bucketName = S3Path.bucketName(uri);
 		final boolean global = bucketName!=null;
-		final AwsClientFactory factory = new AwsClientFactory(awsConfig, Regions.US_EAST_1.getName());
+		final AwsClientFactory factory = new AwsClientFactory(awsConfig, globalRegion(awsConfig));
 		client = new S3Client(factory.getS3Client(clientConfig, global));
 
 		// set the client acl
@@ -852,6 +852,12 @@ protected S3FileSystem createFileSystem(URI uri, AwsConfig awsConfig) {
 		return new S3FileSystem(this, client, uri, props);
 	}
 
+    protected String globalRegion(AwsConfig awsConfig) {
+        return awsConfig.getRegion() != null && awsConfig.getS3Config().isCustomEndpoint()
+                ? awsConfig.getRegion()
+                : Regions.US_EAST_1.getName();
+    }
+
 	protected String getProp(Properties props, String... keys) {
 		for( String k : keys ) {
 			if( props.containsKey(k) ) {
diff --git a/plugins/nf-amazon/src/test/nextflow/cloud/aws/config/AwsS3ConfigTest.groovy b/plugins/nf-amazon/src/test/nextflow/cloud/aws/config/AwsS3ConfigTest.groovy
index 907e211c14..bd786bd849 100644
--- a/plugins/nf-amazon/src/test/nextflow/cloud/aws/config/AwsS3ConfigTest.groovy
+++ b/plugins/nf-amazon/src/test/nextflow/cloud/aws/config/AwsS3ConfigTest.groovy
@@ -39,6 +39,7 @@ class AwsS3ConfigTest extends Specification {
         !client.s3Acl
         !client.pathStyleAccess
         !client.anonymous
+        !client.isCustomEndpoint()
     }
 
     def 'should set config' () {
@@ -139,4 +140,19 @@ class AwsS3ConfigTest extends Specification {
         SysEnv.pop()
 
     }
+
+    @Unroll
+    def 'should check is custom endpoint' () {
+        given:
+        def config = new AwsS3Config(CONFIG)
+
+        expect:
+        config.isCustomEndpoint() == EXPECTED
+
+        where:
+        EXPECTED    | CONFIG
+        false       | [:]
+        false       | [endpoint: 'https://s3.us-east-2.amazonaws.com']
+        true        | [endpoint: 'https://foo.com']
+    }
 }
diff --git a/plugins/nf-amazon/src/test/nextflow/cloud/aws/nio/S3FileSystemProviderTest.groovy b/plugins/nf-amazon/src/test/nextflow/cloud/aws/nio/S3FileSystemProviderTest.groovy
new file mode 100644
index 0000000000..032350fe05
--- /dev/null
+++ b/plugins/nf-amazon/src/test/nextflow/cloud/aws/nio/S3FileSystemProviderTest.groovy
@@ -0,0 +1,47 @@
+/*
+ * Copyright 2013-2023, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package nextflow.cloud.aws.nio
+
+import nextflow.cloud.aws.config.AwsConfig
+import spock.lang.Specification
+import spock.lang.Unroll
+
+/**
+ *
+ * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
+ */
+class S3FileSystemProviderTest extends Specification {
+
+    @Unroll
+    def 'should get global region' () {
+        given:
+        def provider = Spy(S3FileSystemProvider)
+
+        expect:
+        provider.globalRegion(new AwsConfig(CONFIG)) == EXPECTED
+
+        where:
+        EXPECTED    | CONFIG
+        'us-east-1' | [:]
+        'us-east-1' | [region:'foo']
+        'us-east-1' | [region:'foo', client:[endpoint: 'http://s3.us-east-2.amazonaws.com']]
+        'foo'       | [region:'foo', client:[endpoint: 'http://bar.com']]        
+
+    }
+
+}

From f5362a7b067173a29d684663df22bb48fbbf5659 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Mon, 6 Nov 2023 18:50:52 +0100
Subject: [PATCH 247/350] Add support for Singularity OCI mode (#4440)

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Dr Marco Claudio De La Pierre <marco.delapierre@gmail.com>
Co-authored-by: Dr Marco Claudio De La Pierre <marco.delapierre@gmail.com>
---
 docs/config.md                                |  6 ++++
 .../nextflow/container/ContainerConfig.groovy |  4 +++
 .../container/ContainerHandler.groovy         |  4 ++-
 .../container/SingularityBuilder.groovy       | 15 +++++++++-
 .../executor/BashWrapperBuilder.groovy        |  8 +++--
 .../container/ContainerConfigTest.groovy      | 21 ++++++++++++++
 .../container/ContainerHandlerTest.groovy     | 29 +++++++++++--------
 .../container/SingularityBuilderTest.groovy   |  5 ++++
 .../executor/BashWrapperBuilderTest.groovy    | 28 ++++++++++++++++++
 plugins/nf-wave/build.gradle                  |  2 +-
 .../resolver/WaveContainerResolver.groovy     | 14 +++++----
 .../seqera/wave/plugin/WaveClientTest.groovy  |  3 ++
 12 files changed, 116 insertions(+), 23 deletions(-)

diff --git a/docs/config.md b/docs/config.md
index 0486ab7a8e..f271f38a2d 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -1347,6 +1347,12 @@ The following settings are available:
 `singularity.noHttps`
 : Pull the Singularity image with http protocol (default: `false`).
 
+`singularity.oci`
+: :::{versionadded} 23.11.0-edge
+  :::
+: Enable OCI-mode the allows the use of native OCI-compatible containers with Singularity. See [Singularity documentation](https://docs.sylabs.io/guides/4.0/user-guide/oci_runtime.html#oci-mode) for more details and requirements (default: `false`).
+
+
 `singularity.pullTimeout`
 : The amount of time the Singularity pull can last, exceeding which the process is terminated (default: `20 min`).
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/container/ContainerConfig.groovy b/modules/nextflow/src/main/groovy/nextflow/container/ContainerConfig.groovy
index 8b93ac5cfe..78e8caef71 100644
--- a/modules/nextflow/src/main/groovy/nextflow/container/ContainerConfig.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/container/ContainerConfig.groovy
@@ -55,6 +55,10 @@ class ContainerConfig extends LinkedHashMap {
         get('engine')
     }
 
+    boolean singularityOciMode() {
+        getEngine()=='singularity' && get('oci')?.toString() == 'true'
+    }
+
     List<String> getEnvWhitelist() {
         def result = get('envWhitelist')
         if( !result )
diff --git a/modules/nextflow/src/main/groovy/nextflow/container/ContainerHandler.groovy b/modules/nextflow/src/main/groovy/nextflow/container/ContainerHandler.groovy
index aafa544913..524ce6d9e3 100644
--- a/modules/nextflow/src/main/groovy/nextflow/container/ContainerHandler.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/container/ContainerHandler.groovy
@@ -67,6 +67,8 @@ class ContainerHandler {
             final normalizedImageName = normalizeSingularityImageName(imageName)
             if( !config.isEnabled() || !normalizedImageName )
                 return normalizedImageName
+            if( normalizedImageName.startsWith('docker://') && config.singularityOciMode() )
+                return normalizedImageName
             final requiresCaching = normalizedImageName =~ IMAGE_URL_PREFIX
             if( ContainerInspectMode.active() && requiresCaching )
                 return imageName
@@ -192,7 +194,7 @@ class ContainerHandler {
     }
 
 
-    public static final Pattern IMAGE_URL_PREFIX = ~/^[^\/:\. ]+:\/\/(.*)/
+    public static final Pattern IMAGE_URL_PREFIX = ~/^[^\/:. ]+:\/\/(.*)/
 
     /**
      * Normalize Singularity image name resolving the absolute path or
diff --git a/modules/nextflow/src/main/groovy/nextflow/container/SingularityBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/container/SingularityBuilder.groovy
index 5c2d74abfc..6f69c8e116 100644
--- a/modules/nextflow/src/main/groovy/nextflow/container/SingularityBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/container/SingularityBuilder.groovy
@@ -39,6 +39,8 @@ class SingularityBuilder extends ContainerBuilder<SingularityBuilder> {
 
     private String runCmd0
 
+    private Boolean oci
+
     SingularityBuilder(String name) {
         this.image = name
         this.homeMount = defaultHomeMount()
@@ -92,6 +94,9 @@ class SingularityBuilder extends ContainerBuilder<SingularityBuilder> {
         if( params.containsKey('readOnlyInputs') )
             this.readOnlyInputs = params.readOnlyInputs?.toString() == 'true'
 
+        if( params.oci!=null )
+            oci = params.oci.toString() == 'true'
+
         return this
     }
 
@@ -117,9 +122,12 @@ class SingularityBuilder extends ContainerBuilder<SingularityBuilder> {
         if( !homeMount )
             result << '--no-home '
 
-        if( newPidNamespace )
+        if( newPidNamespace && !oci )
             result << '--pid '
 
+        if( oci != null )
+            result << (oci ? '--oci ' : '--no-oci ')
+
         if( autoMounts ) {
             makeVolumes(mounts, result)
         }
@@ -145,6 +153,11 @@ class SingularityBuilder extends ContainerBuilder<SingularityBuilder> {
     protected CharSequence appendEnv(StringBuilder result) {
         makeEnv('TMP',result) .append(' ')
         makeEnv('TMPDIR',result) .append(' ')
+        // add magic variables required by singularity to run in OCI-mode
+        if( oci ) {
+            result .append('${XDG_RUNTIME_DIR:+XDG_RUNTIME_DIR="$XDG_RUNTIME_DIR"} ')
+            result .append('${DBUS_SESSION_BUS_ADDRESS:+DBUS_SESSION_BUS_ADDRESS="$DBUS_SESSION_BUS_ADDRESS"} ')
+        }
         super.appendEnv(result)
     }
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
index bc21186d1a..d53ad6aea1 100644
--- a/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
@@ -480,8 +480,12 @@ class BashWrapperBuilder {
          */
         if( containerBuilder ) {
             String cmd = env ? 'eval $(nxf_container_env); ' + launcher : launcher
-            if( env && !containerConfig.entrypointOverride() ) {
-                if( containerBuilder instanceof SingularityBuilder )
+            // wrap the command with an extra bash invocation either :
+            // - to propagate the container environment or
+            // - to change in the task work directory as required by singularity
+            final needChangeTaskWorkDir = containerBuilder instanceof SingularityBuilder
+            if( (env || needChangeTaskWorkDir) && !containerConfig.entrypointOverride() ) {
+                if( needChangeTaskWorkDir )
                     cmd = 'cd $PWD; ' + cmd
                 cmd = "/bin/bash -c \"$cmd\""
             }
diff --git a/modules/nextflow/src/test/groovy/nextflow/container/ContainerConfigTest.groovy b/modules/nextflow/src/test/groovy/nextflow/container/ContainerConfigTest.groovy
index 6c87437eb7..99ed6439fe 100644
--- a/modules/nextflow/src/test/groovy/nextflow/container/ContainerConfigTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/container/ContainerConfigTest.groovy
@@ -61,6 +61,27 @@ class ContainerConfigTest extends Specification {
 
     }
 
+
+    def 'should validate oci mode' () {
+
+        when:
+        def cfg = new ContainerConfig(OPTS)
+        then:
+        cfg.singularityOciMode() == EXPECTED
+
+        where:
+        OPTS                                | EXPECTED
+        [:]                                 | false
+        [oci:false]                         | false
+        [oci:true]                          | false
+        [engine:'apptainer', oci:true]      | false
+        [engine:'docker', oci:true]         | false
+        [engine:'singularity']              | false
+        [engine:'singularity', oci:false]   | false
+        [engine:'singularity', oci:true]    | true
+
+    }
+
     def 'should get fusion options' () {
         when:
         def cfg = new ContainerConfig(OPTS)
diff --git a/modules/nextflow/src/test/groovy/nextflow/container/ContainerHandlerTest.groovy b/modules/nextflow/src/test/groovy/nextflow/container/ContainerHandlerTest.groovy
index 43129de399..7459c9de21 100644
--- a/modules/nextflow/src/test/groovy/nextflow/container/ContainerHandlerTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/container/ContainerHandlerTest.groovy
@@ -200,11 +200,12 @@ class ContainerHandlerTest extends Specification {
         result == 'shifter://image'
             
     }
+
     @Unroll
     def 'test normalize method for singularity' () {
         given:
         def BASE = Paths.get('/abs/path/')
-        def handler = Spy(new ContainerHandler(engine: 'singularity', enabled: true, baseDir: BASE))
+        def handler = Spy(new ContainerHandler(engine: 'singularity', enabled: true, oci:OCI, baseDir: BASE))
 
         when:
         def result = handler.normalizeImageName(IMAGE)
@@ -215,17 +216,21 @@ class ContainerHandlerTest extends Specification {
         result == EXPECTED
 
         where:
-        IMAGE                                       | NORMALIZED                                        | X           | EXPECTED
-        null                                        | null                                              |           0 | null
-        ''                                          | null                                              |           0 | null
-        '/abs/path/bar.img'                         | '/abs/path/bar.img'                               |           0 | '/abs/path/bar.img'
-        '/abs/path bar.img'                         | '/abs/path bar.img'                               |           0 | '/abs/path\\ bar.img'
-        'file:///abs/path/bar.img'                  | '/abs/path/bar.img'                               |           0 | '/abs/path/bar.img'
-        'foo.img'                                   | Paths.get('foo.img').toAbsolutePath().toString() |       0 | Paths.get('foo.img').toAbsolutePath().toString()
-        'shub://busybox'                            | 'shub://busybox'                                  |           1 | '/path/to/busybox'
-        'docker://library/busybox'                  | 'docker://library/busybox'                        |           1 | '/path/to/busybox'
-        'foo'                                       | 'docker://foo'                                    |           1 | '/path/to/foo'
-        'library://pditommaso/foo/bar.sif:latest'   | 'library://pditommaso/foo/bar.sif:latest'         |           1 | '/path/to/foo-bar-latest.img'
+        IMAGE                                       | NORMALIZED                                        | OCI   | X           | EXPECTED
+        null                                        | null                                              | false |           0 | null
+        ''                                          | null                                              | false |           0 | null
+        '/abs/path/bar.img'                         | '/abs/path/bar.img'                               | false |           0 | '/abs/path/bar.img'
+        '/abs/path bar.img'                         | '/abs/path bar.img'                               | false |           0 | '/abs/path\\ bar.img'
+        'file:///abs/path/bar.img'                  | '/abs/path/bar.img'                               | false |           0 | '/abs/path/bar.img'
+        'foo.img'                                   | Paths.get('foo.img').toAbsolutePath().toString()  | false |           0 | Paths.get('foo.img').toAbsolutePath().toString()
+        'shub://busybox'                            | 'shub://busybox'                                  | false |           1 | '/path/to/busybox'
+        'docker://library/busybox'                  | 'docker://library/busybox'                        | false |           1 | '/path/to/busybox'
+        'foo'                                       | 'docker://foo'                                    | false |           1 | '/path/to/foo'
+        'library://pditommaso/foo/bar.sif:latest'   | 'library://pditommaso/foo/bar.sif:latest'         | false |           1 | '/path/to/foo-bar-latest.img'
+        and:
+        'docker://library/busybox'                  | 'docker://library/busybox'                        | true  |           0 | 'docker://library/busybox'
+        'shub://busybox'                            | 'shub://busybox'                                  | true  |           1 | '/path/to/busybox'
+
     }
 
     def 'should not invoke caching when engine is disabled' () {
diff --git a/modules/nextflow/src/test/groovy/nextflow/container/SingularityBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/container/SingularityBuilderTest.groovy
index 661f459a29..9aad74ffb9 100644
--- a/modules/nextflow/src/test/groovy/nextflow/container/SingularityBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/container/SingularityBuilderTest.groovy
@@ -154,6 +154,11 @@ class SingularityBuilderTest extends Specification {
                 .build()
                 .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home ubuntu'
 
+        new SingularityBuilder('ubuntu')
+            .params(oci: true)
+            .build()
+            .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} ${XDG_RUNTIME_DIR:+XDG_RUNTIME_DIR="$XDG_RUNTIME_DIR"} ${DBUS_SESSION_BUS_ADDRESS:+DBUS_SESSION_BUS_ADDRESS="$DBUS_SESSION_BUS_ADDRESS"} singularity exec --no-home --oci -B "$PWD" ubuntu'
+
     }
 
     def 'should mount home directory if specified' () {
diff --git a/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
index 4a8c012502..03fb0616ea 100644
--- a/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
@@ -996,6 +996,20 @@ class BashWrapperBuilderTest extends Specification {
         binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
     }
 
+    def 'should create wrapper with singularity and no env'() {
+        when:
+        def binding = newBashWrapperBuilder(
+            containerEnabled: true,
+            containerImage: 'docker://ubuntu:latest',
+            environment: [:],
+            containerConfig: [enabled: true, engine: 'singularity'] as ContainerConfig ).makeBinding()
+
+        then:
+        binding.launch_cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} ${NXF_TASK_WORKDIR:+SINGULARITYENV_NXF_TASK_WORKDIR="$NXF_TASK_WORKDIR"} singularity exec --no-home --pid -B /work/dir docker://ubuntu:latest /bin/bash -c "cd $PWD; /bin/bash -ue /work/dir/.command.sh"'
+        binding.cleanup_cmd == ""
+        binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
+    }
+
     def 'should create wrapper with singularity legacy entry'() {
         when:
         def binding = newBashWrapperBuilder(
@@ -1010,6 +1024,20 @@ class BashWrapperBuilderTest extends Specification {
         binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
     }
 
+    def 'should create wrapper with singularity oci mode'() {
+        when:
+        def binding = newBashWrapperBuilder(
+            containerEnabled: true,
+            containerImage: 'docker://ubuntu:latest',
+            environment: [PATH: '/path/to/bin:$PATH', FOO: 'xxx'],
+            containerConfig: [enabled: true, engine: 'singularity', oci: true] as ContainerConfig ).makeBinding()
+
+        then:
+        binding.launch_cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} ${XDG_RUNTIME_DIR:+XDG_RUNTIME_DIR="$XDG_RUNTIME_DIR"} ${DBUS_SESSION_BUS_ADDRESS:+DBUS_SESSION_BUS_ADDRESS="$DBUS_SESSION_BUS_ADDRESS"} ${NXF_TASK_WORKDIR:+SINGULARITYENV_NXF_TASK_WORKDIR="$NXF_TASK_WORKDIR"} singularity exec --no-home --oci -B /work/dir docker://ubuntu:latest /bin/bash -c "cd $PWD; eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
+        binding.cleanup_cmd == ""
+        binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
+    }
+
     def 'should create task and container env' () {
         given:
         def ENV = [FOO: 'hello', BAR: 'hello world', PATH: '/some/path:$PATH']
diff --git a/plugins/nf-wave/build.gradle b/plugins/nf-wave/build.gradle
index f4deb73c9c..93d749fba3 100644
--- a/plugins/nf-wave/build.gradle
+++ b/plugins/nf-wave/build.gradle
@@ -36,7 +36,7 @@ dependencies {
     api 'org.apache.commons:commons-lang3:3.12.0'
     api 'com.google.code.gson:gson:2.10.1'
     api 'org.yaml:snakeyaml:2.0'
-    api 'io.seqera:wave-utils:0.7.9'
+    api 'io.seqera:wave-utils:0.8.0'
 
     testImplementation(testFixtures(project(":nextflow")))
     testImplementation "org.codehaus.groovy:groovy:3.0.19"
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/resolver/WaveContainerResolver.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/resolver/WaveContainerResolver.groovy
index a79d169b2f..28c64973f3 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/resolver/WaveContainerResolver.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/resolver/WaveContainerResolver.groovy
@@ -25,6 +25,7 @@ import groovy.util.logging.Slf4j
 import io.seqera.wave.plugin.WaveClient
 import nextflow.Global
 import nextflow.Session
+import nextflow.container.ContainerConfig
 import nextflow.container.resolver.ContainerInfo
 import nextflow.container.resolver.ContainerResolver
 import nextflow.container.resolver.DefaultContainerResolver
@@ -52,8 +53,7 @@ class WaveContainerResolver implements ContainerResolver {
         return client0 = new WaveClient( Global.session as Session )
     }
 
-    private String getContainerEngine0(TaskRun task) {
-        final config = task.getContainerConfig()
+    private String getContainerEngine0(ContainerConfig config) {
         final result = config.getEngine()
         if( result )
             return result
@@ -68,13 +68,15 @@ class WaveContainerResolver implements ContainerResolver {
             return defaultResolver.resolveImage(task, imageName)
 
         final freeze = client().config().freezeMode()
-        final engine = getContainerEngine0(task)
-        final nativeSingularityBuild = freeze && engine in SINGULARITY_LIKE
+        final config = task.getContainerConfig()
+        final engine = getContainerEngine0(config)
+        final singularityOciMode = config.singularityOciMode()
+        final singularitySpec = freeze && engine in SINGULARITY_LIKE && !singularityOciMode
         if( !imageName ) {
             // when no image name is provided the module bundle should include a
             // Dockerfile or a Conda recipe or a Spack recipe to build
             // an image on-fly with an automatically assigned name
-            return waveContainer(task, null, nativeSingularityBuild)
+            return waveContainer(task, null, singularitySpec)
         }
 
         if( engine in DOCKER_LIKE ) {
@@ -90,7 +92,7 @@ class WaveContainerResolver implements ContainerResolver {
                 return defaultResolver.resolveImage(task, imageName)
             }
             // fetch the wave container name
-            final image = waveContainer(task, imageName, nativeSingularityBuild)
+            final image = waveContainer(task, imageName, singularitySpec)
             // oras prefixed container are served directly
             if( image && image.target.startsWith("oras://") )
                 return image
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
index c0259af468..6842819bb2 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
@@ -534,6 +534,7 @@ class WaveClientTest extends Specification {
                     && micromamba install -y -n base conda-forge::procps-ng \\
                     && micromamba clean -a -y
                 USER root
+                ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
                     '''.stripIndent()
         and:
         !assets.moduleResources
@@ -572,6 +573,7 @@ class WaveClientTest extends Specification {
                     && micromamba install -y -n base conda-forge::procps-ng \\
                     && micromamba clean -a -y
                 USER root
+                ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
                     '''.stripIndent()
         and:
         !assets.moduleResources
@@ -647,6 +649,7 @@ class WaveClientTest extends Specification {
                     && micromamba install -y -n base conda-forge::procps-ng \\
                     && micromamba clean -a -y
                 USER root
+                ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
                     '''.stripIndent()
         and:
         assets.condaFile == condaFile

From f5d7246e7c73930ea7da1e53592e35455259ff36 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Wed, 8 Nov 2023 09:53:56 -0600
Subject: [PATCH 248/350] Return error if plugin version is not specified in
 offline mode (#4487)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 docs/config.md                                 |  5 ++++-
 .../main/nextflow/plugin/PluginUpdater.groovy  | 18 ++++++++++++------
 .../main/nextflow/plugin/PluginsFacade.groovy  |  2 +-
 3 files changed, 17 insertions(+), 8 deletions(-)

diff --git a/docs/config.md b/docs/config.md
index f271f38a2d..954bb43a28 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -1648,10 +1648,13 @@ The following environment variables control the configuration of the Nextflow ru
 : Allows the setting Java VM options. This is similar to `NXF_OPTS` however it's only applied the JVM running Nextflow and not to any java pre-launching commands.
 
 `NXF_OFFLINE`
-: When `true` disables the project automatic download and update from remote repositories (default: `false`).
+: When `true` prevents Nextflow from automatically downloading and updating remote project repositories (default: `false`).
 : :::{versionchanged} 23.09.0-edge
   This option also disables the automatic version check (see `NXF_DISABLE_CHECK_LATEST`).
   :::
+: :::{versionchanged} 23.11.0-edge
+  This option also prevents plugins from being downloaded. Plugin versions must be specified in offline mode, or else Nextflow will fail.
+  :::
 
 `NXF_OPTS`
 : Provides extra options for the Java and Nextflow runtime. It must be a blank separated list of `-Dkey[=value]` properties.
diff --git a/modules/nf-commons/src/main/nextflow/plugin/PluginUpdater.groovy b/modules/nf-commons/src/main/nextflow/plugin/PluginUpdater.groovy
index 4e773877af..98a5739273 100644
--- a/modules/nf-commons/src/main/nextflow/plugin/PluginUpdater.groovy
+++ b/modules/nf-commons/src/main/nextflow/plugin/PluginUpdater.groovy
@@ -224,7 +224,7 @@ class PluginUpdater extends UpdateManager {
             safeMove(dir, pluginPath)
         }
         catch (IOException e) {
-            throw new PluginRuntimeException(e, "Failed to write file '$pluginPath' to plugins folder");
+            throw new PluginRuntimeException(e, "Failed to write file '$pluginPath' to plugins folder")
         }
 
         return pluginPath
@@ -318,8 +318,14 @@ class PluginUpdater extends UpdateManager {
 
         if( version == null )
             version = getLastPluginRelease(id)?.version
-        if( !version )
-            throw new IllegalStateException("Cannot find latest version of $id plugin")
+
+        final offline = SysEnv.get('NXF_OFFLINE')=='true'
+        if( !version ) {
+            final msg = offline
+                ? "Cannot find version for $id plugin -- plugin versions MUST be specified in offline mode"
+                : "Cannot find latest version of $id plugin"
+            throw new IllegalStateException(msg)
+        }
 
         def pluginPath = pluginsStore.resolve("$id-$version")
         if( !FilesEx.exists(pluginPath) ) {
@@ -363,7 +369,7 @@ class PluginUpdater extends UpdateManager {
         // resolve the plugins
         pluginManager.resolvePlugins()
         // finally start it
-        PluginState state = pluginManager.startPlugin(id);
+        PluginState state = pluginManager.startPlugin(id)
         return PluginState.STARTED == state
     }
 
@@ -381,13 +387,13 @@ class PluginUpdater extends UpdateManager {
             throw new PluginRuntimeException("Plugin $id cannot be updated since it is not installed")
         }
 
-        PluginInfo pluginInfo = getPluginsMap().get(id);
+        PluginInfo pluginInfo = getPluginsMap().get(id)
         if (pluginInfo == null) {
             throw new PluginRuntimeException("Plugin $id does not exist in any repository")
         }
 
         if (!pluginManager.deletePlugin(id)) {
-            return false;
+            return false
         }
 
         load0(id, version)
diff --git a/modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy b/modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy
index 5af5b2d2a6..b4320d435e 100644
--- a/modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy
+++ b/modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy
@@ -55,7 +55,7 @@ class PluginsFacade implements PluginStateListener {
     PluginsFacade() {
         mode = getPluginsMode()
         root = getPluginsDir()
-        if( mode=='dev' && root.toString()=='plugins' && !isRunningFromDistArchive() )
+        if( mode==DEV_MODE && root.toString()=='plugins' && !isRunningFromDistArchive() )
             root = detectPluginsDevRoot()
         System.setProperty('pf4j.mode', mode)
     }

From 48ee3c64cafff3c8420458d613c9b19a7bc3f11f Mon Sep 17 00:00:00 2001
From: Dr Marco Claudio De La Pierre <marco.delapierre@gmail.com>
Date: Thu, 9 Nov 2023 00:50:56 +0800
Subject: [PATCH 249/350] Use consistently NXF_TASK_WORKDIR (#4484)

This commit uses `NXF_TASK_WORKDIR` env variable to change in the
task work directory when running a task in a container

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Dr Marco Claudio De La Pierre <marco.delapierre@gmail.com>
Signed-off-by: Dr Marco Claudio De La Pierre <marco.delapierre@seqera.io>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../container/CharliecloudBuilder.groovy      |  2 +-
 .../container/ContainerBuilder.groovy         |  2 +-
 .../nextflow/container/DockerBuilder.groovy   |  2 +-
 .../nextflow/container/PodmanBuilder.groovy   |  2 +-
 .../nextflow/container/SarusBuilder.groovy    |  2 +-
 .../container/SingularityBuilder.groovy       |  2 +-
 .../nextflow/container/UdockerBuilder.groovy  |  2 +-
 .../executor/BashWrapperBuilder.groovy        |  2 +-
 .../nextflow/fusion/FusionHelper.groovy       |  2 +-
 .../container/ApptainerBuilderTest.groovy     | 34 +++++-----
 .../container/CharliecloudBuilderTest.groovy  | 26 ++++----
 .../container/DockerBuilderTest.groovy        | 64 +++++++++----------
 .../container/PodmanBuilderTest.groovy        | 48 +++++++-------
 .../container/SarusBuilderTest.groovy         | 16 ++---
 .../container/SingularityBuilderTest.groovy   | 34 +++++-----
 .../container/UdockerBuilderTest.groovy       | 28 ++++----
 .../executor/BashWrapperBuilderTest.groovy    | 42 ++++++------
 .../seqera/wave/plugin/cli/WaveRunCmd.groovy  |  2 +-
 18 files changed, 156 insertions(+), 156 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/container/CharliecloudBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/container/CharliecloudBuilder.groovy
index e219cddcf4..b72aa61569 100644
--- a/modules/nextflow/src/main/groovy/nextflow/container/CharliecloudBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/container/CharliecloudBuilder.groovy
@@ -61,7 +61,7 @@ class CharliecloudBuilder extends ContainerBuilder<CharliecloudBuilder> {
     CharliecloudBuilder build(StringBuilder result) {
         assert image
 
-        result << 'ch-run --unset-env="*" -c "$PWD" --set-env '
+        result << 'ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env '
         if (!readOnlyInputs)
             result << '-w '
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/container/ContainerBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/container/ContainerBuilder.groovy
index 9f505f0a29..e552a8aaaa 100644
--- a/modules/nextflow/src/main/groovy/nextflow/container/ContainerBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/container/ContainerBuilder.groovy
@@ -295,7 +295,7 @@ abstract class ContainerBuilder<V extends ContainerBuilder> {
 
         // -- append by default the current path -- this is needed when `scratch` is set to true
         if( mountWorkDir ) {
-            result << composeVolumePath('$PWD')
+            result << composeVolumePath('$NXF_TASK_WORKDIR')
             result << ' '
         }
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/container/DockerBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/container/DockerBuilder.groovy
index 8e5e037822..edc5fc9cb0 100644
--- a/modules/nextflow/src/main/groovy/nextflow/container/DockerBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/container/DockerBuilder.groovy
@@ -155,7 +155,7 @@ class DockerBuilder extends ContainerBuilder<DockerBuilder> {
 
         // mount the input folders
         result << makeVolumes(mounts)
-        result << '-w "$PWD" '
+        result << '-w "$NXF_TASK_WORKDIR" '
 
         if( entryPoint )
             result << '--entrypoint ' << entryPoint << ' '
diff --git a/modules/nextflow/src/main/groovy/nextflow/container/PodmanBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/container/PodmanBuilder.groovy
index 649a85c720..84ff98a72f 100644
--- a/modules/nextflow/src/main/groovy/nextflow/container/PodmanBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/container/PodmanBuilder.groovy
@@ -112,7 +112,7 @@ class PodmanBuilder extends ContainerBuilder<PodmanBuilder> {
 
         // mount the input folders
         result << makeVolumes(mounts)
-        result << '-w "$PWD" '
+        result << '-w "$NXF_TASK_WORKDIR" '
 
         if( entryPoint )
             result << '--entrypoint ' << entryPoint << ' '
diff --git a/modules/nextflow/src/main/groovy/nextflow/container/SarusBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/container/SarusBuilder.groovy
index 72306660a8..f73cb2ae27 100644
--- a/modules/nextflow/src/main/groovy/nextflow/container/SarusBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/container/SarusBuilder.groovy
@@ -52,7 +52,7 @@ class SarusBuilder extends ContainerBuilder<SarusBuilder> {
 
         // mount the input folders
         result << makeVolumes(mounts)
-        result << '-w "$PWD" '
+        result << '-w "$NXF_TASK_WORKDIR" '
 
         if( runOptions )
             result << runOptions.join(' ') << ' '
diff --git a/modules/nextflow/src/main/groovy/nextflow/container/SingularityBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/container/SingularityBuilder.groovy
index 6f69c8e116..a4829f0f54 100644
--- a/modules/nextflow/src/main/groovy/nextflow/container/SingularityBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/container/SingularityBuilder.groovy
@@ -225,7 +225,7 @@ class SingularityBuilder extends ContainerBuilder<SingularityBuilder> {
 
         if( launcher ) {
             def result = getRunCommand()
-            result += entryPoint ? " $entryPoint -c \"cd \$PWD; $launcher\"" : " $launcher"
+            result += entryPoint ? " $entryPoint -c \"cd \$NXF_TASK_WORKDIR; $launcher\"" : " $launcher"
             return result
         }
         return getRunCommand() + ' ' + launcher
diff --git a/modules/nextflow/src/main/groovy/nextflow/container/UdockerBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/container/UdockerBuilder.groovy
index afe35cf97d..31bd44332a 100644
--- a/modules/nextflow/src/main/groovy/nextflow/container/UdockerBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/container/UdockerBuilder.groovy
@@ -79,7 +79,7 @@ class UdockerBuilder extends ContainerBuilder<UdockerBuilder> {
 
         // mount the input folders
         result << makeVolumes(mounts)
-        result << '-w "$PWD" --bindhome '
+        result << '-w "$NXF_TASK_WORKDIR" --bindhome '
 
 
         if( runOptions )
diff --git a/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
index d53ad6aea1..613c3dd706 100644
--- a/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy
@@ -486,7 +486,7 @@ class BashWrapperBuilder {
             final needChangeTaskWorkDir = containerBuilder instanceof SingularityBuilder
             if( (env || needChangeTaskWorkDir) && !containerConfig.entrypointOverride() ) {
                 if( needChangeTaskWorkDir )
-                    cmd = 'cd $PWD; ' + cmd
+                    cmd = 'cd $NXF_TASK_WORKDIR; ' + cmd
                 cmd = "/bin/bash -c \"$cmd\""
             }
             launcher = containerBuilder.getRunCommand(cmd)
diff --git a/modules/nextflow/src/main/groovy/nextflow/fusion/FusionHelper.groovy b/modules/nextflow/src/main/groovy/nextflow/fusion/FusionHelper.groovy
index 6298f9583a..4d852ee983 100644
--- a/modules/nextflow/src/main/groovy/nextflow/fusion/FusionHelper.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/fusion/FusionHelper.groovy
@@ -72,7 +72,7 @@ class FusionHelper {
         final containerCmd = containerBuilder
                 .build()
                 .getRunCommand(patchCmd.join(' '))
-                .replaceAll('-w "\\$PWD" ','') // <-- hack to remove the PWD work dir
+                .replaceAll('-w "\\$NXF_TASK_WORKDIR" ','') // <-- hack to remove the PWD work dir
 
         return containerCmd
     }
diff --git a/modules/nextflow/src/test/groovy/nextflow/container/ApptainerBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/container/ApptainerBuilderTest.groovy
index 6552918ea0..0f4404cf95 100644
--- a/modules/nextflow/src/test/groovy/nextflow/container/ApptainerBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/container/ApptainerBuilderTest.groovy
@@ -60,14 +60,14 @@ class ApptainerBuilderTest extends Specification {
                 .addMount(path2)
                 .params(autoMounts: true)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B /foo/data/file1 -B /bar/data/file2 -B "$PWD" ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B /foo/data/file1 -B /bar/data/file2 -B "$NXF_TASK_WORKDIR" ubuntu'
 
         new ApptainerBuilder('ubuntu')
                 .addMount(path1)
                 .addMount(path1)
                 .params(autoMounts: true)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B /foo/data/file1 -B "$PWD" ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B /foo/data/file1 -B "$NXF_TASK_WORKDIR" ubuntu'
 
         new ApptainerBuilder('ubuntu')
                 .addMount(path1)
@@ -75,13 +75,13 @@ class ApptainerBuilderTest extends Specification {
                 .params(autoMounts: true)
                 .params(readOnlyInputs: true)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B /foo/data/file1:/foo/data/file1:ro -B "$PWD" ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B /foo/data/file1:/foo/data/file1:ro -B "$NXF_TASK_WORKDIR" ubuntu'
 
         new ApptainerBuilder('ubuntu')
                 .addMount(path3)
                 .params(autoMounts: true)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B /bar/data\\ file -B "$PWD" ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer run --no-home --pid -B /bar/data\\ file -B "$NXF_TASK_WORKDIR" ubuntu'
 
         new ApptainerBuilder('ubuntu')
                 .params(newPidNamespace: false)
@@ -102,17 +102,17 @@ class ApptainerBuilderTest extends Specification {
         expect:
         new ApptainerBuilder('busybox')
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B "$PWD" busybox'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B "$NXF_TASK_WORKDIR" busybox'
 
         new ApptainerBuilder('busybox')
                 .params(engineOptions: '-q -v')
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer -q -v exec --no-home --pid -B "$PWD" busybox'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer -q -v exec --no-home --pid -B "$NXF_TASK_WORKDIR" busybox'
 
         new ApptainerBuilder('busybox')
                 .params(runOptions: '--contain --writable')
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B "$PWD" --contain --writable busybox'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B "$NXF_TASK_WORKDIR" --contain --writable busybox'
 
         new ApptainerBuilder('ubuntu')
                 .addMount(path1)
@@ -125,14 +125,14 @@ class ApptainerBuilderTest extends Specification {
                 .addMount(path2)
                 .params(autoMounts: true)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B /foo/data/file1 -B /bar/data/file2 -B "$PWD" ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B /foo/data/file1 -B /bar/data/file2 -B "$NXF_TASK_WORKDIR" ubuntu'
 
         new ApptainerBuilder('ubuntu')
                 .addMount(path1)
                 .addMount(path1)
                 .params(autoMounts: true)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B /foo/data/file1 -B "$PWD" ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B /foo/data/file1 -B "$NXF_TASK_WORKDIR" ubuntu'
 
         new ApptainerBuilder('ubuntu')
                 .addMount(path1)
@@ -140,18 +140,18 @@ class ApptainerBuilderTest extends Specification {
                 .params(autoMounts: true)
                 .params(readOnlyInputs: true)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B /foo/data/file1:/foo/data/file1:ro -B "$PWD" ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B /foo/data/file1:/foo/data/file1:ro -B "$NXF_TASK_WORKDIR" ubuntu'
 
         new ApptainerBuilder('ubuntu')
                 .addMount(path3)
                 .params(autoMounts: true)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B /bar/data\\ file -B "$PWD" ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B /bar/data\\ file -B "$NXF_TASK_WORKDIR" ubuntu'
 
         new ApptainerBuilder('ubuntu')
                 .params(newPidNamespace: false)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home -B "$PWD" ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home -B "$NXF_TASK_WORKDIR" ubuntu'
 
     }
 
@@ -201,12 +201,12 @@ class ApptainerBuilderTest extends Specification {
                 .addEnv('X=1')
                 .addEnv(ALPHA:'aaa', BETA: 'bbb')
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} APPTAINERENV_X="1" APPTAINERENV_ALPHA="aaa" APPTAINERENV_BETA="bbb" apptainer exec --no-home --pid -B "$PWD" busybox'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} APPTAINERENV_X="1" APPTAINERENV_ALPHA="aaa" APPTAINERENV_BETA="bbb" apptainer exec --no-home --pid -B "$NXF_TASK_WORKDIR" busybox'
 
         new ApptainerBuilder('busybox')
                 .addEnv('CUDA_VISIBLE_DEVICES')
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} ${CUDA_VISIBLE_DEVICES:+APPTAINERENV_CUDA_VISIBLE_DEVICES="$CUDA_VISIBLE_DEVICES"} apptainer exec --no-home --pid -B "$PWD" busybox'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} ${CUDA_VISIBLE_DEVICES:+APPTAINERENV_CUDA_VISIBLE_DEVICES="$CUDA_VISIBLE_DEVICES"} apptainer exec --no-home --pid -B "$NXF_TASK_WORKDIR" busybox'
 
     }
 
@@ -216,17 +216,17 @@ class ApptainerBuilderTest extends Specification {
         when:
         def cmd = new ApptainerBuilder('ubuntu.img').build().getRunCommand()
         then:
-        cmd == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B "$PWD" ubuntu.img'
+        cmd == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B "$NXF_TASK_WORKDIR" ubuntu.img'
 
         when:
         cmd = new ApptainerBuilder('ubuntu.img').build().getRunCommand('bwa --this --that file.fastq')
         then:
-        cmd == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B "$PWD" ubuntu.img bwa --this --that file.fastq'
+        cmd == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B "$NXF_TASK_WORKDIR" ubuntu.img bwa --this --that file.fastq'
 
         when:
         cmd = new ApptainerBuilder('ubuntu.img').params(entry:'/bin/sh').build().getRunCommand('bwa --this --that file.fastq')
         then:
-        cmd == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B "$PWD" ubuntu.img /bin/sh -c "cd $PWD; bwa --this --that file.fastq"'
+        cmd == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B "$NXF_TASK_WORKDIR" ubuntu.img /bin/sh -c "cd $NXF_TASK_WORKDIR; bwa --this --that file.fastq"'
     }
 
     @Unroll
diff --git a/modules/nextflow/src/test/groovy/nextflow/container/CharliecloudBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/container/CharliecloudBuilderTest.groovy
index d049b59ed9..10b7ff99ae 100644
--- a/modules/nextflow/src/test/groovy/nextflow/container/CharliecloudBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/container/CharliecloudBuilderTest.groovy
@@ -38,34 +38,34 @@ class CharliecloudBuilderTest extends Specification {
         expect:
         new CharliecloudBuilder('busybox')
                 .build()
-                .runCommand == 'ch-run --unset-env="*" -c "$PWD" --set-env -w -b "$PWD" busybox --'
+                .runCommand == 'ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env -w -b "$NXF_TASK_WORKDIR" busybox --'
 
         new CharliecloudBuilder('busybox')
                 .params(runOptions: '-j --no-home')
                 .build()
-                .runCommand == 'ch-run --unset-env="*" -c "$PWD" --set-env -w -b "$PWD" -j --no-home busybox --'
+                .runCommand == 'ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env -w -b "$NXF_TASK_WORKDIR" -j --no-home busybox --'
         
         new CharliecloudBuilder('busybox')
                 .params(temp: '/foo')
                 .build()
-                .runCommand == 'ch-run --unset-env="*" -c "$PWD" --set-env -w -b /foo:/tmp -b "$PWD" busybox --'
+                .runCommand == 'ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env -w -b /foo:/tmp -b "$NXF_TASK_WORKDIR" busybox --'
 
         new CharliecloudBuilder('busybox')
                 .addEnv('X=1')
                 .addEnv(ALPHA:'aaa', BETA: 'bbb')
                 .build()
-                .runCommand == 'ch-run --unset-env="*" -c "$PWD" --set-env -w --set-env=X=1 --set-env=ALPHA=aaa --set-env=BETA=bbb -b "$PWD" busybox --'
+                .runCommand == 'ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env -w --set-env=X=1 --set-env=ALPHA=aaa --set-env=BETA=bbb -b "$NXF_TASK_WORKDIR" busybox --'
 
         new CharliecloudBuilder('ubuntu')
                 .addMount(path1)
                 .build()
-                .runCommand == 'ch-run --unset-env="*" -c "$PWD" --set-env -w -b /foo/data/file1 -b "$PWD" ubuntu --'
+                .runCommand == 'ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env -w -b /foo/data/file1 -b "$NXF_TASK_WORKDIR" ubuntu --'
 
         new CharliecloudBuilder('ubuntu')
                 .addMount(path1)
                 .addMount(path2)
                 .build()
-                .runCommand == 'ch-run --unset-env="*" -c "$PWD" --set-env -w -b /foo/data/file1 -b /bar/data/file2 -b "$PWD" ubuntu --'
+                .runCommand == 'ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env -w -b /foo/data/file1 -b /bar/data/file2 -b "$NXF_TASK_WORKDIR" ubuntu --'
     }
 
     def db_file = Paths.get('/home/db')
@@ -74,27 +74,27 @@ class CharliecloudBuilderTest extends Specification {
         when:
         def cmd = new CharliecloudBuilder('ubuntu').build().getRunCommand()
         then:
-        cmd == 'ch-run --unset-env="*" -c "$PWD" --set-env -w -b "$PWD" ubuntu --'
+        cmd == 'ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env -w -b "$NXF_TASK_WORKDIR" ubuntu --'
 
         when:
         cmd = new CharliecloudBuilder('ubuntu').build().getRunCommand('bwa --this --that file.fastq')
         then:
-        cmd == 'ch-run --unset-env="*" -c "$PWD" --set-env -w -b "$PWD" ubuntu -- bwa --this --that file.fastq'
+        cmd == 'ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env -w -b "$NXF_TASK_WORKDIR" ubuntu -- bwa --this --that file.fastq'
 
         when:
         cmd = new CharliecloudBuilder('ubuntu').params(entry:'/bin/sh').build().getRunCommand('bwa --this --that file.fastq')
         then:
-        cmd == 'ch-run --unset-env="*" -c "$PWD" --set-env -w -b "$PWD" ubuntu -- /bin/sh -c "bwa --this --that file.fastq"'
+        cmd == 'ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env -w -b "$NXF_TASK_WORKDIR" ubuntu -- /bin/sh -c "bwa --this --that file.fastq"'
 
         when:
         cmd = new CharliecloudBuilder('ubuntu').params(entry:'/bin/sh').params(readOnlyInputs: 'true').build().getRunCommand('bwa --this --that file.fastq')
         then:
-        cmd == 'ch-run --unset-env="*" -c "$PWD" --set-env -b "$PWD" ubuntu -- /bin/sh -c "bwa --this --that file.fastq"'
+        cmd == 'ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env -b "$NXF_TASK_WORKDIR" ubuntu -- /bin/sh -c "bwa --this --that file.fastq"'
 
         when:
         cmd = new CharliecloudBuilder('ubuntu').params(entry:'/bin/sh').params(readOnlyInputs: 'false').build().getRunCommand('bwa --this --that file.fastq')
         then:
-        cmd == 'ch-run --unset-env="*" -c "$PWD" --set-env -w -b "$PWD" ubuntu -- /bin/sh -c "bwa --this --that file.fastq"'
+        cmd == 'ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env -w -b "$NXF_TASK_WORKDIR" ubuntu -- /bin/sh -c "bwa --this --that file.fastq"'
 
         when:
         cmd = new CharliecloudBuilder('ubuntu')
@@ -104,7 +104,7 @@ class CharliecloudBuilderTest extends Specification {
             .params(readOnlyInputs: 'true')
             .build().getRunCommand('bwa --this --that file.fastq')
         then:
-        cmd == 'ch-run --unset-env="*" -c "$PWD" --set-env -b /home -b "$PWD" ubuntu -- /bin/sh -c "bwa --this --that file.fastq"'
+        cmd == 'ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env -b /home -b "$NXF_TASK_WORKDIR" ubuntu -- /bin/sh -c "bwa --this --that file.fastq"'
 
         when:
         cmd = new CharliecloudBuilder('ubuntu')
@@ -115,7 +115,7 @@ class CharliecloudBuilderTest extends Specification {
             .build()
             .getRunCommand('bwa --this --that file.fastq')
         then:
-        cmd == 'ch-run --unset-env="*" -c "$PWD" --set-env -w -b /home/db -b "$PWD" ubuntu -- /bin/sh -c "bwa --this --that file.fastq"'
+        cmd == 'ch-run --unset-env="*" -c "$NXF_TASK_WORKDIR" --set-env -w -b /home/db -b "$NXF_TASK_WORKDIR" ubuntu -- /bin/sh -c "bwa --this --that file.fastq"'
     }
 
     @Unroll
diff --git a/modules/nextflow/src/test/groovy/nextflow/container/DockerBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/container/DockerBuilderTest.groovy
index fd94d44262..3a18743f3a 100644
--- a/modules/nextflow/src/test/groovy/nextflow/container/DockerBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/container/DockerBuilderTest.groovy
@@ -38,10 +38,10 @@ class DockerBuilderTest extends Specification {
         def quotes =  [ Paths.get('/folder with blanks/A'), Paths.get('/folder with blanks/B') ]
 
         expect:
-        builder.makeVolumes([]).toString() == '-v "$PWD":"$PWD" '
-        builder.makeVolumes(files).toString() == '-v /folder:/folder -v "$PWD":"$PWD" '
-        builder.makeVolumes(real).toString()  == '-v /user/yo/nextflow:/user/yo/nextflow -v /db/pdb/local/data:/db/pdb/local/data -v "$PWD":"$PWD" '
-        builder.makeVolumes(quotes).toString() == '-v /folder\\ with\\ blanks:/folder\\ with\\ blanks -v "$PWD":"$PWD" '
+        builder.makeVolumes([]).toString() == '-v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" '
+        builder.makeVolumes(files).toString() == '-v /folder:/folder -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" '
+        builder.makeVolumes(real).toString()  == '-v /user/yo/nextflow:/user/yo/nextflow -v /db/pdb/local/data:/db/pdb/local/data -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" '
+        builder.makeVolumes(quotes).toString() == '-v /folder\\ with\\ blanks:/folder\\ with\\ blanks -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" '
 
     }
 
@@ -70,67 +70,67 @@ class DockerBuilderTest extends Specification {
         expect:
         new DockerBuilder('fedora')
                 .build()
-                .runCommand == 'docker run -i -v "$PWD":"$PWD" -w "$PWD" fedora'
+                .runCommand == 'docker run -i -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" fedora'
 
         new DockerBuilder('fedora')
                 .addEnv(env)
                 .build()
-                .runCommand == 'docker run -i -e "FOO=1" -e "BAR=hello world" -v "$PWD":"$PWD" -w "$PWD" fedora'
+                .runCommand == 'docker run -i -e "FOO=1" -e "BAR=hello world" -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" fedora'
 
         new DockerBuilder('ubuntu')
                 .params(temp:'/hola')
                 .build()
-                .runCommand == 'docker run -i -v /hola:/tmp -v "$PWD":"$PWD" -w "$PWD" ubuntu'
+                .runCommand == 'docker run -i -v /hola:/tmp -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" ubuntu'
 
         new DockerBuilder('busybox')
                 .params(sudo: true)
                 .build()
-                .runCommand == 'sudo docker run -i -v "$PWD":"$PWD" -w "$PWD" busybox'
+                .runCommand == 'sudo docker run -i -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" busybox'
 
         new DockerBuilder('busybox')
                 .params(entry: '/bin/bash')
                 .build()
-                .runCommand == 'docker run -i -v "$PWD":"$PWD" -w "$PWD" --entrypoint /bin/bash busybox'
+                .runCommand == 'docker run -i -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" --entrypoint /bin/bash busybox'
 
         new DockerBuilder('busybox')
                 .params(runOptions: '-x --zeta')
                 .build()
-                .runCommand == 'docker run -i -v "$PWD":"$PWD" -w "$PWD" -x --zeta busybox'
+                .runCommand == 'docker run -i -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" -x --zeta busybox'
 
         new DockerBuilder('busybox')
                 .params(userEmulation:true)
                 .build()
-                .runCommand == 'docker run -i -u $(id -u) -e "HOME=${HOME}" -v /etc/passwd:/etc/passwd:ro -v /etc/shadow:/etc/shadow:ro -v /etc/group:/etc/group:ro -v $HOME:$HOME -v "$PWD":"$PWD" -w "$PWD" busybox'
+                .runCommand == 'docker run -i -u $(id -u) -e "HOME=${HOME}" -v /etc/passwd:/etc/passwd:ro -v /etc/shadow:/etc/shadow:ro -v /etc/group:/etc/group:ro -v $HOME:$HOME -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" busybox'
 
         new DockerBuilder('busybox')
                 .setName('hola')
                 .build()
-                .runCommand == 'docker run -i -v "$PWD":"$PWD" -w "$PWD" --name hola busybox'
+                .runCommand == 'docker run -i -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" --name hola busybox'
 
         new DockerBuilder('busybox')
                 .params(engineOptions: '--tlsverify --tlscert="/path/to/my/cert"')
                 .build()
-                .runCommand == 'docker --tlsverify --tlscert="/path/to/my/cert" run -i -v "$PWD":"$PWD" -w "$PWD" busybox'
+                .runCommand == 'docker --tlsverify --tlscert="/path/to/my/cert" run -i -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" busybox'
 
         new DockerBuilder('fedora')
                 .addEnv(env)
                 .addMount(db_file)
                 .addMount(db_file)  // <-- add twice the same to prove that the final string won't contain duplicates
                 .build()
-                .runCommand == 'docker run -i -e "FOO=1" -e "BAR=hello world" -v /home/db:/home/db -v "$PWD":"$PWD" -w "$PWD" fedora'
+                .runCommand == 'docker run -i -e "FOO=1" -e "BAR=hello world" -v /home/db:/home/db -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" fedora'
 
         new DockerBuilder('fedora')
                 .params(readOnlyInputs: true)
                 .addMount(db_file)
                 .build()
-                .runCommand == 'docker run -i -v /home/db:/home/db:ro -v "$PWD":"$PWD" -w "$PWD" fedora'
+                .runCommand == 'docker run -i -v /home/db:/home/db:ro -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" fedora'
 
 
         new DockerBuilder('fedora')
                 .params(mountFlags: 'Z')
                 .addMount(db_file)
                 .build()
-                .runCommand == 'docker run -i -v /home/db:/home/db:Z -v "$PWD":"$PWD":Z -w "$PWD" fedora'
+                .runCommand == 'docker run -i -v /home/db:/home/db:Z -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR":Z -w "$NXF_TASK_WORKDIR" fedora'
     }
 
     def 'test memory and cpuset' () {
@@ -139,58 +139,58 @@ class DockerBuilderTest extends Specification {
         new DockerBuilder('fedora')
                 .setCpus(2)
                 .build()
-                .runCommand == 'docker run -i --cpu-shares 2048 -v "$PWD":"$PWD" -w "$PWD" fedora'
+                .runCommand == 'docker run -i --cpu-shares 2048 -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" fedora'
 
         new DockerBuilder('fedora')
                 .setCpus(1)
                 .build()
-                .runCommand == 'docker run -i --cpu-shares 1024 -v "$PWD":"$PWD" -w "$PWD" fedora'
+                .runCommand == 'docker run -i --cpu-shares 1024 -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" fedora'
 
         new DockerBuilder('fedora')
                 .setCpus(8)
                 .setCpuset('1,2')
                 .build()
-                .runCommand == 'docker run -i --cpu-shares 8192 --cpuset-cpus 1,2 -v "$PWD":"$PWD" -w "$PWD" fedora'
+                .runCommand == 'docker run -i --cpu-shares 8192 --cpuset-cpus 1,2 -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" fedora'
 
         new DockerBuilder('fedora')
                 .params(legacy: true)
                 .setCpuset('1,2')
                 .build()
-                .runCommand == 'docker run -i --cpuset 1,2 -v "$PWD":"$PWD" -w "$PWD" fedora'
+                .runCommand == 'docker run -i --cpuset 1,2 -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" fedora'
 
 
         new DockerBuilder('fedora')
                 .params(legacy: true)
                 .setCpus(1)
                 .build()
-                .runCommand == 'docker run -i -v "$PWD":"$PWD" -w "$PWD" fedora'
+                .runCommand == 'docker run -i -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" fedora'
 
         new DockerBuilder('fedora')
                 .setMemory('10g')
                 .build()
-                .runCommand == 'docker run -i --memory 10g -v "$PWD":"$PWD" -w "$PWD" fedora'
+                .runCommand == 'docker run -i --memory 10g -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" fedora'
 
         new DockerBuilder('fedora')
                 .setMemory(new MemoryUnit('100M'))
                 .build()
-                .runCommand == 'docker run -i --memory 100m -v "$PWD":"$PWD" -w "$PWD" fedora'
+                .runCommand == 'docker run -i --memory 100m -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" fedora'
 
         new DockerBuilder('fedora')
                 .setCpuset('1-3')
                 .setMemory(new MemoryUnit('100M'))
                 .build()
-                .runCommand == 'docker run -i --cpuset-cpus 1-3 --memory 100m -v "$PWD":"$PWD" -w "$PWD" fedora'
+                .runCommand == 'docker run -i --cpuset-cpus 1-3 --memory 100m -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" fedora'
 
         new DockerBuilder('fedora')
                 .params(privileged: true)
                 .build()
-                .runCommand == 'docker run -i -v "$PWD":"$PWD" -w "$PWD" --privileged fedora'
+                .runCommand == 'docker run -i -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" --privileged fedora'
 
         new DockerBuilder('fedora')
                 .params(device: '/dev/fuse')
                 .params(capAdd: 'SYS_ADMIN')
                 .build()
-                .runCommand == 'docker run -i -v "$PWD":"$PWD" -w "$PWD" --device /dev/fuse --cap-add SYS_ADMIN fedora'
+                .runCommand == 'docker run -i -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" --device /dev/fuse --cap-add SYS_ADMIN fedora'
     }
 
     def 'test add mount'() {
@@ -214,14 +214,14 @@ class DockerBuilderTest extends Specification {
         when:
         def docker =  new DockerBuilder('busybox').setName('c1').build()
         then:
-        docker.runCommand == 'docker run -i -v "$PWD":"$PWD" -w "$PWD" --name c1 busybox'
+        docker.runCommand == 'docker run -i -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" --name c1 busybox'
         docker.removeCommand == 'docker rm c1'
         docker.killCommand == 'docker stop c1'
 
         when:
         docker =  new DockerBuilder('busybox').setName('c2').params(sudo: true, remove: true).build()
         then:
-        docker.runCommand == 'sudo docker run -i -v "$PWD":"$PWD" -w "$PWD" --name c2 busybox'
+        docker.runCommand == 'sudo docker run -i -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" --name c2 busybox'
         docker.removeCommand == 'sudo docker rm c2'
         docker.killCommand == 'sudo docker stop c2'
 
@@ -229,7 +229,7 @@ class DockerBuilderTest extends Specification {
         when:
         docker =  new DockerBuilder('busybox').setName('c3').params(remove: true).build()
         then:
-        docker.runCommand == 'docker run -i -v "$PWD":"$PWD" -w "$PWD" --name c3 busybox'
+        docker.runCommand == 'docker run -i -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" --name c3 busybox'
         docker.removeCommand == 'docker rm c3'
         docker.killCommand == 'docker stop c3'
 
@@ -252,17 +252,17 @@ class DockerBuilderTest extends Specification {
         when:
         def cli = new DockerBuilder('ubuntu:14').build().getRunCommand()
         then:
-        cli ==  'docker run -i -v "$PWD":"$PWD" -w "$PWD" ubuntu:14'
+        cli ==  'docker run -i -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" ubuntu:14'
 
         when:
         cli = new DockerBuilder('ubuntu:14').build().getRunCommand('bwa --this --that file.fasta')
         then:
-        cli ==  'docker run -i -v "$PWD":"$PWD" -w "$PWD" ubuntu:14 bwa --this --that file.fasta'
+        cli ==  'docker run -i -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" ubuntu:14 bwa --this --that file.fasta'
 
         when:
         cli = new DockerBuilder('ubuntu:14').params(entry:'/bin/bash').build().getRunCommand('bwa --this --that file.fasta')
         then:
-        cli ==  'docker run -i -v "$PWD":"$PWD" -w "$PWD" --entrypoint /bin/bash ubuntu:14 -c "bwa --this --that file.fasta"'
+        cli ==  'docker run -i -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" --entrypoint /bin/bash ubuntu:14 -c "bwa --this --that file.fasta"'
 
     }
 
diff --git a/modules/nextflow/src/test/groovy/nextflow/container/PodmanBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/container/PodmanBuilderTest.groovy
index 2d57837f84..3cfc0f2c36 100644
--- a/modules/nextflow/src/test/groovy/nextflow/container/PodmanBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/container/PodmanBuilderTest.groovy
@@ -40,10 +40,10 @@ class PodmanBuilderTest extends Specification {
         def quotes =  [ Paths.get('/folder with blanks/A'), Paths.get('/folder with blanks/B') ]
 
         expect:
-        builder.makeVolumes([]).toString() == '-v "$PWD":"$PWD" '
-        builder.makeVolumes(files).toString() == '-v /folder:/folder -v "$PWD":"$PWD" '
-        builder.makeVolumes(real).toString()  == '-v /user/yo/nextflow:/user/yo/nextflow -v /db/pdb/local/data:/db/pdb/local/data -v "$PWD":"$PWD" '
-        builder.makeVolumes(quotes).toString() == '-v /folder\\ with\\ blanks:/folder\\ with\\ blanks -v "$PWD":"$PWD" '
+        builder.makeVolumes([]).toString() == '-v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" '
+        builder.makeVolumes(files).toString() == '-v /folder:/folder -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" '
+        builder.makeVolumes(real).toString()  == '-v /user/yo/nextflow:/user/yo/nextflow -v /db/pdb/local/data:/db/pdb/local/data -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" '
+        builder.makeVolumes(quotes).toString() == '-v /folder\\ with\\ blanks:/folder\\ with\\ blanks -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" '
         and:
         builder.addMountWorkDir(false).makeVolumes([]).toString() == ''
         builder.addMountWorkDir(false).makeVolumes(files).toString() == '-v /folder:/folder '
@@ -74,67 +74,67 @@ class PodmanBuilderTest extends Specification {
         expect:
         new PodmanBuilder('fedora')
                 .build()
-                .runCommand == 'podman run -i -v "$PWD":"$PWD" -w "$PWD" fedora'
+                .runCommand == 'podman run -i -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" fedora'
 
         new PodmanBuilder('fedora')
                 .addEnv(env)
                 .build()
-                .runCommand == 'podman run -i -e "FOO=1" -e "BAR=hello world" -v "$PWD":"$PWD" -w "$PWD" fedora'
+                .runCommand == 'podman run -i -e "FOO=1" -e "BAR=hello world" -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" fedora'
 
         new PodmanBuilder('ubuntu')
                 .params(temp:'/hola')
                 .build()
-                .runCommand == 'podman run -i -v /hola:/tmp -v "$PWD":"$PWD" -w "$PWD" ubuntu'
+                .runCommand == 'podman run -i -v /hola:/tmp -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" ubuntu'
 
         new PodmanBuilder('busybox')
                 .params(entry: '/bin/bash')
                 .build()
-                .runCommand == 'podman run -i -v "$PWD":"$PWD" -w "$PWD" --entrypoint /bin/bash busybox'
+                .runCommand == 'podman run -i -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" --entrypoint /bin/bash busybox'
 
         new PodmanBuilder('busybox')
                 .params(runOptions: '-x --zeta')
                 .build()
-                .runCommand == 'podman run -i -v "$PWD":"$PWD" -w "$PWD" -x --zeta busybox'
+                .runCommand == 'podman run -i -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" -x --zeta busybox'
 
         new PodmanBuilder('busybox')
                 .setName('hola')
                 .build()
-                .runCommand == 'podman run -i -v "$PWD":"$PWD" -w "$PWD" --name hola busybox'
+                .runCommand == 'podman run -i -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" --name hola busybox'
 
         new PodmanBuilder('busybox')
                 .params(engineOptions: '--tls-verify=false --cert-dir "/path/to/my/cert-dir"')
                 .build()
-                .runCommand == 'podman --tls-verify=false --cert-dir "/path/to/my/cert-dir" run -i -v "$PWD":"$PWD" -w "$PWD" busybox'
+                .runCommand == 'podman --tls-verify=false --cert-dir "/path/to/my/cert-dir" run -i -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" busybox'
 
         new PodmanBuilder('fedora')
                 .addEnv(env)
                 .addMount(db_file)
                 .addMount(db_file)  // <-- add twice the same to prove that the final string won't contain duplicates
                 .build()
-                .runCommand == 'podman run -i -e "FOO=1" -e "BAR=hello world" -v /home/db:/home/db -v "$PWD":"$PWD" -w "$PWD" fedora'
+                .runCommand == 'podman run -i -e "FOO=1" -e "BAR=hello world" -v /home/db:/home/db -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" fedora'
 
         new PodmanBuilder('fedora')
                 .params(readOnlyInputs: true)
                 .addMount(db_file)
                 .build()
-                .runCommand == 'podman run -i -v /home/db:/home/db:ro -v "$PWD":"$PWD" -w "$PWD" fedora'
+                .runCommand == 'podman run -i -v /home/db:/home/db:ro -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" fedora'
 
         new PodmanBuilder('fedora')
                 .params(mountFlags: 'Z')
                 .addMount(db_file)
                 .build()
-                .runCommand == 'podman run -i -v /home/db:/home/db:Z -v "$PWD":"$PWD":Z -w "$PWD" fedora'
+                .runCommand == 'podman run -i -v /home/db:/home/db:Z -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR":Z -w "$NXF_TASK_WORKDIR" fedora'
 
         new PodmanBuilder('fedora')
                 .params(privileged: true)
                 .build()
-                .runCommand == 'podman run -i -v "$PWD":"$PWD" -w "$PWD" --privileged fedora'
+                .runCommand == 'podman run -i -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" --privileged fedora'
 
         new PodmanBuilder('fedora')
                 .params(device: '/dev/fuse')
                 .params(capAdd: 'SYS_ADMIN')
                 .build()
-                .runCommand == 'podman run -i -v "$PWD":"$PWD" -w "$PWD" --device /dev/fuse --cap-add SYS_ADMIN fedora'
+                .runCommand == 'podman run -i -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" --device /dev/fuse --cap-add SYS_ADMIN fedora'
     }
 
     def 'test add mount'() {
@@ -158,14 +158,14 @@ class PodmanBuilderTest extends Specification {
         when:
         def podman = new PodmanBuilder('busybox').setName('c1').build()
         then:
-        podman.runCommand == 'podman run -i -v "$PWD":"$PWD" -w "$PWD" --name c1 busybox'
+        podman.runCommand == 'podman run -i -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" --name c1 busybox'
         podman.removeCommand == 'podman rm c1'
         podman.killCommand == 'podman stop c1'
 
         when:
         podman = new PodmanBuilder('busybox').setName('c3').params(remove: true).build()
         then:
-        podman.runCommand == 'podman run -i -v "$PWD":"$PWD" -w "$PWD" --name c3 busybox'
+        podman.runCommand == 'podman run -i -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" --name c3 busybox'
         podman.removeCommand == 'podman rm c3'
         podman.killCommand == 'podman stop c3'
 
@@ -188,17 +188,17 @@ class PodmanBuilderTest extends Specification {
         when:
         def cli = new PodmanBuilder('ubuntu:14').build().getRunCommand()
         then:
-        cli ==  'podman run -i -v "$PWD":"$PWD" -w "$PWD" ubuntu:14'
+        cli ==  'podman run -i -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" ubuntu:14'
 
         when:
         cli = new PodmanBuilder('ubuntu:14').build().getRunCommand('bwa --this --that file.fasta')
         then:
-        cli ==  'podman run -i -v "$PWD":"$PWD" -w "$PWD" ubuntu:14 bwa --this --that file.fasta'
+        cli ==  'podman run -i -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" ubuntu:14 bwa --this --that file.fasta'
 
         when:
         cli = new PodmanBuilder('ubuntu:14').params(entry:'/bin/bash').build().getRunCommand('bwa --this --that file.fasta')
         then:
-        cli ==  'podman run -i -v "$PWD":"$PWD" -w "$PWD" --entrypoint /bin/bash ubuntu:14 -c "bwa --this --that file.fasta"'
+        cli ==  'podman run -i -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" --entrypoint /bin/bash ubuntu:14 -c "bwa --this --that file.fasta"'
 
     }
 
@@ -226,18 +226,18 @@ class PodmanBuilderTest extends Specification {
         new PodmanBuilder('fedora')
                 .setCpus(3)
                 .build()
-                .runCommand == 'podman run -i -v "$PWD":"$PWD" -w "$PWD" --cpu-shares 3072 fedora'
+                .runCommand == 'podman run -i -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" --cpu-shares 3072 fedora'
 
         new PodmanBuilder('fedora')
                 .setMemory(new MemoryUnit('100m'))
                 .build()
-                .runCommand == 'podman run -i -v "$PWD":"$PWD" -w "$PWD" --memory 100m fedora'
+                .runCommand == 'podman run -i -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" --memory 100m fedora'
 
         new PodmanBuilder('fedora')
                 .setCpus(1)
                 .setMemory(new MemoryUnit('400m'))
                 .build()
-                .runCommand == 'podman run -i -v "$PWD":"$PWD" -w "$PWD" --cpu-shares 1024 --memory 400m fedora'
+                .runCommand == 'podman run -i -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" --cpu-shares 1024 --memory 400m fedora'
 
     }
 }
diff --git a/modules/nextflow/src/test/groovy/nextflow/container/SarusBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/container/SarusBuilderTest.groovy
index 986f11d1ae..1f9037b582 100644
--- a/modules/nextflow/src/test/groovy/nextflow/container/SarusBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/container/SarusBuilderTest.groovy
@@ -38,30 +38,30 @@ class SarusrBuilderTest extends Specification {
         expect:
         new SarusBuilder('busybox')
                 .build()
-                .@runCommand == 'sarus run --mount=type=bind,source="$PWD",destination="$PWD" -w "$PWD" busybox'
+                .@runCommand == 'sarus run --mount=type=bind,source="$NXF_TASK_WORKDIR",destination="$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" busybox'
 
         new SarusBuilder('busybox')
                 .params(verbose: true)
                 .build()
-                .@runCommand == 'sarus --verbose run --mount=type=bind,source="$PWD",destination="$PWD" -w "$PWD" busybox'
+                .@runCommand == 'sarus --verbose run --mount=type=bind,source="$NXF_TASK_WORKDIR",destination="$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" busybox'
 
         new SarusBuilder('fedora')
                 .addEnv([VAR_X:1, VAR_Y:2])
                 .addEnv("VAR_Z=3")
                 .build()
-                .@runCommand == 'sarus run -e "VAR_X=1" -e "VAR_Y=2" -e "VAR_Z=3" --mount=type=bind,source="$PWD",destination="$PWD" -w "$PWD" fedora'
+                .@runCommand == 'sarus run -e "VAR_X=1" -e "VAR_Y=2" -e "VAR_Z=3" --mount=type=bind,source="$NXF_TASK_WORKDIR",destination="$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" fedora'
 
         new SarusBuilder('busybox')
                 .params(runOptions: '-x --zeta')
                 .build()
-                .@runCommand == 'sarus run --mount=type=bind,source="$PWD",destination="$PWD" -w "$PWD" -x --zeta busybox'
+                .@runCommand == 'sarus run --mount=type=bind,source="$NXF_TASK_WORKDIR",destination="$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" -x --zeta busybox'
 
         new SarusBuilder('fedora')
                 .addEnv([VAR_X:1, VAR_Y:2])
                 .addMount(Paths.get('/home/db'))
                 .addMount(Paths.get('/home/db'))  // <-- add twice the same to prove that the final string won't contain duplicates
                 .build()
-                .@runCommand == 'sarus run -e "VAR_X=1" -e "VAR_Y=2" --mount=type=bind,source=/home/db,destination=/home/db --mount=type=bind,source="$PWD",destination="$PWD" -w "$PWD" fedora'
+                .@runCommand == 'sarus run -e "VAR_X=1" -e "VAR_Y=2" --mount=type=bind,source=/home/db,destination=/home/db --mount=type=bind,source="$NXF_TASK_WORKDIR",destination="$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" fedora'
 
     }
 
@@ -72,7 +72,7 @@ class SarusrBuilderTest extends Specification {
         then:
         cli ==  '''\
         sarus pull ubuntu:14 1>&2
-        sarus run --mount=type=bind,source="$PWD",destination="$PWD" -w "$PWD" ubuntu:14
+        sarus run --mount=type=bind,source="$NXF_TASK_WORKDIR",destination="$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" ubuntu:14
         '''
         .stripIndent().trim()
 
@@ -81,7 +81,7 @@ class SarusrBuilderTest extends Specification {
         then:
         cli ==  '''\
         sarus pull ubuntu:14 1>&2
-        sarus run --mount=type=bind,source="$PWD",destination="$PWD" -w "$PWD" ubuntu:14 bwa --this --that file.fasta
+        sarus run --mount=type=bind,source="$NXF_TASK_WORKDIR",destination="$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" ubuntu:14 bwa --this --that file.fasta
         '''
         .stripIndent().trim()
 
@@ -90,7 +90,7 @@ class SarusrBuilderTest extends Specification {
         then:
         cli ==  '''\
         sarus pull ubuntu:14 1>&2
-        sarus run --mount=type=bind,source="$PWD",destination="$PWD" -w "$PWD" ubuntu:14 /bin/bash -c "bwa --this --that file.fasta"
+        sarus run --mount=type=bind,source="$NXF_TASK_WORKDIR",destination="$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" ubuntu:14 /bin/bash -c "bwa --this --that file.fasta"
         '''
         .stripIndent().trim()
 
diff --git a/modules/nextflow/src/test/groovy/nextflow/container/SingularityBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/container/SingularityBuilderTest.groovy
index 9aad74ffb9..dd475dc80d 100644
--- a/modules/nextflow/src/test/groovy/nextflow/container/SingularityBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/container/SingularityBuilderTest.groovy
@@ -61,14 +61,14 @@ class SingularityBuilderTest extends Specification {
                 .addMount(path2)
                 .params(autoMounts: true)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity run --no-home --pid -B /foo/data/file1 -B /bar/data/file2 -B "$PWD" ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity run --no-home --pid -B /foo/data/file1 -B /bar/data/file2 -B "$NXF_TASK_WORKDIR" ubuntu'
 
         new SingularityBuilder('ubuntu')
                 .addMount(path1)
                 .addMount(path1)
                 .params(autoMounts: true)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity run --no-home --pid -B /foo/data/file1 -B "$PWD" ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity run --no-home --pid -B /foo/data/file1 -B "$NXF_TASK_WORKDIR" ubuntu'
 
         new SingularityBuilder('ubuntu')
                 .addMount(path1)
@@ -76,13 +76,13 @@ class SingularityBuilderTest extends Specification {
                 .params(autoMounts: true)
                 .params(readOnlyInputs: true)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity run --no-home --pid -B /foo/data/file1:/foo/data/file1:ro -B "$PWD" ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity run --no-home --pid -B /foo/data/file1:/foo/data/file1:ro -B "$NXF_TASK_WORKDIR" ubuntu'
 
         new SingularityBuilder('ubuntu')
                 .addMount(path3)
                 .params(autoMounts: true)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity run --no-home --pid -B /bar/data\\ file -B "$PWD" ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity run --no-home --pid -B /bar/data\\ file -B "$NXF_TASK_WORKDIR" ubuntu'
 
         new SingularityBuilder('ubuntu')
                 .params(newPidNamespace: false)
@@ -103,17 +103,17 @@ class SingularityBuilderTest extends Specification {
         expect:
         new SingularityBuilder('busybox')
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid -B "$PWD" busybox'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid -B "$NXF_TASK_WORKDIR" busybox'
 
         new SingularityBuilder('busybox')
                 .params(engineOptions: '-q -v')
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity -q -v exec --no-home --pid -B "$PWD" busybox'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity -q -v exec --no-home --pid -B "$NXF_TASK_WORKDIR" busybox'
 
         new SingularityBuilder('busybox')
                 .params(runOptions: '--contain --writable')
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid -B "$PWD" --contain --writable busybox'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid -B "$NXF_TASK_WORKDIR" --contain --writable busybox'
 
         new SingularityBuilder('ubuntu')
                 .params(autoMounts: false)
@@ -125,14 +125,14 @@ class SingularityBuilderTest extends Specification {
                 .addMount(path2)
                 .params(autoMounts: true)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid -B /foo/data/file1 -B /bar/data/file2 -B "$PWD" ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid -B /foo/data/file1 -B /bar/data/file2 -B "$NXF_TASK_WORKDIR" ubuntu'
 
         new SingularityBuilder('ubuntu')
                 .addMount(path1)
                 .addMount(path1)
                 .params(autoMounts: true)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid -B /foo/data/file1 -B "$PWD" ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid -B /foo/data/file1 -B "$NXF_TASK_WORKDIR" ubuntu'
 
         new SingularityBuilder('ubuntu')
                 .addMount(path1)
@@ -140,13 +140,13 @@ class SingularityBuilderTest extends Specification {
                 .params(autoMounts: true)
                 .params(readOnlyInputs: true)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid -B /foo/data/file1:/foo/data/file1:ro -B "$PWD" ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid -B /foo/data/file1:/foo/data/file1:ro -B "$NXF_TASK_WORKDIR" ubuntu'
 
         new SingularityBuilder('ubuntu')
                 .addMount(path3)
                 .params(autoMounts: true)
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid -B /bar/data\\ file -B "$PWD" ubuntu'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid -B /bar/data\\ file -B "$NXF_TASK_WORKDIR" ubuntu'
 
         new SingularityBuilder('ubuntu')
                 .params(newPidNamespace: false)
@@ -157,7 +157,7 @@ class SingularityBuilderTest extends Specification {
         new SingularityBuilder('ubuntu')
             .params(oci: true)
             .build()
-            .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} ${XDG_RUNTIME_DIR:+XDG_RUNTIME_DIR="$XDG_RUNTIME_DIR"} ${DBUS_SESSION_BUS_ADDRESS:+DBUS_SESSION_BUS_ADDRESS="$DBUS_SESSION_BUS_ADDRESS"} singularity exec --no-home --oci -B "$PWD" ubuntu'
+            .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} ${XDG_RUNTIME_DIR:+XDG_RUNTIME_DIR="$XDG_RUNTIME_DIR"} ${DBUS_SESSION_BUS_ADDRESS:+DBUS_SESSION_BUS_ADDRESS="$DBUS_SESSION_BUS_ADDRESS"} singularity exec --no-home --oci -B "$NXF_TASK_WORKDIR" ubuntu'
 
     }
 
@@ -207,12 +207,12 @@ class SingularityBuilderTest extends Specification {
                 .addEnv('X=1')
                 .addEnv(ALPHA:'aaa', BETA: 'bbb')
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} SINGULARITYENV_X="1" SINGULARITYENV_ALPHA="aaa" SINGULARITYENV_BETA="bbb" singularity exec --no-home --pid -B "$PWD" busybox'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} SINGULARITYENV_X="1" SINGULARITYENV_ALPHA="aaa" SINGULARITYENV_BETA="bbb" singularity exec --no-home --pid -B "$NXF_TASK_WORKDIR" busybox'
 
         new SingularityBuilder('busybox')
                 .addEnv('CUDA_VISIBLE_DEVICES')
                 .build()
-                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} ${CUDA_VISIBLE_DEVICES:+SINGULARITYENV_CUDA_VISIBLE_DEVICES="$CUDA_VISIBLE_DEVICES"} singularity exec --no-home --pid -B "$PWD" busybox'
+                .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} ${CUDA_VISIBLE_DEVICES:+SINGULARITYENV_CUDA_VISIBLE_DEVICES="$CUDA_VISIBLE_DEVICES"} singularity exec --no-home --pid -B "$NXF_TASK_WORKDIR" busybox'
 
     }
 
@@ -222,17 +222,17 @@ class SingularityBuilderTest extends Specification {
         when:
         def cmd = new SingularityBuilder('ubuntu.img').build().getRunCommand()
         then:
-        cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid -B "$PWD" ubuntu.img'
+        cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid -B "$NXF_TASK_WORKDIR" ubuntu.img'
 
         when:
         cmd = new SingularityBuilder('ubuntu.img').build().getRunCommand('bwa --this --that file.fastq')
         then:
-        cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid -B "$PWD" ubuntu.img bwa --this --that file.fastq'
+        cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid -B "$NXF_TASK_WORKDIR" ubuntu.img bwa --this --that file.fastq'
 
         when:
         cmd = new SingularityBuilder('ubuntu.img').params(entry:'/bin/sh').build().getRunCommand('bwa --this --that file.fastq')
         then:
-        cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid -B "$PWD" ubuntu.img /bin/sh -c "cd $PWD; bwa --this --that file.fastq"'
+        cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} singularity exec --no-home --pid -B "$NXF_TASK_WORKDIR" ubuntu.img /bin/sh -c "cd $NXF_TASK_WORKDIR; bwa --this --that file.fastq"'
     }
 
     @Unroll
diff --git a/modules/nextflow/src/test/groovy/nextflow/container/UdockerBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/container/UdockerBuilderTest.groovy
index 07e374dc9a..3dac89771f 100644
--- a/modules/nextflow/src/test/groovy/nextflow/container/UdockerBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/container/UdockerBuilderTest.groovy
@@ -47,10 +47,10 @@ class UdockerBuilderTest extends Specification {
         def quotes =  [ Paths.get('/folder with blanks/A'), Paths.get('/folder with blanks/B') ]
 
         expect:
-        builder.makeVolumes([]).toString() == '-v "$PWD":"$PWD" '
-        builder.makeVolumes(files).toString() == '-v /folder:/folder -v "$PWD":"$PWD" '
-        builder.makeVolumes(real).toString()  == '-v /user/yo/nextflow:/user/yo/nextflow -v /db/pdb/local/data:/db/pdb/local/data -v "$PWD":"$PWD" '
-        builder.makeVolumes(quotes).toString() == '-v /folder\\ with\\ blanks:/folder\\ with\\ blanks -v "$PWD":"$PWD" '
+        builder.makeVolumes([]).toString() == '-v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" '
+        builder.makeVolumes(files).toString() == '-v /folder:/folder -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" '
+        builder.makeVolumes(real).toString()  == '-v /user/yo/nextflow:/user/yo/nextflow -v /db/pdb/local/data:/db/pdb/local/data -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" '
+        builder.makeVolumes(quotes).toString() == '-v /folder\\ with\\ blanks:/folder\\ with\\ blanks -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" '
 
     }
 
@@ -63,38 +63,38 @@ class UdockerBuilderTest extends Specification {
         expect:
         new UdockerBuilder('fedora')
                 .build()
-                .runCommandRaw == 'udocker.py run --rm -v "$PWD":"$PWD" -w "$PWD" --bindhome $(udocker.py create "fedora:latest")'
+                .runCommandRaw == 'udocker.py run --rm -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" --bindhome $(udocker.py create "fedora:latest")'
 
         new UdockerBuilder('fedora')
                 .addEnv(env)
                 .build()
-                .runCommandRaw == 'udocker.py run --rm -e "FOO=1" -e "BAR=hello world" -v "$PWD":"$PWD" -w "$PWD" --bindhome $(udocker.py create "fedora:latest")'
+                .runCommandRaw == 'udocker.py run --rm -e "FOO=1" -e "BAR=hello world" -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" --bindhome $(udocker.py create "fedora:latest")'
 
         new UdockerBuilder('fedora')
                 .setCpuset('1,2')
                 .build()
-                .runCommandRaw == 'udocker.py run --rm --cpuset-cpus=1,2 -v "$PWD":"$PWD" -w "$PWD" --bindhome $(udocker.py create "fedora:latest")'
+                .runCommandRaw == 'udocker.py run --rm --cpuset-cpus=1,2 -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" --bindhome $(udocker.py create "fedora:latest")'
 
         new UdockerBuilder('fedora')
                 .addMount(db_file)
                 .addEnv(env)
                 .build()
-                .runCommandRaw == 'udocker.py run --rm -e "FOO=1" -e "BAR=hello world" -v /home/db:/home/db -v "$PWD":"$PWD" -w "$PWD" --bindhome $(udocker.py create "fedora:latest")'
+                .runCommandRaw == 'udocker.py run --rm -e "FOO=1" -e "BAR=hello world" -v /home/db:/home/db -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" --bindhome $(udocker.py create "fedora:latest")'
 
         new UdockerBuilder('busybox')
                 .params(remove: false)
                 .build()
-                .runCommandRaw == 'udocker.py run -v "$PWD":"$PWD" -w "$PWD" --bindhome $(udocker.py create "busybox:latest")'
+                .runCommandRaw == 'udocker.py run -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" --bindhome $(udocker.py create "busybox:latest")'
 
         new UdockerBuilder('busybox')
                 .params(runOptions: '-x --zeta')
                 .build()
-                .runCommandRaw == 'udocker.py run --rm -v "$PWD":"$PWD" -w "$PWD" --bindhome -x --zeta $(udocker.py create "busybox:latest")'
+                .runCommandRaw == 'udocker.py run --rm -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" --bindhome -x --zeta $(udocker.py create "busybox:latest")'
 
         new UdockerBuilder('busybox')
                 .params(entry: '/bin/blah')
                 .build()
-                .runCommandRaw == 'udocker.py run --rm -v "$PWD":"$PWD" -w "$PWD" --bindhome $(udocker.py create "busybox:latest")'
+                .runCommandRaw == 'udocker.py run --rm -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" --bindhome $(udocker.py create "busybox:latest")'
 
     }
 
@@ -109,7 +109,7 @@ class UdockerBuilderTest extends Specification {
         result == '''
             ((udocker.py images | grep -E -o "^ubuntu:latest\\s") || udocker.py pull "ubuntu:latest")>/dev/null
             [[ $? != 0 ]] && echo "Udocker failed while pulling container \\`ubuntu:latest\\`" >&2 && exit 1
-            udocker.py run --rm -v "$PWD":"$PWD" -w "$PWD" --bindhome $(udocker.py create "ubuntu:latest")
+            udocker.py run --rm -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" --bindhome $(udocker.py create "ubuntu:latest")
             '''
             .stripIndent().trim()
 
@@ -126,7 +126,7 @@ class UdockerBuilderTest extends Specification {
         result == '''
             ((udocker.py images | grep -E -o "^ubuntu:latest\\s") || udocker.py pull "ubuntu:latest")>/dev/null
             [[ $? != 0 ]] && echo "Udocker failed while pulling container \\`ubuntu:latest\\`" >&2 && exit 1
-            udocker.py run --rm -v "$PWD":"$PWD" -w "$PWD" --bindhome $(udocker.py create "ubuntu:latest") bwa --this --that
+            udocker.py run --rm -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" --bindhome $(udocker.py create "ubuntu:latest") bwa --this --that
             '''
                 .stripIndent().trim()
 
@@ -141,7 +141,7 @@ class UdockerBuilderTest extends Specification {
         result == '''
             ((udocker.py images | grep -E -o "^ubuntu:latest\\s") || udocker.py pull "ubuntu:latest")>/dev/null
             [[ $? != 0 ]] && echo "Udocker failed while pulling container \\`ubuntu:latest\\`" >&2 && exit 1
-            udocker.py run --rm -v "$PWD":"$PWD" -w "$PWD" --bindhome $(udocker.py create "ubuntu:latest") /bin/bash -c "bwa --this --that"
+            udocker.py run --rm -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" --bindhome $(udocker.py create "ubuntu:latest") /bin/bash -c "bwa --this --that"
             '''
                 .stripIndent().trim()
 
diff --git a/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
index 03fb0616ea..34617cdc78 100644
--- a/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/executor/BashWrapperBuilderTest.groovy
@@ -734,7 +734,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'docker', temp: 'auto', enabled: true] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'docker run -i -e "NXF_TASK_WORKDIR" -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'docker run -i -e "NXF_TASK_WORKDIR" -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$NXF_TASK_WORKDIR" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
         binding.cleanup_cmd == 'docker rm $NXF_BOXID &>/dev/null || true\n'
         binding.kill_cmd == 'docker stop $NXF_BOXID'
     }
@@ -748,7 +748,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'docker', temp: 'auto', enabled: true] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'docker run -i -e "NXF_TASK_WORKDIR" -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -c "eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
+        binding.launch_cmd == 'docker run -i -e "NXF_TASK_WORKDIR" -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$NXF_TASK_WORKDIR" --name $NXF_BOXID busybox /bin/bash -c "eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
         binding.cleanup_cmd == 'docker rm $NXF_BOXID &>/dev/null || true\n'
         binding.kill_cmd == 'docker stop $NXF_BOXID'
         and:
@@ -769,7 +769,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'docker', temp: 'auto', enabled: true, entrypointOverride: false] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'docker run -i -e "NXF_TASK_WORKDIR" -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'docker run -i -e "NXF_TASK_WORKDIR" -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$NXF_TASK_WORKDIR" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
         binding.cleanup_cmd == 'docker rm $NXF_BOXID &>/dev/null || true\n'
         binding.kill_cmd == 'docker stop $NXF_BOXID'
     }
@@ -783,7 +783,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'docker', temp: 'auto', enabled: true, entrypointOverride: false] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'docker run -i -e "NXF_TASK_WORKDIR" -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -c "eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
+        binding.launch_cmd == 'docker run -i -e "NXF_TASK_WORKDIR" -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$NXF_TASK_WORKDIR" --name $NXF_BOXID busybox /bin/bash -c "eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
         binding.cleanup_cmd == 'docker rm $NXF_BOXID &>/dev/null || true\n'
         binding.kill_cmd == 'docker stop $NXF_BOXID'
         and:
@@ -804,7 +804,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerEnabled: true  ).makeBinding()
 
         then:
-        binding.launch_cmd == 'sudo docker run -i -e "NXF_TASK_WORKDIR" -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'sudo docker run -i -e "NXF_TASK_WORKDIR" -v /work/dir:/work/dir -w "$NXF_TASK_WORKDIR" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
         binding.cleanup_cmd == 'sudo docker rm $NXF_BOXID &>/dev/null || true\n'
         binding.kill_cmd == 'sudo docker stop $NXF_BOXID'
     }
@@ -817,7 +817,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'docker', temp: 'auto', enabled: true, remove:false, kill: false] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'docker run -i -e "NXF_TASK_WORKDIR" -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID ubuntu /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'docker run -i -e "NXF_TASK_WORKDIR" -v $(nxf_mktemp):/tmp -v /work/dir:/work/dir -w "$NXF_TASK_WORKDIR" --name $NXF_BOXID ubuntu /bin/bash -ue /work/dir/.command.sh'
         binding.cleanup_cmd == ""
         binding.kill_cmd == null
         binding.containsKey('kill_cmd')
@@ -831,7 +831,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'docker', enabled: true, remove:false, kill: 'SIGXXX'] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'docker run -i -e "NXF_TASK_WORKDIR" -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID ubuntu /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'docker run -i -e "NXF_TASK_WORKDIR" -v /work/dir:/work/dir -w "$NXF_TASK_WORKDIR" --name $NXF_BOXID ubuntu /bin/bash -ue /work/dir/.command.sh'
         binding.cleanup_cmd == ""
         binding.kill_cmd == 'docker kill -s SIGXXX $NXF_BOXID'
         binding.containsKey('kill_cmd')
@@ -846,7 +846,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'docker', enabled: true] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'docker run -i -e "NXF_TASK_WORKDIR" -v /folder\\ with\\ blanks:/folder\\ with\\ blanks -v /work/dir:/work/dir -w "\$PWD" --name \$NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'docker run -i -e "NXF_TASK_WORKDIR" -v /folder\\ with\\ blanks:/folder\\ with\\ blanks -v /work/dir:/work/dir -w "\$NXF_TASK_WORKDIR" --name \$NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
         binding.cleanup_cmd == 'docker rm $NXF_BOXID &>/dev/null || true\n'
         binding.kill_cmd == 'docker stop $NXF_BOXID'
     }
@@ -861,7 +861,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'docker', sudo: true, enabled: true] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'sudo docker run -i -e "NXF_TASK_WORKDIR" -v /work/dir:/work/dir -v "$PWD":"$PWD" -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'sudo docker run -i -e "NXF_TASK_WORKDIR" -v /work/dir:/work/dir -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
         binding.kill_cmd == 'sudo docker stop $NXF_BOXID'
         binding.cleanup_cmd == '''\
                 (sudo -n true && sudo rm -rf "$NXF_SCRATCH" || rm -rf "$NXF_SCRATCH")&>/dev/null || true
@@ -878,7 +878,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'docker', enabled: true] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'docker run -i -e "NXF_TASK_WORKDIR" -v /work/dir:/work/dir -w "$PWD" -v /foo:/bar --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'docker run -i -e "NXF_TASK_WORKDIR" -v /work/dir:/work/dir -w "$NXF_TASK_WORKDIR" -v /foo:/bar --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
         binding.kill_cmd == 'docker stop $NXF_BOXID'
         binding.cleanup_cmd == 'docker rm $NXF_BOXID &>/dev/null || true\n'
     }
@@ -893,7 +893,7 @@ class BashWrapperBuilderTest extends Specification {
         then:
         binding.launch_cmd == '''\
         sarus pull busybox 1>&2
-        sarus run -e "NXF_TASK_WORKDIR" --mount=type=bind,source=/work/dir,destination=/work/dir -w "$PWD" busybox /bin/bash -ue /work/dir/.command.sh
+        sarus run -e "NXF_TASK_WORKDIR" --mount=type=bind,source=/work/dir,destination=/work/dir -w "$NXF_TASK_WORKDIR" busybox /bin/bash -ue /work/dir/.command.sh
         '''.stripIndent().rightTrim()
         binding.cleanup_cmd == ""
         binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
@@ -910,7 +910,7 @@ class BashWrapperBuilderTest extends Specification {
         then:
         binding.launch_cmd == '''\
         sarus pull busybox 1>&2
-        sarus run -e "NXF_TASK_WORKDIR" --mount=type=bind,source=/work/dir,destination=/work/dir -w "$PWD" busybox /bin/bash -c "eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"
+        sarus run -e "NXF_TASK_WORKDIR" --mount=type=bind,source=/work/dir,destination=/work/dir -w "$NXF_TASK_WORKDIR" busybox /bin/bash -c "eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"
         '''.stripIndent().rightTrim()
         binding.cleanup_cmd == ""
         binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
@@ -935,7 +935,7 @@ class BashWrapperBuilderTest extends Specification {
         then:
         binding.launch_cmd == '''\
         sarus pull busybox 1>&2
-        sarus run -e "NXF_TASK_WORKDIR" --mount=type=bind,source=/folder\\ with\\ blanks,destination=/folder\\ with\\ blanks --mount=type=bind,source=/work/dir,destination=/work/dir -w "$PWD" busybox /bin/bash -ue /work/dir/.command.sh
+        sarus run -e "NXF_TASK_WORKDIR" --mount=type=bind,source=/folder\\ with\\ blanks,destination=/folder\\ with\\ blanks --mount=type=bind,source=/work/dir,destination=/work/dir -w "$NXF_TASK_WORKDIR" busybox /bin/bash -ue /work/dir/.command.sh
         '''.stripIndent().rightTrim()
         binding.cleanup_cmd == ""
         binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
@@ -952,7 +952,7 @@ class BashWrapperBuilderTest extends Specification {
         then:
         binding.launch_cmd == '''\
         sarus pull busybox 1>&2
-        sarus run -e "NXF_TASK_WORKDIR" --mount=type=bind,source=/work/dir,destination=/work/dir -w "$PWD" --mount=type=bind,source=/foo,destination=/bar busybox /bin/bash -ue /work/dir/.command.sh
+        sarus run -e "NXF_TASK_WORKDIR" --mount=type=bind,source=/work/dir,destination=/work/dir -w "$NXF_TASK_WORKDIR" --mount=type=bind,source=/foo,destination=/bar busybox /bin/bash -ue /work/dir/.command.sh
         '''.stripIndent().rightTrim()
         binding.cleanup_cmd == ""
         binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
@@ -991,7 +991,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [enabled: true, engine: 'singularity'] as ContainerConfig ).makeBinding()
 
         then:
-        binding.launch_cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} ${NXF_TASK_WORKDIR:+SINGULARITYENV_NXF_TASK_WORKDIR="$NXF_TASK_WORKDIR"} singularity exec --no-home --pid -B /work/dir docker://ubuntu:latest /bin/bash -c "cd $PWD; eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
+        binding.launch_cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} ${NXF_TASK_WORKDIR:+SINGULARITYENV_NXF_TASK_WORKDIR="$NXF_TASK_WORKDIR"} singularity exec --no-home --pid -B /work/dir docker://ubuntu:latest /bin/bash -c "cd $NXF_TASK_WORKDIR; eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
         binding.cleanup_cmd == ""
         binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
     }
@@ -1005,7 +1005,7 @@ class BashWrapperBuilderTest extends Specification {
             containerConfig: [enabled: true, engine: 'singularity'] as ContainerConfig ).makeBinding()
 
         then:
-        binding.launch_cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} ${NXF_TASK_WORKDIR:+SINGULARITYENV_NXF_TASK_WORKDIR="$NXF_TASK_WORKDIR"} singularity exec --no-home --pid -B /work/dir docker://ubuntu:latest /bin/bash -c "cd $PWD; /bin/bash -ue /work/dir/.command.sh"'
+        binding.launch_cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} ${NXF_TASK_WORKDIR:+SINGULARITYENV_NXF_TASK_WORKDIR="$NXF_TASK_WORKDIR"} singularity exec --no-home --pid -B /work/dir docker://ubuntu:latest /bin/bash -c "cd $NXF_TASK_WORKDIR; /bin/bash -ue /work/dir/.command.sh"'
         binding.cleanup_cmd == ""
         binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
     }
@@ -1019,7 +1019,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [enabled: true, engine: 'singularity', entrypointOverride: true] as ContainerConfig ).makeBinding()
 
         then:
-        binding.launch_cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} ${NXF_TASK_WORKDIR:+SINGULARITYENV_NXF_TASK_WORKDIR="$NXF_TASK_WORKDIR"} singularity exec --no-home --pid -B /work/dir docker://ubuntu:latest /bin/bash -c "cd $PWD; eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
+        binding.launch_cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} ${NXF_TASK_WORKDIR:+SINGULARITYENV_NXF_TASK_WORKDIR="$NXF_TASK_WORKDIR"} singularity exec --no-home --pid -B /work/dir docker://ubuntu:latest /bin/bash -c "cd $NXF_TASK_WORKDIR; eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
         binding.cleanup_cmd == ""
         binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
     }
@@ -1033,7 +1033,7 @@ class BashWrapperBuilderTest extends Specification {
             containerConfig: [enabled: true, engine: 'singularity', oci: true] as ContainerConfig ).makeBinding()
 
         then:
-        binding.launch_cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} ${XDG_RUNTIME_DIR:+XDG_RUNTIME_DIR="$XDG_RUNTIME_DIR"} ${DBUS_SESSION_BUS_ADDRESS:+DBUS_SESSION_BUS_ADDRESS="$DBUS_SESSION_BUS_ADDRESS"} ${NXF_TASK_WORKDIR:+SINGULARITYENV_NXF_TASK_WORKDIR="$NXF_TASK_WORKDIR"} singularity exec --no-home --oci -B /work/dir docker://ubuntu:latest /bin/bash -c "cd $PWD; eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
+        binding.launch_cmd == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} ${XDG_RUNTIME_DIR:+XDG_RUNTIME_DIR="$XDG_RUNTIME_DIR"} ${DBUS_SESSION_BUS_ADDRESS:+DBUS_SESSION_BUS_ADDRESS="$DBUS_SESSION_BUS_ADDRESS"} ${NXF_TASK_WORKDIR:+SINGULARITYENV_NXF_TASK_WORKDIR="$NXF_TASK_WORKDIR"} singularity exec --no-home --oci -B /work/dir docker://ubuntu:latest /bin/bash -c "cd $NXF_TASK_WORKDIR; eval $(nxf_container_env); /bin/bash -ue /work/dir/.command.sh"'
         binding.cleanup_cmd == ""
         binding.kill_cmd == '[[ "$pid" ]] && nxf_kill $pid'
     }
@@ -1173,7 +1173,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'podman', enabled: true] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'podman run -i -e "NXF_TASK_WORKDIR" -v /work/dir:/work/dir -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'podman run -i -e "NXF_TASK_WORKDIR" -v /work/dir:/work/dir -w "$NXF_TASK_WORKDIR" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
         binding.cleanup_cmd == 'podman rm $NXF_BOXID &>/dev/null || true\n'
         binding.kill_cmd == 'podman stop $NXF_BOXID'
     }
@@ -1186,7 +1186,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'podman', enabled: true, entrypointOverride: true] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'podman run -i -e "NXF_TASK_WORKDIR" -v /work/dir:/work/dir -w "$PWD" --entrypoint /bin/bash --name $NXF_BOXID busybox -c "/bin/bash -ue /work/dir/.command.sh"'
+        binding.launch_cmd == 'podman run -i -e "NXF_TASK_WORKDIR" -v /work/dir:/work/dir -w "$NXF_TASK_WORKDIR" --entrypoint /bin/bash --name $NXF_BOXID busybox -c "/bin/bash -ue /work/dir/.command.sh"'
         binding.cleanup_cmd == 'podman rm $NXF_BOXID &>/dev/null || true\n'
         binding.kill_cmd == 'podman stop $NXF_BOXID'
     }
@@ -1200,7 +1200,7 @@ class BashWrapperBuilderTest extends Specification {
                 containerConfig: [engine: 'podman', enabled: true] ).makeBinding()
 
         then:
-        binding.launch_cmd == 'podman run -i -e "NXF_TASK_WORKDIR" -v /work/dir:/work/dir -v "$PWD":"$PWD" -w "$PWD" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
+        binding.launch_cmd == 'podman run -i -e "NXF_TASK_WORKDIR" -v /work/dir:/work/dir -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" --name $NXF_BOXID busybox /bin/bash -ue /work/dir/.command.sh'
         binding.cleanup_cmd == 'rm -rf $NXF_SCRATCH || true\npodman rm $NXF_BOXID &>/dev/null || true\n'
         binding.kill_cmd == 'podman stop $NXF_BOXID'
     }
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/cli/WaveRunCmd.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/cli/WaveRunCmd.groovy
index c9aaafc287..5f076694b3 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/cli/WaveRunCmd.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/cli/WaveRunCmd.groovy
@@ -87,7 +87,7 @@ class WaveRunCmd {
         final containerCmd = containerBuilder
                 .build()
                 .getRunCommand(args.join(' '))
-                .replaceAll('-w "\\$PWD" ','') // <-- hack to remove the PWD work dir
+                .replaceAll('-w "\\$NXF_TASK_WORKDIR" ','') // <-- hack to remove the PWD work dir
 
         log.debug "Running: $containerCmd"
         final process = new ProcessBuilder()

From dfc7b7c81ee9eed474adf4a2e22c450ffb5f0df6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Robin=20G=C3=B6gge?= <r.goegge@gmail.com>
Date: Wed, 8 Nov 2023 18:14:06 +0100
Subject: [PATCH 250/350] Add support for K8s schedulerName pod spec (#4485)
 [ci fast]
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Signed-off-by: Robin Gögge <r.goegge@gmail.com>
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Co-authored-by: Ben Sherman <bentshermann@gmail.com>
---
 docs/process.md                                   |  3 +++
 .../groovy/nextflow/k8s/model/PodOptions.groovy   | 10 ++++++++++
 .../nextflow/k8s/model/PodSpecBuilder.groovy      |  7 +++++++
 .../nextflow/k8s/model/PodOptionsTest.groovy      | 12 ++++++++++++
 .../nextflow/k8s/model/PodSpecBuilderTest.groovy  | 15 +++++++++++++++
 5 files changed, 47 insertions(+)

diff --git a/docs/process.md b/docs/process.md
index 7f99670ed5..03a1a6938f 100644
--- a/docs/process.md
+++ b/docs/process.md
@@ -2075,6 +2075,9 @@ The following options are available:
 `runAsUser: '<uid>'`
 : Specifies the user ID with which to run the container. Shortcut for the `securityContext` option.
 
+`schedulerName: '<name>'`
+: Specifies which [scheduler](https://kubernetes.io/docs/tasks/extend-kubernetes/configure-multiple-schedulers/#specify-schedulers-for-pods) is used to schedule the container. 
+
 `secret: '<secret>/<key>', mountPath: '</absolute/path>'`
 : *Can be specified multiple times*
 : Mounts a [Secret](https://kubernetes.io/docs/concepts/configuration/secret/) with name and optional key to the given path. If the key is omitted, the path is interpreted as a directory and all entries in the `Secret` are exposed in that path.
diff --git a/modules/nextflow/src/main/groovy/nextflow/k8s/model/PodOptions.groovy b/modules/nextflow/src/main/groovy/nextflow/k8s/model/PodOptions.groovy
index 19ddc6d8d2..4c1d0000e8 100644
--- a/modules/nextflow/src/main/groovy/nextflow/k8s/model/PodOptions.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/k8s/model/PodOptions.groovy
@@ -67,6 +67,8 @@ class PodOptions {
     private List<Map> tolerations
 
     private Boolean privileged
+
+    private String schedulerName
     
     PodOptions( List<Map> options=null ) {
         int size = options ? options.size() : 0
@@ -156,6 +158,9 @@ class PodOptions {
         else if( entry.privileged instanceof Boolean ) {
             this.privileged = entry.privileged as Boolean
         }
+        else if( entry.schedulerName ) {
+            this.schedulerName = entry.schedulerName
+        }
         else
             throw new IllegalArgumentException("Unknown pod options: $entry")
     }
@@ -218,6 +223,8 @@ class PodOptions {
 
     String getPriorityClassName() { priorityClassName }
 
+    String getSchedulerName() { schedulerName }
+
     List<Map> getTolerations() { tolerations }
 
     Boolean getPrivileged() { privileged }
@@ -297,6 +304,9 @@ class PodOptions {
         //  privileged execution
         result.privileged = other.privileged!=null ? other.privileged : this.privileged
 
+        // scheduler name
+        result.schedulerName = other.schedulerName ?: this.schedulerName
+
         return result
     }
 }
diff --git a/modules/nextflow/src/main/groovy/nextflow/k8s/model/PodSpecBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/k8s/model/PodSpecBuilder.groovy
index e87c0abeb2..24c56bc308 100644
--- a/modules/nextflow/src/main/groovy/nextflow/k8s/model/PodSpecBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/k8s/model/PodSpecBuilder.groovy
@@ -118,6 +118,8 @@ class PodSpecBuilder {
 
     Map<String,?> resourcesLimits
 
+    String schedulerName
+
     /**
      * @return A sequential volume unique identifier
      */
@@ -374,6 +376,8 @@ class PodSpecBuilder {
             tolerations.addAll(opts.tolerations)
         // -- privileged
         privileged = opts.privileged
+        // -- scheduler name
+        schedulerName = opts.schedulerName
 
         return this
     }
@@ -436,6 +440,9 @@ class PodSpecBuilder {
         if( nodeSelector )
             spec.nodeSelector = nodeSelector.toSpec()
 
+        if( schedulerName )
+            spec.schedulerName = schedulerName
+
         if( affinity )
             spec.affinity = affinity
 
diff --git a/modules/nextflow/src/test/groovy/nextflow/k8s/model/PodOptionsTest.groovy b/modules/nextflow/src/test/groovy/nextflow/k8s/model/PodOptionsTest.groovy
index 9070458eef..18f2592f78 100644
--- a/modules/nextflow/src/test/groovy/nextflow/k8s/model/PodOptionsTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/k8s/model/PodOptionsTest.groovy
@@ -553,4 +553,16 @@ class PodOptionsTest extends Specification {
         then:
         opts.getPrivileged()
     }
+
+    def 'should set pod schedulerName' () {
+        when:
+        def opts = new PodOptions()
+        then:
+        opts.getSchedulerName() == null
+
+        when:
+        opts = new PodOptions([ [schedulerName:'my-scheduler'] ])
+        then:
+        opts.getSchedulerName() == 'my-scheduler'
+    }
 }
diff --git a/modules/nextflow/src/test/groovy/nextflow/k8s/model/PodSpecBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/k8s/model/PodSpecBuilderTest.groovy
index 188e72dc81..dfb406c2be 100644
--- a/modules/nextflow/src/test/groovy/nextflow/k8s/model/PodSpecBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/k8s/model/PodSpecBuilderTest.groovy
@@ -581,6 +581,21 @@ class PodSpecBuilderTest extends Specification {
 
     }
 
+    def 'should create pod spec with schedulerName' () {
+
+        when:
+        def pod = new PodSpecBuilder()
+                .withPodName('foo')
+                .withImageName('busybox')
+                .withCommand(['echo', 'hello'])
+                .withPodOptions(new PodOptions(schedulerName: 'my-scheduler'))
+                .build()
+
+        then:
+        pod.spec.schedulerName == 'my-scheduler'
+
+    }
+
     def 'should create image pull request map' () {
         given:
         def builder = new PodSpecBuilder(imagePullSecret: 'MySecret')

From 3e66fba44292cb2283f5e40472efb499f4e009d3 Mon Sep 17 00:00:00 2001
From: Alan Hoyle <alan@alanhoyle.com>
Date: Wed, 8 Nov 2023 12:30:51 -0500
Subject: [PATCH 251/350] Add section about sharing modules (#4482)

Signed-off-by: Alan Hoyle <alan@alanhoyle.com>
Signed-off-by: Phil Ewels <phil.ewels@seqera.io>
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Co-authored-by: Phil Ewels <phil.ewels@seqera.io>
Co-authored-by: Ben Sherman <bentshermann@gmail.com>
---
 docs/module.md | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/docs/module.md b/docs/module.md
index 11298699dc..59fc886887 100644
--- a/docs/module.md
+++ b/docs/module.md
@@ -270,3 +270,11 @@ Those scripts will be made accessible like any other command in the task environ
 :::{note}
 This feature requires the use of a local or shared file system for the pipeline work directory, or {ref}`wave-page` when using cloud-based executors.
 :::
+
+## Sharing modules
+
+Modules are designed to be easy to share and re-use across different pipelines, which helps eliminate duplicate work and spread improvements throughout the community. While Nextflow does not provide an explicit mechanism for sharing modules, there are several ways to do it:
+
+- Simply copy the module files into your pipeline repository
+- Use [Git submodules](https://git-scm.com/book/en/v2/Git-Tools-Submodules) to fetch modules from other Git repositories without maintaining a separate copy
+- Use the [nf-core](https://nf-co.re/tools#modules) CLI to install and update modules with a standard approach used by the nf-core community

From d9ee987073eac4c591c4292552c1ff1027f722f9 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Wed, 8 Nov 2023 11:33:54 -0600
Subject: [PATCH 252/350] Add section on process directives to plugin docs
 (#4477)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 docs/plugins.md | 27 +++++++++++++++++++++++++++
 docs/process.md | 15 +++++++++++++--
 2 files changed, 40 insertions(+), 2 deletions(-)

diff --git a/docs/plugins.md b/docs/plugins.md
index 061207a9b9..1ceeb18bb1 100644
--- a/docs/plugins.md
+++ b/docs/plugins.md
@@ -249,6 +249,33 @@ channel
 The above snippet is based on the [nf-sqldb](https://github.com/nextflow-io/nf-sqldb) plugin. The `fromQuery` factory 
 is included under the alias `fromTable`.
 
+### Process directives
+
+Plugins that implement a [custom executor](#executors) will likely need to access {ref}`process directives <process-directives>` that affect the task execution. When an executor receives a task, the process directives can be accessed through that task's configuration. As a best practice, custom executors should try to support all process directives that have executor-specific behavior and are relevant to your executor.
+
+Nextflow does not provide the ability to define custom process directives in a plugin. Instead, you can use the {ref}`process-ext` directive to provide custom process settings to your executor. Try to use specific names that are not likely to conflict with other plugins or existing pipelines.
+
+Here is an example of a custom executor that uses existing process directives as well as a custom setting through the `ext` directive:
+
+```groovy
+class MyExecutor extends Executor {
+
+    @Override
+    TaskHandler createTaskHandler(TaskRun task) {
+        final cpus = task.config.cpus
+        final memory = task.config.memory
+        final myOption = task.config.ext.myOption
+
+        println "This task is configured with cpus=${cpus}, memory=${memory}, myOption=${myOption}"
+
+        // ...
+    }
+
+    // ...
+
+}
+```
+
 ### Trace observers
 
 A *trace observer* in Nextflow is an entity that can listen and react to workflow events, such as when a workflow starts, a task completes, a file is published, etc. Several components in Nextflow, such as the execution report and DAG visualization, are implemented as trace observers.
diff --git a/docs/process.md b/docs/process.md
index 03a1a6938f..845d0c22b5 100644
--- a/docs/process.md
+++ b/docs/process.md
@@ -1653,15 +1653,26 @@ process mapping {
   tuple val(sampleId), path(reads)
 
   """
-  STAR --genomeDir $genome --readFilesIn $reads
+  STAR --genomeDir $genome --readFilesIn $reads ${task.ext.args ?: ''}
   """
 }
 ```
 
-In the above example, the process uses a container whose version is controlled by the `ext.version` property. This can be defined in the `nextflow.config` file as shown below:
+In the above example, the process container version is controlled by `ext.version`, and the script supports additional command line arguments through `ext.args`.
+
+The `ext` directive can be set in the process definition:
+
+```groovy
+process mapping {
+  ext version: '2.5.3', args: '--foo --bar'
+}
+```
+
+Or in the Nextflow configuration:
 
 ```groovy
 process.ext.version = '2.5.3'
+process.ext.args = '--foo --bar'
 ```
 
 (process-fair)=

From 13aa1b60ffd45cf1141204afdf13385309ebf6e2 Mon Sep 17 00:00:00 2001
From: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
Date: Wed, 8 Nov 2023 14:50:56 -0300
Subject: [PATCH 253/350] Document `emit` option in process outputs (#4437)

Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Ben Sherman <bentshermann@gmail.com>
---
 docs/process.md  | 46 ++++++++++++++++++++++++++++++++++++++++++++++
 docs/workflow.md |  4 ++++
 2 files changed, 50 insertions(+)

diff --git a/docs/process.md b/docs/process.md
index 845d0c22b5..73d6dec191 100644
--- a/docs/process.md
+++ b/docs/process.md
@@ -1177,6 +1177,52 @@ output:
 
 In this example, the process is normally expected to produce an `output.txt` file, but in the cases where the file is legitimately missing, the process does not fail. The output channel will only contain values for those processes that produce `output.txt`.
 
+(process-multiple-outputs)=
+
+### Multiple outputs
+
+When a process declares multiple outputs, each output can be accessed by index. The following example prints the second process output (indexes start at zero):
+
+```groovy
+process FOO {
+    output:
+    path 'bye_file.txt'
+    path 'hi_file.txt'
+
+    """
+    echo "bye" > bye_file.txt
+    echo "hi" > hi_file.txt
+    """
+}
+
+workflow {
+    FOO()
+    FOO.out[1].view()
+}
+```
+
+You can also use the `emit` option to assign a name to each output and access them by name:
+
+```groovy
+process FOO {
+    output:
+    path 'bye_file.txt', emit: bye_file
+    path 'hi_file.txt',  emit: hi_file
+
+    """
+    echo "bye" > bye_file.txt
+    echo "hi" > hi_file.txt
+    """
+}
+
+workflow {
+    FOO()
+    FOO.out.hi_file.view()
+}
+```
+
+See {ref}`workflow-process-invocation` for more details.
+
 ## When
 
 The `when` block allows you to define a condition that must be satisfied in order to execute the process. The condition can be any expression that returns a boolean value.
diff --git a/docs/workflow.md b/docs/workflow.md
index 209b3e769b..a81dcc1a83 100644
--- a/docs/workflow.md
+++ b/docs/workflow.md
@@ -41,6 +41,8 @@ The `main:` label can be omitted if there are no `take:` or `emit:` blocks.
 Workflows were introduced in DSL2. If you are still using DSL1, see the {ref}`dsl1-page` page to learn how to migrate your Nextflow pipelines to DSL2.
 :::
 
+(workflow-process-invocation)=
+
 ## Process invocation
 
 A process can be invoked like a function in a workflow definition, passing the expected input channels like function arguments. For example:
@@ -142,6 +144,8 @@ workflow {
 }
 ```
 
+See {ref}`process-multiple-outputs` for more details.
+
 ### Process named stdout
 
 The `emit` option can also be used to name a `stdout` output:

From d49f02aeb4c44287f64b2df7a5d25a5a073581f8 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Wed, 8 Nov 2023 12:44:30 -0600
Subject: [PATCH 254/350] Add ability detect Google Batch spot interruption
 (#4462)

This commit adds the ability to detect Google Batch spot interruption.

When a spot instance is reclaimed nextflow now detect the event and return
the value 50001 as `task.exitStatus`. The developer can use this information
to re-execute the task using a dynamic errorStrategy, for example:

```
errorStrategy = { task.exitStatus==50001 ? 'retry' : 'terminate' }
```


Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/google.md                                |  5 ++-
 plugins/nf-google/build.gradle                |  2 +-
 .../batch/GoogleBatchTaskHandler.groovy       | 22 ++++++++++++-
 .../batch/GoogleBatchTaskHandlerTest.groovy   | 31 +++++++++++++++++++
 4 files changed, 57 insertions(+), 3 deletions(-)

diff --git a/docs/google.md b/docs/google.md
index 36a8846598..1dcddfc2d8 100644
--- a/docs/google.md
+++ b/docs/google.md
@@ -175,11 +175,14 @@ google {
 }
 ```
 
+:::{versionadded} 23.11.0-edge
+:::
+
 Since this type of virtual machines can be retired by the provider before the job completion, it is advisable to add the following retry strategy to your config file to instruct Nextflow to automatically re-execute a job if the virtual machine was terminated preemptively:
 
 ```groovy
 process {
-    errorStrategy = { task.exitStatus==14 ? 'retry' : 'terminate' }
+    errorStrategy = { task.exitStatus==50001 ? 'retry' : 'terminate' }
     maxRetries = 5
 }
 ```
diff --git a/plugins/nf-google/build.gradle b/plugins/nf-google/build.gradle
index 644aa9502e..b1c9178d6f 100644
--- a/plugins/nf-google/build.gradle
+++ b/plugins/nf-google/build.gradle
@@ -39,7 +39,7 @@ dependencies {
 
     api 'com.google.apis:google-api-services-lifesciences:v2beta-rev20210527-1.31.5'
     api 'com.google.auth:google-auth-library-oauth2-http:0.18.0'
-    api 'com.google.cloud:google-cloud-batch:0.10.0'
+    api 'com.google.cloud:google-cloud-batch:0.29.0'
     api 'com.google.cloud:google-cloud-logging:3.8.0'
     api 'com.google.cloud:google-cloud-nio:0.124.8'
     api 'com.google.cloud:google-cloud-storage:2.9.3'
diff --git a/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchTaskHandler.groovy b/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchTaskHandler.groovy
index 5fe5c45548..7bd4e1367f 100644
--- a/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchTaskHandler.groovy
+++ b/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchTaskHandler.groovy
@@ -378,7 +378,9 @@ class GoogleBatchTaskHandler extends TaskHandler implements FusionAwareTask {
         if( state in TERMINATED ) {
             log.debug "[GOOGLE BATCH] Process `${task.lazyName()}` - terminated job=$jobId; state=$state"
             // finalize the task
-            task.exitStatus = readExitFile()
+            task.exitStatus = getJobExitCode()
+            if( task.exitStatus == null )
+                task.exitStatus = readExitFile()
             if( state == 'FAILED' ) {
                 task.stdout = executor.logging.stdout(uid) ?: outputFile
                 task.stderr = executor.logging.stderr(uid) ?: errorFile
@@ -394,6 +396,24 @@ class GoogleBatchTaskHandler extends TaskHandler implements FusionAwareTask {
         return false
     }
 
+    protected Integer getJobExitCode() {
+        try {
+            final status = client.getJobStatus(jobId)
+            final eventsCount = status.getStatusEventsCount()
+            final lastEvent = eventsCount > 0 ? status.getStatusEvents(eventsCount - 1) : null
+            log.debug "[GOOGLE BATCH] Process `${task.lazyName()}` - last event: ${lastEvent}"
+
+            if( lastEvent?.getDescription()?.contains('due to Spot VM preemption with exit code 50001') ) {
+                return 50001
+            }
+        }
+        catch (Throwable t) {
+            log.debug "[GOOGLE BATCH] Unable to fetch task `${task.lazyName()}` exit code - cause: ${t.message}"
+        }
+
+        return null
+    }
+
     @PackageScope Integer readExitFile() {
         try {
             exitFile.text as Integer
diff --git a/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchTaskHandlerTest.groovy b/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchTaskHandlerTest.groovy
index 846969f971..4d0d36c6f1 100644
--- a/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchTaskHandlerTest.groovy
+++ b/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchTaskHandlerTest.groovy
@@ -18,6 +18,9 @@
 package nextflow.cloud.google.batch
 
 import com.google.cloud.batch.v1.GCS
+import com.google.cloud.batch.v1.JobStatus
+import com.google.cloud.batch.v1.StatusEvent
+import com.google.cloud.batch.v1.TaskExecution
 import com.google.cloud.batch.v1.Volume
 import com.google.cloud.storage.contrib.nio.CloudStorageFileSystem
 import nextflow.cloud.google.batch.client.BatchClient
@@ -330,4 +333,32 @@ class GoogleBatchTaskHandlerTest extends Specification {
         req.getAllocationPolicy().getInstances(0).policy.getMachineType() == ""
 
     }
+
+    JobStatus makeJobStatus(String desc) {
+        JobStatus.newBuilder()
+            .addStatusEvents(
+                StatusEvent.newBuilder()
+                    .setDescription(desc)
+            )
+            .build()
+    }
+
+    def 'should detect spot failures from status event'() {
+        given:
+        def jobId = 'job-id'
+        def client = Mock(BatchClient)
+        def task = Mock(TaskRun) {
+            lazyName() >> 'foo (1)'
+        }
+        def handler = Spy(new GoogleBatchTaskHandler(jobId: jobId, client: client, task: task))
+
+        when:
+        client.getJobStatus(jobId) >>> [
+            makeJobStatus('Task failed due to Spot VM preemption with exit code 50001.'),
+            makeJobStatus('Task succeeded')
+        ]
+        then:
+        handler.getJobExitCode() == 50001
+        handler.getJobExitCode() == null
+    }
 }

From 0356178bedd1215df5235f70ef0650a12f449af1 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Thu, 9 Nov 2023 01:47:51 -0600
Subject: [PATCH 255/350] Fix rounding error with long durations (#4496) [ci
 fast]

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 modules/nf-commons/src/main/nextflow/util/Duration.groovy   | 6 +++---
 .../nf-commons/src/test/nextflow/util/DurationTest.groovy   | 2 ++
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/modules/nf-commons/src/main/nextflow/util/Duration.groovy b/modules/nf-commons/src/main/nextflow/util/Duration.groovy
index feb54dfb5e..3322d5b638 100644
--- a/modules/nf-commons/src/main/nextflow/util/Duration.groovy
+++ b/modules/nf-commons/src/main/nextflow/util/Duration.groovy
@@ -146,7 +146,7 @@ class Duration implements Comparable<Duration>, Serializable, Cloneable {
                 def digit = groups[1]
                 def unit = groups[2]
 
-                result += convert( digit.toFloat(), unit )
+                result += convert( digit.toDouble(), unit )
                 str = str.substring(all.length()).trim()
                 continue
             }
@@ -166,7 +166,7 @@ class Duration implements Comparable<Duration>, Serializable, Cloneable {
      * @param unit A valid duration unit e.g. {@code d}, {@code d}, {@code h}, {@code hour}, etc
      * @return The duration in millisecond
      */
-    private long convert( float digit, String unit ) {
+    private long convert( double digit, String unit ) {
 
         if( unit in MILLIS ) {
             return Math.round(digit)
@@ -283,7 +283,7 @@ class Duration implements Comparable<Duration>, Serializable, Cloneable {
 
         // when less than 60 seconds round up to 100th of millis
         if( durationInMillis < 60_000 ) {
-            return String.valueOf( Math.round(durationInMillis / 1_000 * 10 as float) / 10 ) + 's'
+            return String.valueOf( Math.round(durationInMillis / 1_000 * 10 as double) / 10 ) + 's'
         }
 
         def secs
diff --git a/modules/nf-commons/src/test/nextflow/util/DurationTest.groovy b/modules/nf-commons/src/test/nextflow/util/DurationTest.groovy
index a818b05af7..ba69a151b3 100644
--- a/modules/nf-commons/src/test/nextflow/util/DurationTest.groovy
+++ b/modules/nf-commons/src/test/nextflow/util/DurationTest.groovy
@@ -62,6 +62,8 @@ class DurationTest extends Specification {
         Duration.of('1day').toHours() == 24
         Duration.of('1d').toHours() == 24
 
+        Duration.of('30d').toMillis() == 30 * DAY
+
     }
 
     def 'should not be parsed as a duration' () {

From 66a3ed1986d52c44f844913fb9806bd81073ce99 Mon Sep 17 00:00:00 2001
From: zetxqx <118311804+zetxqx@users.noreply.github.com>
Date: Wed, 8 Nov 2023 23:51:05 -0800
Subject: [PATCH 256/350] Update logging filter for Google Batch provider.
 (#4488)

Batch used to use generic_task as monitored resource type. However, the type is not only for Batch.
Google Batch is planning to switch it's own monitored resource type which is "batch.googleapis.com/Job".
To have a smooth changing, add a OR filter to have the new monitored resource type included.
After the transition is finished, the generic_task filter will be removed.

Signed-off-by: zetxqx <118311804+zetxqx@users.noreply.github.com>
---
 .../nextflow/cloud/google/batch/logging/BatchLogging.groovy     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/plugins/nf-google/src/main/nextflow/cloud/google/batch/logging/BatchLogging.groovy b/plugins/nf-google/src/main/nextflow/cloud/google/batch/logging/BatchLogging.groovy
index ce2cedfe76..da394dd39d 100644
--- a/plugins/nf-google/src/main/nextflow/cloud/google/batch/logging/BatchLogging.groovy
+++ b/plugins/nf-google/src/main/nextflow/cloud/google/batch/logging/BatchLogging.groovy
@@ -70,7 +70,7 @@ class BatchLogging implements Closeable {
         final stdout = new StringBuilder()
         final stderr = new StringBuilder()
         // use logging here
-        final filter = "resource.type=generic_task AND logName=\"projects/${projectId}/logs/batch_task_logs\" AND labels.job_uid=$uid"
+        final filter = "resource.type=generic_task OR resource.type=\"batch.googleapis.com/Job\" AND logName=\"projects/${projectId}/logs/batch_task_logs\" AND labels.job_uid=$uid"
         final entries = loggingService().listLogEntries(
                 Logging.EntryListOption.filter(filter),
                 Logging.EntryListOption.pageSize(1000) )

From 8ec14dd230321b74a1a237993d69934a051e91fe Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Thu, 9 Nov 2023 12:22:36 +0100
Subject: [PATCH 257/350] Fix Bug in JsonSplitter ordering [ci fast]

This change fixed a weird bug where the JSON splitter would fail
when parsing an object with a null value in it. It also makes the key
order consistent which is good for the CI test.

Credits Ben Sherman <ben.sherman@seqera.io>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../src/main/groovy/nextflow/splitter/JsonSplitter.groovy   | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/splitter/JsonSplitter.groovy b/modules/nextflow/src/main/groovy/nextflow/splitter/JsonSplitter.groovy
index 66dcb40b4b..d68b2ed070 100644
--- a/modules/nextflow/src/main/groovy/nextflow/splitter/JsonSplitter.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/splitter/JsonSplitter.groovy
@@ -219,9 +219,9 @@ class JsonSplitter extends AbstractTextSplitter {
                 break
             }
 
-            final map = Map.of(
-                 OBJECT_KEY, reader.nextName(),
-                 OBJECT_VALUE, fromJson(reader))
+            final map = new LinkedHashMap<>(1)
+            map[OBJECT_KEY] = reader.nextName()
+            map[OBJECT_VALUE] = fromJson(reader)
 
             // -- apply the splitting logic for the fetched record
             result = processChunk( map )

From 0ff3b3057ad83aee5a1be0d1115315f0f59c6e83 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Thu, 9 Nov 2023 05:26:02 -0600
Subject: [PATCH 258/350] Add doc tests, move some snippets to separate files
 (#3959)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .github/workflows/build.yml                   |    2 +-
 docs/doctests/choice.nf                       |    7 -
 docs/doctests/collateSize.nf                  |    5 -
 docs/doctests/collateStep.nf                  |    4 -
 docs/doctests/combs.nf                        |   12 -
 docs/doctests/cond.nf                         |    9 -
 docs/doctests/count.nf                        |   16 -
 docs/doctests/create-image-doc-tracing-io.nf  |   14 -
 .../create-image-doc-tracing-job-duration.nf  |   43 -
 .../create-image-doc-tracing-memory.nf        |   21 -
 docs/doctests/cross.nf                        |    5 -
 docs/doctests/env.nf                          |    6 -
 docs/doctests/flat_map.nf                     |    4 -
 docs/doctests/into.nf                         |   10 -
 docs/doctests/print_count.nf                  |   16 -
 docs/doctests/random.nf                       |   12 -
 docs/doctests/rec.nf                          |   14 -
 docs/doctests/reduce.nf                       |    4 -
 docs/doctests/saveHello.nf                    |   15 -
 docs/doctests/sepa.nf                         |    9 -
 docs/doctests/set.nf                          |   13 -
 docs/doctests/split.nf                        |   12 -
 docs/doctests/stdout.nf                       |    9 -
 docs/doctests/storedir.nf                     |   22 -
 docs/doctests/sum.nf                          |    4 -
 docs/operator.md                              | 1166 ++++++-----------
 docs/snippets/.gitignore                      |    2 +
 docs/snippets/branch-criteria.nf              |   12 +
 docs/snippets/branch-criteria.out             |    5 +
 docs/snippets/branch-with-fallback.nf         |   11 +
 docs/snippets/branch-with-fallback.out        |    5 +
 docs/snippets/branch-with-mapper.nf           |   16 +
 docs/snippets/branch-with-mapper.out          |    5 +
 docs/snippets/branch.nf                       |    9 +
 docs/snippets/branch.out                      |    5 +
 docs/snippets/buffer-with-closing.nf          |    3 +
 docs/snippets/buffer-with-closing.out         |    2 +
 docs/snippets/buffer-with-opening-closing.nf  |    4 +
 docs/snippets/buffer-with-opening-closing.out |    2 +
 docs/snippets/buffer-with-size-remainder.nf   |    3 +
 docs/snippets/buffer-with-size-remainder.out  |    4 +
 docs/snippets/buffer-with-size-skip.nf        |    3 +
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 docs/snippets/buffer-with-size.nf             |    3 +
 docs/snippets/buffer-with-size.out            |    3 +
 docs/snippets/collate-with-no-remainder.nf    |    3 +
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 docs/snippets/collate-with-step.nf            |    3 +
 docs/snippets/collate-with-step.out           |    4 +
 docs/snippets/collate.nf                      |    3 +
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 docs/snippets/collectfile-closure.out         |   11 +
 docs/snippets/collectfile.nf                  |    6 +
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 docs/snippets/combine-by.out                  |    6 +
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 docs/snippets/view.out                        |    3 +
 docs/snippets/your-first-script.nf            |    2 +-
 validation/test.sh                            |   24 +-
 193 files changed, 1193 insertions(+), 1080 deletions(-)
 delete mode 100644 docs/doctests/choice.nf
 delete mode 100644 docs/doctests/collateSize.nf
 delete mode 100644 docs/doctests/collateStep.nf
 delete mode 100644 docs/doctests/combs.nf
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index d1d2e1025b..d2cb25c27f 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -99,7 +99,7 @@ jobs:
       fail-fast: false
       matrix:
         java_version: [11, 21]
-        test_mode: ["test_integration", "test_aws", "test_azure", "test_google", "test_wave"]
+        test_mode: ["test_integration", "test_docs", "test_aws", "test_azure", "test_google", "test_wave"]
     steps:
       - name: Checkout
         uses: actions/checkout@v3
diff --git a/docs/doctests/choice.nf b/docs/doctests/choice.nf
deleted file mode 100644
index 4caecc4a21..0000000000
--- a/docs/doctests/choice.nf
+++ /dev/null
@@ -1,7 +0,0 @@
-   source = Channel.from 'Hello world', 'Hola', 'Hello John'
-    queue1 = Channel.create()
-    queue2 = Channel.create()
-    
-    source.choice(queue1, queue2) { a -> a =~ /^Hello.*/ ? 0 : 1 }
-
-    queue1.subscribe { println it }
diff --git a/docs/doctests/collateSize.nf b/docs/doctests/collateSize.nf
deleted file mode 100644
index 0730171bba..0000000000
--- a/docs/doctests/collateSize.nf
+++ /dev/null
@@ -1,5 +0,0 @@
-    Channel
-        .from(1,2,3,1,2,3,1)
-        .collate( 3, false )
-	.subscribe { println it  }
-
diff --git a/docs/doctests/collateStep.nf b/docs/doctests/collateStep.nf
deleted file mode 100644
index eac1793a92..0000000000
--- a/docs/doctests/collateStep.nf
+++ /dev/null
@@ -1,4 +0,0 @@
-Channel
-  .from(1,2,3,4)
-  .collate( 3, 1 )
-  .subscribe { println it }
diff --git a/docs/doctests/combs.nf b/docs/doctests/combs.nf
deleted file mode 100644
index 9429e848bc..0000000000
--- a/docs/doctests/combs.nf
+++ /dev/null
@@ -1,12 +0,0 @@
-    shapes = Channel.from('circle','square', 'triangle' )
-
-    process combine {
-      debug true
-      input:
-      val shape from shapes
-      each color from 'red','blue'
-      each size from 1,2,3
-
-      "echo draw $shape $color with size: $size"
-
-    }
diff --git a/docs/doctests/cond.nf b/docs/doctests/cond.nf
deleted file mode 100644
index 7b9517a1d0..0000000000
--- a/docs/doctests/cond.nf
+++ /dev/null
@@ -1,9 +0,0 @@
-    x = Channel.from( 'a', 'b', 'c')   
-
-    process simpleSum {
-        input: 
-        val x 
-
-        exec:
-        println "Hello Mr. $x"
-    }
diff --git a/docs/doctests/count.nf b/docs/doctests/count.nf
deleted file mode 100644
index 4d670f0780..0000000000
--- a/docs/doctests/count.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-Channel
-    .from(4,1,7,1,1)
-    .count(1)
-    .subscribe { println "literal $it" }
- // -> 3
-
-Channel
-    .from('a','c','c','q','b')
-    .count ( ~/c/ )
-    .subscribe { println "regexp: $it" }
-// -> 2
-
-Channel
-    .from('a','c','c','q','b')
-    .count { it <= 'c' }
-    .subscribe { println "predicate: $it" }
diff --git a/docs/doctests/create-image-doc-tracing-io.nf b/docs/doctests/create-image-doc-tracing-io.nf
deleted file mode 100644
index f89b44316f..0000000000
--- a/docs/doctests/create-image-doc-tracing-io.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-  
-  process io_read_write_1G {
-    """
-    dd if=/dev/zero of=/dev/null bs=1G count=1
-    """
-  }
-
-  
-  process io_read_write_256M {
-    """
-    dd if=/dev/zero of=/dev/null bs=256M count=1
-    """
-  }
diff --git a/docs/doctests/create-image-doc-tracing-job-duration.nf b/docs/doctests/create-image-doc-tracing-job-duration.nf
deleted file mode 100644
index 25fd6f0067..0000000000
--- a/docs/doctests/create-image-doc-tracing-job-duration.nf
+++ /dev/null
@@ -1,43 +0,0 @@
-process stress_1cpu {
-  """
-  stress -c 1 -t 5
-  """
-}
-
-process stress_2cpu {
-  cpus 2
-  """
-  stress -c 2 -t 10
-  """
-}
-
-process stress_100M_RAM {
-  memory 110.MB
-  """
-  stress -m 1 --vm-bytes 100000000 -t 10
-  """
-}
-
-process stress_1G_RAM {
-  memory 1.1.GB
-  """
-  stress -m 1 --vm-bytes 1000000000 -t 5
-  """
-}
-
-
-
-process io_read_write_1G {
-  """
-  dd if=/dev/zero of=1giga.img bs=1G count=1
-  """
-}
-
-process io_read_write_200M {
-  cpus 2
-  """
-  dd if=/dev/zero of=100mega.img bs=100M count=1
-  dd if=/dev/zero of=100mega.img bs=100M count=1
-  """
-}
-
diff --git a/docs/doctests/create-image-doc-tracing-memory.nf b/docs/doctests/create-image-doc-tracing-memory.nf
deleted file mode 100644
index ab33e50ef4..0000000000
--- a/docs/doctests/create-image-doc-tracing-memory.nf
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/usr/bin/env nextflow
-
-process foo {
-
-    memory '1.5 GB'
-
-    """
-    memory_vmem_1GiB_ram_0Gib
-    """
-
-}
-
-process bar {
-
-    memory '1.5 GB'
-
-    """
-    memory_vmem_1GiB_ram_1Gib
-    """
-
-}
diff --git a/docs/doctests/cross.nf b/docs/doctests/cross.nf
deleted file mode 100644
index 2bb12560a7..0000000000
--- a/docs/doctests/cross.nf
+++ /dev/null
@@ -1,5 +0,0 @@
-
-source = Channel.from( [1, 'alpha'], [2, 'beta'] )
-target = Channel.from( [1, 'x'], [1, 'y'], [1, 'z'], [2,'p'], [2,'q'], [2,'t'] )
-
-target.cross(source).subscribe { println it }
\ No newline at end of file
diff --git a/docs/doctests/env.nf b/docs/doctests/env.nf
deleted file mode 100644
index d398e38ea9..0000000000
--- a/docs/doctests/env.nf
+++ /dev/null
@@ -1,6 +0,0 @@
-process env {
-  debug true
-
-  'echo $MYPATH'
-
-}
diff --git a/docs/doctests/flat_map.nf b/docs/doctests/flat_map.nf
deleted file mode 100644
index 5f2fc45944..0000000000
--- a/docs/doctests/flat_map.nf
+++ /dev/null
@@ -1,4 +0,0 @@
-
-    Channel.from ( 1, 2, 3 )
-           .flatMap { it -> [ number: it, square: it*it ] }
-           .subscribe { println it.key + ': ' + it.value }
\ No newline at end of file
diff --git a/docs/doctests/into.nf b/docs/doctests/into.nf
deleted file mode 100644
index ff4a91ea7b..0000000000
--- a/docs/doctests/into.nf
+++ /dev/null
@@ -1,10 +0,0 @@
-
-     alpha = Channel.create()
-     delta = Channel.create()
-
-     Channel
-        .from([1,2], ['a','b'], ['p','q'])
-        .into( alpha, delta )
-
-     alpha.subscribe { println "first : $it" }
-     delta.subscribe { println "second: $it" }
diff --git a/docs/doctests/print_count.nf b/docs/doctests/print_count.nf
deleted file mode 100644
index 72de97df5c..0000000000
--- a/docs/doctests/print_count.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-    process printCount {
-
-      input:
-      val cheers from 'Bonjour', 'Ciao', 'Hello', 'Hola'
-
-      share:
-      val count from 1 into result
-
-      script:
-      count += count
-      "echo $cheers world! "
-
-    }
-
-
-    result.subscribe  { println "Process result: $it" }
diff --git a/docs/doctests/random.nf b/docs/doctests/random.nf
deleted file mode 100644
index f3f1ebba00..0000000000
--- a/docs/doctests/random.nf
+++ /dev/null
@@ -1,12 +0,0 @@
-    process randomNum {
-    
-       output:
-       file 'random_out' into numbers
-
-       '''
-       echo $RANDOM > random_out
-       '''
-
-    }
-    
-   numbers.subscribe { println "Received: " + it.text }
diff --git a/docs/doctests/rec.nf b/docs/doctests/rec.nf
deleted file mode 100644
index 2aff1ccdf2..0000000000
--- a/docs/doctests/rec.nf
+++ /dev/null
@@ -1,14 +0,0 @@
- methods = ['prot','dna', 'rna']
-
-   process anyValue {
-     input:
-     val x from methods
-
-     output:
-     val x into receiver
-
-     "echo $x > file"
-
-   }
-
-   receiver.subscribe { println "Received: $it" }
diff --git a/docs/doctests/reduce.nf b/docs/doctests/reduce.nf
deleted file mode 100644
index 38f154282d..0000000000
--- a/docs/doctests/reduce.nf
+++ /dev/null
@@ -1,4 +0,0 @@
-    Channel
-        .from( 1, 2, 3, 4, 5 )
-        .reduce { a, b ->  println "a: $a	b: $b"; return a+b }
-        .subscribe { println "result = $it" }
\ No newline at end of file
diff --git a/docs/doctests/saveHello.nf b/docs/doctests/saveHello.nf
deleted file mode 100644
index defa469e27..0000000000
--- a/docs/doctests/saveHello.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-    process saveHello {
-      input:
-      val cheers from 'Bonjour', 'Ciao', 'Hello', 'Hola'
-
-      share:
-      file greetings into result
-      
-      "echo '$cheers' >> $greetings "
-
-    }
-
-
-    result.subscribe { println it.text  }  
-
-
diff --git a/docs/doctests/sepa.nf b/docs/doctests/sepa.nf
deleted file mode 100644
index da481b4697..0000000000
--- a/docs/doctests/sepa.nf
+++ /dev/null
@@ -1,9 +0,0 @@
-    queue1 = Channel.create()
-    queue2 = Channel.create()
-
-    Channel
-        .from ( 2,4,8 ) 
-        .separate( queue1, queue2 ) { a -> [a+1, a*a] }
-
-    queue1.subscribe { println "Channel 1: $it" }
-    queue2.subscribe { println "Channel 2: $it" }
diff --git a/docs/doctests/set.nf b/docs/doctests/set.nf
deleted file mode 100644
index 61825f2d5b..0000000000
--- a/docs/doctests/set.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-     tuple = Channel.from( [1, 'alpha', 'Lorem ipsum dolor sit amet'], [2, 'beta', 'consectetur adipiscing elit'] )
-
-     process setExample {
-         input:
-         set val(x), env(VAR_X), file('latin.txt')  from tuple 
-
-         """
-         echo Processing $x
-         cat latin.txt
-         """
-
-     }
-
diff --git a/docs/doctests/split.nf b/docs/doctests/split.nf
deleted file mode 100644
index aade294fd7..0000000000
--- a/docs/doctests/split.nf
+++ /dev/null
@@ -1,12 +0,0 @@
-    process splitLetters {
-
-        output:
-        file 'chunk_*' into letters
-
-        '''
-        printf 'Hola' | split -b 1 - chunk_
-        '''
-    }
-
-    letters.subscribe { println it *. text }
-
diff --git a/docs/doctests/stdout.nf b/docs/doctests/stdout.nf
deleted file mode 100644
index 1d18349b63..0000000000
--- a/docs/doctests/stdout.nf
+++ /dev/null
@@ -1,9 +0,0 @@
-    process echoSomething {
-        output: 
-        stdout channel
-    
-        "echo Hello world!"
-      
-    }
-    
-    channel.subscribe { print "I say..  $it" }
diff --git a/docs/doctests/storedir.nf b/docs/doctests/storedir.nf
deleted file mode 100644
index bf13689175..0000000000
--- a/docs/doctests/storedir.nf
+++ /dev/null
@@ -1,22 +0,0 @@
-genomes = Channel.path( params.genomes )
-
-  process formatBlastDatabases {
-
-    storeDir 'blastdb'
-
-    input:
-    file species from genomes
-
-    output:
-    file "${dbName}.*" into blastDb
-
-    script:
-    dbName = species.baseName
-    """
-    makeblastdb -dbtype prot -in ${species} -out ${dbName}
-    """
-
-  }
-
-blastDb.subscribe { println it  }
-
diff --git a/docs/doctests/sum.nf b/docs/doctests/sum.nf
deleted file mode 100644
index 558676a9a9..0000000000
--- a/docs/doctests/sum.nf
+++ /dev/null
@@ -1,4 +0,0 @@
-	Channel
-		.from( 4, 1, 7, 5 )
-		.sum { it * it } 
-		.subscribe {  println "Square: $it" } 
diff --git a/docs/operator.md b/docs/operator.md
index 5d92cdf130..a54f0b022e 100644
--- a/docs/operator.md
+++ b/docs/operator.md
@@ -27,25 +27,12 @@ The `branch` operator allows you to forward the items emitted by a source channe
 
 The selection criteria is defined by specifying a {ref}`closure <script-closure>` that provides one or more boolean expression, each of which is identified by a unique label. On the first expression that evaluates to a *true* value, the current item is bound to a named channel as the label identifier. For example:
 
-```groovy
-Channel
-    .of(1, 2, 3, 40, 50)
-    .branch {
-        small: it < 10
-        large: it > 10
-    }
-    .set { result }
-
- result.small.view { "$it is small" }
- result.large.view { "$it is large" }
+```{literalinclude} snippets/branch.nf
+:language: groovy
 ```
 
-```
-1 is small
-2 is small
-3 is small
-40 is large
-50 is large
+```{literalinclude} snippets/branch.out
+:language: console
 ```
 
 :::{note}
@@ -54,31 +41,22 @@ The above *small* and *large* strings may be printed in any order due to the asy
 
 A default fallback condition can be specified using `true` as the last branch condition:
 
-```groovy
-Channel
-    .from(1, 2, 3, 40, 50)
-    .branch {
-        small: it < 10
-        large: it < 50
-        other: true
-    }
+```{literalinclude} snippets/branch-with-fallback.nf
+:language: groovy
 ```
 
-The value returned by each branch condition can be customised by specifying an optional expression statement(s) just after the condition expression. For example:
+```{literalinclude} snippets/branch-with-fallback.out
+:language: console
+```
 
-```groovy
-Channel
-    .from(1, 2, 3, 40, 50)
-    .branch {
-        foo: it < 10
-            return it+2
+The value returned by each branch condition can be customised by specifying an optional expression statement(s) just after the condition expression. For example:
 
-        bar: it < 50
-            return it-2
+```{literalinclude} snippets/branch-with-mapper.nf
+:language: groovy
+```
 
-        other: true
-            return 0
-    }
+```{literalinclude} snippets/branch-with-mapper.out
+:language: console
 ```
 
 :::{tip}
@@ -87,14 +65,12 @@ When the `return` keyword is omitted, the value of the last expression statement
 
 To create a branch criteria as variable that can be passed as an argument to more than one `branch` operator use the `branchCriteria` built-in method as shown below:
 
-```groovy
-def criteria = branchCriteria {
-    small: it < 10
-    large: it > 10
-}
+```{literalinclude} snippets/branch-criteria.nf
+:language: groovy
+```
 
-Channel.of(1, 2, 30).branch(criteria).set { ch1 }
-Channel.of(10, 20, 1).branch(criteria).set { ch2 }
+```{literalinclude} snippets/branch-criteria.out
+:language: console
 ```
 
 ## buffer
@@ -107,70 +83,52 @@ There are a number of ways you can regulate how `buffer` gathers the items from
 
 - `buffer( closingCondition )`: starts to collect the items emitted by the channel into a subset until the `closingCondition` is verified. After that the subset is emitted to the resulting channel and new items are gathered into a new subset. The process is repeated until the last value in the source channel is sent. The `closingCondition` can be specified either as a {ref}`regular expression <script-regexp>`, a Java class, a literal value, or a boolean predicate that has to be satisfied. For example:
 
-  ```groovy
-  Channel
-      .of( 1, 2, 3, 1, 2, 3 )
-      .buffer { it == 2 }
-      .view()
+  ```{literalinclude} snippets/buffer-with-closing.nf
+  :language: groovy
+  ```
 
-  // emitted values
-  [1,2]
-  [3,1,2]
+  ```{literalinclude} snippets/buffer-with-closing.out
+  :language: console
   ```
 
 - `buffer( openingCondition, closingCondition )`: starts to gather the items emitted by the channel as soon as one of the them verify the `openingCondition` and it continues until there is one item which verify the `closingCondition`. After that the subset is emitted and it continues applying the described logic until the last channel item is emitted. Both conditions can be defined either as a {ref}`regular expression <script-regexp>`, a literal value, a Java class, or a boolean predicate that need to be satisfied. For example:
 
-  ```groovy
-  Channel
-      .of( 1, 2, 3, 4, 5, 1, 2, 3, 4, 5, 1, 2 )
-      .buffer( 2, 4 )
-      .view()
+  ```{literalinclude} snippets/buffer-with-opening-closing.nf
+  :language: groovy
+  ```
 
-  // emits bundles starting with '2' and ending with'4'
-  [2,3,4]
-  [2,3,4]
+  ```{literalinclude} snippets/buffer-with-opening-closing.out
+  :language: console
   ```
 
 - `buffer( size: n )`: transform the source channel in such a way that it emits tuples made up of `n` elements. An incomplete tuple is discarded. For example:
 
-  ```groovy
-  Channel
-      .of( 1, 2, 3, 1, 2, 3, 1 )
-      .buffer( size: 2 )
-      .view()
+  ```{literalinclude} snippets/buffer-with-size.nf
+  :language: groovy
+  ```
 
-  // emitted values
-  [1, 2]
-  [3, 1]
-  [2, 3]
+  ```{literalinclude} snippets/buffer-with-size.out
+  :language: console
   ```
 
   If you want to emit the last items in a tuple containing less than `n` elements, simply add the parameter `remainder` specifying `true`, for example:
 
-  ```groovy
-  Channel
-      .of( 1, 2, 3, 1, 2, 3, 1 )
-      .buffer( size: 2, remainder: true )
-      .view()
-
-  // emitted values
-  [1, 2]
-  [3, 1]
-  [2, 3]
-  [1]
+  ```{literalinclude} snippets/buffer-with-size-remainder.nf
+  :language: groovy
+  ```
+
+  ```{literalinclude} snippets/buffer-with-size-remainder.out
+  :language: console
   ```
 
 - `buffer( size: n, skip: m )`: as in the previous example, it emits tuples containing `n` elements, but skips `m` values before starting to collect the values for the next tuple (including the first emission). For example:
 
-  ```groovy
-  Channel
-      .of( 1, 2, 3, 4, 5, 1, 2, 3, 4, 5, 1, 2 )
-      .buffer( size:3, skip:2 )
-      .view()
+  ```{literalinclude} snippets/buffer-with-size-skip.nf
+  :language: groovy
+  ```
 
-  // emitted values
-  [3, 4, 5]
-  [3, 4, 5]
+  ```{literalinclude} snippets/buffer-with-size-skip.out
+  :language: console
   ```
 
   If you want to emit the remaining items in a tuple containing less than `n` elements, simply add the parameter `remainder` specifying `true`, as shown in the previous example.
@@ -183,47 +141,32 @@ See also: [collate](#collate) operator.
 
 The `collate` operator transforms a channel in such a way that the emitted values are grouped in tuples containing `n` items. For example:
 
-```groovy
-Channel
-    .of(1,2,3,1,2,3,1)
-    .collate( 3 )
-    .view()
+```{literalinclude} snippets/collate.nf
+:language: groovy
 ```
 
-```
-[1, 2, 3]
-[1, 2, 3]
-[1]
+```{literalinclude} snippets/collate.out
+:language: console
 ```
 
 As shown in the above example the last tuple may be incomplete e.g. contain fewer elements than the specified size. If you want to avoid this, specify `false` as the second parameter. For example:
 
-```groovy
-Channel
-    .of(1,2,3,1,2,3,1)
-    .collate( 3, false )
-    .view()
+```{literalinclude} snippets/collate-with-no-remainder.nf
+:language: groovy
 ```
 
-```
-[1, 2, 3]
-[1, 2, 3]
+```{literalinclude} snippets/collate-with-no-remainder.out
+:language: console
 ```
 
 A second version of the `collate` operator allows you to specify, after the `size`, the `step` by which elements are collected in tuples. For example:
 
-```groovy
-Channel
-    .of(1,2,3,4)
-    .collate( 3, 1 )
-    .view()
+```{literalinclude} snippets/collate-with-step.nf
+:language: groovy
 ```
 
-```
-[1, 2, 3]
-[2, 3, 4]
-[3, 4]
-[4]
+```{literalinclude} snippets/collate-with-step.out
+:language: console
 ```
 
 As before, if you don't want to emit the last items which do not complete a tuple, specify `false` as the third parameter.
@@ -238,28 +181,22 @@ See also: [buffer](#buffer) operator.
 
 The `collect` operator collects all the items emitted by a channel to a `List` and return the resulting object as a sole emission. For example:
 
-```groovy
-Channel
-    .of( 1, 2, 3, 4 )
-    .collect()
-    .view()
+```{literalinclude} snippets/collect.nf
+:language: groovy
 ```
 
-```
-[1,2,3,4]
+```{literalinclude} snippets/collect.out
+:language: console
 ```
 
 An optional {ref}`closure <script-closure>` can be specified to transform each item before adding it to the resulting list. For example:
 
-```groovy
-Channel
-    .of( 'hello', 'ciao', 'bonjour' )
-    .collect { it.length() }
-    .view()
+```{literalinclude} snippets/collect-with-mapper.nf
+:language: groovy
 ```
 
-```
-[5,4,7]
+```{literalinclude} snippets/collect-with-mapper.out
+:language: console
 ```
 
 Available options:
@@ -280,42 +217,21 @@ The `collectFile` operator allows you to gather the items emitted by a channel a
 
 In the simplest case, just specify the name of a file where the entries have to be stored. For example:
 
-```groovy
-Channel
-    .of('alpha', 'beta', 'gamma')
-    .collectFile(name: 'sample.txt', newLine: true)
-    .subscribe {
-        println "Entries are saved to file: $it"
-        println "File content is: ${it.text}"
-    }
+```{literalinclude} snippets/collectfile.nf
+:language: groovy
 ```
 
+
 A second version of the `collectFile` operator allows you to gather the items emitted by a channel and group them together into files whose name can be defined by a dynamic criteria. The grouping criteria is specified by a {ref}`closure <script-closure>` that must return a pair in which the first element defines the file name for the group and the second element the actual value to be appended to that file. For example:
 
-```groovy
-Channel
-    .of('Hola', 'Ciao', 'Hello', 'Bonjour', 'Halo')
-    .collectFile() { item ->
-        [ "${item[0]}.txt", item + '\n' ]
-    }
-    .subscribe {
-        println "File ${it.name} contains:"
-        println it.text
-    }
+```{literalinclude} snippets/collectfile-closure.nf
+:language: groovy
 ```
 
+```{literalinclude} snippets/collectfile-closure.out
+:language: console
 ```
-File 'B.txt' contains:
-Bonjour
-
-File 'C.txt' contains:
-Ciao
 
-File 'H.txt' contains:
-Halo
-Hola
-Hello
-```
 
 :::{tip}
 When the items emitted by the source channel are files, the grouping criteria can be omitted. In this case the items content will be grouped into file(s) having the same name as the source items.
@@ -400,41 +316,22 @@ The `collectFile` operator needs to store files in a temporary folder that is au
 
 The `combine` operator combines (cartesian product) the items emitted by two channels or by a channel and a `Collection` object (as right operand). For example:
 
-```groovy
-numbers = Channel.of(1, 2, 3)
-words = Channel.of('hello', 'ciao')
-numbers
-    .combine(words)
-    .view()
+```{literalinclude} snippets/combine.nf
+:language: groovy
 ```
 
-```
-[1, hello]
-[2, hello]
-[3, hello]
-[1, ciao]
-[2, ciao]
-[3, ciao]
+```{literalinclude} snippets/combine.out
+:language: console
 ```
 
 A second version of the `combine` operator allows you to combine items that share a common matching key. The index of the key element is specified by using the `by` parameter (zero-based index, multiple indices can be specified as a list of integers). For example:
 
-```groovy
-left = Channel.of(['A', 1], ['B', 2], ['A', 3])
-right = Channel.of(['B', 'x'], ['B', 'y'], ['A', 'z'], ['A', 'w'])
-
-left
-    .combine(right, by: 0)
-    .view()
+```{literalinclude} snippets/combine-by.nf
+:language: groovy
 ```
 
-```
-[A, 1, z]
-[A, 3, z]
-[A, 1, w]
-[A, 3, w]
-[B, 2, x]
-[B, 2, y]
+```{literalinclude} snippets/combine-by.out
+:language: console
 ```
 
 See also [join](#join) and [cross](#cross).
@@ -451,23 +348,12 @@ In other words, given *N* channels, the items from the *i+1 th* channel are emit
 
 For example:
 
-```groovy
-a = Channel.of('a', 'b', 'c')
-b = Channel.of(1, 2, 3)
-c = Channel.of('p', 'q')
-
-c.concat( b, a ).view()
+```{literalinclude} snippets/concat.nf
+:language: groovy
 ```
 
-```
-p
-q
-1
-2
-3
-a
-b
-c
+```{literalinclude} snippets/concat.out
+:language: console
 ```
 
 (operator-count)=
@@ -478,34 +364,38 @@ c
 
 The `count` operator creates a channel that emits a single item: a number that represents the total number of items emitted by the source channel. For example:
 
-```groovy
-Channel
-    .of(9,1,7,5)
-    .count()
-    .view()
-// -> 4
+```{literalinclude} snippets/count.nf
+:language: groovy
+```
+
+```{literalinclude} snippets/count.out
+:language: console
 ```
 
 An optional parameter can be provided to select which items are to be counted. The selection criteria can be specified either as a {ref}`regular expression <script-regexp>`, a literal value, a Java class, or a boolean predicate that needs to be satisfied. For example:
 
-```groovy
-Channel
-    .of(4,1,7,1,1)
-    .count(1)
-    .view()
-// -> 3
+```{literalinclude} snippets/count-with-filter-number.nf
+:language: groovy
+```
 
-Channel
-    .of('a','c','c','q','b')
-    .count ( ~/c/ )
-    .view()
-// -> 2
+```{literalinclude} snippets/count-with-filter-number.out
+:language: console
+```
 
-Channel
-    .of('a','c','c','q','b')
-    .count { it <= 'c' }
-    .view()
-// -> 4
+```{literalinclude} snippets/count-with-filter-regex.nf
+:language: groovy
+```
+
+```{literalinclude} snippets/count-with-filter-regex.out
+:language: console
+```
+
+```{literalinclude} snippets/count-with-filter-closure.nf
+:language: groovy
+```
+
+```{literalinclude} snippets/count-with-filter-closure.out
+:language: console
 ```
 
 (operator-countfasta)=
@@ -550,20 +440,12 @@ The `cross` operator allows you to combine the items of two channels in such a w
 
 The key is defined, by default, as the first entry in an array, a list or map object, or the value itself for any other data type. For example:
 
-```groovy
-source = Channel.of( [1, 'alpha'], [2, 'beta'] )
-target = Channel.of( [1, 'x'], [1, 'y'], [1, 'z'], [2, 'p'], [2, 'q'], [2, 't'] )
-
-source.cross(target).view()
+```{literalinclude} snippets/cross.nf
+:language: groovy
 ```
 
-```
-[ [1, alpha], [1, x] ]
-[ [1, alpha], [1, y] ]
-[ [1, alpha], [1, z] ]
-[ [2, beta],  [2, p] ]
-[ [2, beta],  [2, q] ]
-[ [2, beta],  [2, t] ]
+```{literalinclude} snippets/cross.out
+:language: console
 ```
 
 The above example shows how the items emitted by the source channels are associated to the ones emitted by the target channel (on the right) having the same key.
@@ -573,7 +455,15 @@ There are two important caveats when using the `cross` operator:
 1. The operator is not `commutative`, i.e. the result of `a.cross(b)` is different from `b.cross(a)`
 2. The source channel should emits items for which there's no key repetition i.e. the emitted items have an unique key identifier.
 
-Optionally, a mapping function can be specified in order to provide a custom rule to associate an item to a key.
+An optional closure can be used to define the matching key for each item:
+
+```{literalinclude} snippets/cross-with-mapper.nf
+:language: groovy
+```
+
+```{literalinclude} snippets/cross-with-mapper.out
+:language: console
+```
 
 ## distinct
 
@@ -581,38 +471,22 @@ Optionally, a mapping function can be specified in order to provide a custom rul
 
 The `distinct` operator allows you to remove *consecutive* duplicated items from a channel, so that each emitted item is different from the preceding one. For example:
 
-```groovy
-Channel
-    .of( 1,1,2,2,2,3,1,1,2,2,3 )
-    .distinct()
-    .subscribe onNext: { println it }, onComplete: { println 'Done' }
+```{literalinclude} snippets/distinct.nf
+:language: groovy
 ```
 
-```
-1
-2
-3
-1
-2
-3
-Done
+```{literalinclude} snippets/distinct.out
+:language: console
 ```
 
 You can also specify an optional {ref}`closure <script-closure>` that customizes the way it distinguishes between distinct items. For example:
 
-```groovy
-Channel
-    .of( 1,1,2,2,2,3,1,1,2,4,6 )
-    .distinct { it % 2 }
-    .subscribe onNext: { println it }, onComplete: { println 'Done' }
+```{literalinclude} snippets/distinct-with-mapper.nf
+:language: groovy
 ```
 
-```
-1
-2
-3
-2
-Done
+```{literalinclude} snippets/distinct-with-mapper.out
+:language: console
 ```
 
 (operator-dump)=
@@ -627,29 +501,21 @@ This is useful to enable the debugging of one or more channel content on-demand
 
 An optional `tag` parameter allows you to select which channel to dump. For example:
 
-```groovy
-Channel
-    .of(1,2,3)
-    .map { it+1 }
-    .dump(tag: 'foo')
-
-Channel
-    .of(1,2,3)
-    .map { it^2 }
-    .dump(tag: 'bar')
+```{literalinclude} snippets/dump.nf
+:language: groovy
 ```
 
-Then you will be able to specify the tag `foo` or `bar` as an argument of the `-dump-channels` option to print either the content of the first or the second channel. Multiple tag names can be specified separating them with a `,` character.
+Then, you can run your pipeline with `-dump-channels foo` or `-dump-channels bar` to dump the content of either channel. Multiple tag names can be specified as a comma-separated list.
 
-:::{versionadded} 22.10.0
-The output can be formatted by enabling the `pretty` option:
+Available options:
 
-```groovy
-Channel
-    .fromSRA('SRP043510')
-    .dump(tag: 'foo', pretty: true)
-```
-:::
+`pretty`
+: :::{versionadded} 22.10.0
+  :::
+: When `true`, format the output as pretty-printed JSON (default: `false`).
+
+`tag`
+: Associate the channel with a tag that can be specified with the `-dump-channels` option to select which channels to dump.
 
 ## filter
 
@@ -659,45 +525,32 @@ The `filter` operator allows you to get only the items emitted by a channel that
 
 The following example shows how to filter a channel by using a regular expression that returns only strings that begin with `a`:
 
-```groovy
-Channel
-    .of( 'a', 'b', 'aa', 'bc', 3, 4.5 )
-    .filter( ~/^a.*/ )
-    .view()
+```{literalinclude} snippets/filter-regex.nf
+:language: groovy
 ```
 
-```
-a
-aa
+```{literalinclude} snippets/filter-regex.out
+:language: console
 ```
 
 The following example shows how to filter a channel by specifying the type qualifier `Number` so that only numbers are returned:
 
-```groovy
-Channel
-    .of( 'a', 'b', 'aa', 'bc', 3, 4.5 )
-    .filter( Number )
-    .view()
+```{literalinclude} snippets/filter-type.nf
+:language: groovy
 ```
 
-```
-3
-4.5
+```{literalinclude} snippets/filter-type.out
+:language: console
 ```
 
 Finally, a filtering condition can be defined by using any a boolean predicate. A predicate is expressed by a {ref}`closure <script-closure>` returning a boolean value. For example the following fragment shows how filter a channel emitting numbers so that the odd values are returned:
 
-```groovy
-Channel
-    .of( 1, 2, 3, 4, 5 )
-    .filter { it % 2 == 1 }
-    .view()
+```{literalinclude} snippets/filter-closure.nf
+:language: groovy
 ```
 
-```
-1
-3
-5
+```{literalinclude} snippets/filter-closure.out
+:language: console
 ```
 
 :::{tip}
@@ -712,30 +565,8 @@ In the above example the filter condition is wrapped in curly brackets, instead
 
 The `first` operator creates a channel that returns the first item emitted by the source channel, or eventually the first item that matches an optional condition. The condition can be specified by using a {ref}`regular expression<script-regexp>`, a Java `class` type or any boolean predicate. For example:
 
-```groovy
-// no condition is specified, emits the very first item: 1
-Channel
-    .of( 1, 2, 3 )
-    .first()
-    .view()
-
-// emits the first String value: 'a'
-Channel
-    .of( 1, 2, 'a', 'b', 3 )
-    .first( String )
-    .view()
-
-// emits the first item matching the regular expression: 'aa'
-Channel
-    .of( 'a', 'aa', 'aaa' )
-    .first( ~/aa.*/ )
-    .view()
-
-// emits the first item for which the predicate evaluates to true: 4
-Channel
-    .of( 1,2,3,4,5 )
-    .first { it > 3 }
-    .view()
+```{literalinclude} snippets/first.nf
+:language: groovy
 ```
 
 (operator-flatmap)=
@@ -744,47 +575,26 @@ Channel
 
 *Returns: queue channel*
 
-The `flatMap` operator applies a function of your choosing to every item emitted by a channel, and returns the items so obtained as a new channel. Whereas the mapping function returns a list of items, this list is flattened so that each single item is emitted on its own.
+The `flatMap` operator applies a *mapping function* to each item from a source channel.
 
-For example:
-
-```groovy
-// create a channel of numbers
-numbers = Channel.of( 1, 2, 3 )
+When the mapping function returns a list, each element in the list is emitted separately:
 
-// map each number to a tuple (array), which items are emitted separately
-results = numbers.flatMap { n -> [ n*2, n*3 ] }
-
-// print the final results
-results.subscribe onNext: { println it }, onComplete: { println 'Done' }
+```{literalinclude} snippets/flatmap-list.nf
+:language: groovy
 ```
 
-```
-2
-3
-4
-6
-6
-9
-Done
+```{literalinclude} snippets/flatmap-list.out
+:language: console
 ```
 
-Associative arrays are handled in the same way, so that each array entry is emitted as a single key-value pair. For example:
+When the mapping function returns a map, each key-value pair in the map is emitted separately:
 
-```groovy
-Channel
-    .of ( 1, 2, 3 )
-    .flatMap { it -> [ number: it, square: it*it ] }
-    .view { it.key + ': ' + it.value }
+```{literalinclude} snippets/flatmap-map.nf
+:language: groovy
 ```
 
-```
-number: 1
-square: 1
-number: 2
-square: 4
-number: 3
-square: 9
+```{literalinclude} snippets/flatmap-map.out
+:language: console
 ```
 
 (operator-flatten)=
@@ -795,20 +605,12 @@ square: 9
 
 The `flatten` operator transforms a channel in such a way that every item of type `Collection` or `Array` is flattened so that each single entry is emitted separately by the resulting channel. For example:
 
-```groovy
-Channel
-    .of( [1,[2,3]], 4, [5,[6]] )
-    .flatten()
-    .view()
+```{literalinclude} snippets/flatten.nf
+:language: groovy
 ```
 
-```
-1
-2
-3
-4
-5
-6
+```{literalinclude} snippets/flatten.out
+:language: console
 ```
 
 See also: [flatMap](#flatmap) operator.
@@ -825,55 +627,32 @@ In other words, the operator transforms a sequence of tuple like *(K, V, W, ..)*
 
 For example:
 
-```groovy
-Channel
-    .of( [1, 'A'], [1, 'B'], [2, 'C'], [3, 'B'], [1, 'C'], [2, 'A'], [3, 'D'] )
-    .groupTuple()
-    .view()
+```{literalinclude} snippets/grouptuple.nf
+:language: groovy
 ```
 
-```
-[1, [A, B, C]]
-[2, [C, A]]
-[3, [B, D]]
+```{literalinclude} snippets/grouptuple.out
+:language: console
 ```
 
 By default the first entry in the tuple is used as grouping key. A different key can be chosen by using the `by` parameter and specifying the index of the entry to be used as key (the index is zero-based). For example, grouping by the second value in each tuple:
 
-```groovy
-Channel
-    .of( [1, 'A'], [1, 'B'], [2, 'C'], [3, 'B'], [1, 'C'], [2, 'A'], [3, 'D'] )
-    .groupTuple(by: 1)
-    .view()
+```{literalinclude} snippets/grouptuple-by.nf
+:language: groovy
 ```
 
-```
-[[1, 2], A]
-[[1, 3], B]
-[[2, 1], C]
-[[3], D]
+```{literalinclude} snippets/grouptuple-by.out
+:language: console
 ```
 
 By default, if you don't specify a size, the `groupTuple` operator will not emit any groups until *all* inputs have been received. If possible, you should always try to specify the number of expected elements in each group using the `size` option, so that each group can be emitted as soon as it's ready. In cases where the size of each group varies based on the grouping key, you can use the built-in `groupKey` function, which allows you to create a special grouping key with an associated size:
 
-```groovy
-chr_frequency = [ "chr1": 2, "chr2": 3 ]
-
-Channel.of(
-        [ 'region1', 'chr1', '/path/to/region1_chr1.vcf' ],
-        [ 'region2', 'chr1', '/path/to/region2_chr1.vcf' ],
-        [ 'region1', 'chr2', '/path/to/region1_chr2.vcf' ],
-        [ 'region2', 'chr2', '/path/to/region2_chr2.vcf' ],
-        [ 'region3', 'chr2', '/path/to/region3_chr2.vcf' ]
-    )
-    .map { region, chr, vcf -> tuple( groupKey(chr, chr_frequency[chr]), vcf ) }
-    .groupTuple()
-    .view()
+```{literalinclude} snippets/grouptuple-groupkey.nf
+:language: groovy
 ```
 
-```
-[chr1, [/path/to/region1_chr1.vcf, /path/to/region2_chr1.vcf]]
-[chr2, [/path/to/region1_chr2.vcf, /path/to/region2_chr2.vcf, /path/to/region3_chr2.vcf]]
+```{literalinclude} snippets/grouptuple-groupkey.out
+:language: console
 ```
 
 Available options:
@@ -906,24 +685,22 @@ The `ifEmpty` operator creates a channel which emits a default value, specified
 
 Thus, the following example prints:
 
-```groovy
-Channel .of(1,2,3) .ifEmpty('Hello') .view()
+```{literalinclude} snippets/ifempty-1.nf
+:language: groovy
 ```
 
-```
-1
-2
-3
+```{literalinclude} snippets/ifempty-1.out
+:language: console
 ```
 
 Instead, this one prints:
 
-```groovy
-Channel .empty() .ifEmpty('Hello') .view()
+```{literalinclude} snippets/ifempty-2.nf
+:language: groovy
 ```
 
-```
-Hello
+```{literalinclude} snippets/ifempty-2.out
+:language: console
 ```
 
 The `ifEmpty` value parameter can be defined with a {ref}`closure <script-closure>`. In this case the result value of the closure evaluation will be emitted when the empty condition is satisfied.
@@ -940,33 +717,24 @@ The `join` operator creates a channel that joins together the items emitted by t
 
 For example:
 
-```groovy
-left  = Channel.of(['X', 1], ['Y', 2], ['Z', 3], ['P', 7])
-right = Channel.of(['Z', 6], ['Y', 5], ['X', 4])
-left.join(right).view()
+```{literalinclude} snippets/join.nf
+:language: groovy
 ```
 
-```
-[Z, 3, 6]
-[Y, 2, 5]
-[X, 1, 4]
+```{literalinclude} snippets/join.out
+:language: console
 ```
 
 The `index` of a different matching element can be specified by using the `by` parameter.
 
 The `join` operator can emit all the pairs that are incomplete, i.e. the items for which a matching element is missing, by specifying the optional parameter `remainder` as shown below:
 
-```groovy
-left  = Channel.of(['X', 1], ['Y', 2], ['Z', 3], ['P', 7])
-right = Channel.of(['Z', 6], ['Y', 5], ['X', 4])
-left.join(right, remainder: true).view()
+```{literalinclude} snippets/join-with-remainder.nf
+:language: groovy
 ```
 
-```
-[Y, 2, 5]
-[Z, 3, 6]
-[X, 1, 4]
-[P, 7, null]
+```{literalinclude} snippets/join-with-remainder.out
+:language: console
 ```
 
 Available options:
@@ -991,15 +759,12 @@ Available options:
 
 The `last` operator creates a channel that only returns the last item emitted by the source channel. For example:
 
-```groovy
-Channel
-    .of( 1,2,3,4,5,6 )
-    .last()
-    .view()
+```{literalinclude} snippets/last.nf
+:language: groovy
 ```
 
-```
-6
+```{literalinclude} snippets/last.out
+:language: console
 ```
 
 (operator-map)=
@@ -1010,20 +775,12 @@ Channel
 
 The `map` operator applies a function of your choosing to every item emitted by a channel, and returns the items so obtained as a new channel. The function applied is called the mapping function and is expressed with a {ref}`closure <script-closure>` as shown in the example below:
 
-```groovy
-Channel
-    .of( 1, 2, 3, 4, 5 )
-    .map { it * it }
-    .subscribe onNext: { println it }, onComplete: { println 'Done' }
+```{literalinclude} snippets/map.nf
+:language: groovy
 ```
 
-```
-1
-4
-9
-16
-25
-Done
+```{literalinclude} snippets/map.out
+:language: console
 ```
 
 (operator-max)=
@@ -1034,37 +791,32 @@ Done
 
 The `max` operator waits until the source channel completes, and then emits the item that has the greatest value. For example:
 
-```groovy
-Channel
-    .of( 8, 6, 2, 5 )
-    .max()
-    .view { "Max value is $it" }
+```{literalinclude} snippets/max.nf
+:language: groovy
 ```
 
-```
-Max value is 8
+```{literalinclude} snippets/max.out
+:language: console
 ```
 
 An optional {ref}`closure <script-closure>` parameter can be specified in order to provide a function that returns the value to be compared. The example below shows how to find the string item that has the maximum length:
 
-```groovy
-Channel
-    .of("hello","hi","hey")
-    .max { it.size() }
-    .view()
+```{literalinclude} snippets/max-with-mapper.nf
+:language: groovy
 ```
 
-```
-"hello"
+```{literalinclude} snippets/max-with-mapper.out
+:language: console
 ```
 
 Alternatively it is possible to specify a comparator function i.e. a {ref}`closure <script-closure>` taking two parameters that represent two emitted items to be compared. For example:
 
-```groovy
-Channel
-    .of("hello","hi","hey")
-    .max { a,b -> a.size() <=> b.size() }
-    .view()
+```{literalinclude} snippets/max-with-comparator.nf
+:language: groovy
+```
+
+```{literalinclude} snippets/max-with-comparator.out
+:language: console
 ```
 
 (operator-merge)=
@@ -1077,30 +829,22 @@ The `merge` operator lets you join items emitted by two (or more) channels into
 
 For example, the following code merges two channels together: one which emits a series of odd integers and the other which emits a series of even integers:
 
-```groovy
-odds  = Channel.of(1, 3, 5, 7, 9)
-evens = Channel.of(2, 4, 6)
-
-odds
-    .merge( evens )
-    .view()
+```{literalinclude} snippets/merge.nf
+:language: groovy
 ```
 
-```
-[1, 2]
-[3, 4]
-[5, 6]
+```{literalinclude} snippets/merge.out
+:language: console
 ```
 
 An optional closure can be provided to customise the items emitted by the resulting merged channel. For example:
 
-```groovy
-odds  = Channel.of(1, 3, 5, 7, 9)
-evens = Channel.of(2, 4, 6)
+```{literalinclude} snippets/merge-with-mapper.nf
+:language: groovy
+```
 
-odds
-    .merge( evens ) { a, b -> tuple(b*b, a) }
-    .view()
+```{literalinclude} snippets/merge-with-mapper.out
+:language: console
 ```
 
 :::{danger}
@@ -1117,37 +861,32 @@ You should always use a matching key (e.g. sample ID) to merge multiple channels
 
 The `min` operator waits until the source channel completes, and then emits the item that has the lowest value. For example:
 
-```groovy
-Channel
-    .of( 8, 6, 2, 5 )
-    .min()
-    .view { "Min value is $it" }
+```{literalinclude} snippets/min.nf
+:language: groovy
 ```
 
-```
-Min value is 2
+```{literalinclude} snippets/min.out
+:language: console
 ```
 
 An optional {ref}`closure <script-closure>` parameter can be specified in order to provide a function that returns the value to be compared. The example below shows how to find the string item that has the minimum length:
 
-```groovy
-Channel
-    .of("hello","hi","hey")
-    .min { it.size() }
-    .view()
+```{literalinclude} snippets/min-with-mapper.nf
+:language: groovy
 ```
 
-```
-"hi"
+```{literalinclude} snippets/min-with-mapper.out
+:language: console
 ```
 
 Alternatively it is possible to specify a comparator function i.e. a {ref}`closure <script-closure>` taking two parameters that represent two emitted items to be compared. For example:
 
-```groovy
-Channel
-    .of("hello","hi","hey")
-    .min { a,b -> a.size() <=> b.size() }
-    .view()
+```{literalinclude} snippets/min-with-comparator.nf
+:language: groovy
+```
+
+```{literalinclude} snippets/min-with-comparator.out
+:language: console
 ```
 
 (operator-mix)=
@@ -1160,22 +899,12 @@ The `mix` operator combines the items emitted by two (or more) channels into a s
 
 For example:
 
-```groovy
-c1 = Channel.of( 1, 2, 3 )
-c2 = Channel.of( 'a', 'b' )
-c3 = Channel.of( 'z' )
-
-c1.mix(c2,c3)
-    .subscribe onNext: { println it }, onComplete: { println 'Done' }
+```{literalinclude} snippets/mix.nf
+:language: groovy
 ```
 
-```
-1
-2
-3
-'a'
-'b'
-'z'
+```{literalinclude} snippets/mix.out
+:language: console
 ```
 
 :::{note}
@@ -1206,50 +935,30 @@ The mapping criteria is defined with a {ref}`closure <script-closure>` that spec
 
 For example:
 
-```groovy
-Channel.of(1, 2, 3, 4)
-    .multiMap { it ->
-        foo: it + 1
-        bar: it * it
-    }
-    .set { result }
-
-result.foo.view { "foo $it" }
-result.bar.view { "bar $it" }
+```{literalinclude} snippets/multimap.nf
+:language: groovy
 ```
 
-```
-foo 2
-foo 3
-foo 4
-foo 5
-bar 1
-bar 4
-bar 9
-bar 16
+```{literalinclude} snippets/multimap.out
+:language: console
 ```
 
 The mapping expression can be omitted when the value to be emitted is the same as the following one. If you just need to forward the same value to multiple channels, you can use the following shorthand:
 
-```groovy
-Channel
-    .of(1,2,3)
-    .multiMap { it -> foo: bar: it }
-    .set { result }
+```{literalinclude} snippets/multimap-shared.nf
+:language: groovy
+```
+
+```{literalinclude} snippets/multimap-shared.out
+:language: console
 ```
 
 As before, this creates two channels, but now both of them receive the same source items.
 
 You can use the `multiMapCriteria` method to create a multi-map criteria as a variable that can be passed as an argument to one or more `multiMap` operations, as shown below:
 
-```groovy
-def criteria = multiMapCriteria {
-    small: it < 10
-    large: it > 10
-}
-
-Channel.of(1, 2, 30).multiMap(criteria).set { ch1 }
-Channel.of(10, 20, 1).multiMap(criteria).set { ch2 }
+```{literalinclude} snippets/multimap-criteria.nf
+:language: groovy
 ```
 
 :::{note}
@@ -1264,22 +973,16 @@ If you use `multiMap` to split a tuple or map into multiple channels, it is reco
 
 The `randomSample` operator allows you to create a channel emitting the specified number of items randomly taken from the channel to which is applied. For example:
 
-```groovy
-Channel
-    .of( 1..100 )
-    .randomSample( 10 )
-    .view()
+```{literalinclude} snippets/random-sample.nf
+:language: groovy
 ```
 
 The above snippet will print 10 numbers in the range from 1 to 100.
 
 The operator supports a second parameter that allows you to set the initial `seed` for the random number generator. By setting it, the `randomSample` operator will always return the same pseudo-random sequence. For example:
 
-```groovy
-Channel
-    .of( 1..100 )
-    .randomSample( 10, 234 )
-    .view()
+```{literalinclude} snippets/random-sample-with-seed.nf
+:language: groovy
 ```
 
 The above example will print 10 random numbers in the range between 1 and 100. At each run of the script, the same sequence will be returned.
@@ -1296,19 +999,12 @@ Finally, the `reduce` operator emits the result of the last invocation of your f
 
 For example:
 
-```groovy
-Channel
-    .of( 1, 2, 3, 4, 5 )
-    .reduce { a, b -> println "a: $a b: $b"; return a+b }
-    .view { "result = $it" }
+```{literalinclude} snippets/reduce.nf
+:language: groovy
 ```
 
-```
-a: 1 b: 2
-a: 3 b: 3
-a: 6 b: 4
-a: 10 b: 5
-result = 15
+```{literalinclude} snippets/reduce.out
+:language: console
 ```
 
 :::{tip}
@@ -1317,8 +1013,12 @@ A common use case for this operator is to use the first parameter as an accumula
 
 Optionally you can specify an initial value for the accumulator as shown below:
 
-```groovy
-myChannel.reduce( initialValue ) { a, b -> ... }
+```{literalinclude} snippets/reduce-with-initial-value.nf
+:language: groovy
+```
+
+```{literalinclude} snippets/reduce-with-initial-value.out
+:language: console
 ```
 
 (operator-set)=
@@ -1351,39 +1051,36 @@ The `splitCsv` operator allows you to parse text items emitted by a channel, tha
 
 In the simplest case just apply the `splitCsv` operator to a channel emitting a CSV formatted text files or text entries. For example:
 
-```groovy
-Channel
-    .of( 'alpha,beta,gamma\n10,20,30\n70,80,90' )
-    .splitCsv()
-    .view { row -> "${row[0]} - ${row[1]} - ${row[2]}" }
+```{literalinclude} snippets/splitcsv.nf
+:language: groovy
+```
+
+```{literalinclude} snippets/splitcsv.out
+:language: console
 ```
 
 The above example shows hows CSV text is parsed and is split into single rows. Values can be accessed by its column index in the row object.
 
 When the CSV begins with a header line defining the column names, you can specify the parameter `header: true` which allows you to reference each value by its name, as shown in the following example:
 
-```groovy
-Channel
-    .of( 'alpha,beta,gamma\n10,20,30\n70,80,90' )
-    .splitCsv(header: true)
-    .view { row -> "${row.alpha} - ${row.beta} - ${row.gamma}" }
+```{literalinclude} snippets/splitcsv-with-header.nf
+:language: groovy
 ```
 
-It will print
-
-```
-10 - 20 - 30
-70 - 80 - 90
+```{literalinclude} snippets/splitcsv-with-header.out
+:language: console
 ```
 
 Alternatively you can provide custom header names by specifying a the list of strings in the `header` parameter as shown below:
 
-```groovy
-Channel
-    .of( 'alpha,beta,gamma\n10,20,30\n70,80,90' )
-    .splitCsv(header: ['col1', 'col2', 'col3'], skip: 1 )
-    .view { row -> "${row.col1} - ${row.col2} - ${row.col3}" }
+```{literalinclude} snippets/splitcsv-with-columns.nf
+:language: groovy
+```
+
+```{literalinclude} snippets/splitcsv-with-columns.out
+:language: console
 ```
+
 :::{note}
 - By default, the `splitCsv` operator returns each row as a *list* object. Items are accessed by using the 0-based column index.
 - When the `header` is specified each row is returned as a *map* object (also known as dictionary). Items are accessed via the corresponding column name. 
@@ -1590,51 +1287,32 @@ The `splitJson` operator allows you to split a JSON document from a source chann
 
 An example with a JSON array:
 
-```groovy
-Channel.of('[1,null,["A",{}],true]')
-    .splitJson()
-    .view{"Item: ${it}"}
+```{literalinclude} snippets/splitjson-array.nf
+:language: groovy
 ```
 
-Produces the following output:
-
-```
-Item: 1
-Item: null
-Item: [A, [:]]
-Item: true
+```{literalinclude} snippets/splitjson-array.out
+:language: console
 ```
 
 An example with a JSON object:
 
-```groovy
-Channel.of('{"A":1,"B":[1,2,3],"C":{"D":null}}')
-    .splitJson()
-    .view{"Item: ${it}"}
+```{literalinclude} snippets/splitjson-object.nf
+:language: groovy
 ```
 
-Produces the following output:
-
-```
-Item: [value:1, key:A]
-Item: [value:[1, 2, 3], key:B]
-Item: [value:[D:null], key:C]
+```{literalinclude} snippets/splitjson-object.out
+:language: console
 ```
 
 You can optionally query a section of the JSON document to parse and split, using the `path` option:
 
-```groovy
-Channel.of('{"A":1,"B":[2,3,{"C":{"D":null,"E":4,"F":5}}]}')
-    .splitJson(path: "B[2].C")
-    .view{"Item: ${it}"}
+```{literalinclude} snippets/splitjson-with-path.nf
+:language: groovy
 ```
 
-Produces the following output:
-
-```
-Item: [value:null, key:D]
-Item: [value:4, key:E]
-Item: [value:5, key:F]
+```{literalinclude} snippets/splitjson-with-path.out
+:language: console
 ```
 
 Available options:
@@ -1729,18 +1407,12 @@ The `subscribe` operator allows you to execute a user defined function each time
 
 The emitted value is passed implicitly to the specified function. For example:
 
-```groovy
-// define a channel emitting three values
-source = Channel.of( 'alpha', 'beta', 'delta' )
-
-// subscribe a function to the channel printing the emitted values
-source.subscribe { println "Got: $it" }
+```{literalinclude} snippets/subscribe.nf
+:language: groovy
 ```
 
-```
-Got: alpha
-Got: beta
-Got: delta
+```{literalinclude} snippets/subscribe.out
+:language: console
 ```
 
 :::{note}
@@ -1749,18 +1421,15 @@ In Groovy, the language on which Nextflow is based, the user defined function is
 
 If needed the closure parameter can be defined explicitly, using a name other than `it` and, optionally, specifying the expected value type, as shown in the following example:
 
-```groovy
-Channel
-    .of( 'alpha', 'beta', 'lambda' )
-    .subscribe { String str ->
-        println "Got: ${str}; len: ${str.size()}"
-    }
+```{literalinclude} snippets/subscribe-with-param.nf
+:language: groovy
+```
+
+```{literalinclude} snippets/subscribe-with-param.out
+:language: console
 ```
 
 ```
-Got: alpha; len: 5
-Got: beta; len: 4
-Got: lambda; len: 6
 ```
 
 The `subscribe` operator may accept one or more of the following event handlers:
@@ -1771,17 +1440,12 @@ The `subscribe` operator may accept one or more of the following event handlers:
 
 For example:
 
-```groovy
-Channel
-    .of( 1, 2, 3 )
-    .subscribe onNext: { println it }, onComplete: { println 'Done' }
+```{literalinclude} snippets/subscribe-with-on-complete.nf
+:language: groovy
 ```
 
-```
-1
-2
-3
-Done
+```{literalinclude} snippets/subscribe-with-on-complete.out
+:language: console
 ```
 
 (operator-sum)=
@@ -1792,28 +1456,22 @@ Done
 
 The `sum` operator creates a channel that emits the sum of all the items emitted by the channel itself. For example:
 
-```groovy
-Channel
-    .of( 8, 6, 2, 5 )
-    .sum()
-    .view { "The sum is $it" }
+```{literalinclude} snippets/sum.nf
+:language: groovy
 ```
 
-```
-The sum is 21
+```{literalinclude} snippets/sum.out
+:language: console
 ```
 
 An optional {ref}`closure <script-closure>` parameter can be specified in order to provide a function that, given an item, returns the value to be summed. For example:
 
-```groovy
-Channel
-    .of( 4, 1, 7, 5 )
-    .sum { it * it }
-    .view { "Square: $it" }
+```{literalinclude} snippets/sum-with-mapper.nf
+:language: groovy
 ```
 
-```
-Square: 91
+```{literalinclude} snippets/sum-with-mapper.out
+:language: console
 ```
 
 ## take
@@ -1822,18 +1480,12 @@ Square: 91
 
 The `take` operator allows you to filter only the first `n` items emitted by a channel. For example:
 
-```groovy
-Channel
-    .of( 1, 2, 3, 4, 5, 6 )
-    .take( 3 )
-    .subscribe onNext: { println it }, onComplete: { println 'Done' }
+```{literalinclude} snippets/take.nf
+:language: groovy
 ```
 
-```
-1
-2
-3
-Done
+```{literalinclude} snippets/take.out
+:language: console
 ```
 
 :::{tip}
@@ -1850,31 +1502,12 @@ The `tap` operator is like the [set](#set) operator in that it assigns a source
 but it also emits the source channel for downstream use. This operator is a useful way to extract intermediate
 output channels from a chain of operators. For example:
 
-```groovy
-Channel
-    .of ( 'a', 'b', 'c' )
-    .tap { log1 }
-    .map { it * 2 }
-    .tap { log2 }
-    .map { it.toUpperCase() }
-    .view { "Result: $it" }
-
-log1.view { "Log 1: $it" }
-log2.view { "Log 2: $it" }
+```{literalinclude} snippets/tap.nf
+:language: groovy
 ```
 
-```
-Result: AA
-Result: BB
-Result: CC
-
-Log 1: a
-Log 1: b
-Log 1: c
-
-Log 2: aa
-Log 2: bb
-Log 2: cc
+```{literalinclude} snippets/tap.out
+:language: console
 ```
 
 ## toInteger
@@ -1883,12 +1516,12 @@ Log 2: cc
 
 The `toInteger` operator allows you to convert the string values emitted by a channel to `Integer` values. For example:
 
-```groovy
-Channel
-    .of( '1', '7', '12' )
-    .toInteger()
-    .sum()
-    .view()
+```{literalinclude} snippets/tointeger.nf
+:language: groovy
+```
+
+```{literalinclude} snippets/tointeger.out
+:language: console
 ```
 
 :::{tip}
@@ -1901,16 +1534,12 @@ You can also use `toLong`, `toFloat`, and `toDouble` to convert to other numeric
 
 The `toList` operator collects all the items emitted by a channel to a `List` object and emits the resulting collection as a single item. For example:
 
-```groovy
-Channel
-    .of( 1, 2, 3, 4 )
-    .toList()
-    .subscribe onNext: { println it }, onComplete: { println 'Done' }
+```{literalinclude} snippets/tolist.nf
+:language: groovy
 ```
 
-```
-[1,2,3,4]
-Done
+```{literalinclude} snippets/tolist.out
+:language: console
 ```
 
 :::{note}
@@ -1934,29 +1563,23 @@ See also: [collect](#collect) operator.
 
 The `toSortedList` operator collects all the items emitted by a channel to a `List` object where they are sorted and emits the resulting collection as a single item. For example:
 
-```groovy
-Channel
-    .of( 3, 2, 1, 4 )
-    .toSortedList()
-    .subscribe onNext: { println it }, onComplete: { println 'Done' }
+```{literalinclude} snippets/tosortedlist.nf
+:language: groovy
 ```
 
-```
-[1,2,3,4]
-Done
+```{literalinclude} snippets/tosortedlist.out
+:language: console
 ```
 
 You may also pass a comparator closure as an argument to the `toSortedList` operator to customize the sorting criteria. For example, to sort by the second element of a tuple in descending order:
 
-```groovy
-Channel
-    .of( ["homer", 5], ["bart", 2], ["lisa", 10], ["marge", 3], ["maggie", 7] )
-    .toSortedList( { a, b -> b[1] <=> a[1] } )
-    .view()
-```
 
+```{literalinclude} snippets/tosortedlist-with-comparator.nf
+:language: groovy
 ```
-[[lisa, 10], [maggie, 7], [homer, 5], [marge, 3], [bart, 2]]
+
+```{literalinclude} snippets/tosortedlist-with-comparator.out
+:language: console
 ```
 
 See also: [collect](#collect) operator.
@@ -1967,26 +1590,12 @@ See also: [collect](#collect) operator.
 
 The `transpose` operator transforms a channel in such a way that the emitted items are the result of a transposition of all tuple elements in each item. For example:
 
-```groovy
-Channel.of(
-        [1, ['A', 'B', 'C']],
-        [2, ['C', 'A']],
-        [3, ['B', 'D']]
-    )
-    .transpose()
-    .view()
+```{literalinclude} snippets/transpose.nf
+:language: groovy
 ```
 
-The above snippet prints:
-
-```
-[1, A]
-[1, B]
-[1, C]
-[2, C]
-[2, A]
-[3, B]
-[3, D]
+```{literalinclude} snippets/transpose.out
+:language: console
 ```
 
 If each element of the channel has more than 2 items, these will be flattened by the first item in the element and only emit an element when the element is complete:
@@ -2046,32 +1655,22 @@ The `unique` operator allows you to remove duplicate items from a channel and on
 
 For example:
 
-```groovy
-Channel
-    .of( 1, 1, 1, 5, 7, 7, 7, 3, 3 )
-    .unique()
-    .view()
+```{literalinclude} snippets/unique.nf
+:language: groovy
 ```
 
-```
-1
-5
-7
-3
+```{literalinclude} snippets/unique.out
+:language: console
 ```
 
 You can also specify an optional {ref}`closure <script-closure>` that customizes the way it distinguishes between unique items. For example:
 
-```groovy
-Channel
-    .of(1, 3, 4, 5)
-    .unique { it % 2 }
-    .view()
+```{literalinclude} snippets/unique-with-mapper.nf
+:language: groovy
 ```
 
-```
-1
-4
+```{literalinclude} snippets/unique-with-mapper.out
+:language: console
 ```
 
 ## until
@@ -2080,17 +1679,12 @@ Channel
 
 The `until` operator creates a channel that returns the items emitted by the source channel and stop when the condition specified is verified. For example:
 
-```groovy
-Channel
-    .of( 3, 2, 1, 5, 1, 5 )
-    .until { it == 5 }
-    .view()
+```{literalinclude} snippets/until.nf
+:language: groovy
 ```
 
-```
-3
-2
-1
+```{literalinclude} snippets/until.out
+:language: console
 ```
 
 See also [take](#take).
@@ -2103,28 +1697,24 @@ See also [take](#take).
 
 The `view` operator prints the items emitted by a channel to the console standard output. For example:
 
-```groovy
-Channel.of(1, 2, 3).view()
+```{literalinclude} snippets/view.nf
+:language: groovy
+```
 
-1
-2
-3
+```{literalinclude} snippets/view.out
+:language: console
 ```
 
 Each item is printed on a separate line unless otherwise specified by using the `newLine: false` optional parameter.
 
 How the channel items are printed can be controlled by using an optional closure parameter. The closure must return the actual value of the item to be printed:
 
-```groovy
-Channel.of(1, 2, 3)
-    .map { it -> [it, it*it] }
-    .view { num, sqr -> "Square of: $num is $sqr" }
+```{literalinclude} snippets/view-with-mapper.nf
+:language: groovy
 ```
 
-```
-Square of: 1 is 1
-Square of: 2 is 4
-Square of: 3 is 9
+```{literalinclude} snippets/view-with-mapper.out
+:language: console
 ```
 
 The `view` operator also emits every item that it receives, allowing it to be chained with other operators.
diff --git a/docs/snippets/.gitignore b/docs/snippets/.gitignore
new file mode 100644
index 0000000000..7ca126b99d
--- /dev/null
+++ b/docs/snippets/.gitignore
@@ -0,0 +1,2 @@
+.nextflow*
+work
\ No newline at end of file
diff --git a/docs/snippets/branch-criteria.nf b/docs/snippets/branch-criteria.nf
new file mode 100644
index 0000000000..9730317433
--- /dev/null
+++ b/docs/snippets/branch-criteria.nf
@@ -0,0 +1,12 @@
+def criteria = branchCriteria {
+    small: it < 10
+    large: it > 10
+}
+
+Channel.of(1, 2, 30).branch(criteria).set { ch1 }
+Channel.of(10, 20, 3).branch(criteria).set { ch2 }
+
+ch1.small.view { "$it is small" }
+ch1.large.view { "$it is large" }
+ch2.small.view { "$it is small" }
+ch2.large.view { "$it is large" }
\ No newline at end of file
diff --git a/docs/snippets/branch-criteria.out b/docs/snippets/branch-criteria.out
new file mode 100644
index 0000000000..6f8490b73d
--- /dev/null
+++ b/docs/snippets/branch-criteria.out
@@ -0,0 +1,5 @@
+1 is small
+2 is small
+3 is small
+20 is large
+30 is large
\ No newline at end of file
diff --git a/docs/snippets/branch-with-fallback.nf b/docs/snippets/branch-with-fallback.nf
new file mode 100644
index 0000000000..b9ed430843
--- /dev/null
+++ b/docs/snippets/branch-with-fallback.nf
@@ -0,0 +1,11 @@
+Channel.of(1, 2, 3, 40, 50)
+    .branch {
+        small: it < 10
+        large: it < 50
+        other: true
+    }
+    .set { result }
+
+result.small.view { "$it is small" }
+result.large.view { "$it is large" }
+result.other.view { "$it is other" }
\ No newline at end of file
diff --git a/docs/snippets/branch-with-fallback.out b/docs/snippets/branch-with-fallback.out
new file mode 100644
index 0000000000..c292f25e26
--- /dev/null
+++ b/docs/snippets/branch-with-fallback.out
@@ -0,0 +1,5 @@
+1 is small
+2 is small
+3 is small
+40 is large
+50 is other
\ No newline at end of file
diff --git a/docs/snippets/branch-with-mapper.nf b/docs/snippets/branch-with-mapper.nf
new file mode 100644
index 0000000000..b7e98adb1a
--- /dev/null
+++ b/docs/snippets/branch-with-mapper.nf
@@ -0,0 +1,16 @@
+Channel.of(1, 2, 3, 40, 50)
+    .branch {
+        foo: it < 10
+            return it+2
+
+        bar: it < 50
+            return it-2
+
+        other: true
+            return 0
+    }
+    .set { result }
+
+result.foo.view { "$it is foo" }
+result.bar.view { "$it is bar" }
+result.other.view { "$it is other" }
\ No newline at end of file
diff --git a/docs/snippets/branch-with-mapper.out b/docs/snippets/branch-with-mapper.out
new file mode 100644
index 0000000000..3d8a973d3b
--- /dev/null
+++ b/docs/snippets/branch-with-mapper.out
@@ -0,0 +1,5 @@
+3 is foo
+4 is foo
+5 is foo
+38 is bar
+0 is other
\ No newline at end of file
diff --git a/docs/snippets/branch.nf b/docs/snippets/branch.nf
new file mode 100644
index 0000000000..973fd46800
--- /dev/null
+++ b/docs/snippets/branch.nf
@@ -0,0 +1,9 @@
+Channel.of(1, 2, 3, 40, 50)
+    .branch {
+        small: it < 10
+        large: it > 10
+    }
+    .set { result }
+
+result.small.view { "$it is small" }
+result.large.view { "$it is large" }
\ No newline at end of file
diff --git a/docs/snippets/branch.out b/docs/snippets/branch.out
new file mode 100644
index 0000000000..ac05166f6b
--- /dev/null
+++ b/docs/snippets/branch.out
@@ -0,0 +1,5 @@
+1 is small
+2 is small
+3 is small
+40 is large
+50 is large
\ No newline at end of file
diff --git a/docs/snippets/buffer-with-closing.nf b/docs/snippets/buffer-with-closing.nf
new file mode 100644
index 0000000000..36739fecf8
--- /dev/null
+++ b/docs/snippets/buffer-with-closing.nf
@@ -0,0 +1,3 @@
+Channel.of( 1, 2, 3, 1, 2, 3 )
+    .buffer { it == 2 }
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/buffer-with-closing.out b/docs/snippets/buffer-with-closing.out
new file mode 100644
index 0000000000..b64a302e78
--- /dev/null
+++ b/docs/snippets/buffer-with-closing.out
@@ -0,0 +1,2 @@
+[1, 2]
+[3, 1, 2]
\ No newline at end of file
diff --git a/docs/snippets/buffer-with-opening-closing.nf b/docs/snippets/buffer-with-opening-closing.nf
new file mode 100644
index 0000000000..fcc2cecfaa
--- /dev/null
+++ b/docs/snippets/buffer-with-opening-closing.nf
@@ -0,0 +1,4 @@
+// emits bundles starting with `2` and ending with `4`
+Channel.of( 1, 2, 3, 4, 5, 1, 2, 3, 4, 5, 1, 2 )
+    .buffer( 2, 4 )
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/buffer-with-opening-closing.out b/docs/snippets/buffer-with-opening-closing.out
new file mode 100644
index 0000000000..61105ec0d7
--- /dev/null
+++ b/docs/snippets/buffer-with-opening-closing.out
@@ -0,0 +1,2 @@
+[2, 3, 4]
+[2, 3, 4]
\ No newline at end of file
diff --git a/docs/snippets/buffer-with-size-remainder.nf b/docs/snippets/buffer-with-size-remainder.nf
new file mode 100644
index 0000000000..9ca0842fbf
--- /dev/null
+++ b/docs/snippets/buffer-with-size-remainder.nf
@@ -0,0 +1,3 @@
+Channel.of( 1, 2, 3, 1, 2, 3, 1 )
+    .buffer( size: 2, remainder: true )
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/buffer-with-size-remainder.out b/docs/snippets/buffer-with-size-remainder.out
new file mode 100644
index 0000000000..8f9461c767
--- /dev/null
+++ b/docs/snippets/buffer-with-size-remainder.out
@@ -0,0 +1,4 @@
+[1, 2]
+[3, 1]
+[2, 3]
+[1]
\ No newline at end of file
diff --git a/docs/snippets/buffer-with-size-skip.nf b/docs/snippets/buffer-with-size-skip.nf
new file mode 100644
index 0000000000..602f0b42ea
--- /dev/null
+++ b/docs/snippets/buffer-with-size-skip.nf
@@ -0,0 +1,3 @@
+Channel.of( 1, 2, 3, 4, 5, 1, 2, 3, 4, 5, 1, 2 )
+    .buffer( size: 3, skip: 2 )
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/buffer-with-size-skip.out b/docs/snippets/buffer-with-size-skip.out
new file mode 100644
index 0000000000..8354fe8d6f
--- /dev/null
+++ b/docs/snippets/buffer-with-size-skip.out
@@ -0,0 +1,2 @@
+[3, 4, 5]
+[3, 4, 5]
\ No newline at end of file
diff --git a/docs/snippets/buffer-with-size.nf b/docs/snippets/buffer-with-size.nf
new file mode 100644
index 0000000000..7848fc0701
--- /dev/null
+++ b/docs/snippets/buffer-with-size.nf
@@ -0,0 +1,3 @@
+Channel.of( 1, 2, 3, 1, 2, 3, 1 )
+    .buffer( size: 2 )
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/buffer-with-size.out b/docs/snippets/buffer-with-size.out
new file mode 100644
index 0000000000..a8c6fc4922
--- /dev/null
+++ b/docs/snippets/buffer-with-size.out
@@ -0,0 +1,3 @@
+[1, 2]
+[3, 1]
+[2, 3]
\ No newline at end of file
diff --git a/docs/snippets/collate-with-no-remainder.nf b/docs/snippets/collate-with-no-remainder.nf
new file mode 100644
index 0000000000..24517a111d
--- /dev/null
+++ b/docs/snippets/collate-with-no-remainder.nf
@@ -0,0 +1,3 @@
+Channel.of(1, 2, 3, 1, 2, 3, 1)
+    .collate( 3, false )
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/collate-with-no-remainder.out b/docs/snippets/collate-with-no-remainder.out
new file mode 100644
index 0000000000..10ea892304
--- /dev/null
+++ b/docs/snippets/collate-with-no-remainder.out
@@ -0,0 +1,2 @@
+[1, 2, 3]
+[1, 2, 3]
\ No newline at end of file
diff --git a/docs/snippets/collate-with-step.nf b/docs/snippets/collate-with-step.nf
new file mode 100644
index 0000000000..4da5e35997
--- /dev/null
+++ b/docs/snippets/collate-with-step.nf
@@ -0,0 +1,3 @@
+Channel.of(1, 2, 3, 4)
+    .collate( 3, 1 )
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/collate-with-step.out b/docs/snippets/collate-with-step.out
new file mode 100644
index 0000000000..d92034b5c4
--- /dev/null
+++ b/docs/snippets/collate-with-step.out
@@ -0,0 +1,4 @@
+[1, 2, 3]
+[2, 3, 4]
+[3, 4]
+[4]
\ No newline at end of file
diff --git a/docs/snippets/collate.nf b/docs/snippets/collate.nf
new file mode 100644
index 0000000000..b6898986ab
--- /dev/null
+++ b/docs/snippets/collate.nf
@@ -0,0 +1,3 @@
+Channel.of(1, 2, 3, 1, 2, 3, 1)
+    .collate( 3 )
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/collate.out b/docs/snippets/collate.out
new file mode 100644
index 0000000000..cc547cb82b
--- /dev/null
+++ b/docs/snippets/collate.out
@@ -0,0 +1,3 @@
+[1, 2, 3]
+[1, 2, 3]
+[1]
\ No newline at end of file
diff --git a/docs/snippets/collect-with-mapper.nf b/docs/snippets/collect-with-mapper.nf
new file mode 100644
index 0000000000..ba9eda1ab3
--- /dev/null
+++ b/docs/snippets/collect-with-mapper.nf
@@ -0,0 +1,3 @@
+Channel.of( 'hello', 'ciao', 'bonjour' )
+    .collect { it.length() }
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/collect-with-mapper.out b/docs/snippets/collect-with-mapper.out
new file mode 100644
index 0000000000..23b386f57b
--- /dev/null
+++ b/docs/snippets/collect-with-mapper.out
@@ -0,0 +1 @@
+[5, 4, 7]
\ No newline at end of file
diff --git a/docs/snippets/collect.nf b/docs/snippets/collect.nf
new file mode 100644
index 0000000000..c93ece639f
--- /dev/null
+++ b/docs/snippets/collect.nf
@@ -0,0 +1,3 @@
+Channel.of( 1, 2, 3, 4 )
+    .collect()
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/collect.out b/docs/snippets/collect.out
new file mode 100644
index 0000000000..98d20c4307
--- /dev/null
+++ b/docs/snippets/collect.out
@@ -0,0 +1 @@
+[1, 2, 3, 4]
\ No newline at end of file
diff --git a/docs/snippets/collectfile-closure.nf b/docs/snippets/collectfile-closure.nf
new file mode 100644
index 0000000000..c31e4e45f6
--- /dev/null
+++ b/docs/snippets/collectfile-closure.nf
@@ -0,0 +1,8 @@
+Channel.of('Hola', 'Ciao', 'Hello', 'Bonjour', 'Halo')
+    .collectFile { item ->
+        [ "${item[0]}.txt", item + '\n' ]
+    }
+    .subscribe {
+        println "File '${it.name}' contains:"
+        println it.text
+    }
\ No newline at end of file
diff --git a/docs/snippets/collectfile-closure.out b/docs/snippets/collectfile-closure.out
new file mode 100644
index 0000000000..c930bc0b9a
--- /dev/null
+++ b/docs/snippets/collectfile-closure.out
@@ -0,0 +1,11 @@
+File 'B.txt' contains:
+Bonjour
+
+File 'C.txt' contains:
+Ciao
+
+File 'H.txt' contains:
+Halo
+Hola
+Hello
+
diff --git a/docs/snippets/collectfile.nf b/docs/snippets/collectfile.nf
new file mode 100644
index 0000000000..c2295baa4c
--- /dev/null
+++ b/docs/snippets/collectfile.nf
@@ -0,0 +1,6 @@
+Channel.of('alpha', 'beta', 'gamma')
+    .collectFile(name: 'sample.txt', newLine: true)
+    .subscribe {
+        println "Entries are saved to file: $it"
+        println "File content is: ${it.text}"
+    }
\ No newline at end of file
diff --git a/docs/snippets/combine-by.nf b/docs/snippets/combine-by.nf
new file mode 100644
index 0000000000..e49d94775f
--- /dev/null
+++ b/docs/snippets/combine-by.nf
@@ -0,0 +1,4 @@
+source = Channel.of( [1, 'alpha'], [2, 'beta'] )
+target = Channel.of( [1, 'x'], [1, 'y'], [1, 'z'], [2, 'p'], [2, 'q'], [2, 't'] )
+
+source.combine(target, by: 0).view()
\ No newline at end of file
diff --git a/docs/snippets/combine-by.out b/docs/snippets/combine-by.out
new file mode 100644
index 0000000000..5f391a56fa
--- /dev/null
+++ b/docs/snippets/combine-by.out
@@ -0,0 +1,6 @@
+[1, alpha, x]
+[1, alpha, y]
+[1, alpha, z]
+[2, beta, p]
+[2, beta, q]
+[2, beta, t]
\ No newline at end of file
diff --git a/docs/snippets/combine.nf b/docs/snippets/combine.nf
new file mode 100644
index 0000000000..fa113d3ad2
--- /dev/null
+++ b/docs/snippets/combine.nf
@@ -0,0 +1,6 @@
+numbers = Channel.of(1, 2, 3)
+words = Channel.of('hello', 'ciao')
+
+numbers
+    .combine(words)
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/combine.out b/docs/snippets/combine.out
new file mode 100644
index 0000000000..67944a86ba
--- /dev/null
+++ b/docs/snippets/combine.out
@@ -0,0 +1,6 @@
+[1, hello]
+[2, hello]
+[3, hello]
+[1, ciao]
+[2, ciao]
+[3, ciao]
\ No newline at end of file
diff --git a/docs/snippets/concat.nf b/docs/snippets/concat.nf
new file mode 100644
index 0000000000..9b5fd58a3a
--- /dev/null
+++ b/docs/snippets/concat.nf
@@ -0,0 +1,5 @@
+a = Channel.of( 'a', 'b', 'c' )
+b = Channel.of( 1, 2, 3 )
+c = Channel.of( 'p', 'q' )
+
+c.concat( b, a ).view()
\ No newline at end of file
diff --git a/docs/snippets/concat.out b/docs/snippets/concat.out
new file mode 100644
index 0000000000..3138a55a6d
--- /dev/null
+++ b/docs/snippets/concat.out
@@ -0,0 +1,8 @@
+p
+q
+1
+2
+3
+a
+b
+c
\ No newline at end of file
diff --git a/docs/snippets/count-with-filter-closure.nf b/docs/snippets/count-with-filter-closure.nf
new file mode 100644
index 0000000000..7282cce013
--- /dev/null
+++ b/docs/snippets/count-with-filter-closure.nf
@@ -0,0 +1,3 @@
+Channel.of('a', 'c', 'c', 'q', 'b')
+    .count { it <= 'c' }
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/count-with-filter-closure.out b/docs/snippets/count-with-filter-closure.out
new file mode 100644
index 0000000000..bf0d87ab1b
--- /dev/null
+++ b/docs/snippets/count-with-filter-closure.out
@@ -0,0 +1 @@
+4
\ No newline at end of file
diff --git a/docs/snippets/count-with-filter-number.nf b/docs/snippets/count-with-filter-number.nf
new file mode 100644
index 0000000000..56a91264f6
--- /dev/null
+++ b/docs/snippets/count-with-filter-number.nf
@@ -0,0 +1,3 @@
+Channel.of(4, 1, 7, 1, 1)
+    .count(1)
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/count-with-filter-number.out b/docs/snippets/count-with-filter-number.out
new file mode 100644
index 0000000000..e440e5c842
--- /dev/null
+++ b/docs/snippets/count-with-filter-number.out
@@ -0,0 +1 @@
+3
\ No newline at end of file
diff --git a/docs/snippets/count-with-filter-regex.nf b/docs/snippets/count-with-filter-regex.nf
new file mode 100644
index 0000000000..852e630478
--- /dev/null
+++ b/docs/snippets/count-with-filter-regex.nf
@@ -0,0 +1,3 @@
+Channel.of('a', 'c', 'c', 'q', 'b')
+    .count( ~/c/ )
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/count-with-filter-regex.out b/docs/snippets/count-with-filter-regex.out
new file mode 100644
index 0000000000..d8263ee986
--- /dev/null
+++ b/docs/snippets/count-with-filter-regex.out
@@ -0,0 +1 @@
+2
\ No newline at end of file
diff --git a/docs/snippets/count.nf b/docs/snippets/count.nf
new file mode 100644
index 0000000000..b874b8b9fd
--- /dev/null
+++ b/docs/snippets/count.nf
@@ -0,0 +1,3 @@
+Channel.of(9, 1, 7, 5)
+    .count()
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/count.out b/docs/snippets/count.out
new file mode 100644
index 0000000000..bf0d87ab1b
--- /dev/null
+++ b/docs/snippets/count.out
@@ -0,0 +1 @@
+4
\ No newline at end of file
diff --git a/docs/snippets/cross-with-mapper.nf b/docs/snippets/cross-with-mapper.nf
new file mode 100644
index 0000000000..7e20c3d6cc
--- /dev/null
+++ b/docs/snippets/cross-with-mapper.nf
@@ -0,0 +1,4 @@
+source = Channel.of( [1, 'alpha'], [2, 'beta'] )
+target = Channel.of( [1, 'a'], [1, 'b'], [2, 'a'], [2, 'b'] )
+
+source .cross(target) { it[1][0] } .view()
\ No newline at end of file
diff --git a/docs/snippets/cross-with-mapper.out b/docs/snippets/cross-with-mapper.out
new file mode 100644
index 0000000000..1d1dfc8fcf
--- /dev/null
+++ b/docs/snippets/cross-with-mapper.out
@@ -0,0 +1,4 @@
+[[1, alpha], [1, a]]
+[[1, alpha], [2, a]]
+[[2, beta], [1, b]]
+[[2, beta], [2, b]]
\ No newline at end of file
diff --git a/docs/snippets/cross.nf b/docs/snippets/cross.nf
new file mode 100644
index 0000000000..dff9010e16
--- /dev/null
+++ b/docs/snippets/cross.nf
@@ -0,0 +1,4 @@
+source = Channel.of( [1, 'alpha'], [2, 'beta'] )
+target = Channel.of( [1, 'x'], [1, 'y'], [1, 'z'], [2, 'p'], [2, 'q'], [2, 't'] )
+
+source.cross(target).view()
\ No newline at end of file
diff --git a/docs/snippets/cross.out b/docs/snippets/cross.out
new file mode 100644
index 0000000000..c83035ade5
--- /dev/null
+++ b/docs/snippets/cross.out
@@ -0,0 +1,6 @@
+[[1, alpha], [1, x]]
+[[1, alpha], [1, y]]
+[[1, alpha], [1, z]]
+[[2, beta], [2, p]]
+[[2, beta], [2, q]]
+[[2, beta], [2, t]]
\ No newline at end of file
diff --git a/docs/snippets/distinct-with-mapper.nf b/docs/snippets/distinct-with-mapper.nf
new file mode 100644
index 0000000000..b35422e4ee
--- /dev/null
+++ b/docs/snippets/distinct-with-mapper.nf
@@ -0,0 +1,3 @@
+Channel.of( 1, 1, 2, 2, 2, 3, 1, 1, 2, 4, 6 )
+    .distinct { it % 2 }
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/distinct-with-mapper.out b/docs/snippets/distinct-with-mapper.out
new file mode 100644
index 0000000000..fa2fa9f9b9
--- /dev/null
+++ b/docs/snippets/distinct-with-mapper.out
@@ -0,0 +1,4 @@
+1
+2
+3
+2
\ No newline at end of file
diff --git a/docs/snippets/distinct.nf b/docs/snippets/distinct.nf
new file mode 100644
index 0000000000..3e74c2153e
--- /dev/null
+++ b/docs/snippets/distinct.nf
@@ -0,0 +1,3 @@
+Channel.of( 1, 1, 2, 2, 2, 3, 1, 1, 2, 2, 3 )
+    .distinct()
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/distinct.out b/docs/snippets/distinct.out
new file mode 100644
index 0000000000..c7a7acee13
--- /dev/null
+++ b/docs/snippets/distinct.out
@@ -0,0 +1,6 @@
+1
+2
+3
+1
+2
+3
\ No newline at end of file
diff --git a/docs/snippets/dump.nf b/docs/snippets/dump.nf
new file mode 100644
index 0000000000..7f3b482698
--- /dev/null
+++ b/docs/snippets/dump.nf
@@ -0,0 +1,7 @@
+Channel.of( 1, 2, 3 )
+    .map { it+1 }
+    .dump(tag: 'foo')
+
+Channel.of( 1, 2, 3 )
+    .map { it^2 }
+    .dump(tag: 'bar')
\ No newline at end of file
diff --git a/docs/snippets/filter-closure.nf b/docs/snippets/filter-closure.nf
new file mode 100644
index 0000000000..59578268e7
--- /dev/null
+++ b/docs/snippets/filter-closure.nf
@@ -0,0 +1,3 @@
+Channel.of( 1, 2, 3, 4, 5 )
+    .filter { it % 2 == 1 }
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/filter-closure.out b/docs/snippets/filter-closure.out
new file mode 100644
index 0000000000..b2a630f360
--- /dev/null
+++ b/docs/snippets/filter-closure.out
@@ -0,0 +1,3 @@
+1
+3
+5
\ No newline at end of file
diff --git a/docs/snippets/filter-regex.nf b/docs/snippets/filter-regex.nf
new file mode 100644
index 0000000000..4d7806d3f2
--- /dev/null
+++ b/docs/snippets/filter-regex.nf
@@ -0,0 +1,3 @@
+Channel.of( 'a', 'b', 'aa', 'bc', 3, 4.5 )
+    .filter( ~/^a.*/ )
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/filter-regex.out b/docs/snippets/filter-regex.out
new file mode 100644
index 0000000000..20c5a71c64
--- /dev/null
+++ b/docs/snippets/filter-regex.out
@@ -0,0 +1,2 @@
+a
+aa
\ No newline at end of file
diff --git a/docs/snippets/filter-type.nf b/docs/snippets/filter-type.nf
new file mode 100644
index 0000000000..959af7961f
--- /dev/null
+++ b/docs/snippets/filter-type.nf
@@ -0,0 +1,3 @@
+Channel.of( 'a', 'b', 'aa', 'bc', 3, 4.5 )
+    .filter( Number )
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/filter-type.out b/docs/snippets/filter-type.out
new file mode 100644
index 0000000000..589bf560b8
--- /dev/null
+++ b/docs/snippets/filter-type.out
@@ -0,0 +1,2 @@
+3
+4.5
\ No newline at end of file
diff --git a/docs/snippets/first.nf b/docs/snippets/first.nf
new file mode 100644
index 0000000000..d4ec5d15df
--- /dev/null
+++ b/docs/snippets/first.nf
@@ -0,0 +1,19 @@
+// no condition is specified, emits the very first item: 1
+Channel.of( 1, 2, 3 )
+    .first()
+    .view()
+
+// emits the first item matching the regular expression: 'aa'
+Channel.of( 'a', 'aa', 'aaa' )
+    .first( ~/aa.*/ )
+    .view()
+
+// emits the first String value: 'a'
+Channel.of( 1, 2, 'a', 'b', 3 )
+    .first( String )
+    .view()
+
+// emits the first item for which the predicate evaluates to true: 4
+Channel.of( 1, 2, 3, 4, 5 )
+    .first { it > 3 }
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/first.out b/docs/snippets/first.out
new file mode 100644
index 0000000000..63db24ea5e
--- /dev/null
+++ b/docs/snippets/first.out
@@ -0,0 +1,4 @@
+1
+a
+aa
+4
\ No newline at end of file
diff --git a/docs/snippets/flatmap-list.nf b/docs/snippets/flatmap-list.nf
new file mode 100644
index 0000000000..e8ccc175b2
--- /dev/null
+++ b/docs/snippets/flatmap-list.nf
@@ -0,0 +1,3 @@
+Channel.of( 1, 2, 3 )
+    .flatMap { n -> [ n, n*2, n*3 ] }
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/flatmap-list.out b/docs/snippets/flatmap-list.out
new file mode 100644
index 0000000000..68effb8e5e
--- /dev/null
+++ b/docs/snippets/flatmap-list.out
@@ -0,0 +1,9 @@
+1
+2
+3
+2
+4
+6
+3
+6
+9
\ No newline at end of file
diff --git a/docs/snippets/flatmap-map.nf b/docs/snippets/flatmap-map.nf
new file mode 100644
index 0000000000..fd78c38674
--- /dev/null
+++ b/docs/snippets/flatmap-map.nf
@@ -0,0 +1,3 @@
+Channel.of( 1, 2, 3 )
+    .flatMap { n -> [ number: n, square: n*n, cube: n*n*n ] }
+    .view { "${it.key}: ${it.value}" }
\ No newline at end of file
diff --git a/docs/snippets/flatmap-map.out b/docs/snippets/flatmap-map.out
new file mode 100644
index 0000000000..a269dccd60
--- /dev/null
+++ b/docs/snippets/flatmap-map.out
@@ -0,0 +1,9 @@
+number: 1
+square: 1
+cube: 1
+number: 2
+square: 4
+cube: 8
+number: 3
+square: 9
+cube: 27
\ No newline at end of file
diff --git a/docs/snippets/flatten.nf b/docs/snippets/flatten.nf
new file mode 100644
index 0000000000..396efac437
--- /dev/null
+++ b/docs/snippets/flatten.nf
@@ -0,0 +1,3 @@
+Channel.of( [1, [2, 3]], 4, [5, [6]] )
+    .flatten()
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/flatten.out b/docs/snippets/flatten.out
new file mode 100644
index 0000000000..cf0389a5af
--- /dev/null
+++ b/docs/snippets/flatten.out
@@ -0,0 +1,6 @@
+1
+2
+3
+4
+5
+6
\ No newline at end of file
diff --git a/docs/snippets/grouptuple-by.nf b/docs/snippets/grouptuple-by.nf
new file mode 100644
index 0000000000..3673710f9a
--- /dev/null
+++ b/docs/snippets/grouptuple-by.nf
@@ -0,0 +1,3 @@
+Channel.of( [1, 'A'], [1, 'B'], [2, 'C'], [3, 'B'], [1, 'C'], [2, 'A'], [3, 'D'] )
+    .groupTuple(by: 1)
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/grouptuple-by.out b/docs/snippets/grouptuple-by.out
new file mode 100644
index 0000000000..70fb39833d
--- /dev/null
+++ b/docs/snippets/grouptuple-by.out
@@ -0,0 +1,4 @@
+[[1, 2], A]
+[[1, 3], B]
+[[2, 1], C]
+[[3], D]
\ No newline at end of file
diff --git a/docs/snippets/grouptuple-groupkey.nf b/docs/snippets/grouptuple-groupkey.nf
new file mode 100644
index 0000000000..fa9f08c6fd
--- /dev/null
+++ b/docs/snippets/grouptuple-groupkey.nf
@@ -0,0 +1,12 @@
+chr_frequency = ["chr1": 2, "chr2": 3]
+
+Channel.of(
+        ['region1', 'chr1', '/path/to/region1_chr1.vcf'],
+        ['region2', 'chr1', '/path/to/region2_chr1.vcf'],
+        ['region1', 'chr2', '/path/to/region1_chr2.vcf'],
+        ['region2', 'chr2', '/path/to/region2_chr2.vcf'],
+        ['region3', 'chr2', '/path/to/region3_chr2.vcf']
+    )
+    .map { region, chr, vcf -> tuple( groupKey(chr, chr_frequency[chr]), vcf ) }
+    .groupTuple()
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/grouptuple-groupkey.out b/docs/snippets/grouptuple-groupkey.out
new file mode 100644
index 0000000000..e97159c872
--- /dev/null
+++ b/docs/snippets/grouptuple-groupkey.out
@@ -0,0 +1,2 @@
+[chr1, [/path/to/region1_chr1.vcf, /path/to/region2_chr1.vcf]]
+[chr2, [/path/to/region1_chr2.vcf, /path/to/region2_chr2.vcf, /path/to/region3_chr2.vcf]]
\ No newline at end of file
diff --git a/docs/snippets/grouptuple.nf b/docs/snippets/grouptuple.nf
new file mode 100644
index 0000000000..653ee170cd
--- /dev/null
+++ b/docs/snippets/grouptuple.nf
@@ -0,0 +1,3 @@
+Channel.of( [1, 'A'], [1, 'B'], [2, 'C'], [3, 'B'], [1, 'C'], [2, 'A'], [3, 'D'] )
+    .groupTuple()
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/grouptuple.out b/docs/snippets/grouptuple.out
new file mode 100644
index 0000000000..4d11258ce8
--- /dev/null
+++ b/docs/snippets/grouptuple.out
@@ -0,0 +1,3 @@
+[1, [A, B, C]]
+[2, [C, A]]
+[3, [B, D]]
\ No newline at end of file
diff --git a/docs/snippets/ifempty-1.nf b/docs/snippets/ifempty-1.nf
new file mode 100644
index 0000000000..f18604d55f
--- /dev/null
+++ b/docs/snippets/ifempty-1.nf
@@ -0,0 +1 @@
+Channel .of(1, 2, 3) .ifEmpty('Hello') .view()
\ No newline at end of file
diff --git a/docs/snippets/ifempty-1.out b/docs/snippets/ifempty-1.out
new file mode 100644
index 0000000000..5f5fbe759f
--- /dev/null
+++ b/docs/snippets/ifempty-1.out
@@ -0,0 +1,3 @@
+1
+2
+3
\ No newline at end of file
diff --git a/docs/snippets/ifempty-2.nf b/docs/snippets/ifempty-2.nf
new file mode 100644
index 0000000000..3fdc4abacb
--- /dev/null
+++ b/docs/snippets/ifempty-2.nf
@@ -0,0 +1 @@
+Channel .empty() .ifEmpty('Hello') .view()
\ No newline at end of file
diff --git a/docs/snippets/ifempty-2.out b/docs/snippets/ifempty-2.out
new file mode 100644
index 0000000000..5ab2f8a432
--- /dev/null
+++ b/docs/snippets/ifempty-2.out
@@ -0,0 +1 @@
+Hello
\ No newline at end of file
diff --git a/docs/snippets/join-with-remainder.nf b/docs/snippets/join-with-remainder.nf
new file mode 100644
index 0000000000..0b940155e3
--- /dev/null
+++ b/docs/snippets/join-with-remainder.nf
@@ -0,0 +1,4 @@
+left  = Channel.of( ['X', 1], ['Y', 2], ['Z', 3], ['P', 7] )
+right = Channel.of( ['Z', 6], ['Y', 5], ['X', 4] )
+
+left.join(right, remainder: true).view()
\ No newline at end of file
diff --git a/docs/snippets/join-with-remainder.out b/docs/snippets/join-with-remainder.out
new file mode 100644
index 0000000000..2f37fc3195
--- /dev/null
+++ b/docs/snippets/join-with-remainder.out
@@ -0,0 +1,4 @@
+[Y, 2, 5]
+[Z, 3, 6]
+[X, 1, 4]
+[P, 7, null]
\ No newline at end of file
diff --git a/docs/snippets/join.nf b/docs/snippets/join.nf
new file mode 100644
index 0000000000..0e5161cb13
--- /dev/null
+++ b/docs/snippets/join.nf
@@ -0,0 +1,4 @@
+left  = Channel.of( ['X', 1], ['Y', 2], ['Z', 3], ['P', 7] )
+right = Channel.of( ['Z', 6], ['Y', 5], ['X', 4] )
+
+left.join(right).view()
\ No newline at end of file
diff --git a/docs/snippets/join.out b/docs/snippets/join.out
new file mode 100644
index 0000000000..69ebb21e93
--- /dev/null
+++ b/docs/snippets/join.out
@@ -0,0 +1,3 @@
+[Z, 3, 6]
+[Y, 2, 5]
+[X, 1, 4]
\ No newline at end of file
diff --git a/docs/snippets/last.nf b/docs/snippets/last.nf
new file mode 100644
index 0000000000..912864017f
--- /dev/null
+++ b/docs/snippets/last.nf
@@ -0,0 +1,3 @@
+Channel.of( 1, 2, 3, 4, 5, 6 )
+    .last()
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/last.out b/docs/snippets/last.out
new file mode 100644
index 0000000000..62f9457511
--- /dev/null
+++ b/docs/snippets/last.out
@@ -0,0 +1 @@
+6
\ No newline at end of file
diff --git a/docs/snippets/map.nf b/docs/snippets/map.nf
new file mode 100644
index 0000000000..a4df86f706
--- /dev/null
+++ b/docs/snippets/map.nf
@@ -0,0 +1,3 @@
+Channel.of( 1, 2, 3, 4, 5 )
+    .map { it * it }
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/map.out b/docs/snippets/map.out
new file mode 100644
index 0000000000..1ba204d253
--- /dev/null
+++ b/docs/snippets/map.out
@@ -0,0 +1,5 @@
+1
+4
+9
+16
+25
\ No newline at end of file
diff --git a/docs/snippets/max-with-comparator.nf b/docs/snippets/max-with-comparator.nf
new file mode 100644
index 0000000000..9be747b11c
--- /dev/null
+++ b/docs/snippets/max-with-comparator.nf
@@ -0,0 +1,4 @@
+// comparator function
+Channel.of( "hello", "hi", "hey" )
+    .max { a, b -> a.size() <=> b.size() }
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/max-with-comparator.out b/docs/snippets/max-with-comparator.out
new file mode 100644
index 0000000000..b6fc4c620b
--- /dev/null
+++ b/docs/snippets/max-with-comparator.out
@@ -0,0 +1 @@
+hello
\ No newline at end of file
diff --git a/docs/snippets/max-with-mapper.nf b/docs/snippets/max-with-mapper.nf
new file mode 100644
index 0000000000..e047f1a4ea
--- /dev/null
+++ b/docs/snippets/max-with-mapper.nf
@@ -0,0 +1,4 @@
+// mapping function
+Channel.of( "hello", "hi", "hey" )
+    .max { it.size() }
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/max-with-mapper.out b/docs/snippets/max-with-mapper.out
new file mode 100644
index 0000000000..b6fc4c620b
--- /dev/null
+++ b/docs/snippets/max-with-mapper.out
@@ -0,0 +1 @@
+hello
\ No newline at end of file
diff --git a/docs/snippets/max.nf b/docs/snippets/max.nf
new file mode 100644
index 0000000000..d2b321416a
--- /dev/null
+++ b/docs/snippets/max.nf
@@ -0,0 +1,3 @@
+Channel.of( 8, 6, 2, 5 )
+    .max()
+    .view { "Max value is $it" }
\ No newline at end of file
diff --git a/docs/snippets/max.out b/docs/snippets/max.out
new file mode 100644
index 0000000000..3c19a5458f
--- /dev/null
+++ b/docs/snippets/max.out
@@ -0,0 +1 @@
+Max value is 8
\ No newline at end of file
diff --git a/docs/snippets/merge-with-mapper.nf b/docs/snippets/merge-with-mapper.nf
new file mode 100644
index 0000000000..62465ddfa3
--- /dev/null
+++ b/docs/snippets/merge-with-mapper.nf
@@ -0,0 +1,6 @@
+odds  = Channel.of(1, 3, 5, 7, 9)
+evens = Channel.of(2, 4, 6)
+
+odds
+    .merge( evens ) { a, b -> tuple(b*b, a) }
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/merge-with-mapper.out b/docs/snippets/merge-with-mapper.out
new file mode 100644
index 0000000000..00cb7ff5af
--- /dev/null
+++ b/docs/snippets/merge-with-mapper.out
@@ -0,0 +1,3 @@
+[16, 3]
+[36, 5]
+[4, 1]
\ No newline at end of file
diff --git a/docs/snippets/merge.nf b/docs/snippets/merge.nf
new file mode 100644
index 0000000000..2b19e96e83
--- /dev/null
+++ b/docs/snippets/merge.nf
@@ -0,0 +1,6 @@
+odds  = Channel.of(1, 3, 5, 7, 9)
+evens = Channel.of(2, 4, 6)
+
+odds
+    .merge( evens )
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/merge.out b/docs/snippets/merge.out
new file mode 100644
index 0000000000..f6c49d0277
--- /dev/null
+++ b/docs/snippets/merge.out
@@ -0,0 +1,3 @@
+[1, 2]
+[3, 4]
+[5, 6]
\ No newline at end of file
diff --git a/docs/snippets/min-with-comparator.nf b/docs/snippets/min-with-comparator.nf
new file mode 100644
index 0000000000..3392c95a0e
--- /dev/null
+++ b/docs/snippets/min-with-comparator.nf
@@ -0,0 +1,4 @@
+// comparator function
+Channel.of( "hello", "hi", "hey" )
+    .min { a, b -> a.size() <=> b.size() }
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/min-with-comparator.out b/docs/snippets/min-with-comparator.out
new file mode 100644
index 0000000000..32f95c0d12
--- /dev/null
+++ b/docs/snippets/min-with-comparator.out
@@ -0,0 +1 @@
+hi
\ No newline at end of file
diff --git a/docs/snippets/min-with-mapper.nf b/docs/snippets/min-with-mapper.nf
new file mode 100644
index 0000000000..32ab5287f3
--- /dev/null
+++ b/docs/snippets/min-with-mapper.nf
@@ -0,0 +1,4 @@
+// mapping function
+Channel.of( "hello", "hi", "hey" )
+    .min { it.size() }
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/min-with-mapper.out b/docs/snippets/min-with-mapper.out
new file mode 100644
index 0000000000..32f95c0d12
--- /dev/null
+++ b/docs/snippets/min-with-mapper.out
@@ -0,0 +1 @@
+hi
\ No newline at end of file
diff --git a/docs/snippets/min.nf b/docs/snippets/min.nf
new file mode 100644
index 0000000000..78ab2571fe
--- /dev/null
+++ b/docs/snippets/min.nf
@@ -0,0 +1,3 @@
+Channel.of( 8, 6, 2, 5 )
+    .min()
+    .view { "Min value is $it" }
\ No newline at end of file
diff --git a/docs/snippets/min.out b/docs/snippets/min.out
new file mode 100644
index 0000000000..d2da450bea
--- /dev/null
+++ b/docs/snippets/min.out
@@ -0,0 +1 @@
+Min value is 2
\ No newline at end of file
diff --git a/docs/snippets/mix.nf b/docs/snippets/mix.nf
new file mode 100644
index 0000000000..84f122060f
--- /dev/null
+++ b/docs/snippets/mix.nf
@@ -0,0 +1,5 @@
+c1 = Channel.of( 1, 2, 3 )
+c2 = Channel.of( 'a', 'b' )
+c3 = Channel.of( 'z' )
+
+c1.mix(c2, c3).view()
\ No newline at end of file
diff --git a/docs/snippets/mix.out b/docs/snippets/mix.out
new file mode 100644
index 0000000000..a2d71225e4
--- /dev/null
+++ b/docs/snippets/mix.out
@@ -0,0 +1,6 @@
+1
+2
+3
+a
+b
+z
\ No newline at end of file
diff --git a/docs/snippets/multimap-criteria.nf b/docs/snippets/multimap-criteria.nf
new file mode 100644
index 0000000000..7b15740d97
--- /dev/null
+++ b/docs/snippets/multimap-criteria.nf
@@ -0,0 +1,12 @@
+def criteria = multiMapCriteria {
+    small: [it, it < 10]
+    large: [it, it > 10]
+}
+
+Channel.of(1, 2, 30).multiMap(criteria).set { ch1 }
+Channel.of(10, 20, 1).multiMap(criteria).set { ch2 }
+
+ch1.small.view { v, is_small -> "ch1: $v is small: $is_small" }
+ch1.large.view { v, is_large -> "ch1: $v is large: $is_large" }
+ch2.small.view { v, is_small -> "ch2: $v is small: $is_small" }
+ch2.large.view { v, is_large -> "ch2: $v is large: $is_large" }
\ No newline at end of file
diff --git a/docs/snippets/multimap-criteria.out b/docs/snippets/multimap-criteria.out
new file mode 100644
index 0000000000..5657e20905
--- /dev/null
+++ b/docs/snippets/multimap-criteria.out
@@ -0,0 +1,12 @@
+ch1: 1 is large: false
+ch1: 1 is small: true
+ch1: 2 is large: false
+ch1: 2 is small: true
+ch1: 30 is large: true
+ch1: 30 is small: false
+ch2: 1 is large: false
+ch2: 1 is small: true
+ch2: 10 is large: false
+ch2: 10 is small: false
+ch2: 20 is large: true
+ch2: 20 is small: false
\ No newline at end of file
diff --git a/docs/snippets/multimap-shared.nf b/docs/snippets/multimap-shared.nf
new file mode 100644
index 0000000000..0573f53199
--- /dev/null
+++ b/docs/snippets/multimap-shared.nf
@@ -0,0 +1,6 @@
+Channel.of( 1, 2, 3 )
+    .multiMap { it -> foo: bar: it }
+    .set { result }
+
+result.foo.view { "foo $it" }
+result.bar.view { "bar $it" }
\ No newline at end of file
diff --git a/docs/snippets/multimap-shared.out b/docs/snippets/multimap-shared.out
new file mode 100644
index 0000000000..4e1ceb9afb
--- /dev/null
+++ b/docs/snippets/multimap-shared.out
@@ -0,0 +1,6 @@
+bar 1
+bar 2
+bar 3
+foo 1
+foo 2
+foo 3
\ No newline at end of file
diff --git a/docs/snippets/multimap.nf b/docs/snippets/multimap.nf
new file mode 100644
index 0000000000..52ab934aca
--- /dev/null
+++ b/docs/snippets/multimap.nf
@@ -0,0 +1,9 @@
+Channel.of( 1, 2, 3, 4 )
+    .multiMap { it ->
+        foo: it + 1
+        bar: it * it
+    }
+    .set { result }
+
+result.foo.view { "foo $it" }
+result.bar.view { "bar $it" }
\ No newline at end of file
diff --git a/docs/snippets/multimap.out b/docs/snippets/multimap.out
new file mode 100644
index 0000000000..1855cec8ef
--- /dev/null
+++ b/docs/snippets/multimap.out
@@ -0,0 +1,8 @@
+foo 2
+foo 3
+foo 4
+foo 5
+bar 1
+bar 4
+bar 9
+bar 16
\ No newline at end of file
diff --git a/docs/snippets/random-sample-with-seed.nf b/docs/snippets/random-sample-with-seed.nf
new file mode 100644
index 0000000000..79d2c5d6a0
--- /dev/null
+++ b/docs/snippets/random-sample-with-seed.nf
@@ -0,0 +1,3 @@
+Channel.of( 1..100 )
+    .randomSample( 10, 234 )
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/random-sample.nf b/docs/snippets/random-sample.nf
new file mode 100644
index 0000000000..c66e6e9c1f
--- /dev/null
+++ b/docs/snippets/random-sample.nf
@@ -0,0 +1,3 @@
+Channel.of( 1..100 )
+    .randomSample( 10 )
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/reduce-with-initial-value.nf b/docs/snippets/reduce-with-initial-value.nf
new file mode 100644
index 0000000000..28427b32a8
--- /dev/null
+++ b/docs/snippets/reduce-with-initial-value.nf
@@ -0,0 +1,6 @@
+Channel.of( 1, 2, 3, 4, 5 )
+    .reduce( 'result:' ) { accum, v ->
+        println accum
+        accum + ' ' + v
+    }
+    .view { "final $it" }
\ No newline at end of file
diff --git a/docs/snippets/reduce-with-initial-value.out b/docs/snippets/reduce-with-initial-value.out
new file mode 100644
index 0000000000..9737132fa4
--- /dev/null
+++ b/docs/snippets/reduce-with-initial-value.out
@@ -0,0 +1,6 @@
+result:
+result: 1
+result: 1 2
+result: 1 2 3
+result: 1 2 3 4
+final result: 1 2 3 4 5
\ No newline at end of file
diff --git a/docs/snippets/reduce.nf b/docs/snippets/reduce.nf
new file mode 100644
index 0000000000..f4c0402269
--- /dev/null
+++ b/docs/snippets/reduce.nf
@@ -0,0 +1,6 @@
+Channel.of( 1, 2, 3, 4, 5 )
+    .reduce { a, b ->
+        println "a: $a b: $b"
+        a + b
+    }
+    .view { "result = $it" }
\ No newline at end of file
diff --git a/docs/snippets/reduce.out b/docs/snippets/reduce.out
new file mode 100644
index 0000000000..5ed1862ac3
--- /dev/null
+++ b/docs/snippets/reduce.out
@@ -0,0 +1,5 @@
+a: 1 b: 2
+a: 3 b: 3
+a: 6 b: 4
+a: 10 b: 5
+result = 15
\ No newline at end of file
diff --git a/docs/snippets/splitcsv-with-columns.nf b/docs/snippets/splitcsv-with-columns.nf
new file mode 100644
index 0000000000..9a6888994d
--- /dev/null
+++ b/docs/snippets/splitcsv-with-columns.nf
@@ -0,0 +1,3 @@
+Channel.of( 'alpha,beta,gamma\n10,20,30\n70,80,90' )
+    .splitCsv( header: ['col1', 'col2', 'col3'], skip: 1 )
+    .view { row -> "${row.col1} - ${row.col2} - ${row.col3}" }
\ No newline at end of file
diff --git a/docs/snippets/splitcsv-with-columns.out b/docs/snippets/splitcsv-with-columns.out
new file mode 100644
index 0000000000..7214f60d10
--- /dev/null
+++ b/docs/snippets/splitcsv-with-columns.out
@@ -0,0 +1,2 @@
+10 - 20 - 30
+70 - 80 - 90
\ No newline at end of file
diff --git a/docs/snippets/splitcsv-with-header.nf b/docs/snippets/splitcsv-with-header.nf
new file mode 100644
index 0000000000..2a887c4198
--- /dev/null
+++ b/docs/snippets/splitcsv-with-header.nf
@@ -0,0 +1,3 @@
+Channel.of( 'alpha,beta,gamma\n10,20,30\n70,80,90' )
+    .splitCsv( header: true )
+    .view { row -> "${row.alpha} - ${row.beta} - ${row.gamma}" }
\ No newline at end of file
diff --git a/docs/snippets/splitcsv-with-header.out b/docs/snippets/splitcsv-with-header.out
new file mode 100644
index 0000000000..7214f60d10
--- /dev/null
+++ b/docs/snippets/splitcsv-with-header.out
@@ -0,0 +1,2 @@
+10 - 20 - 30
+70 - 80 - 90
\ No newline at end of file
diff --git a/docs/snippets/splitcsv.nf b/docs/snippets/splitcsv.nf
new file mode 100644
index 0000000000..59af507f7f
--- /dev/null
+++ b/docs/snippets/splitcsv.nf
@@ -0,0 +1,3 @@
+Channel.of( '10,20,30\n70,80,90' )
+    .splitCsv()
+    .view { row -> "${row[0]} - ${row[1]} - ${row[2]}" }
\ No newline at end of file
diff --git a/docs/snippets/splitcsv.out b/docs/snippets/splitcsv.out
new file mode 100644
index 0000000000..7214f60d10
--- /dev/null
+++ b/docs/snippets/splitcsv.out
@@ -0,0 +1,2 @@
+10 - 20 - 30
+70 - 80 - 90
\ No newline at end of file
diff --git a/docs/snippets/splitjson-array.nf b/docs/snippets/splitjson-array.nf
new file mode 100644
index 0000000000..99b81ab1b8
--- /dev/null
+++ b/docs/snippets/splitjson-array.nf
@@ -0,0 +1,4 @@
+// Example with a JSON array
+Channel.of('[1, null, ["A", {}], true]')
+    .splitJson()
+    .view{"Item: ${it}"}
\ No newline at end of file
diff --git a/docs/snippets/splitjson-array.out b/docs/snippets/splitjson-array.out
new file mode 100644
index 0000000000..a64844cb9f
--- /dev/null
+++ b/docs/snippets/splitjson-array.out
@@ -0,0 +1,4 @@
+Item: 1
+Item: null
+Item: [A, [:]]
+Item: true
\ No newline at end of file
diff --git a/docs/snippets/splitjson-error.log b/docs/snippets/splitjson-error.log
new file mode 100644
index 0000000000..035b4bf959
--- /dev/null
+++ b/docs/snippets/splitjson-error.log
@@ -0,0 +1,106 @@
+May-18 21:16:09.405 [main] DEBUG nextflow.cli.Launcher - $> ../../launch.sh -q run splitjson-with-path.nf
+May-18 21:16:09.489 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 23.05.0-edge
+May-18 21:16:09.531 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=dev; embedded=false; plugins-dir=/home/bent/projects/nextflow-io_nextflow/plugins; core-plugins: nf-amazon@2.0.0,nf-azure@1.1.0,nf-codecommit@0.1.5,nf-console@1.0.6,nf-ga4gh@1.0.6,nf-google@1.7.4,nf-tower@1.5.13,nf-wave@0.9.0
+May-18 21:16:09.531 [main] DEBUG nextflow.plugin.DevPluginManager - Add plugin root repository: /home/bent/projects/nextflow-io_nextflow/plugins
+May-18 21:16:09.535 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
+May-18 21:16:09.536 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
+May-18 21:16:09.542 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'development' mode
+May-18 21:16:09.553 [main] DEBUG nextflow.plugin.DevPluginClasspath - Groovy DEV plugin classpath: classes-dirs=[build/classes/groovy/main, build/classes/main, build/resources/main]; jars-dirs=[build/target/libs]
+May-18 21:16:09.564 [main] INFO  org.pf4j.AbstractPluginManager - Plugin 'nf-wave@0.9.0' resolved
+May-18 21:16:09.564 [main] INFO  org.pf4j.AbstractPluginManager - Plugin 'nf-amazon@2.0.0' resolved
+May-18 21:16:09.564 [main] INFO  org.pf4j.AbstractPluginManager - Plugin 'nf-google@1.7.4' resolved
+May-18 21:16:09.564 [main] INFO  org.pf4j.AbstractPluginManager - Plugin 'nf-ga4gh@1.0.6' resolved
+May-18 21:16:09.564 [main] INFO  org.pf4j.AbstractPluginManager - Plugin 'nf-tower@1.5.13' resolved
+May-18 21:16:09.564 [main] INFO  org.pf4j.AbstractPluginManager - Plugin 'nf-codecommit@0.1.5' resolved
+May-18 21:16:09.564 [main] INFO  org.pf4j.AbstractPluginManager - Plugin 'nf-console@1.0.6' resolved
+May-18 21:16:09.565 [main] INFO  org.pf4j.AbstractPluginManager - Plugin 'nf-azure@1.1.0' resolved
+May-18 21:16:09.612 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 by global default
+May-18 21:16:09.623 [main] INFO  nextflow.cli.CmdRun - Launching `splitjson-with-path.nf` [sad_hawking] DSL2 - revision: 75f20d5d34
+May-18 21:16:09.624 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
+May-18 21:16:09.624 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
+May-18 21:16:09.634 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/bent/.nextflow/secrets/store.json
+May-18 21:16:09.638 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@72805168] - activable => nextflow.secret.LocalSecretsProvider@72805168
+May-18 21:16:09.687 [main] DEBUG nextflow.Session - Session UUID: cd50afbf-cb5d-4dc2-87de-474cdc70dcc6
+May-18 21:16:09.687 [main] DEBUG nextflow.Session - Run name: sad_hawking
+May-18 21:16:09.688 [main] DEBUG nextflow.Session - Executor pool size: 12
+May-18 21:16:09.693 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
+May-18 21:16:09.697 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=36; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
+May-18 21:16:09.718 [main] DEBUG nextflow.cli.CmdRun - 
+  Version: 23.05.0-edge build 5864
+  Created: 19-05-2023 02:15 UTC (18-05-2023 21:15 CDT)
+  System: Linux 5.10.16.3-microsoft-standard-WSL2
+  Runtime: Groovy 3.0.17 on OpenJDK 64-Bit Server VM 17.0.6+10
+  Encoding: UTF-8 (UTF-8)
+  Process: 31895@LAPTOP-2GR8K3GP [127.0.1.1]
+  CPUs: 12 - Mem: 7.6 GB (4.5 GB) - Swap: 2 GB (2 GB)
+May-18 21:16:09.744 [main] DEBUG nextflow.Session - Work-dir: /home/bent/projects/nextflow-io_nextflow/docs/snippets/work [ext2/ext3]
+May-18 21:16:09.745 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /home/bent/projects/nextflow-io_nextflow/docs/snippets/bin
+May-18 21:16:09.752 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
+May-18 21:16:09.759 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
+May-18 21:16:09.771 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
+May-18 21:16:09.777 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 13; maxThreads: 1000
+May-18 21:16:09.841 [main] DEBUG nextflow.Session - Session start
+May-18 21:16:10.198 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
+May-18 21:16:10.259 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: 
+May-18 21:16:10.260 [main] DEBUG nextflow.Session - Igniting dataflow network (1)
+May-18 21:16:10.260 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination 
+May-18 21:16:10.260 [main] DEBUG nextflow.Session - Session await
+May-18 21:16:10.260 [main] DEBUG nextflow.Session - Session await > all processes finished
+May-18 21:16:10.261 [main] DEBUG nextflow.Session - Session await > all barriers passed
+May-18 21:16:10.265 [Actor Thread 3] ERROR nextflow.extension.DataflowHelper - @unknown
+java.lang.IllegalStateException: Error while parsing JSON content - cause: java.lang.NullPointerException
+	at nextflow.splitter.JsonSplitter.process(JsonSplitter.groovy:95)
+	at nextflow.splitter.JsonSplitter.process(JsonSplitter.groovy)
+	at nextflow.splitter.AbstractSplitter.apply(AbstractSplitter.groovy:154)
+	at nextflow.extension.SplitOp$_applySplittingOperator_closure1.doCall(SplitOp.groovy:190)
+	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
+	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
+	at java.base/java.lang.reflect.Method.invoke(Method.java:568)
+	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
+	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
+	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274)
+	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
+	at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:38)
+	at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
+	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
+	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139)
+	at nextflow.extension.DataflowHelper$_subscribeImpl_closure2.doCall(DataflowHelper.groovy:284)
+	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
+	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
+	at java.base/java.lang.reflect.Method.invoke(Method.java:568)
+	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
+	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
+	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274)
+	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
+	at groovy.lang.Closure.call(Closure.java:412)
+	at groovyx.gpars.dataflow.operator.DataflowOperatorActor.startTask(DataflowOperatorActor.java:120)
+	at groovyx.gpars.dataflow.operator.DataflowOperatorActor.onMessage(DataflowOperatorActor.java:108)
+	at groovyx.gpars.actor.impl.SDAClosure$1.call(SDAClosure.java:43)
+	at groovyx.gpars.actor.AbstractLoopingActor.runEnhancedWithoutRepliesOnMessages(AbstractLoopingActor.java:293)
+	at groovyx.gpars.actor.AbstractLoopingActor.access$400(AbstractLoopingActor.java:30)
+	at groovyx.gpars.actor.AbstractLoopingActor$1.handleMessage(AbstractLoopingActor.java:93)
+	at groovyx.gpars.util.AsyncMessagingCore.run(AsyncMessagingCore.java:132)
+	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
+	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
+	at java.base/java.lang.Thread.run(Thread.java:833)
+Caused by: java.lang.NullPointerException: null
+	at java.base/java.util.Objects.requireNonNull(Objects.java:208)
+	at java.base/java.util.ImmutableCollections$MapN.<init>(ImmutableCollections.java:1186)
+	at java.base/java.util.Map.of(Map.java:1373)
+	at nextflow.splitter.JsonSplitter.processObject(JsonSplitter.groovy:224)
+	at nextflow.splitter.JsonSplitter.scanJsonForPath(JsonSplitter.groovy:138)
+	at nextflow.splitter.JsonSplitter.scanJsonForPath(JsonSplitter.groovy:144)
+	at nextflow.splitter.JsonSplitter.scanJsonForPath(JsonSplitter.groovy:128)
+	at nextflow.splitter.JsonSplitter.scanJsonForPath(JsonSplitter.groovy:144)
+	at nextflow.splitter.JsonSplitter.process(JsonSplitter.groovy:88)
+	... 35 common frames omitted
+May-18 21:16:10.271 [Actor Thread 3] DEBUG nextflow.Session - Session aborted -- Cause: Error while parsing JSON content - cause: java.lang.NullPointerException
+May-18 21:16:10.307 [Actor Thread 3] DEBUG nextflow.Session - The following nodes are still active:
+  [operator] splitJson
+  [operator] view
+
+May-18 21:16:10.343 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=0; peakCpus=0; peakMemory=0; ]
+May-18 21:16:10.363 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
+May-18 21:16:10.392 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye
diff --git a/docs/snippets/splitjson-object.nf b/docs/snippets/splitjson-object.nf
new file mode 100644
index 0000000000..8f403576f6
--- /dev/null
+++ b/docs/snippets/splitjson-object.nf
@@ -0,0 +1,4 @@
+// Example with a JSON object
+Channel.of('{"A": 1, "B": [1, 2, 3], "C": {"D": null}}')
+    .splitJson()
+    .view{"Item: ${it}"}
\ No newline at end of file
diff --git a/docs/snippets/splitjson-object.out b/docs/snippets/splitjson-object.out
new file mode 100644
index 0000000000..0870901294
--- /dev/null
+++ b/docs/snippets/splitjson-object.out
@@ -0,0 +1,3 @@
+Item: [key:A, value:1]
+Item: [key:B, value:[1, 2, 3]]
+Item: [key:C, value:[D:null]]
\ No newline at end of file
diff --git a/docs/snippets/splitjson-with-path.nf b/docs/snippets/splitjson-with-path.nf
new file mode 100644
index 0000000000..15a652d53b
--- /dev/null
+++ b/docs/snippets/splitjson-with-path.nf
@@ -0,0 +1,3 @@
+Channel.of('{"A": 1, "B": [2, 3, {"C": {"D": null, "E": 4, "F": 5}}]}')
+    .splitJson(path: 'B[2].C')
+    .view{"Item: ${it}"}
\ No newline at end of file
diff --git a/docs/snippets/splitjson-with-path.out b/docs/snippets/splitjson-with-path.out
new file mode 100644
index 0000000000..93b88e977b
--- /dev/null
+++ b/docs/snippets/splitjson-with-path.out
@@ -0,0 +1,3 @@
+Item: [key:D, value:null]
+Item: [key:E, value:4]
+Item: [key:F, value:5]
\ No newline at end of file
diff --git a/docs/snippets/subscribe-with-on-complete.nf b/docs/snippets/subscribe-with-on-complete.nf
new file mode 100644
index 0000000000..fa44724378
--- /dev/null
+++ b/docs/snippets/subscribe-with-on-complete.nf
@@ -0,0 +1,2 @@
+Channel.of( 1, 2, 3 )
+    .subscribe onNext: { println it }, onComplete: { println 'Done' }
\ No newline at end of file
diff --git a/docs/snippets/subscribe-with-on-complete.out b/docs/snippets/subscribe-with-on-complete.out
new file mode 100644
index 0000000000..42244bce80
--- /dev/null
+++ b/docs/snippets/subscribe-with-on-complete.out
@@ -0,0 +1,4 @@
+1
+2
+3
+Done
\ No newline at end of file
diff --git a/docs/snippets/subscribe-with-param.nf b/docs/snippets/subscribe-with-param.nf
new file mode 100644
index 0000000000..273e519ce3
--- /dev/null
+++ b/docs/snippets/subscribe-with-param.nf
@@ -0,0 +1,5 @@
+Channel
+    .of( 'alpha', 'beta', 'lambda' )
+    .subscribe { String str ->
+        println "Got: ${str}; len: ${str.size()}"
+    }
\ No newline at end of file
diff --git a/docs/snippets/subscribe-with-param.out b/docs/snippets/subscribe-with-param.out
new file mode 100644
index 0000000000..3be852e6b9
--- /dev/null
+++ b/docs/snippets/subscribe-with-param.out
@@ -0,0 +1,3 @@
+Got: alpha; len: 5
+Got: beta; len: 4
+Got: lambda; len: 6
\ No newline at end of file
diff --git a/docs/snippets/subscribe.nf b/docs/snippets/subscribe.nf
new file mode 100644
index 0000000000..e5a4a3b8f0
--- /dev/null
+++ b/docs/snippets/subscribe.nf
@@ -0,0 +1,5 @@
+// define a channel emitting three values
+source = Channel.of( 'alpha', 'beta', 'delta' )
+
+// subscribe to the channel with a function that prints each value
+source.subscribe { println "Got: $it" }
\ No newline at end of file
diff --git a/docs/snippets/subscribe.out b/docs/snippets/subscribe.out
new file mode 100644
index 0000000000..27a68821f4
--- /dev/null
+++ b/docs/snippets/subscribe.out
@@ -0,0 +1,3 @@
+Got: alpha
+Got: beta
+Got: delta
\ No newline at end of file
diff --git a/docs/snippets/sum-with-mapper.nf b/docs/snippets/sum-with-mapper.nf
new file mode 100644
index 0000000000..9824e9bade
--- /dev/null
+++ b/docs/snippets/sum-with-mapper.nf
@@ -0,0 +1,3 @@
+Channel.of( 4, 1, 7, 5 )
+    .sum { it * it }
+    .view { "Square: $it" }
\ No newline at end of file
diff --git a/docs/snippets/sum-with-mapper.out b/docs/snippets/sum-with-mapper.out
new file mode 100644
index 0000000000..095ddac1e4
--- /dev/null
+++ b/docs/snippets/sum-with-mapper.out
@@ -0,0 +1 @@
+Square: 91
\ No newline at end of file
diff --git a/docs/snippets/sum.nf b/docs/snippets/sum.nf
new file mode 100644
index 0000000000..add3d63e1f
--- /dev/null
+++ b/docs/snippets/sum.nf
@@ -0,0 +1,3 @@
+Channel.of( 8, 6, 2, 5 )
+    .sum()
+    .view { "The sum is $it" }
\ No newline at end of file
diff --git a/docs/snippets/sum.out b/docs/snippets/sum.out
new file mode 100644
index 0000000000..2c4b1b41ff
--- /dev/null
+++ b/docs/snippets/sum.out
@@ -0,0 +1 @@
+The sum is 21
\ No newline at end of file
diff --git a/docs/snippets/take.nf b/docs/snippets/take.nf
new file mode 100644
index 0000000000..9aeeaefb59
--- /dev/null
+++ b/docs/snippets/take.nf
@@ -0,0 +1,3 @@
+Channel.of( 1..10 )
+    .take( 3 )
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/take.out b/docs/snippets/take.out
new file mode 100644
index 0000000000..5f5fbe759f
--- /dev/null
+++ b/docs/snippets/take.out
@@ -0,0 +1,3 @@
+1
+2
+3
\ No newline at end of file
diff --git a/docs/snippets/tap.nf b/docs/snippets/tap.nf
new file mode 100644
index 0000000000..41278f9711
--- /dev/null
+++ b/docs/snippets/tap.nf
@@ -0,0 +1,9 @@
+Channel.of( 'a', 'b', 'c' )
+    .tap { log1 }
+    .map { it * 2 }
+    .tap { log2 }
+    .map { it.toUpperCase() }
+    .view { "Result: $it" }
+
+log1.view { "Log 1: $it" }
+log2.view { "Log 2: $it" }
\ No newline at end of file
diff --git a/docs/snippets/tap.out b/docs/snippets/tap.out
new file mode 100644
index 0000000000..85b5cb1377
--- /dev/null
+++ b/docs/snippets/tap.out
@@ -0,0 +1,9 @@
+Result: AA
+Result: BB
+Result: CC
+Log 1: a
+Log 1: b
+Log 1: c
+Log 2: aa
+Log 2: bb
+Log 2: cc
\ No newline at end of file
diff --git a/docs/snippets/test.sh b/docs/snippets/test.sh
new file mode 100755
index 0000000000..c71497f5b4
--- /dev/null
+++ b/docs/snippets/test.sh
@@ -0,0 +1,26 @@
+#!/bin/bash
+
+NXF_CMD=${NXF_CMD:-nextflow}
+NXF_FILES=${*:-'*.nf'}
+
+for pipeline in $NXF_FILES ; do
+
+    echo "> Running test: $pipeline"
+
+    # run the pipeline
+    $NXF_CMD -q run "$pipeline" > .out
+
+    # verify output (if ground truth exists)
+    outfile="$(basename "$pipeline" .nf).out"
+
+    if [[ -f "$outfile" ]] ; then
+        sort "$outfile" > a.out
+        sort .out > b.out
+        diff a.out b.out
+    else
+        echo "> $outfile not found, skipping"
+    fi
+
+done
+
+rm -rf .nextflow* work .out a.out b.out
diff --git a/docs/snippets/tointeger.nf b/docs/snippets/tointeger.nf
new file mode 100644
index 0000000000..14435cb1df
--- /dev/null
+++ b/docs/snippets/tointeger.nf
@@ -0,0 +1,4 @@
+Channel.of( '1', '7', '12' )
+    .toInteger()
+    .sum()
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/tointeger.out b/docs/snippets/tointeger.out
new file mode 100644
index 0000000000..2edeafb09d
--- /dev/null
+++ b/docs/snippets/tointeger.out
@@ -0,0 +1 @@
+20
\ No newline at end of file
diff --git a/docs/snippets/tolist.nf b/docs/snippets/tolist.nf
new file mode 100644
index 0000000000..d3275bbab3
--- /dev/null
+++ b/docs/snippets/tolist.nf
@@ -0,0 +1,3 @@
+Channel.of( 1, 2, 3, 4 )
+    .toList()
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/tolist.out b/docs/snippets/tolist.out
new file mode 100644
index 0000000000..98d20c4307
--- /dev/null
+++ b/docs/snippets/tolist.out
@@ -0,0 +1 @@
+[1, 2, 3, 4]
\ No newline at end of file
diff --git a/docs/snippets/tosortedlist-with-comparator.nf b/docs/snippets/tosortedlist-with-comparator.nf
new file mode 100644
index 0000000000..55b6d887bc
--- /dev/null
+++ b/docs/snippets/tosortedlist-with-comparator.nf
@@ -0,0 +1,3 @@
+Channel.of( ['homer', 5], ['bart', 2], ['lisa', 10], ['marge', 3], ['maggie', 7] )
+    .toSortedList { a, b -> b[1] <=> a[1] }
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/tosortedlist-with-comparator.out b/docs/snippets/tosortedlist-with-comparator.out
new file mode 100644
index 0000000000..ba7635ebd6
--- /dev/null
+++ b/docs/snippets/tosortedlist-with-comparator.out
@@ -0,0 +1 @@
+[[lisa, 10], [maggie, 7], [homer, 5], [marge, 3], [bart, 2]]
\ No newline at end of file
diff --git a/docs/snippets/tosortedlist.nf b/docs/snippets/tosortedlist.nf
new file mode 100644
index 0000000000..654afa6686
--- /dev/null
+++ b/docs/snippets/tosortedlist.nf
@@ -0,0 +1,3 @@
+Channel.of( 3, 2, 1, 4 )
+    .toSortedList()
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/tosortedlist.out b/docs/snippets/tosortedlist.out
new file mode 100644
index 0000000000..98d20c4307
--- /dev/null
+++ b/docs/snippets/tosortedlist.out
@@ -0,0 +1 @@
+[1, 2, 3, 4]
\ No newline at end of file
diff --git a/docs/snippets/transpose.nf b/docs/snippets/transpose.nf
new file mode 100644
index 0000000000..8300eb1f86
--- /dev/null
+++ b/docs/snippets/transpose.nf
@@ -0,0 +1,7 @@
+Channel.of(
+        [1, ['A', 'B', 'C']],
+        [2, ['C', 'A']],
+        [3, ['B', 'D']]
+    )
+    .transpose()
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/transpose.out b/docs/snippets/transpose.out
new file mode 100644
index 0000000000..b7670a313e
--- /dev/null
+++ b/docs/snippets/transpose.out
@@ -0,0 +1,7 @@
+[1, A]
+[1, B]
+[1, C]
+[2, C]
+[2, A]
+[3, B]
+[3, D]
\ No newline at end of file
diff --git a/docs/snippets/unique-with-mapper.nf b/docs/snippets/unique-with-mapper.nf
new file mode 100644
index 0000000000..3eee3005f0
--- /dev/null
+++ b/docs/snippets/unique-with-mapper.nf
@@ -0,0 +1,3 @@
+Channel.of( 1, 1, 2, 2, 2, 3, 1, 1, 2, 4, 6 )
+    .unique { it % 2 }
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/unique-with-mapper.out b/docs/snippets/unique-with-mapper.out
new file mode 100644
index 0000000000..7a754f414c
--- /dev/null
+++ b/docs/snippets/unique-with-mapper.out
@@ -0,0 +1,2 @@
+1
+2
\ No newline at end of file
diff --git a/docs/snippets/unique.nf b/docs/snippets/unique.nf
new file mode 100644
index 0000000000..a53a861235
--- /dev/null
+++ b/docs/snippets/unique.nf
@@ -0,0 +1,3 @@
+Channel.of( 1, 1, 2, 2, 2, 3, 1, 1, 2, 2, 3 )
+    .unique()
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/unique.out b/docs/snippets/unique.out
new file mode 100644
index 0000000000..5f5fbe759f
--- /dev/null
+++ b/docs/snippets/unique.out
@@ -0,0 +1,3 @@
+1
+2
+3
\ No newline at end of file
diff --git a/docs/snippets/until.nf b/docs/snippets/until.nf
new file mode 100644
index 0000000000..9fe22e26fa
--- /dev/null
+++ b/docs/snippets/until.nf
@@ -0,0 +1,3 @@
+Channel.of( 3, 2, 1, 5, 1, 5 )
+    .until { it == 5 }
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/until.out b/docs/snippets/until.out
new file mode 100644
index 0000000000..339b1ea033
--- /dev/null
+++ b/docs/snippets/until.out
@@ -0,0 +1,3 @@
+3
+2
+1
\ No newline at end of file
diff --git a/docs/snippets/view-with-mapper.nf b/docs/snippets/view-with-mapper.nf
new file mode 100644
index 0000000000..643cfd4394
--- /dev/null
+++ b/docs/snippets/view-with-mapper.nf
@@ -0,0 +1,3 @@
+Channel.of(1, 2, 3)
+    .map { it -> [it, it*it] }
+    .view { num, sqr -> "The square of $num is $sqr" }
\ No newline at end of file
diff --git a/docs/snippets/view-with-mapper.out b/docs/snippets/view-with-mapper.out
new file mode 100644
index 0000000000..4244d7cbfa
--- /dev/null
+++ b/docs/snippets/view-with-mapper.out
@@ -0,0 +1,3 @@
+The square of 1 is 1
+The square of 2 is 4
+The square of 3 is 9
\ No newline at end of file
diff --git a/docs/snippets/view.nf b/docs/snippets/view.nf
new file mode 100644
index 0000000000..f329abd2c2
--- /dev/null
+++ b/docs/snippets/view.nf
@@ -0,0 +1 @@
+Channel.of(1, 2, 3).view()
\ No newline at end of file
diff --git a/docs/snippets/view.out b/docs/snippets/view.out
new file mode 100644
index 0000000000..5f5fbe759f
--- /dev/null
+++ b/docs/snippets/view.out
@@ -0,0 +1,3 @@
+1
+2
+3
\ No newline at end of file
diff --git a/docs/snippets/your-first-script.nf b/docs/snippets/your-first-script.nf
index f457ff3deb..6fe3710e9b 100644
--- a/docs/snippets/your-first-script.nf
+++ b/docs/snippets/your-first-script.nf
@@ -23,4 +23,4 @@ process convertToUpper {
 
 workflow {
     splitLetters | flatten | convertToUpper | view { it.trim() }
-}
\ No newline at end of file
+}
diff --git a/validation/test.sh b/validation/test.sh
index a8734027aa..3ca483728c 100755
--- a/validation/test.sh
+++ b/validation/test.sh
@@ -33,7 +33,7 @@ if [[ $TEST_MODE == 'test_integration' ]]; then
     #
     git clone https://github.com/nextflow-io/hello
     (
-      cd hello;
+      cd hello
       $NXF_CMD run .
       $NXF_CMD run . -resume
     )
@@ -49,6 +49,19 @@ if [[ $TEST_MODE == 'test_integration' ]]; then
     exit 0
 fi
 
+#
+# Documentation tests
+#
+if [[ $TEST_MODE == 'test_docs' ]]; then
+
+    (
+      echo "Documentation tests"
+      cd ../docs/snippets/
+      bash test.sh
+    )
+
+fi
+
 if [ "$GITHUB_EVENT_NAME" = "pull_request" ]; then
   if [ "$(jq -r '.pull_request.head.repo.fork' $GITHUB_EVENT_PATH)" = "true" ]; then
     echo "Skipping cloud integration tests on external PR event"
@@ -81,17 +94,20 @@ if [[ $TEST_MODE == 'test_azure' ]]; then
 fi
 
 #
-# Google Life Sciences
+# Google Batch
 #
 if [[ $TEST_MODE == 'test_google' ]]; then
     if [ "$GOOGLE_SECRET" ]; then
-      echo "Google LS tests"
+      echo "Google Batch tests"
       bash google.sh
     else
-      echo "Missing GOOGLE_SECRET variable -- Skipping Google LS tests"
+      echo "Missing GOOGLE_SECRET variable -- Skipping Google Batch tests"
     fi
 fi
 
+#
+# Wave
+#
 if [[ $TEST_MODE == 'test_wave' ]]; then
       echo "Wave tests"
       bash wave.sh

From 4d326551226e699e62654affa6fd28a82520e31d Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Fri, 10 Nov 2023 00:11:12 -0600
Subject: [PATCH 259/350] Fix doc tests to fail on test failure (#4505)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 docs/snippets/test.sh | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/docs/snippets/test.sh b/docs/snippets/test.sh
index c71497f5b4..42bd7236a9 100755
--- a/docs/snippets/test.sh
+++ b/docs/snippets/test.sh
@@ -1,5 +1,7 @@
 #!/bin/bash
 
+exit_status=0
+
 NXF_CMD=${NXF_CMD:-nextflow}
 NXF_FILES=${*:-'*.nf'}
 
@@ -17,6 +19,7 @@ for pipeline in $NXF_FILES ; do
         sort "$outfile" > a.out
         sort .out > b.out
         diff a.out b.out
+        status=$? ; [ $status -eq 0 ] || exit_status=$status
     else
         echo "> $outfile not found, skipping"
     fi
@@ -24,3 +27,5 @@ for pipeline in $NXF_FILES ; do
 done
 
 rm -rf .nextflow* work .out a.out b.out
+
+[ $exit_status -eq 0 ] || false

From b8907ccbcfd5b598affafb5a55f59a02f59aecac Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Fri, 10 Nov 2023 13:10:40 -0600
Subject: [PATCH 260/350] Fix Checkout remote tag if checkout remote branch
 fails (#4247)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../groovy/nextflow/scm/AssetManager.groovy   | 25 +++++++++++++------
 .../nextflow/scm/AssetManagerTest.groovy      | 21 ++++++++++++++++
 2 files changed, 38 insertions(+), 8 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/scm/AssetManager.groovy b/modules/nextflow/src/main/groovy/nextflow/scm/AssetManager.groovy
index 683a4673f5..a38ec5b2ec 100644
--- a/modules/nextflow/src/main/groovy/nextflow/scm/AssetManager.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/scm/AssetManager.groovy
@@ -628,8 +628,11 @@ class AssetManager {
              * Try to checkout it from a remote branch and return
              */
             catch ( RefNotFoundException e ) {
-                def ref = checkoutRemoteBranch(revision)
-                return "checkout-out at ${ref.getObjectId().name()}"
+                final ref = checkoutRemoteBranch(revision)
+                final commitId = ref?.getObjectId()
+                return commitId
+                    ? "checked out at ${commitId.name()}"
+                    : "checked out revision ${revision}"
             }
         }
 
@@ -943,12 +946,18 @@ class AssetManager {
                 fetch.setRecurseSubmodules(FetchRecurseSubmodulesMode.YES)
             }
             fetch.call()
-            git.checkout()
-                    .setCreateBranch(true)
-                    .setName(revision)
-                    .setUpstreamMode(CreateBranchCommand.SetupUpstreamMode.TRACK)
-                    .setStartPoint("origin/" + revision)
-                    .call()
+
+            try {
+                return git.checkout()
+                        .setCreateBranch(true)
+                        .setName(revision)
+                        .setUpstreamMode(CreateBranchCommand.SetupUpstreamMode.TRACK)
+                        .setStartPoint("origin/" + revision)
+                        .call()
+            }
+            catch (RefNotFoundException e) {
+                return git.checkout() .setName(revision) .call()
+            }
         }
         catch (RefNotFoundException e) {
             throw new AbortOperationException("Cannot find revision `$revision` -- Make sure that it exists in the remote repository `$repositoryUrl`", e)
diff --git a/modules/nextflow/src/test/groovy/nextflow/scm/AssetManagerTest.groovy b/modules/nextflow/src/test/groovy/nextflow/scm/AssetManagerTest.groovy
index 0e239fc0a5..e17022f58a 100644
--- a/modules/nextflow/src/test/groovy/nextflow/scm/AssetManagerTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/scm/AssetManagerTest.groovy
@@ -580,4 +580,25 @@ class AssetManagerTest extends Specification {
 
     }
 
+    @Requires({System.getenv('NXF_GITHUB_ACCESS_TOKEN')})
+    def 'should download tag specified'() {
+
+        given:
+        def folder = tempDir.getRoot()
+        def token = System.getenv('NXF_GITHUB_ACCESS_TOKEN')
+        def manager = new AssetManager().build('nextflow-io/nf-test-branch', [providers: [github: [auth: token]]])
+
+        when:
+        manager.download("v0.1")
+        then:
+        folder.resolve('nextflow-io/nf-test-branch/.git').isDirectory()
+        and:
+        folder.resolve('nextflow-io/nf-test-branch/workflow.nf').text == "println 'Hello'\n"
+
+        when:
+        manager.download()
+        then:
+        noExceptionThrown()
+    }
+
 }

From 54bc0b7d88402532e8d77cd430dbc7ad493c5f42 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Mon, 13 Nov 2023 09:40:20 -0600
Subject: [PATCH 261/350] Remove incorrect note about workflow inputs (#4509)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 docs/workflow.md | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/docs/workflow.md b/docs/workflow.md
index a81dcc1a83..260ebeb37e 100644
--- a/docs/workflow.md
+++ b/docs/workflow.md
@@ -247,10 +247,6 @@ workflow {
 }
 ```
 
-:::{note}
-Workflow inputs are always channels by definition. If a basic data type, such as a number, string, list, etc, is provided, it is implicitly converted to a {ref}`value channel <channel-type-value>`.
-:::
-
 ### Workflow outputs
 
 A workflow can declare one or more output channels using the `emit` keyword. For example:

From 89f09fe0315c2d57a02d3e32f7bdc9984f63b726 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Mon, 13 Nov 2023 15:01:05 -0600
Subject: [PATCH 262/350] Fix Fusion symlinks when publishing files (#4348)

This commit fix the invalid resolution for Fusion symlink in publishDir directive
when the output file is the same as an input file.

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Robert Syme <rob.syme@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../nextflow/processor/PublishDir.groovy      | 77 +++++++++++++------
 .../groovy/nextflow/processor/TaskRun.groovy  |  4 +-
 .../nextflow/extension/PublishOpTest.groovy   |  1 +
 .../nextflow/processor/PublishDirTest.groovy  |  4 +-
 .../processor/PublishDirS3Test.groovy         | 34 +++++++-
 tests/checks/fusion-symlink.nf/.checks        | 25 ++++++
 tests/checks/fusion-symlink.nf/.config        |  4 +
 tests/checks/fusion-symlink.nf/.expected      |  1 +
 tests/fusion-symlink.nf                       | 61 +++++++++++++++
 9 files changed, 180 insertions(+), 31 deletions(-)
 create mode 100644 tests/checks/fusion-symlink.nf/.checks
 create mode 100644 tests/checks/fusion-symlink.nf/.config
 create mode 100644 tests/checks/fusion-symlink.nf/.expected
 create mode 100644 tests/fusion-symlink.nf

diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/PublishDir.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/PublishDir.groovy
index 8013f97fea..0a503ab920 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/PublishDir.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/PublishDir.groovy
@@ -25,10 +25,12 @@ import java.nio.file.NoSuchFileException
 import java.nio.file.Path
 import java.nio.file.PathMatcher
 import java.util.concurrent.ExecutorService
+import java.util.regex.Pattern
 
 import groovy.transform.CompileDynamic
 import groovy.transform.CompileStatic
 import groovy.transform.EqualsAndHashCode
+import groovy.transform.Memoized
 import groovy.transform.PackageScope
 import groovy.transform.ToString
 import groovy.util.logging.Slf4j
@@ -38,6 +40,7 @@ import nextflow.Session
 import nextflow.extension.FilesEx
 import nextflow.file.FileHelper
 import nextflow.file.TagAwareFile
+import nextflow.fusion.FusionHelper
 import nextflow.util.PathTrie
 /**
  * Implements the {@code publishDir} directory. It create links or copies the output
@@ -51,10 +54,14 @@ import nextflow.util.PathTrie
 @CompileStatic
 class PublishDir {
 
+    final static private Pattern FUSION_PATH_REGEX = ~/^\/fusion\/([^\/]+)\/(.*)/
+
     enum Mode { SYMLINK, LINK, COPY, MOVE, COPY_NO_FOLLOW, RELLINK }
 
     private Map<Path,Boolean> makeCache = new HashMap<>()
 
+    private Session session = Global.session as Session
+
     /**
      * The target path where create the links or copy the output files
      */
@@ -117,10 +124,18 @@ class PublishDir {
 
     private boolean nullPathWarn
 
-    private String taskName
+    private TaskRun task
 
     @Lazy
-    private ExecutorService threadPool = { def sess = Global.session as Session; sess.publishDirExecutorService() }()
+    private ExecutorService threadPool = { session.publishDirExecutorService() }()
+
+    protected String getTaskName() {
+        return task?.getName()
+    }
+
+    protected Map<String,Path> getTaskInputs() {
+        return task?.getInputFilesMap()
+    }
 
     void setPath( def value ) {
         final resolved = value instanceof Closure ? value.call() : value
@@ -202,7 +217,6 @@ class PublishDir {
         return result
     }
 
-    @CompileStatic
     protected void apply0(Set<Path> files) {
         assert path
 
@@ -266,7 +280,6 @@ class PublishDir {
      * @param files Set of output files
      * @param task The task whose output need to be published
      */
-    @CompileStatic
     void apply( Set<Path> files, TaskRun task ) {
 
         if( !files || !enabled )
@@ -281,13 +294,10 @@ class PublishDir {
         this.sourceDir = task.targetDir
         this.sourceFileSystem = sourceDir.fileSystem
         this.stageInMode = task.config.stageInMode
-        this.taskName = task.name
 
         apply0(files)
     }
 
-
-    @CompileStatic
     protected void apply1(Path source, boolean inProcess ) {
 
         def target = sourceDir ? sourceDir.relativize(source) : source.getFileName()
@@ -328,7 +338,6 @@ class PublishDir {
 
     }
 
-    @CompileStatic
     protected Path resolveDestination(target) {
 
         if( target instanceof Path ) {
@@ -347,7 +356,6 @@ class PublishDir {
         throw new IllegalArgumentException("Not a valid publish target path: `$target` [${target?.class?.name}]")
     }
 
-    @CompileStatic
     protected void safeProcessFile(Path source, Path target) {
         try {
             processFile(source, target)
@@ -355,15 +363,20 @@ class PublishDir {
         catch( Throwable e ) {
             log.warn "Failed to publish file: ${source.toUriString()}; to: ${target.toUriString()} [${mode.toString().toLowerCase()}] -- See log file for details", e
             if( NF.strictMode || failOnError){
-                final session = Global.session as Session
                 session?.abort(e)
             }
         }
     }
 
-    @CompileStatic
     protected void processFile( Path source, Path destination ) {
 
+        // resolve Fusion symlink if applicable
+        if( FusionHelper.isFusionEnabled(session) ) {
+            final inputs = getTaskInputs()
+            if( source.name in inputs )
+                source = resolveFusionLink(inputs[source.name])
+        }
+
         // create target dirs if required
         makeDirs(destination.parent)
 
@@ -387,6 +400,29 @@ class PublishDir {
         notifyFilePublish(destination, source)
     }
 
+    /**
+     * Resolve a Fusion symlink by following the .fusion.symlinks
+     * file in the task directory until the original file is reached.
+     *
+     * @param file
+     */
+    protected Path resolveFusionLink(Path file) {
+        while( file.name in getFusionLinks(file.parent) )
+            file = file.text.replaceFirst(FUSION_PATH_REGEX) { _, scheme, path -> "${scheme}://${path}" } as Path
+        return file
+    }
+
+    @Memoized
+    protected List<String> getFusionLinks(Path workDir) {
+        try {
+            final file = workDir.resolve('.fusion.symlinks')
+            return file.text.tokenize('\n')
+        }
+        catch( NoSuchFileException e ) {
+            return List.of()
+        }
+    }
+
     private String real0(Path p) {
         try {
             // resolve symlink if it's file in the default (posix) file system
@@ -422,8 +458,9 @@ class PublishDir {
         final s1 = real0(sourceDir)
         if( t1.startsWith(s1) ) {
             def msg = "Refusing to publish file since destination path conflicts with the task work directory!"
-            if( taskName )
-                msg += "\n- offending task  : $taskName"
+            def name0 = getTaskName()
+            if( name0 )
+                msg += "\n- offending task  : $name0"
             msg += "\n- offending file  : $target"
             if( t1 != target.toString() )
                 msg += "\n- real destination: $t1"
@@ -438,7 +475,6 @@ class PublishDir {
         return !mode || mode == Mode.SYMLINK || mode == Mode.RELLINK
     }
 
-    @CompileStatic
     protected void processFileImpl( Path source, Path destination ) {
         log.trace "publishing file: $source -[$mode]-> $destination"
 
@@ -466,13 +502,11 @@ class PublishDir {
         }
     }
 
-    @CompileStatic
-    private void createPublishDir() {
+    protected void createPublishDir() {
         makeDirs(this.path)
     }
 
-    @CompileStatic
-    private void makeDirs(Path dir) {
+    protected void makeDirs(Path dir) {
         if( !dir || makeCache.containsKey(dir) )
             return
 
@@ -491,7 +525,6 @@ class PublishDir {
      * That valid publish mode has been selected
      * Note: link and symlinks are not allowed across different file system
      */
-    @CompileStatic
     @PackageScope
     void validatePublishMode() {
         if( log.isTraceEnabled() )
@@ -512,11 +545,7 @@ class PublishDir {
     }
 
     protected void notifyFilePublish(Path destination, Path source=null) {
-        final sess = Global.session
-        if (sess instanceof Session) {
-            sess.notifyFilePublish(destination, source)
-        }
+        session.notifyFilePublish(destination, source)
     }
 
-
 }
diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskRun.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskRun.groovy
index 205951016e..23672e4a42 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskRun.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskRun.groovy
@@ -433,8 +433,8 @@ class TaskRun implements Cloneable {
      */
     Map<String,Path> getInputFilesMap() {
 
-        def result = [:]
-        def allFiles = getInputFiles().values()
+        final allFiles = getInputFiles().values()
+        final result = new HashMap<String,Path>(allFiles.size())
         for( List<FileHolder> entry : allFiles ) {
             if( entry ) for( FileHolder it : entry ) {
                 result[ it.stageName ] = it.storePath
diff --git a/modules/nextflow/src/test/groovy/nextflow/extension/PublishOpTest.groovy b/modules/nextflow/src/test/groovy/nextflow/extension/PublishOpTest.groovy
index b968b284c7..e904387db3 100644
--- a/modules/nextflow/src/test/groovy/nextflow/extension/PublishOpTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/extension/PublishOpTest.groovy
@@ -42,6 +42,7 @@ class PublishOpTest extends BaseSpec {
         def BASE = folder
         def sess = Mock(Session) {
             getWorkDir() >> BASE
+            getConfig() >> [:]
         }
         Global.session = sess
 
diff --git a/modules/nextflow/src/test/groovy/nextflow/processor/PublishDirTest.groovy b/modules/nextflow/src/test/groovy/nextflow/processor/PublishDirTest.groovy
index 3c858344cb..613fead059 100644
--- a/modules/nextflow/src/test/groovy/nextflow/processor/PublishDirTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/processor/PublishDirTest.groovy
@@ -20,6 +20,7 @@ import java.nio.file.FileSystems
 import java.nio.file.Files
 import java.nio.file.Paths
 
+import nextflow.Global
 import nextflow.Session
 import spock.lang.Specification
 import test.TestHelper
@@ -114,8 +115,9 @@ class PublishDirTest extends Specification {
     }
 
     def 'should create symlinks for output files' () {
-
         given:
+        Global.session = Mock(Session) { getConfig()>>[:] }
+        and:
         def folder = Files.createTempDirectory('nxf')
         folder.resolve('work-dir').mkdir()
         folder.resolve('work-dir/file1.txt').text = 'aaa'
diff --git a/plugins/nf-amazon/src/test/nextflow/processor/PublishDirS3Test.groovy b/plugins/nf-amazon/src/test/nextflow/processor/PublishDirS3Test.groovy
index 460de36581..4e92cb97e7 100644
--- a/plugins/nf-amazon/src/test/nextflow/processor/PublishDirS3Test.groovy
+++ b/plugins/nf-amazon/src/test/nextflow/processor/PublishDirS3Test.groovy
@@ -16,14 +16,14 @@
 
 package nextflow.processor
 
+import java.nio.file.FileSystems
 import java.nio.file.Files
 
+import nextflow.Global
+import nextflow.Session
 import nextflow.cloud.aws.nio.S3Path
-import spock.lang.Specification
-
-import java.nio.file.FileSystems
-
 import nextflow.file.FileHelper
+import spock.lang.Specification
 
 /**
  *
@@ -73,4 +73,30 @@ class PublishDirS3Test extends Specification {
         folder?.deleteDir()
     }
 
+    def 'should resolve fusion symlinks' () {
+        given:
+        Global.session = Mock(Session) {
+            config >> [fusion: [enabled: true]]
+        }
+        and:
+        def prev = FileHelper.asPath('s3://bucket/work/0/foo.txt')
+        def file = FileHelper.asPath('s3://bucket/work/1/foo.txt')
+        def taskInputs = ['foo.txt': file]
+        and:
+        def targetDir = FileHelper.asPath('s3://bucket/results')
+        def target = targetDir.resolve('foo.txt')
+        def publisher = Spy(new PublishDir(path: targetDir)) { getTaskInputs()>>taskInputs }
+
+        when:
+        publisher.processFile(file, target)
+        then:
+        1 * publisher.resolveFusionLink(file) >> prev
+        _ * publisher.makeDirs(target.parent) >> _
+        1 * publisher.processFileImpl(prev, target) >> _
+        1 * publisher.notifyFilePublish(target, prev) >> _
+
+        cleanup:
+        Global.session = null
+    }
+
 }
diff --git a/tests/checks/fusion-symlink.nf/.checks b/tests/checks/fusion-symlink.nf/.checks
new file mode 100644
index 0000000000..a28366d245
--- /dev/null
+++ b/tests/checks/fusion-symlink.nf/.checks
@@ -0,0 +1,25 @@
+#!/bin/bash
+
+# Skip test if AWS keys are missing
+if [ -z "$AWS_ACCESS_KEY_ID" ]; then 
+  echo "Missing AWS credentials -- Skipping test"
+  exit 0
+fi
+
+#
+# normal run
+#
+echo initial run
+$NXF_RUN -c .config
+
+$NXF_CMD fs cp s3://nextflow-ci/work/ci-test/fusion-symlink/data.txt data.txt
+cmp data.txt .expected || false
+
+#
+# resume run
+#
+echo resumed run
+$NXF_RUN -c .config -resume
+
+$NXF_CMD fs cp s3://nextflow-ci/work/ci-test/fusion-symlink/data.txt data.txt
+cmp data.txt .expected || false
diff --git a/tests/checks/fusion-symlink.nf/.config b/tests/checks/fusion-symlink.nf/.config
new file mode 100644
index 0000000000..630af142fa
--- /dev/null
+++ b/tests/checks/fusion-symlink.nf/.config
@@ -0,0 +1,4 @@
+workDir = 's3://nextflow-ci/work'
+fusion.enabled = true
+fusion.exportStorageCredentials = true
+wave.enabled = true
\ No newline at end of file
diff --git a/tests/checks/fusion-symlink.nf/.expected b/tests/checks/fusion-symlink.nf/.expected
new file mode 100644
index 0000000000..e427984d4a
--- /dev/null
+++ b/tests/checks/fusion-symlink.nf/.expected
@@ -0,0 +1 @@
+HELLO
diff --git a/tests/fusion-symlink.nf b/tests/fusion-symlink.nf
new file mode 100644
index 0000000000..30d0cee56d
--- /dev/null
+++ b/tests/fusion-symlink.nf
@@ -0,0 +1,61 @@
+#!/usr/bin/env nextflow
+/*
+ * Copyright 2013-2023, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+process CREATE {
+
+    output:
+    path "data.txt"
+
+    script:
+    """
+    echo HELLO > data.txt
+    """
+}
+
+process FORWARD {
+
+    input:
+    path "data.txt"
+
+    output:
+    path "data.txt"
+
+    script:
+    """
+    echo AND
+    """
+}
+
+process PUBLISH {
+    publishDir "s3://nextflow-ci/work/ci-test/fusion-symlink"
+
+    input:
+    path "data.txt"
+
+    output:
+    path "data.txt"
+
+    script:
+    """
+    echo BYE
+    """
+}
+
+workflow {
+    CREATE | FORWARD | PUBLISH
+}

From 82e56799654eab43f37fb41ada579b34637f56f6 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Wed, 15 Nov 2023 11:09:30 -0600
Subject: [PATCH 263/350] Add note about limitations of glacier auto retrieval
 (#4514)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 docs/config.md | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/docs/config.md b/docs/config.md
index 954bb43a28..c51e86e38b 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -220,7 +220,10 @@ The following settings are available:
 : :::{versionadded} 22.12.0-edge
   :::
 : *Experimental: may change in a future release.*
-: Enable auto retrieval of S3 objects stored with Glacier class store (default: `false`).
+: Enable auto retrieval of S3 objects with a Glacier storage class (default: `false`).
+: :::{note}
+  This feature only works for S3 objects that are downloaded by Nextflow directly. It is not supported for tasks (e.g. when using the AWS Batch executor), since that would lead to many tasks sitting idle for several hours and wasting resources. If you need to restore many objects from Glacier, consider restoring them in a script prior to launching the pipeline.
+  :::
 
 `aws.client.glacierExpirationDays`
 : :::{versionadded} 22.12.0-edge

From 2faadc224fd5c484c5ff4909fa30c61e31a0fb8b Mon Sep 17 00:00:00 2001
From: Jordi Deu-Pons <jordi@jordeu.net>
Date: Sat, 18 Nov 2023 08:47:58 +0100
Subject: [PATCH 264/350] Add "fusion.cacheSize" config option (#4518)

Signed-off-by: Jordi Deu-Pons <jordi@jordeu.net>
---
 docs/fusion.md                                  | 11 ++++++++---
 .../groovy/nextflow/fusion/FusionConfig.groovy  |  6 ++++++
 .../nextflow/fusion/FusionEnvProvider.groovy    |  2 ++
 .../nextflow/fusion/FusionConfigTest.groovy     | 17 ++++++++++++++++-
 4 files changed, 32 insertions(+), 4 deletions(-)

diff --git a/docs/fusion.md b/docs/fusion.md
index 186837e76b..2479e097e3 100644
--- a/docs/fusion.md
+++ b/docs/fusion.md
@@ -184,15 +184,20 @@ The following configuration options are available:
 `fusion.enabled`
 : Enable/disable the use of Fusion file system.
 
+`fusion.cacheSize`
+: :::{versionadded} 23.11.0-edge
+:::
+: The maximum size of the local cache used by the Fusion client.
+
+`fusion.containerConfigUrl`
+: The URL from where the container layer provisioning the Fusion client is downloaded.
+
 `fusion.exportStorageCredentials`
 : :::{versionadded} 23.05.0-edge
   This option was previously named `fusion.exportAwsAccessKeys`.
   :::
 : When `true` the access credentials required by the underlying object storage are exported the pipeline jobs execution environment.
 
-`fusion.containerConfigUrl`
-: The URL from where the container layer provisioning the Fusion client is downloaded. 
-
 `fusion.logLevel`
 : The level of logging emitted by the Fusion client.
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/fusion/FusionConfig.groovy b/modules/nextflow/src/main/groovy/nextflow/fusion/FusionConfig.groovy
index e6b71f0dd0..e67006cb14 100644
--- a/modules/nextflow/src/main/groovy/nextflow/fusion/FusionConfig.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/fusion/FusionConfig.groovy
@@ -21,6 +21,8 @@ import groovy.transform.CompileStatic
 import groovy.transform.Memoized
 import nextflow.Global
 import nextflow.SysEnv
+import nextflow.util.MemoryUnit
+
 /**
  * Model Fusion config options
  *
@@ -44,6 +46,7 @@ class FusionConfig {
     final private boolean tagsEnabled
     final private String tagsPattern
     final private boolean privileged
+    final private MemoryUnit cacheSize
 
     boolean enabled() { enabled }
 
@@ -63,6 +66,8 @@ class FusionConfig {
 
     String tagsPattern() { tagsPattern }
 
+    MemoryUnit cacheSize() { cacheSize }
+
     URL containerConfigUrl() {
         this.containerConfigUrl ? new URL(this.containerConfigUrl) : null
     }
@@ -81,6 +86,7 @@ class FusionConfig {
         this.tagsEnabled = opts.tags==null || opts.tags.toString()!='false'
         this.tagsPattern = (opts.tags==null || (opts.tags instanceof Boolean && opts.tags)) ? DEFAULT_TAGS : ( opts.tags !instanceof Boolean ? opts.tags as String : null )
         this.privileged = opts.privileged==null || opts.privileged.toString()=='true'
+        this.cacheSize = opts.cacheSize as MemoryUnit
         if( containerConfigUrl && !validProtocol(containerConfigUrl))
             throw new IllegalArgumentException("Fusion container config URL should start with 'http:' or 'https:' protocol prefix - offending value: $containerConfigUrl")
     }
diff --git a/modules/nextflow/src/main/groovy/nextflow/fusion/FusionEnvProvider.groovy b/modules/nextflow/src/main/groovy/nextflow/fusion/FusionEnvProvider.groovy
index a1c2f6e7e3..b31e11e5d9 100644
--- a/modules/nextflow/src/main/groovy/nextflow/fusion/FusionEnvProvider.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/fusion/FusionEnvProvider.groovy
@@ -42,6 +42,8 @@ class FusionEnvProvider {
             result.FUSION_LOG_OUTPUT = config.logOutput()
         if( config.logLevel() )
             result.FUSION_LOG_LEVEL = config.logLevel()
+        if( config.cacheSize() )
+            result.FUSION_CACHE_SIZE = "${config.cacheSize().toMega()}M"
         return result
     }
 }
diff --git a/modules/nextflow/src/test/groovy/nextflow/fusion/FusionConfigTest.groovy b/modules/nextflow/src/test/groovy/nextflow/fusion/FusionConfigTest.groovy
index b6d176038f..d5e511d365 100644
--- a/modules/nextflow/src/test/groovy/nextflow/fusion/FusionConfigTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/fusion/FusionConfigTest.groovy
@@ -17,7 +17,7 @@
 
 package nextflow.fusion
 
-
+import nextflow.util.MemoryUnit
 import spock.lang.Specification
 import spock.lang.Unroll
 /**
@@ -85,6 +85,21 @@ class FusionConfigTest extends Specification {
         [logOutput: 'stdout']           | null      | 'stdout'
     }
 
+    def 'should configure cache size' () {
+        given:
+        def opts = new FusionConfig(OPTS)
+        expect:
+        opts.cacheSize() == SIZE
+
+        where:
+        OPTS                            | SIZE
+        [:]                             | null
+        [cacheSize: 100]                | MemoryUnit.of(100)
+        [cacheSize: '100']              | MemoryUnit.of(100)
+        [cacheSize: '100.MB']           | MemoryUnit.of('100.MB')
+    }
+
+
     @Unroll
     def 'should configure tags' () {
         given:

From 4f3aa631752d105086e2c9c2c63298268b6e0816 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 18 Nov 2023 09:26:20 +0100
Subject: [PATCH 265/350] Add support for Fusion when using Singularity OCI
 mode (#4508)

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../src/main/groovy/nextflow/container/ContainerConfig.groovy  | 2 ++
 .../test/groovy/nextflow/container/ContainerConfigTest.groovy  | 3 +++
 2 files changed, 5 insertions(+)

diff --git a/modules/nextflow/src/main/groovy/nextflow/container/ContainerConfig.groovy b/modules/nextflow/src/main/groovy/nextflow/container/ContainerConfig.groovy
index 78e8caef71..71fb346713 100644
--- a/modules/nextflow/src/main/groovy/nextflow/container/ContainerConfig.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/container/ContainerConfig.groovy
@@ -93,6 +93,8 @@ class ContainerConfig extends LinkedHashMap {
             return null
         if( eng=='docker' || eng=='podman' )
             return '--rm --privileged'
+        if( singularityOciMode() )
+            return '-B /dev/fuse'
         if( eng=='singularity' || eng=='apptainer' )
             return null
         log.warn "Fusion file system is not supported by '$eng' container engine"
diff --git a/modules/nextflow/src/test/groovy/nextflow/container/ContainerConfigTest.groovy b/modules/nextflow/src/test/groovy/nextflow/container/ContainerConfigTest.groovy
index 99ed6439fe..29ce5704e4 100644
--- a/modules/nextflow/src/test/groovy/nextflow/container/ContainerConfigTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/container/ContainerConfigTest.groovy
@@ -95,6 +95,9 @@ class ContainerConfigTest extends Specification {
         [engine:'docker']                               | '--rm --privileged'
         [engine:'podman']                               | '--rm --privileged'
         and:
+        [engine: 'singularity']                         | null
+        [engine: 'singularity', oci:true]               | '-B /dev/fuse'
+        and:
         [engine:'docker', fusionOptions:'--cap-add foo']| '--cap-add foo'
         [engine:'podman', fusionOptions:'--cap-add bar']| '--cap-add bar'
         and:

From 4c6f2e8541afae3a3960b04e71aaa62f744c1866 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 18 Nov 2023 10:11:08 +0100
Subject: [PATCH 266/350] Fix container hashing for Singularity + Wave
 containers

This commit fixes an issue in the container unique hashing
when using Singularity containers along with Wave container
provisioning that was causing the invalidation of task cache.

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../resolver/DefaultContainerResolver.groovy       | 14 ++++++++++++--
 .../plugin/resolver/WaveContainerResolver.groovy   | 12 ++++++++----
 .../resolver/WaveContainerResolverTest.groovy      |  2 +-
 3 files changed, 21 insertions(+), 7 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/container/resolver/DefaultContainerResolver.groovy b/modules/nextflow/src/main/groovy/nextflow/container/resolver/DefaultContainerResolver.groovy
index 54432faefa..34cafe65b5 100644
--- a/modules/nextflow/src/main/groovy/nextflow/container/resolver/DefaultContainerResolver.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/container/resolver/DefaultContainerResolver.groovy
@@ -39,10 +39,20 @@ class DefaultContainerResolver implements ContainerResolver {
             return ContainerInfo.EMPTY
         }
 
+        final ret = resolveImage0(task, imageName)
+        return new ContainerInfo(imageName, ret, ret)
+    }
+
+    private String resolveImage0(TaskRun task, String imageName) {
         final cfg = task.getContainerConfig()
         final handler = new ContainerHandler(cfg)
-        final ret = handler.normalizeImageName(imageName)
-        return new ContainerInfo(imageName, ret, ret)
+        return handler.normalizeImageName(imageName)
+    }
+
+    ContainerInfo resolveImage(TaskRun task, String imageName, String hashKey) {
+        assert imageName
+        final ret = resolveImage0(task, imageName)
+        return new ContainerInfo(imageName, ret, hashKey)
     }
 
 }
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/resolver/WaveContainerResolver.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/resolver/WaveContainerResolver.groovy
index 28c64973f3..8049d292da 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/resolver/WaveContainerResolver.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/resolver/WaveContainerResolver.groovy
@@ -41,7 +41,7 @@ import nextflow.processor.TaskRun
 @Priority(-10)  // <-- lower is higher, this is needed to override default provider behavior
 class WaveContainerResolver implements ContainerResolver {
 
-    private ContainerResolver defaultResolver = new DefaultContainerResolver()
+    private DefaultContainerResolver defaultResolver = new DefaultContainerResolver()
     static final private List<String> DOCKER_LIKE = ['docker','podman','sarus']
     static final private List<String> SINGULARITY_LIKE = ['singularity','apptainer']
     static final private String DOCKER_PREFIX = 'docker://'
@@ -93,11 +93,15 @@ class WaveContainerResolver implements ContainerResolver {
             }
             // fetch the wave container name
             final image = waveContainer(task, imageName, singularitySpec)
+            // when wave returns no info, just default to standard behaviour
+            if( !image ) {
+                return defaultResolver.resolveImage(task, imageName)
+            }
             // oras prefixed container are served directly
-            if( image && image.target.startsWith("oras://") )
+            if( image.target.startsWith("oras://") )
                 return image
-            // otherwise adapt it to singularity format
-            return defaultResolver.resolveImage(task, image.target)
+            // otherwise adapt it to singularity format using the target containerInfo to avoid the cache invalidation
+            return defaultResolver.resolveImage(task, image.target, image.hashKey)
         }
         else
             throw new IllegalArgumentException("Wave does not support '$engine' container engine")
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/resolver/WaveContainerResolverTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/resolver/WaveContainerResolverTest.groovy
index 8f46949bf4..74f2db4519 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/resolver/WaveContainerResolverTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/resolver/WaveContainerResolverTest.groovy
@@ -67,7 +67,7 @@ class WaveContainerResolverTest extends Specification {
         _ * task.getContainerConfig() >> Mock(ContainerConfig) { getEngine()>>'singularity' }
         and:
         1 * resolver.waveContainer(task, CONTAINER_NAME, false) >> WAVE_CONTAINER
-        1 * defaultResolver.resolveImage(task, WAVE_CONTAINER.target) >> SINGULARITY_CONTAINER
+        1 * defaultResolver.resolveImage(task, WAVE_CONTAINER.target, WAVE_CONTAINER.hashKey) >> SINGULARITY_CONTAINER
         and:
         result == SINGULARITY_CONTAINER
 

From 7f8f20d3243d5d5f837ab4adc27281be8ae9e5e8 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Mon, 20 Nov 2023 03:43:49 -0600
Subject: [PATCH 267/350] Fix Bypass Google Batch Price query if task cpus and
 memory are defined (#4521)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 .../cloud/google/batch/GoogleBatchMachineTypeSelector.groovy | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchMachineTypeSelector.groovy b/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchMachineTypeSelector.groovy
index 2e21d54042..61b5c4cb8a 100644
--- a/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchMachineTypeSelector.groovy
+++ b/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchMachineTypeSelector.groovy
@@ -90,7 +90,6 @@ class GoogleBatchMachineTypeSelector {
     }
 
     MachineType bestMachineType(int cpus, int memoryMB, String region, boolean spot, boolean fusionEnabled, List<String> families) {
-        final machineTypes = getAvailableMachineTypes(region, spot)
         if (families == null)
             families = Collections.<String>emptyList()
 
@@ -100,7 +99,7 @@ class GoogleBatchMachineTypeSelector {
             if (familyOrType.contains("custom-"))
                 return new MachineType(type: familyOrType, family: 'custom', cpusPerVm: cpus, memPerVm: memoryMB, location: region, priceModel: spot ? PriceModel.spot : PriceModel.standard)
 
-            final machineType = machineTypes.find { it.type == familyOrType }
+            final machineType = getAvailableMachineTypes(region, spot).find { it.type == familyOrType }
             if( machineType )
                 return machineType
         }
@@ -117,7 +116,7 @@ class GoogleBatchMachineTypeSelector {
         final matchMachineType = {String type -> !families || families.find { matchType(it, type) }}
 
         // find machines with enough resources and SSD local disk
-        final validMachineTypes = machineTypes.findAll {
+        final validMachineTypes = getAvailableMachineTypes(region, spot).findAll {
                     it.cpusPerVm >= cpus &&
                     it.memPerVm >= memoryGB &&
                     matchMachineType(it.type)

From 6b1ea7266455b82b716b93b23ee298c3a4cdf70e Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Mon, 20 Nov 2023 04:00:03 -0600
Subject: [PATCH 268/350] Fix typos (#4519) [ci fast]

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 .../nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy   | 4 ++--
 .../groovy/nextflow/container/SingularityCache.groovy     | 2 +-
 .../main/groovy/nextflow/executor/GridTaskHandler.groovy  | 2 +-
 .../main/groovy/nextflow/extension/GroupTupleOp.groovy    | 2 +-
 .../src/main/groovy/nextflow/file/FileCollector.groovy    | 2 +-
 .../main/groovy/nextflow/processor/TaskProcessor.groovy   | 2 +-
 .../src/test/groovy/nextflow/cli/CmdRunTest.groovy        | 2 +-
 .../src/main/nextflow/plugin/PluginUpdater.groovy         | 2 +-
 packing.gradle                                            | 2 +-
 .../main/nextflow/cloud/aws/nio/S3FileSystemProvider.java | 8 ++++----
 .../cloud/aws/nio/util/S3ObjectSummaryLookup.java         | 4 ++--
 11 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
index 7fa7d65298..ac66878d64 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
@@ -677,7 +677,7 @@ class CmdRun extends CmdBase implements HubOptions {
             result.putAll(json)
         }
         catch (NoSuchFileException | FileNotFoundException e) {
-            throw new AbortOperationException("Specified params file does not exists: ${file.toUriString()}")
+            throw new AbortOperationException("Specified params file does not exist: ${file.toUriString()}")
         }
         catch( Exception e ) {
             throw new AbortOperationException("Cannot parse params file: ${file.toUriString()} - Cause: ${e.message}", e)
@@ -691,7 +691,7 @@ class CmdRun extends CmdBase implements HubOptions {
             result.putAll(yaml)
         }
         catch (NoSuchFileException | FileNotFoundException e) {
-            throw new AbortOperationException("Specified params file does not exists: ${file.toUriString()}")
+            throw new AbortOperationException("Specified params file does not exist: ${file.toUriString()}")
         }
         catch( Exception e ) {
             throw new AbortOperationException("Cannot parse params file: ${file.toUriString()}", e)
diff --git a/modules/nextflow/src/main/groovy/nextflow/container/SingularityCache.groovy b/modules/nextflow/src/main/groovy/nextflow/container/SingularityCache.groovy
index 7e2134aa67..2fa7c85db4 100644
--- a/modules/nextflow/src/main/groovy/nextflow/container/SingularityCache.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/container/SingularityCache.groovy
@@ -99,7 +99,7 @@ class SingularityCache {
     }
 
     /**
-     * Create the specified directory if not exists
+     * Create the specified directory if it does not exist
      *
      * @param
      *      str A path string representing a folder where store the singularity images once downloaded
diff --git a/modules/nextflow/src/main/groovy/nextflow/executor/GridTaskHandler.groovy b/modules/nextflow/src/main/groovy/nextflow/executor/GridTaskHandler.groovy
index 143703b551..3ad6430856 100644
--- a/modules/nextflow/src/main/groovy/nextflow/executor/GridTaskHandler.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/executor/GridTaskHandler.groovy
@@ -478,7 +478,7 @@ class GridTaskHandler extends TaskHandler implements FusionAwareTask {
                 return true
             }
             // if the task is not complete (ie submitted or running)
-            // AND the work-dir does not exists ==> something is wrong
+            // AND the work-dir does not exist ==> something is wrong
             task.error = new ProcessException("Task work directory is missing (!)")
             // sanity check does not pass
             return false
diff --git a/modules/nextflow/src/main/groovy/nextflow/extension/GroupTupleOp.groovy b/modules/nextflow/src/main/groovy/nextflow/extension/GroupTupleOp.groovy
index 36e8d2f1a8..e51a3b6bc7 100644
--- a/modules/nextflow/src/main/groovy/nextflow/extension/GroupTupleOp.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/extension/GroupTupleOp.groovy
@@ -96,7 +96,7 @@ class GroupTupleOp {
         final len = tuple.size()
 
         final List items = groups.getOrCreate(key) {    // get the group for the specified key
-            def result = new ArrayList(len)             // create if does not exists
+            def result = new ArrayList(len)             // create if does not exist
             for( int i=0; i<len; i++ )
                 result[i] = (i in indices ? tuple[i] : new ArrayBag())
             return result
diff --git a/modules/nextflow/src/main/groovy/nextflow/file/FileCollector.groovy b/modules/nextflow/src/main/groovy/nextflow/file/FileCollector.groovy
index 4135e8b2d7..de20b47cd3 100644
--- a/modules/nextflow/src/main/groovy/nextflow/file/FileCollector.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/file/FileCollector.groovy
@@ -217,7 +217,7 @@ abstract class FileCollector implements Closeable {
      * Save the entries collected grouping them into files whose name is given by the
      * correspondent group key
      *
-     * @param target A {@link Path} to the folder where files will be saved. If the folder does not exists, is created
+     * @param target A {@link Path} to the folder where files will be saved. If the folder does not exist, is created
      *              automatically
      * @return The list of files where entries have been saved.
      */
diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
index 69b95e689a..134d6b28b8 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
@@ -857,7 +857,7 @@ class TaskProcessor {
         }
 
         if( !task.config.getStoreDir().exists() ) {
-            log.trace "[${safeTaskName(task)}] Store dir does not exists > ${task.config.storeDir} -- return false"
+            log.trace "[${safeTaskName(task)}] Store dir does not exist > ${task.config.storeDir} -- return false"
             // no folder -> no cached result
             return false
         }
diff --git a/modules/nextflow/src/test/groovy/nextflow/cli/CmdRunTest.groovy b/modules/nextflow/src/test/groovy/nextflow/cli/CmdRunTest.groovy
index e18b401a76..004128cc22 100644
--- a/modules/nextflow/src/test/groovy/nextflow/cli/CmdRunTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/cli/CmdRunTest.groovy
@@ -172,7 +172,7 @@ class CmdRunTest extends Specification {
         cmd.parsedParams()
         then:
         def e = thrown(AbortOperationException)
-        e.message == 'Specified params file does not exists: /missing/path.yml'
+        e.message == 'Specified params file does not exist: /missing/path.yml'
 
         cleanup:
         folder?.delete()
diff --git a/modules/nf-commons/src/main/nextflow/plugin/PluginUpdater.groovy b/modules/nf-commons/src/main/nextflow/plugin/PluginUpdater.groovy
index 98a5739273..0fab0ba1c5 100644
--- a/modules/nf-commons/src/main/nextflow/plugin/PluginUpdater.groovy
+++ b/modules/nf-commons/src/main/nextflow/plugin/PluginUpdater.groovy
@@ -121,7 +121,7 @@ class PluginUpdater extends UpdateManager {
                 uri = 'file://' + temp.absolutePath
             }
             catch (FileNotFoundException e) {
-                throw new IllegalArgumentException("Provided repository URL does not exists or cannot be accessed: $uri")
+                throw new IllegalArgumentException("Provided repository URL does not exist or cannot be accessed: $uri")
             }
         }
         // create the update repository instance
diff --git a/packing.gradle b/packing.gradle
index 05993e0465..fe90d5e48d 100644
--- a/packing.gradle
+++ b/packing.gradle
@@ -225,7 +225,7 @@ task deploy( type: Exec, dependsOn: [clean, compile, pack]) {
         checkVersionExits(version)
         
         def path = new File(releaseDir)
-        if( !path.exists() ) error("Releases path does not exists: $path")
+        if( !path.exists() ) error("Releases path does not exist: $path")
         path.eachFile {
             if( it.name.startsWith("nextflow-$version"))
                 files << it
diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3FileSystemProvider.java b/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3FileSystemProvider.java
index b376ba7532..b0e1e763d9 100644
--- a/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3FileSystemProvider.java
+++ b/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3FileSystemProvider.java
@@ -496,7 +496,7 @@ public void delete(Path path) throws IOException {
 		S3Path s3Path = (S3Path) path;
 
         if (Files.notExists(path)){
-            throw new NoSuchFileException("the path: " + path + " not exists");
+            throw new NoSuchFileException("the path: " + path + " does not exist");
         }
 
         if (Files.isDirectory(path)){
@@ -711,11 +711,11 @@ private S3FileAttributes readAttr0(S3Path s3Path) throws IOException {
 		boolean directory = false;
 		boolean regularFile = false;
 		String key = objectSummary.getKey();
-		// check if is a directory and exists the key of this directory at amazon s3
+		// check if is a directory and the key of this directory exists in amazon s3
 		if (objectSummary.getKey().equals(s3Path.getKey() + "/") && objectSummary.getKey().endsWith("/")) {
 			directory = true;
 		}
-		// is a directory but not exists at amazon s3
+		// is a directory but does not exist in amazon s3
 		else if ((!objectSummary.getKey().equals(s3Path.getKey()) || "".equals(s3Path.getKey())) && objectSummary.getKey().startsWith(s3Path.getKey())){
 			directory = true;
 			// no metadata, we fake one
@@ -910,7 +910,7 @@ private boolean exists(S3Path path) {
 	}
 
 	/**
-	 * Get the Control List, if the path not exists
+	 * Get the Control List, if the path does not exist
      * (because the path is a directory and this key isn't created at amazon s3)
      * then return the ACL of the first child.
      *
diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/util/S3ObjectSummaryLookup.java b/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/util/S3ObjectSummaryLookup.java
index 9354f8456b..ce1e0e75cd 100644
--- a/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/util/S3ObjectSummaryLookup.java
+++ b/plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/util/S3ObjectSummaryLookup.java
@@ -37,7 +37,7 @@ public class S3ObjectSummaryLookup {
     private static final Logger log = LoggerFactory.getLogger(S3ObjectSummary.class);
 
     /**
-     * Get the {@link com.amazonaws.services.s3.model.S3ObjectSummary} that represent this Path or her first child if this path not exists
+     * Get the {@link com.amazonaws.services.s3.model.S3ObjectSummary} that represent this Path or its first child if the path does not exist
      * @param s3Path {@link S3Path}
      * @return {@link com.amazonaws.services.s3.model.S3ObjectSummary}
      * @throws java.nio.file.NoSuchFileException if not found the path and any child
@@ -139,7 +139,7 @@ public ObjectMetadata getS3ObjectMetadata(S3Path s3Path) {
     /**
      * get S3Object represented by this S3Path try to access with or without end slash '/'
      * @param s3Path S3Path
-     * @return S3Object or null if not exists
+     * @return S3Object or null if it does not exist
      */
     @Deprecated
     private S3Object getS3Object(S3Path s3Path){

From 2ccb05d06869cc7fafe292de0db6ae78a55ba71e Mon Sep 17 00:00:00 2001
From: Dr Marco Claudio De La Pierre <marco.delapierre@gmail.com>
Date: Mon, 20 Nov 2023 18:00:37 +0800
Subject: [PATCH 269/350] Makefile clean to also remove buildSrc/build (#4517)

Signed-off-by: Dr Marco Claudio De La Pierre <marco.delapierre@gmail.com>
---
 Makefile | 1 +
 1 file changed, 1 insertion(+)

diff --git a/Makefile b/Makefile
index 6d21ea1548..fb508c68a4 100644
--- a/Makefile
+++ b/Makefile
@@ -33,6 +33,7 @@ clean:
 	rm -rf modules/nextflow/.nextflow*
 	rm -rf modules/nextflow/work
 	rm -rf build
+	rm -rf buildSrc/build
 	rm -rf modules/*/build
 	rm -rf plugins/*/build
 	./gradlew clean

From 8320ea10a74897cca3dbe544bd5fc83cee9dd2c9 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Tue, 21 Nov 2023 16:54:41 +0100
Subject: [PATCH 270/350] Add support for Azure low-priority pool (#4527)

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/config.md                                |  4 +
 .../cloud/azure/batch/AzBatchService.groovy   | 26 +++--
 .../cloud/azure/config/AzPoolOpts.groovy      |  3 +
 .../azure/batch/AzBatchServiceTest.groovy     | 14 ++-
 .../cloud/azure/config/AzPoolOptsTest.groovy  | 94 +++++++++++++++++++
 5 files changed, 130 insertions(+), 11 deletions(-)
 create mode 100644 plugins/nf-azure/src/test/nextflow/cloud/azure/config/AzPoolOptsTest.groovy

diff --git a/docs/config.md b/docs/config.md
index c51e86e38b..406e579901 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -366,6 +366,10 @@ The following settings are available:
 : *New in `nf-azure` version `0.11.0`*
 : If mounting File Shares, this is the internal root mounting point. Must be `/mnt/resource/batch/tasks/fsmounts` for CentOS nodes or `/mnt/batch/tasks/fsmounts` for Ubuntu nodes (default is for CentOS).
 
+`azure.batch.pools.<name>.lowPriority`
+: *New in `nf-azure` version `1.4.0`*
+: Enable the use of low-priority VMs (default: `false`).
+
 `azure.batch.pools.<name>.maxVmCount`
 : Specify the max of virtual machine when using auto scale option.
 
diff --git a/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchService.groovy b/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchService.groovy
index a16506e4ad..170a0f6e11 100644
--- a/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchService.groovy
+++ b/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchService.groovy
@@ -749,7 +749,12 @@ class AzBatchService implements Closeable {
                     .withAutoScaleEvaluationInterval( new Period().withSeconds(interval) )
                     .withAutoScaleFormula(scaleFormula(spec.opts))
         }
-        else {
+        else if( spec.opts.lowPriority ) {
+            log.debug "Creating low-priority pool with id: ${spec.poolId}; vmCount=${spec.opts.vmCount};"
+            poolParams
+                .withTargetLowPriorityNodes(spec.opts.vmCount)
+        }
+        else  {
             log.debug "Creating fixed pool with id: ${spec.poolId}; vmCount=${spec.opts.vmCount};"
             poolParams
                     .withTargetDedicatedNodes(spec.opts.vmCount)
@@ -759,23 +764,24 @@ class AzBatchService implements Closeable {
     }
 
     protected String scaleFormula(AzPoolOpts opts) {
+        final target = opts.lowPriority ? 'TargetLowPriorityNodes' : 'TargetDedicatedNodes'
         // https://docs.microsoft.com/en-us/azure/batch/batch-automatic-scaling
-        def DEFAULT_FORMULA = '''
+        final DEFAULT_FORMULA = """
             // Get pool lifetime since creation.
             lifespan = time() - time("{{poolCreationTime}}");
             interval = TimeInterval_Minute * {{scaleInterval}};
             
             // Compute the target nodes based on pending tasks.
-            // $PendingTasks == The sum of $ActiveTasks and $RunningTasks
-            $samples = $PendingTasks.GetSamplePercent(interval);
-            $tasks = $samples < 70 ? max(0, $PendingTasks.GetSample(1)) : max( $PendingTasks.GetSample(1), avg($PendingTasks.GetSample(interval)));
-            $targetVMs = $tasks > 0 ? $tasks : max(0, $TargetDedicatedNodes/2);
-            targetPoolSize = max(0, min($targetVMs, {{maxVmCount}}));
+            // \$PendingTasks == The sum of \$ActiveTasks and \$RunningTasks
+            \$samples = \$PendingTasks.GetSamplePercent(interval);
+            \$tasks = \$samples < 70 ? max(0, \$PendingTasks.GetSample(1)) : max( \$PendingTasks.GetSample(1), avg(\$PendingTasks.GetSample(interval)));
+            \$targetVMs = \$tasks > 0 ? \$tasks : max(0, \$TargetDedicatedNodes/2);
+            targetPoolSize = max(0, min(\$targetVMs, {{maxVmCount}}));
             
             // For first interval deploy 1 node, for other intervals scale up/down as per tasks.
-            $TargetDedicatedNodes = lifespan < interval ? {{vmCount}} : targetPoolSize;
-            $NodeDeallocationOption = taskcompletion;
-            '''.stripIndent(true)
+            \$${target} = lifespan < interval ? {{vmCount}} : targetPoolSize;
+            \$NodeDeallocationOption = taskcompletion;
+            """.stripIndent(true)
 
         final scaleFormula = opts.scaleFormula ?: DEFAULT_FORMULA
         final vars = poolCreationBindings(opts, Instant.now())
diff --git a/plugins/nf-azure/src/main/nextflow/cloud/azure/config/AzPoolOpts.groovy b/plugins/nf-azure/src/main/nextflow/cloud/azure/config/AzPoolOpts.groovy
index 178c34e47f..c17b818c9d 100644
--- a/plugins/nf-azure/src/main/nextflow/cloud/azure/config/AzPoolOpts.groovy
+++ b/plugins/nf-azure/src/main/nextflow/cloud/azure/config/AzPoolOpts.groovy
@@ -66,6 +66,7 @@ class AzPoolOpts implements CacheFunnel {
     String password
 
     String virtualNetwork
+    boolean lowPriority
 
     AzPoolOpts() {
         this(Collections.emptyMap())
@@ -89,6 +90,7 @@ class AzPoolOpts implements CacheFunnel {
         this.userName = opts.userName
         this.password = opts.password
         this.virtualNetwork = opts.virtualNetwork
+        this.lowPriority = opts.lowPriority as boolean
     }
 
     @Override
@@ -108,6 +110,7 @@ class AzPoolOpts implements CacheFunnel {
         hasher.putUnencodedChars(scaleFormula ?: '')
         hasher.putUnencodedChars(schedulePolicy ?: '')
         hasher.putUnencodedChars(virtualNetwork ?: '')
+        hasher.putBoolean(lowPriority)
         return hasher
     }
 
diff --git a/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchServiceTest.groovy b/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchServiceTest.groovy
index 0b00cc9a38..10c2a6836f 100644
--- a/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchServiceTest.groovy
+++ b/plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchServiceTest.groovy
@@ -237,6 +237,18 @@ class AzBatchServiceTest extends Specification {
         formula.contains '$TargetDedicatedNodes = lifespan < interval ? 3 : targetPoolSize;'
     }
 
+    def 'should check scaling formula for low-priority' () {
+        given:
+        def exec = Mock(AzBatchExecutor) { getConfig() >> new AzConfig([:]) }
+        def svc = new AzBatchService(exec)
+
+        when:
+        def formula = svc.scaleFormula( new AzPoolOpts(lowPriority: true, vmCount: 3, maxVmCount: 10, scaleInterval: Duration.of('5 min')) )
+        then:
+        formula.contains 'interval = TimeInterval_Minute * 5;'
+        formula.contains '$TargetLowPriorityNodes = lifespan < interval ? 3 : targetPoolSize;'
+    }
+
     def 'should  check formula vars' () {
         given:
         def exec = Mock(AzBatchExecutor) { getConfig() >> new AzConfig([:]) }
@@ -347,7 +359,7 @@ class AzBatchServiceTest extends Specification {
         then:
         1 * svc.guessBestVm(LOC, CPUS, MEM, TYPE) >> VM
         and:
-        spec.poolId == 'nf-pool-9022a3fbfb5f93028d78fefaea5e21ab-Standard_X1'
+        spec.poolId == 'nf-pool-6e9cf97d3d846621464131d3842265ce-Standard_X1'
         spec.metadata == [foo: 'bar']
 
     }
diff --git a/plugins/nf-azure/src/test/nextflow/cloud/azure/config/AzPoolOptsTest.groovy b/plugins/nf-azure/src/test/nextflow/cloud/azure/config/AzPoolOptsTest.groovy
new file mode 100644
index 0000000000..ca57b5f4ec
--- /dev/null
+++ b/plugins/nf-azure/src/test/nextflow/cloud/azure/config/AzPoolOptsTest.groovy
@@ -0,0 +1,94 @@
+/*
+ * Copyright 2013-2023, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package nextflow.cloud.azure.config
+
+import nextflow.util.Duration
+import spock.lang.Specification
+/**
+ *
+ * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
+ */
+class AzPoolOptsTest extends Specification {
+
+    def 'should create pool options' () {
+        when:
+        def opts = new AzPoolOpts()
+        then:
+        !opts.runAs
+        !opts.privileged
+        opts.publisher == AzPoolOpts.DEFAULT_PUBLISHER
+        opts.offer == AzPoolOpts.DEFAULT_OFFER
+        opts.sku == AzPoolOpts.DEFAULT_SKU
+        opts.vmType == AzPoolOpts.DEFAULT_VM_TYPE
+        opts.fileShareRootPath == '/mnt/batch/tasks/fsmounts'
+        opts.vmCount == 1
+        !opts.autoScale
+        !opts.scaleFormula
+        !opts.schedulePolicy
+        opts.scaleInterval == AzPoolOpts.DEFAULT_SCALE_INTERVAL
+        opts.maxVmCount == opts.vmCount *3
+        !opts.registry
+        !opts.userName
+        !opts.password
+        !opts.virtualNetwork
+        !opts.lowPriority
+    }
+
+    def 'should create pool with custom options' () {
+        when:
+        def opts = new AzPoolOpts([
+            runAs:'foo',
+            privileged: true,
+            publisher: 'some-pub',
+            offer: 'some-offer',
+            sku: 'some-sku',
+            vmType: 'some-vmtype',
+            vmCount: 10,
+            autoScale: true,
+            scaleFormula: 'some-formula',
+            schedulePolicy: 'some-policy',
+            scaleInterval: Duration.of('10s'),
+            maxVmCount: 100,
+            registry: 'some-reg',
+            userName: 'some-user',
+            password: 'some-pwd',
+            virtualNetwork: 'some-vnet',
+            lowPriority: true
+        ])
+        then:
+        opts.runAs == 'foo'
+        opts.privileged
+        opts.publisher == 'some-pub'
+        opts.offer == 'some-offer'
+        opts.sku == 'some-sku'
+        opts.vmType == 'some-vmtype'
+        opts.fileShareRootPath == ''
+        opts.vmCount == 10
+        opts.autoScale
+        opts.scaleFormula == 'some-formula'
+        opts.schedulePolicy == 'some-policy'
+        opts.scaleInterval == Duration.of('10s')
+        opts.maxVmCount == 100
+        opts.registry == 'some-reg'
+        opts.userName == 'some-user'
+        opts.password == 'some-pwd'
+        opts.virtualNetwork == 'some-vnet'
+        opts.lowPriority
+    }
+
+}

From f6a53a6aff86daf6ecfaa939c0e380ba76f0e33a Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Tue, 21 Nov 2023 18:23:31 +0100
Subject: [PATCH 271/350] Fix Google creds for CI tests

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 validation/google.sh | 11 +----------
 1 file changed, 1 insertion(+), 10 deletions(-)

diff --git a/validation/google.sh b/validation/google.sh
index e0f7792870..d97fedd4c1 100644
--- a/validation/google.sh
+++ b/validation/google.sh
@@ -6,16 +6,7 @@ get_abs_filename() {
 
 export NXF_CMD=${NXF_CMD:-$(get_abs_filename ../launch.sh)}
 
-#
-# setup credentials:
-#  1. decrypt credentials file
-#  2. export required env var
-# Note: file was encrypted with the command:
-#  gpg --symmetric --cipher-algo AES256 --output ./google_credentials.gpg $GOOGLE_APPLICATION_CREDENTIALS
-#
-# More details https://help.github.com/en/actions/automating-your-workflow-with-github-actions/creating-and-using-encrypted-secrets
-#   
-gpg --quiet --batch --yes --decrypt --passphrase=$GOOGLE_SECRET --output google_credentials.json ./google_credentials.gpg
+echo $GOOGLE_SECRET | base64 -d > $PWD/google_credentials.json
 export GOOGLE_APPLICATION_CREDENTIALS=$PWD/google_credentials.json
 
 [[ $TOWER_ACCESS_TOKEN ]] && OPTS='-with-tower' || OPTS=''

From a310c77704a9d1dc301dec004a1be1d905c33589 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Tue, 21 Nov 2023 13:09:48 -0600
Subject: [PATCH 272/350] Fix security vulnerabilities (#4513)

This commit bumps:
- org.eclipse.jgit:6.6.1.202309021850
- pf4j:3.10.0
- ivy:2.5.2

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 docker/Dockerfile                                |  2 +-
 modules/nextflow/build.gradle                    |  4 ++--
 modules/nf-commons/build.gradle                  |  2 +-
 .../nextflow/plugin/CustomPluginManager.groovy   |  2 +-
 .../plugin/TestPluginDescriptorFinder.groovy     | 16 ++++++++++------
 packing.gradle                                   |  2 +-
 plugins/nf-amazon/build.gradle                   |  2 +-
 plugins/nf-azure/build.gradle                    |  2 +-
 plugins/nf-cloudcache/build.gradle               |  2 +-
 plugins/nf-codecommit/build.gradle               |  2 +-
 plugins/nf-console/build.gradle                  |  2 +-
 plugins/nf-ga4gh/build.gradle                    |  2 +-
 plugins/nf-google/build.gradle                   |  2 +-
 plugins/nf-tower/build.gradle                    |  2 +-
 plugins/nf-wave/build.gradle                     |  2 +-
 15 files changed, 25 insertions(+), 21 deletions(-)

diff --git a/docker/Dockerfile b/docker/Dockerfile
index de56944d02..e016583e98 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -1,4 +1,4 @@
-FROM amazoncorretto:17.0.8
+FROM amazoncorretto:17.0.9
 RUN yum install -y procps-ng shadow-utils which
 
 ENV NXF_HOME=/.nextflow
diff --git a/modules/nextflow/build.gradle b/modules/nextflow/build.gradle
index 4b468ecc14..c24f235cdc 100644
--- a/modules/nextflow/build.gradle
+++ b/modules/nextflow/build.gradle
@@ -36,13 +36,13 @@ dependencies {
     api "com.beust:jcommander:1.35"
     api("com.esotericsoftware.kryo:kryo:2.24.0") { exclude group: 'com.esotericsoftware.minlog', module: 'minlog' }
     api('org.iq80.leveldb:leveldb:0.12')
-    api('org.eclipse.jgit:org.eclipse.jgit:6.5.0.202303070854-r')
+    api('org.eclipse.jgit:org.eclipse.jgit:6.6.1.202309021850-r')
     api ('javax.activation:activation:1.1.1')
     api ('javax.mail:mail:1.4.7')
     api ('org.yaml:snakeyaml:2.0')
     api ('org.jsoup:jsoup:1.15.4')
     api 'jline:jline:2.9'
-    api 'org.pf4j:pf4j:3.4.1'
+    api 'org.pf4j:pf4j:3.10.0'
     api 'dev.failsafe:failsafe:3.1.0'
 
     testImplementation 'org.subethamail:subethasmtp:3.1.7'
diff --git a/modules/nf-commons/build.gradle b/modules/nf-commons/build.gradle
index e3a00932d9..1d09cf4f76 100644
--- a/modules/nf-commons/build.gradle
+++ b/modules/nf-commons/build.gradle
@@ -30,7 +30,7 @@ dependencies {
     api "org.codehaus.groovy:groovy-nio:3.0.19"
     api "commons-lang:commons-lang:2.6"
     api 'com.google.guava:guava:31.1-jre'
-    api 'org.pf4j:pf4j:3.4.1'
+    api 'org.pf4j:pf4j:3.10.0'
     api 'org.pf4j:pf4j-update:2.3.0'
     api 'dev.failsafe:failsafe:3.1.0'
     // patch gson dependency required by pf4j
diff --git a/modules/nf-commons/src/main/nextflow/plugin/CustomPluginManager.groovy b/modules/nf-commons/src/main/nextflow/plugin/CustomPluginManager.groovy
index 2dcf244478..db6b79e783 100644
--- a/modules/nf-commons/src/main/nextflow/plugin/CustomPluginManager.groovy
+++ b/modules/nf-commons/src/main/nextflow/plugin/CustomPluginManager.groovy
@@ -64,6 +64,6 @@ class CustomPluginManager extends DefaultPluginManager {
 
     @Override
     protected ExtensionFactory createExtensionFactory() {
-        return new SingletonExtensionFactory()
+        return new SingletonExtensionFactory(this)
     }
 }
diff --git a/modules/nf-commons/src/testFixtures/groovy/nextflow/plugin/TestPluginDescriptorFinder.groovy b/modules/nf-commons/src/testFixtures/groovy/nextflow/plugin/TestPluginDescriptorFinder.groovy
index 66b40e2669..a7ca0ef139 100644
--- a/modules/nf-commons/src/testFixtures/groovy/nextflow/plugin/TestPluginDescriptorFinder.groovy
+++ b/modules/nf-commons/src/testFixtures/groovy/nextflow/plugin/TestPluginDescriptorFinder.groovy
@@ -19,6 +19,7 @@ package nextflow.plugin
 
 import java.nio.file.Files
 import java.nio.file.Path
+import java.util.jar.Manifest
 
 import org.pf4j.ManifestPluginDescriptorFinder
 /**
@@ -30,12 +31,15 @@ import org.pf4j.ManifestPluginDescriptorFinder
 class TestPluginDescriptorFinder extends ManifestPluginDescriptorFinder {
 
     @Override
-    protected Path getManifestPath(Path pluginPath) {
-        if (Files.isDirectory(pluginPath)) {
-            final manifest = pluginPath.resolve('build/resources/testFixtures/META-INF/MANIFEST.MF')
-            return Files.exists(manifest) ? manifest : null
-        }
+    protected Manifest readManifestFromDirectory(Path pluginPath) {
+        if( !Files.isDirectory(pluginPath) )
+            return null
 
-        return null;
+        final manifestPath = pluginPath.resolve('build/resources/testFixtures/META-INF/MANIFEST.MF')
+        if( !Files.exists(manifestPath) )
+            return null
+
+        final input = Files.newInputStream(manifestPath)
+        return new Manifest(input)
     }
 }
diff --git a/packing.gradle b/packing.gradle
index fe90d5e48d..8587735102 100644
--- a/packing.gradle
+++ b/packing.gradle
@@ -15,7 +15,7 @@ configurations {
 dependencies {
     api project(':nextflow')
     // include Ivy at runtime in order to have Grape @Grab work correctly
-    defaultCfg "org.apache.ivy:ivy:2.5.1"
+    defaultCfg "org.apache.ivy:ivy:2.5.2"
     // default cfg = runtime + httpfs + amazon + tower client + wave client
     defaultCfg project(':nf-httpfs')
     // Capsule manages the fat jar building process
diff --git a/plugins/nf-amazon/build.gradle b/plugins/nf-amazon/build.gradle
index fad4a22db4..de082b0fc2 100644
--- a/plugins/nf-amazon/build.gradle
+++ b/plugins/nf-amazon/build.gradle
@@ -35,7 +35,7 @@ configurations {
 dependencies {
     compileOnly project(':nextflow')
     compileOnly 'org.slf4j:slf4j-api:2.0.7'
-    compileOnly 'org.pf4j:pf4j:3.4.1'
+    compileOnly 'org.pf4j:pf4j:3.10.0'
 
     api ('javax.xml.bind:jaxb-api:2.3.1')
     api ('com.amazonaws:aws-java-sdk-s3:1.12.429')
diff --git a/plugins/nf-azure/build.gradle b/plugins/nf-azure/build.gradle
index c74ef70fe8..284e994fa4 100644
--- a/plugins/nf-azure/build.gradle
+++ b/plugins/nf-azure/build.gradle
@@ -35,7 +35,7 @@ configurations {
 dependencies {
     compileOnly project(':nextflow')
     compileOnly 'org.slf4j:slf4j-api:2.0.7'
-    compileOnly 'org.pf4j:pf4j:3.4.1'
+    compileOnly 'org.pf4j:pf4j:3.10.0'
     api('com.azure:azure-storage-blob:12.22.1') {
         exclude group: 'org.slf4j', module: 'slf4j-api'
     }
diff --git a/plugins/nf-cloudcache/build.gradle b/plugins/nf-cloudcache/build.gradle
index d37b5354c9..d8ebde2e0a 100644
--- a/plugins/nf-cloudcache/build.gradle
+++ b/plugins/nf-cloudcache/build.gradle
@@ -32,7 +32,7 @@ configurations {
 dependencies {
     compileOnly project(':nextflow')
     compileOnly 'org.slf4j:slf4j-api:2.0.7'
-    compileOnly 'org.pf4j:pf4j:3.4.1'
+    compileOnly 'org.pf4j:pf4j:3.10.0'
 
     testImplementation(testFixtures(project(":nextflow")))
     testImplementation "org.codehaus.groovy:groovy:3.0.19"
diff --git a/plugins/nf-codecommit/build.gradle b/plugins/nf-codecommit/build.gradle
index 0137c25c5a..c2b9dabaf7 100644
--- a/plugins/nf-codecommit/build.gradle
+++ b/plugins/nf-codecommit/build.gradle
@@ -35,7 +35,7 @@ configurations {
 dependencies {
     compileOnly project(':nextflow')
     compileOnly 'org.slf4j:slf4j-api:2.0.7'
-    compileOnly 'org.pf4j:pf4j:3.4.1'
+    compileOnly 'org.pf4j:pf4j:3.10.0'
 
     api ('javax.xml.bind:jaxb-api:2.3.1')
     api ('com.amazonaws:aws-java-sdk-codecommit:1.12.429')
diff --git a/plugins/nf-console/build.gradle b/plugins/nf-console/build.gradle
index 9b88a1daf2..33d5bc1add 100644
--- a/plugins/nf-console/build.gradle
+++ b/plugins/nf-console/build.gradle
@@ -35,7 +35,7 @@ configurations {
 dependencies {
     compileOnly project(':nextflow')
     compileOnly 'org.slf4j:slf4j-api:2.0.7'
-    compileOnly 'org.pf4j:pf4j:3.4.1'
+    compileOnly 'org.pf4j:pf4j:3.10.0'
 
     api("org.codehaus.groovy:groovy-console:3.0.19") { transitive=false }
     api("org.codehaus.groovy:groovy-swing:3.0.19")  { transitive=false }
diff --git a/plugins/nf-ga4gh/build.gradle b/plugins/nf-ga4gh/build.gradle
index 1f87616d4d..6767558fe7 100644
--- a/plugins/nf-ga4gh/build.gradle
+++ b/plugins/nf-ga4gh/build.gradle
@@ -35,7 +35,7 @@ configurations {
 dependencies {
     compileOnly project(':nextflow')
     compileOnly 'org.slf4j:slf4j-api:2.0.7'
-    compileOnly 'org.pf4j:pf4j:3.4.1'
+    compileOnly 'org.pf4j:pf4j:3.10.0'
 
     api 'javax.annotation:javax.annotation-api:1.3.2'
     api 'io.swagger:swagger-annotations:1.5.15'
diff --git a/plugins/nf-google/build.gradle b/plugins/nf-google/build.gradle
index b1c9178d6f..a9b51fe048 100644
--- a/plugins/nf-google/build.gradle
+++ b/plugins/nf-google/build.gradle
@@ -35,7 +35,7 @@ configurations {
 dependencies {
     compileOnly project(':nextflow')
     compileOnly 'org.slf4j:slf4j-api:2.0.7'
-    compileOnly 'org.pf4j:pf4j:3.4.1'
+    compileOnly 'org.pf4j:pf4j:3.10.0'
 
     api 'com.google.apis:google-api-services-lifesciences:v2beta-rev20210527-1.31.5'
     api 'com.google.auth:google-auth-library-oauth2-http:0.18.0'
diff --git a/plugins/nf-tower/build.gradle b/plugins/nf-tower/build.gradle
index bb5980c1a8..e32f582ede 100644
--- a/plugins/nf-tower/build.gradle
+++ b/plugins/nf-tower/build.gradle
@@ -31,7 +31,7 @@ configurations {
 dependencies {
     compileOnly project(':nextflow')
     compileOnly 'org.slf4j:slf4j-api:2.0.7'
-    compileOnly 'org.pf4j:pf4j:3.4.1'
+    compileOnly 'org.pf4j:pf4j:3.10.0'
 
     api "com.fasterxml.jackson.dataformat:jackson-dataformat-yaml:2.15.0"
     api "com.fasterxml.jackson.core:jackson-databind:2.12.7.1"
diff --git a/plugins/nf-wave/build.gradle b/plugins/nf-wave/build.gradle
index 93d749fba3..ed170126a5 100644
--- a/plugins/nf-wave/build.gradle
+++ b/plugins/nf-wave/build.gradle
@@ -31,7 +31,7 @@ configurations {
 dependencies {
     compileOnly project(':nextflow')
     compileOnly 'org.slf4j:slf4j-api:2.0.7'
-    compileOnly 'org.pf4j:pf4j:3.4.1'
+    compileOnly 'org.pf4j:pf4j:3.10.0'
     api 'org.apache.commons:commons-compress:1.21'
     api 'org.apache.commons:commons-lang3:3.12.0'
     api 'com.google.code.gson:gson:2.10.1'

From 38210e117bb37b02f59471c02f26aa44f3e06cf6 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Tue, 21 Nov 2023 13:12:24 -0600
Subject: [PATCH 273/350] Improve operator docs (#4502)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/config.md                                |   4 +-
 docs/mail.md                                  |   2 +-
 docs/operator.md                              | 715 +++++++++---------
 docs/process.md                               |   8 +-
 docs/script.md                                |  46 +-
 .../snippets/{transpose.nf => transpose-1.nf} |   0
 .../{transpose.out => transpose-1.out}        |   0
 docs/snippets/transpose-2-with-remainder.nf   |   7 +
 docs/snippets/transpose-2-with-remainder.out  |   6 +
 docs/snippets/transpose-2.nf                  |   7 +
 docs/snippets/transpose-2.out                 |   5 +
 11 files changed, 434 insertions(+), 366 deletions(-)
 rename docs/snippets/{transpose.nf => transpose-1.nf} (100%)
 rename docs/snippets/{transpose.out => transpose-1.out} (100%)
 create mode 100644 docs/snippets/transpose-2-with-remainder.nf
 create mode 100644 docs/snippets/transpose-2-with-remainder.out
 create mode 100644 docs/snippets/transpose-2.nf
 create mode 100644 docs/snippets/transpose-2.out

diff --git a/docs/config.md b/docs/config.md
index 406e579901..d9641dbcb1 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -279,7 +279,7 @@ The following settings are available:
 `aws.client.storageKmsKeyId`
 : :::{versionadded} 22.05.0-edge
   :::
-: The AWS KMS key Id to be used to encrypt files stored in the target S3 bucket ().
+: The AWS KMS key Id to be used to encrypt files stored in the target S3 bucket.
 
 `aws.client.userAgent`
 : The HTTP user agent header passed with all HTTP requests.
@@ -1097,7 +1097,7 @@ Read the {ref}`sharing-page` page to learn how to publish your pipeline to GitHu
 The `notification` scope allows you to define the automatic sending of a notification email message when the workflow execution terminates.
 
 `notification.binding`
-: An associative array modelling the variables in the template file.
+: A map modelling the variables in the template file.
 
 `notification.enabled`
 : Enables the sending of a notification message when the workflow execution completes.
diff --git a/docs/mail.md b/docs/mail.md
index 59ce19890a..093b56fb1c 100644
--- a/docs/mail.md
+++ b/docs/mail.md
@@ -10,7 +10,7 @@ The built-in function `sendMail` allows you to send a mail message from a workfl
 
 ### Basic mail
 
-The mail attributes are specified as named parameters or providing an equivalent associative array as argument. For example:
+The mail attributes are specified as named parameters or an equivalent map. For example:
 
 ```groovy
 sendMail(
diff --git a/docs/operator.md b/docs/operator.md
index a54f0b022e..8ba07a7cc7 100644
--- a/docs/operator.md
+++ b/docs/operator.md
@@ -8,7 +8,7 @@ This page is a comprehensive reference for all Nextflow operators. However, if y
 
 - Filtering: [filter](#filter), [randomSample](#randomsample), [take](#take), [unique](#unique)
 - Reduction: [collect](#collect), [groupTuple](#grouptuple), [reduce](#reduce)
-- Parsing text data: [splitCsv](#splitcsv), [splitJson](#splitjson), [splitText](#splittext)
+- Text processing: [splitCsv](#splitcsv), [splitJson](#splitjson), [splitText](#splittext)
 - Combining channels: [combine](#combine), [concat](#concat), [join](#join), [mix](#mix)
 - Forking channels: [branch](#branch), [multiMap](#multimap)
 - Maths: [count](#count), [max](#max), [min](#min), [sum](#sum)
@@ -23,9 +23,9 @@ This page is a comprehensive reference for all Nextflow operators. However, if y
 
 *Returns: map of queue channels*
 
-The `branch` operator allows you to forward the items emitted by a source channel to one or more output channels, choosing one out of them at a time.
+The `branch` operator forwards each item from a source channel to one of multiple output channels, based on a selection criteria.
 
-The selection criteria is defined by specifying a {ref}`closure <script-closure>` that provides one or more boolean expression, each of which is identified by a unique label. On the first expression that evaluates to a *true* value, the current item is bound to a named channel as the label identifier. For example:
+The selection criteria is a {ref}`closure <script-closure>` that defines, for each output channel, a unique label followed by a boolean expression. When an item is received, it is routed to the first output channel whose expression evaluates to `true`. For example:
 
 ```{literalinclude} snippets/branch.nf
 :language: groovy
@@ -36,10 +36,10 @@ The selection criteria is defined by specifying a {ref}`closure <script-closure>
 ```
 
 :::{note}
-The above *small* and *large* strings may be printed in any order due to the asynchronous execution of the `view` operator.
+The above output may be printed in any order since the two `view` operations are executed asynchronously.
 :::
 
-A default fallback condition can be specified using `true` as the last branch condition:
+A fallback condition can be specified using `true` as the last branch condition:
 
 ```{literalinclude} snippets/branch-with-fallback.nf
 :language: groovy
@@ -49,7 +49,7 @@ A default fallback condition can be specified using `true` as the last branch co
 :language: console
 ```
 
-The value returned by each branch condition can be customised by specifying an optional expression statement(s) just after the condition expression. For example:
+The value emitted to each branch can be customized with an expression statement (or statements) after the branch condition:
 
 ```{literalinclude} snippets/branch-with-mapper.nf
 :language: groovy
@@ -63,7 +63,7 @@ The value returned by each branch condition can be customised by specifying an o
 When the `return` keyword is omitted, the value of the last expression statement is implicitly returned.
 :::
 
-To create a branch criteria as variable that can be passed as an argument to more than one `branch` operator use the `branchCriteria` built-in method as shown below:
+The `branchCriteria()` method can be used to create a branch criteria as a variable that can be passed as an argument to any number of `branch` operations, as shown below:
 
 ```{literalinclude} snippets/branch-criteria.nf
 :language: groovy
@@ -77,11 +77,13 @@ To create a branch criteria as variable that can be passed as an argument to mor
 
 *Returns: queue channel*
 
-The `buffer` operator gathers the items emitted by the source channel into subsets and emits these subsets separately.
+The `buffer` operator collects items from a source channel into subsets and emits each subset separately.
 
-There are a number of ways you can regulate how `buffer` gathers the items from the source channel into subsets:
+This operator has multiple variants:
 
-- `buffer( closingCondition )`: starts to collect the items emitted by the channel into a subset until the `closingCondition` is verified. After that the subset is emitted to the resulting channel and new items are gathered into a new subset. The process is repeated until the last value in the source channel is sent. The `closingCondition` can be specified either as a {ref}`regular expression <script-regexp>`, a Java class, a literal value, or a boolean predicate that has to be satisfied. For example:
+`buffer( closingCondition )`
+
+: Emits each subset when `closingCondition` is satisfied. The closing condition can be a literal value, a {ref}`regular expression <script-regexp>`, a type qualifier (i.e. Java class), or a boolean predicate. For example:
 
   ```{literalinclude} snippets/buffer-with-closing.nf
   :language: groovy
@@ -91,7 +93,9 @@ There are a number of ways you can regulate how `buffer` gathers the items from
   :language: console
   ```
 
-- `buffer( openingCondition, closingCondition )`: starts to gather the items emitted by the channel as soon as one of the them verify the `openingCondition` and it continues until there is one item which verify the `closingCondition`. After that the subset is emitted and it continues applying the described logic until the last channel item is emitted. Both conditions can be defined either as a {ref}`regular expression <script-regexp>`, a literal value, a Java class, or a boolean predicate that need to be satisfied. For example:
+`buffer( openingCondition, closingCondition )`
+
+: Creates a new subset when `openingCondition` is satisfied and emits the subset when is `closingCondition` is satisfied. The opening and closing conditions can each be a literal value, a {ref}`regular expression <script-regexp>`, a type qualifier (i.e. Java class), or a boolean predicate. For example:
 
   ```{literalinclude} snippets/buffer-with-opening-closing.nf
   :language: groovy
@@ -101,7 +105,9 @@ There are a number of ways you can regulate how `buffer` gathers the items from
   :language: console
   ```
 
-- `buffer( size: n )`: transform the source channel in such a way that it emits tuples made up of `n` elements. An incomplete tuple is discarded. For example:
+`buffer( size: n )`
+
+: Emits a new subset for every `n` items. Remaining items are discarded. For example:
 
   ```{literalinclude} snippets/buffer-with-size.nf
   :language: groovy
@@ -111,7 +117,7 @@ There are a number of ways you can regulate how `buffer` gathers the items from
   :language: console
   ```
 
-  If you want to emit the last items in a tuple containing less than `n` elements, simply add the parameter `remainder` specifying `true`, for example:
+  The `remainder` option can be used to emit any remaining items as a partial subset:
 
   ```{literalinclude} snippets/buffer-with-size-remainder.nf
   :language: groovy
@@ -121,7 +127,9 @@ There are a number of ways you can regulate how `buffer` gathers the items from
   :language: console
   ```
 
-- `buffer( size: n, skip: m )`: as in the previous example, it emits tuples containing `n` elements, but skips `m` values before starting to collect the values for the next tuple (including the first emission). For example:
+`buffer( size: n, skip: m )`
+
+: Emits a new subset for every `n` items, skipping `m` items before collecting each subset. For example:
 
   ```{literalinclude} snippets/buffer-with-size-skip.nf
   :language: groovy
@@ -131,47 +139,59 @@ There are a number of ways you can regulate how `buffer` gathers the items from
   :language: console
   ```
 
-  If you want to emit the remaining items in a tuple containing less than `n` elements, simply add the parameter `remainder` specifying `true`, as shown in the previous example.
+  The `remainder` option can be used to emit any remaining items as a partial subset.
 
-See also: [collate](#collate) operator.
+See also: [collate](#collate)
 
 ## collate
 
 *Returns: queue channel*
 
-The `collate` operator transforms a channel in such a way that the emitted values are grouped in tuples containing `n` items. For example:
+The `collate` operator collects items from a source channel into groups of *N* items.
 
-```{literalinclude} snippets/collate.nf
-:language: groovy
-```
+This operator has multiple variants:
 
-```{literalinclude} snippets/collate.out
-:language: console
-```
+`collate( size, remainder = true )`
 
-As shown in the above example the last tuple may be incomplete e.g. contain fewer elements than the specified size. If you want to avoid this, specify `false` as the second parameter. For example:
+: Collects items into groups of `size` items:
 
-```{literalinclude} snippets/collate-with-no-remainder.nf
-:language: groovy
-```
+  ```{literalinclude} snippets/collate.nf
+  :language: groovy
+  ```
 
-```{literalinclude} snippets/collate-with-no-remainder.out
-:language: console
-```
+  ```{literalinclude} snippets/collate.out
+  :language: console
+  ```
 
-A second version of the `collate` operator allows you to specify, after the `size`, the `step` by which elements are collected in tuples. For example:
+  By default, any remaining items are emitted as a partial group. You can specify `false` as the second parameter to discard them instead:
 
-```{literalinclude} snippets/collate-with-step.nf
-:language: groovy
-```
+  ```{literalinclude} snippets/collate-with-no-remainder.nf
+  :language: groovy
+  ```
 
-```{literalinclude} snippets/collate-with-step.out
-:language: console
-```
+  ```{literalinclude} snippets/collate-with-no-remainder.out
+  :language: console
+  ```
 
-As before, if you don't want to emit the last items which do not complete a tuple, specify `false` as the third parameter.
+  :::{note}
+  This version of `collate` is equivalent to `buffer( size: n, remainder: true | false )`.
+  :::
+
+`collate( size, step, remainder = true )`
+
+: Collects items into groups of `size` items using a *sliding window* that moves by `step` items at a time:
+
+  ```{literalinclude} snippets/collate-with-step.nf
+  :language: groovy
+  ```
 
-See also: [buffer](#buffer) operator.
+  ```{literalinclude} snippets/collate-with-step.out
+  :language: console
+  ```
+
+  You can specify `false` as the third parameter to discard any remaining items.
+
+See also: [buffer](#buffer)
 
 (operator-collect)=
 
@@ -179,7 +199,7 @@ See also: [buffer](#buffer) operator.
 
 *Returns: value channel*
 
-The `collect` operator collects all the items emitted by a channel to a `List` and return the resulting object as a sole emission. For example:
+The `collect` operator collects all items from a source channel into a list and emits it as a single item:
 
 ```{literalinclude} snippets/collect.nf
 :language: groovy
@@ -189,7 +209,7 @@ The `collect` operator collects all the items emitted by a channel to a `List` a
 :language: console
 ```
 
-An optional {ref}`closure <script-closure>` can be specified to transform each item before adding it to the resulting list. For example:
+An optional {ref}`closure <script-closure>` can be used to transform each item before it is collected:
 
 ```{literalinclude} snippets/collect-with-mapper.nf
 :language: groovy
@@ -202,39 +222,57 @@ An optional {ref}`closure <script-closure>` can be specified to transform each i
 Available options:
 
 `flat`
-: When `true` nested list structures are normalised and their items are added to the resulting list object (default: `true`).
+: When `true`, nested list structures are flattened and their items are collected individually (default: `true`).
 
 `sort`
-: When `true` the items in the resulting list are sorted by their natural ordering. It is possible to provide a custom ordering criteria by using either a {ref}`closure <script-closure>` or a [Comparator](https://docs.oracle.com/javase/8/docs/api/java/util/Comparator.html) object (default: `false`).
+: When `true`, the collected items are sorted by their natural ordering (default: `false`). Can also be a {ref}`closure <script-closure>` or a [Comparator](https://docs.oracle.com/javase/8/docs/api/java/util/Comparator.html) which defines how items are compared during sorting.
 
-See also: [toList](#tolist) and [toSortedList](#tosortedlist) operator.
+See also: [toList](#tolist), [toSortedList](#tosortedlist)
 
 ## collectFile
 
 *Returns: queue channel*
 
-The `collectFile` operator allows you to gather the items emitted by a channel and save them to one or more files. The operator returns a new channel that emits the collected file(s).
+The `collectFile` operator collects the items from a source channel and saves them to one or more files, emitting the collected file(s).
 
-In the simplest case, just specify the name of a file where the entries have to be stored. For example:
+This operator has multiple variants:
 
-```{literalinclude} snippets/collectfile.nf
-:language: groovy
-```
+`collectFile( name: '...', options = [:] )`
 
+: Collects the items and saves them to a single file specified by the `name` option:
 
-A second version of the `collectFile` operator allows you to gather the items emitted by a channel and group them together into files whose name can be defined by a dynamic criteria. The grouping criteria is specified by a {ref}`closure <script-closure>` that must return a pair in which the first element defines the file name for the group and the second element the actual value to be appended to that file. For example:
+  ```{literalinclude} snippets/collectfile.nf
+  :language: groovy
+  ```
 
-```{literalinclude} snippets/collectfile-closure.nf
-:language: groovy
-```
+`collectFile( closure, options = [:] )`
 
-```{literalinclude} snippets/collectfile-closure.out
-:language: console
-```
+: Collects the items into groups and saves each group to a file, using a grouping criteria. The grouping criteria is a {ref}`closure <script-closure>` that maps each item to a pair, where the first element is the file name for the group and the second element is the content to be appended to that file. For example:
 
+  ```{literalinclude} snippets/collectfile-closure.nf
+  :language: groovy
+  ```
 
-:::{tip}
-When the items emitted by the source channel are files, the grouping criteria can be omitted. In this case the items content will be grouped into file(s) having the same name as the source items.
+  ```{literalinclude} snippets/collectfile-closure.out
+  :language: console
+  ```
+
+  When the items from the source channel are files, the grouping criteria can be omitted. In this case, the items will be grouped by their source filename.
+
+The following example shows how to use a closure to collect and sort all sequences in a FASTA file from shortest to longest:
+
+```groovy
+Channel
+    .fromPath('/data/sequences.fa')
+    .splitFasta( record: [id: true, sequence: true] )
+    .collectFile( name: 'result.fa', sort: { it.size() } ) {
+        it.sequence
+    }
+    .view { it.text }
+```
+
+:::{warning}
+The `collectFile` operator needs to store files in a temporary directory that is automatically deleted on workflow completion. For performance reasons, this directory is located in the machine's local storage, and it should have as much free space as the data that is being collected. The `tempDir` option can be used to specify a different temporary directory.
 :::
 
 Available options:
@@ -243,7 +281,7 @@ Available options:
 : Controls the caching ability of the `collectFile` operator when using the *resume* feature. It follows the same semantic of the {ref}`process-cache` directive (default: `true`).
 
 `keepHeader`
-: Prepend the resulting file with the header fetched in the first collected file. The header size (ie. lines) can be specified by using the `skip` parameter (default: `false`), to determine how many lines to remove from all collected files except for the first (where no lines will be removed).
+: Prepend the resulting file with the header fetched in the first collected file. The header size (ie. lines) can be specified by using the `skip` option (default: `0`), to determine how many lines to remove from all collected files except for the first (where no lines will be removed).
 
 `name`
 : Name of the file where all received values are stored.
@@ -252,10 +290,10 @@ Available options:
 : Appends a `newline` character automatically after each entry (default: `false`).
 
 `seed`
-: A value or a map of values used to initialise the files content.
+: A value or a map of values used to initialize the files content.
 
 `skip`
-: Skip the first `n` lines e.g. `skip: 1`.
+: Skip the first `n` lines e.g. `skip: 1` (default: `0`).
 
 `sort`
 : Defines sorting criteria of content in resulting file(s). Can be one of the following values:
@@ -265,56 +303,25 @@ Available options:
   - `'index'`: Order the content by the incremental index number assigned to each entry while they are collected.
   - `'hash'`: (default) Order the content by the hash number associated to each entry
   - `'deep'`: Similar to the previous, but the hash number is created on actual entries content e.g. when the entry is a file the hash is created on the actual file content.
-  - A custom sorting criteria can be specified by using either a {ref}`Closure <script-closure>` or a [Comparator](http://docs.oracle.com/javase/7/docs/api/java/util/Comparator.html) object.
+  - A custom sorting criteria can be specified with a {ref}`Closure <script-closure>` or a [Comparator](http://docs.oracle.com/javase/7/docs/api/java/util/Comparator.html) object.
 
   The file content is sorted in such a way that it does not depend on the order in which entries were added to it, which guarantees that it is consistent (i.e. does not change) across different executions with the same data.
 
 `storeDir`
-: Folder where the resulting file(s) are be stored.
+: Folder where the resulting file(s) are stored.
 
 `tempDir`
 : Folder where temporary files, used by the collecting process, are stored.
 
-The following snippet shows how sort the content of the result file alphabetically:
-
-```groovy
-Channel
-    .of('Z'..'A')
-    .collectFile(name:'result', sort: true, newLine: true)
-    .view { it.text }
-```
-
-```
-A
-B
-C
-:
-Z
-```
-
-The following example shows how use a `closure` to collect and sort all sequences in a FASTA file from shortest to longest:
-
-```groovy
-Channel
-    .fromPath('/data/sequences.fa')
-    .splitFasta( record: [id: true, sequence: true] )
-    .collectFile( name:'result.fa', sort: { it.size() } ) {
-        it.sequence
-    }
-    .view { it.text }
-```
-
-:::{warning}
-The `collectFile` operator needs to store files in a temporary folder that is automatically deleted on workflow completion. For performance reasons this folder is located in the machine's local storage, and it will require as much free space as the data that is being collected. Optionally, a different temporary data folder can be specified by using the `tempDir` parameter.
-:::
-
 (operator-combine)=
 
 ## combine
 
 *Returns: queue channel*
 
-The `combine` operator combines (cartesian product) the items emitted by two channels or by a channel and a `Collection` object (as right operand). For example:
+The `combine` operator produces the combinations (i.e. cross product, "Cartesian" product) of two source channels, or a channel and a list (as the right operand), emitting each combination separately.
+
+For example:
 
 ```{literalinclude} snippets/combine.nf
 :language: groovy
@@ -324,7 +331,7 @@ The `combine` operator combines (cartesian product) the items emitted by two cha
 :language: console
 ```
 
-A second version of the `combine` operator allows you to combine items that share a common matching key. The index of the key element is specified by using the `by` parameter (zero-based index, multiple indices can be specified as a list of integers). For example:
+The `by` option can be used to combine items that share a matching key. The value should be the zero-based index of the tuple, or a list of indices. For example:
 
 ```{literalinclude} snippets/combine-by.nf
 :language: groovy
@@ -334,7 +341,17 @@ A second version of the `combine` operator allows you to combine items that shar
 :language: console
 ```
 
-See also [join](#join) and [cross](#cross).
+:::{note}
+The `combine` operator is similar to `cross` and `join`, making them easy to confuse. Their differences can be summarized as follows:
+
+- `combine` and `cross` both produce an *outer product* or *cross product*, whereas `join` produces an *inner product*.
+
+- `combine` filters pairs with a matching key only if the `by` option is used, whereas `cross` always filters pairs with a matching key.
+
+- `combine` with the `by` option merges and flattens each pair, whereas `cross` does not. Compare the examples for `combine` and `cross` to see this difference.
+:::
+
+See also: [cross](#cross), [join](#join)
 
 (operator-concat)=
 
@@ -342,9 +359,9 @@ See also [join](#join) and [cross](#cross).
 
 *Returns: queue channel*
 
-The `concat` operator allows you to *concatenate* the items emitted by two or more channels to a new channel. The items emitted by the resulting channel are in the same order as specified in the operator arguments.
+The `concat` operator emits the items from two or more source channels into a single output channel. Each source channel is emitted in the order in which it was specified.
 
-In other words, given *N* channels, the items from the *i+1 th* channel are emitted only after all of the items from the *i th* channel have been emitted.
+In other words, given *N* channels, the items from the *i+1*-th channel are emitted only after all of the items from the *i*-th channel have been emitted.
 
 For example:
 
@@ -356,13 +373,15 @@ For example:
 :language: console
 ```
 
+See also: [mix](#mix)
+
 (operator-count)=
 
 ## count
 
 *Returns: value channel*
 
-The `count` operator creates a channel that emits a single item: a number that represents the total number of items emitted by the source channel. For example:
+The `count` operator computes the total number of items in a source channel and emits it:
 
 ```{literalinclude} snippets/count.nf
 :language: groovy
@@ -372,7 +391,7 @@ The `count` operator creates a channel that emits a single item: a number that r
 :language: console
 ```
 
-An optional parameter can be provided to select which items are to be counted. The selection criteria can be specified either as a {ref}`regular expression <script-regexp>`, a literal value, a Java class, or a boolean predicate that needs to be satisfied. For example:
+An optional filter can be provided to select which items to count. The selection criteria can be a literal value, a {ref}`regular expression <script-regexp>`, a type qualifier (i.e. Java class), or a boolean predicate. For example:
 
 ```{literalinclude} snippets/count-with-filter-number.nf
 :language: groovy
@@ -436,9 +455,9 @@ Counts the total number of lines in a channel of text files, equivalent to `spli
 
 *Returns: queue channel*
 
-The `cross` operator allows you to combine the items of two channels in such a way that the items of the source channel are emitted along with the items emitted by the target channel for which they have a matching key.
+The `cross` operator emits every pairwise combination of two channels for which the pair has a matching key.
 
-The key is defined, by default, as the first entry in an array, a list or map object, or the value itself for any other data type. For example:
+By default, the key is defined as the first entry in a list or map, or the value itself for any other data type. For example:
 
 ```{literalinclude} snippets/cross.nf
 :language: groovy
@@ -448,13 +467,6 @@ The key is defined, by default, as the first entry in an array, a list or map ob
 :language: console
 ```
 
-The above example shows how the items emitted by the source channels are associated to the ones emitted by the target channel (on the right) having the same key.
-
-There are two important caveats when using the `cross` operator:
-
-1. The operator is not `commutative`, i.e. the result of `a.cross(b)` is different from `b.cross(a)`
-2. The source channel should emits items for which there's no key repetition i.e. the emitted items have an unique key identifier.
-
 An optional closure can be used to define the matching key for each item:
 
 ```{literalinclude} snippets/cross-with-mapper.nf
@@ -465,11 +477,18 @@ An optional closure can be used to define the matching key for each item:
 :language: console
 ```
 
+There are two important caveats when using the `cross` operator:
+
+1. The operator is not *commutative*, i.e. `a.cross(b)` is not the same as `b.cross(a)`
+2. Each source channel should not emit any items with duplicate keys, i.e. each item should have a unique key.
+
+See also: [combine](#combine)
+
 ## distinct
 
 *Returns: queue channel*
 
-The `distinct` operator allows you to remove *consecutive* duplicated items from a channel, so that each emitted item is different from the preceding one. For example:
+The `distinct` operator forwards a source channel with *consecutively* repeated items removed, such that each emitted item is different from the preceding one:
 
 ```{literalinclude} snippets/distinct.nf
 :language: groovy
@@ -479,7 +498,7 @@ The `distinct` operator allows you to remove *consecutive* duplicated items from
 :language: console
 ```
 
-You can also specify an optional {ref}`closure <script-closure>` that customizes the way it distinguishes between distinct items. For example:
+An optional {ref}`closure <script-closure>` can be used to transform each value before it is evaluated for distinct-ness:
 
 ```{literalinclude} snippets/distinct-with-mapper.nf
 :language: groovy
@@ -489,17 +508,17 @@ You can also specify an optional {ref}`closure <script-closure>` that customizes
 :language: console
 ```
 
+See also: [unique](#unique)
+
 (operator-dump)=
 
 ## dump
 
 *Returns: queue channel or value channel, depending on the input*
 
-The `dump` operator prints the items emitted by the channel to which is applied only when the option `-dump-channels` is specified on the `run` command line, otherwise it is ignored.
-
-This is useful to enable the debugging of one or more channel content on-demand by using a command line option instead of modifying your script code.
+The `dump` operator prints each item in a source channel when the pipeline is executed with the `-dump-channels` command-line option, otherwise it does nothing. It is a useful way to inspect and debug channels quickly without having to modify the pipeline script.
 
-An optional `tag` parameter allows you to select which channel to dump. For example:
+The `tag` option can be used to select which channels to dump:
 
 ```{literalinclude} snippets/dump.nf
 :language: groovy
@@ -521,9 +540,9 @@ Available options:
 
 *Returns: queue channel*
 
-The `filter` operator allows you to get only the items emitted by a channel that satisfy a condition and discarding all the others. The filtering condition can be specified by using either a {ref}`regular expression <script-regexp>`, a literal value, a type qualifier (i.e. a Java class) or any boolean predicate.
+The `filter` operator emits the items from a source channel that satisfy a condition, discarding all other items. The filter condition can be a literal value, a {ref}`regular expression <script-regexp>`, a type qualifier (i.e. Java class), or a boolean predicate.
 
-The following example shows how to filter a channel by using a regular expression that returns only strings that begin with `a`:
+The following example filters a channel with a regular expression that only matches strings beginning with `a`:
 
 ```{literalinclude} snippets/filter-regex.nf
 :language: groovy
@@ -533,7 +552,7 @@ The following example shows how to filter a channel by using a regular expressio
 :language: console
 ```
 
-The following example shows how to filter a channel by specifying the type qualifier `Number` so that only numbers are returned:
+The following example filters a channel with the `Number` type qualifier so that only numbers are emitted:
 
 ```{literalinclude} snippets/filter-type.nf
 :language: groovy
@@ -543,7 +562,7 @@ The following example shows how to filter a channel by specifying the type quali
 :language: console
 ```
 
-Finally, a filtering condition can be defined by using any a boolean predicate. A predicate is expressed by a {ref}`closure <script-closure>` returning a boolean value. For example the following fragment shows how filter a channel emitting numbers so that the odd values are returned:
+The following example filters a channel using a boolean predicate, which is a {ref}`closure <script-closure>` that returns a boolean value. In this case, the predicate is used to select only odd numbers:
 
 ```{literalinclude} snippets/filter-closure.nf
 :language: groovy
@@ -553,17 +572,13 @@ Finally, a filtering condition can be defined by using any a boolean predicate.
 :language: console
 ```
 
-:::{tip}
-In the above example the filter condition is wrapped in curly brackets, instead of parentheses, because it specifies a {ref}`closure <script-closure>` as the operator's argument. In reality it is just syntactic sugar for `filter({ it % 2 == 1 })`
-:::
-
 (operator-first)=
 
 ## first
 
 *Returns: value channel*
 
-The `first` operator creates a channel that returns the first item emitted by the source channel, or eventually the first item that matches an optional condition. The condition can be specified by using a {ref}`regular expression<script-regexp>`, a Java `class` type or any boolean predicate. For example:
+The `first` operator emits the first item in a source channel, or the first item that matches a condition. The condition can be a {ref}`regular expression<script-regexp>`, a type qualifier (i.e. Java class), or a boolean predicate. For example:
 
 ```{literalinclude} snippets/first.nf
 :language: groovy
@@ -603,7 +618,7 @@ When the mapping function returns a map, each key-value pair in the map is emitt
 
 *Returns: queue channel*
 
-The `flatten` operator transforms a channel in such a way that every item of type `Collection` or `Array` is flattened so that each single entry is emitted separately by the resulting channel. For example:
+The `flatten` operator flattens each item from a source channel that is a list or other collection, such that each element in each collection is emitted separately:
 
 ```{literalinclude} snippets/flatten.nf
 :language: groovy
@@ -613,7 +628,9 @@ The `flatten` operator transforms a channel in such a way that every item of typ
 :language: console
 ```
 
-See also: [flatMap](#flatmap) operator.
+As shown in the above example, deeply nested collections are also flattened.
+
+See also: [flatMap](#flatmap)
 
 (operator-grouptuple)=
 
@@ -621,9 +638,9 @@ See also: [flatMap](#flatmap) operator.
 
 *Returns: queue channel*
 
-The `groupTuple` operator collects tuples (or lists) of values emitted by the source channel grouping together the elements that share the same key. Finally it emits a new tuple object for each distinct key collected.
+The `groupTuple` operator collects lists (i.e. *tuples*) from a source channel into groups based on a grouping key. A new tuple is emitted for each distinct key.
 
-In other words, the operator transforms a sequence of tuple like *(K, V, W, ..)* into a new channel emitting a sequence of *(K, list(V), list(W), ..)*
+To be more precise, the operator transforms a sequence of tuples like *(K, V, W, ..)* into a sequence of tuples like *(K, list(V), list(W), ..)*.
 
 For example:
 
@@ -635,7 +652,7 @@ For example:
 :language: console
 ```
 
-By default the first entry in the tuple is used as grouping key. A different key can be chosen by using the `by` parameter and specifying the index of the entry to be used as key (the index is zero-based). For example, grouping by the second value in each tuple:
+By default, the first element of each tuple is used as the grouping key. The `by` option can be used to specify a different index, or list of indices. For example, to group by the second element of each tuple:
 
 ```{literalinclude} snippets/grouptuple-by.nf
 :language: groovy
@@ -645,7 +662,7 @@ By default the first entry in the tuple is used as grouping key. A different key
 :language: console
 ```
 
-By default, if you don't specify a size, the `groupTuple` operator will not emit any groups until *all* inputs have been received. If possible, you should always try to specify the number of expected elements in each group using the `size` option, so that each group can be emitted as soon as it's ready. In cases where the size of each group varies based on the grouping key, you can use the built-in `groupKey` function, which allows you to create a special grouping key with an associated size:
+By default, if you don't specify a size, the `groupTuple` operator will not emit any groups until *all* inputs have been received. If possible, you should always try to specify the number of expected elements in each group using the `size` option, so that each group can be emitted as soon as it's ready. In cases where the size of each group varies based on the grouping key, you can use the built-in `groupKey()` function, which allows you to define a different expected size for each group:
 
 ```{literalinclude} snippets/grouptuple-groupkey.nf
 :language: groovy
@@ -658,22 +675,22 @@ By default, if you don't specify a size, the `groupTuple` operator will not emit
 Available options:
 
 `by`
-: The index (zero based) of the element to be used as grouping key. A key composed by multiple elements can be defined specifying a list of indices e.g. `by: [0,2]`
+: The zero-based index of the element to use as the grouping key. Can also be a list of indices, e.g. `by: [0,2]` (default: `[0]`).
 
 `remainder`
-: When `false` incomplete tuples (i.e. with less than `size` grouped items) are discarded (default). When `true` incomplete tuples are emitted as the ending emission. Only valid when a `size` parameter is specified.
+: When `true`, incomplete tuples (i.e. groups with less than `size` items) are emitted as partial groups, otherwise they are discarded (default: `false`). This option can only be used with `size`.
 
 `size`
-: The number of items the grouped list(s) has to contain. When the specified size is reached, the tuple is emitted.
+: The required number of items for each group. When a group reaches the required size, it is emitted.
 
 `sort`
 : Defines the sorting criteria for the grouped items. Can be one of the following values:
 
   - `false`: No sorting is applied (default).
   - `true`: Order the grouped items by the item's natural ordering i.e. numerical for number, lexicographic for string, etc. See the [Java documentation](http://docs.oracle.com/javase/tutorial/collections/interfaces/order.html) for more information.
-  - `hash`: Order the grouped items by the hash number associated to each entry.
-  - `deep`: Similar to the previous, but the hash number is created on actual entries content e.g. when the item is a file, the hash is created on the actual file content.
-  - A custom sorting criteria used to order the tuples element holding list of values. It can be specified by using either a {ref}`Closure <script-closure>` or a [Comparator](http://docs.oracle.com/javase/7/docs/api/java/util/Comparator.html) object.
+  - `'hash'`: Order the grouped items by the hash number associated to each entry.
+  - `'deep'`: Similar to the previous, but the hash number is created on actual entries content e.g. when the item is a file, the hash is created on the actual file content.
+  - A custom sorting criteria used to order the nested list elements of each tuple. It can be a {ref}`Closure <script-closure>` or a [Comparator](http://docs.oracle.com/javase/7/docs/api/java/util/Comparator.html) object.
 
 (operator-ifempty)=
 
@@ -681,9 +698,7 @@ Available options:
 
 *Returns: value channel*
 
-The `ifEmpty` operator creates a channel which emits a default value, specified as the operator parameter, when the channel to which is applied is *empty* i.e. doesn't emit any value. Otherwise it will emit the same sequence of entries as the original channel.
-
-Thus, the following example prints:
+The `ifEmpty` operator emits a source channel, or a default value if the source channel is *empty* (doesn't emit any value):
 
 ```{literalinclude} snippets/ifempty-1.nf
 :language: groovy
@@ -693,8 +708,6 @@ Thus, the following example prints:
 :language: console
 ```
 
-Instead, this one prints:
-
 ```{literalinclude} snippets/ifempty-2.nf
 :language: groovy
 ```
@@ -703,9 +716,9 @@ Instead, this one prints:
 :language: console
 ```
 
-The `ifEmpty` value parameter can be defined with a {ref}`closure <script-closure>`. In this case the result value of the closure evaluation will be emitted when the empty condition is satisfied.
+The default value can also be a {ref}`closure <script-closure>`, in which case the closure is evaluated and the result is emitted when the source channel is empty.
 
-See also: {ref}`channel-empty` method.
+See also: {ref}`channel-empty` channel factory
 
 (operator-join)=
 
@@ -713,7 +726,9 @@ See also: {ref}`channel-empty` method.
 
 *Returns: queue channel*
 
-The `join` operator creates a channel that joins together the items emitted by two channels for which exists a matching key. The key is defined, by default, as the first element in each item emitted.
+The `join` operator emits the inner product of two source channels using a matching key.
+
+To be more precise, the operator transforms a sequence of tuples like *(K, V1, V2, ..)* and *(K, W1, W1, ..)* into a sequence of tuples like *(K, V1, V2, .., W1, W2, ..)*. It is equivalent to an *inner join* in SQL, or an *outer join* when `remainder` is `true`.
 
 For example:
 
@@ -725,9 +740,9 @@ For example:
 :language: console
 ```
 
-The `index` of a different matching element can be specified by using the `by` parameter.
+By default, the first element of each item is used as the key. The `by` option can be used to specify a different index, or list of indices.
 
-The `join` operator can emit all the pairs that are incomplete, i.e. the items for which a matching element is missing, by specifying the optional parameter `remainder` as shown below:
+By default, unmatched items are discarded. The `remainder` option can be used to emit them at the end:
 
 ```{literalinclude} snippets/join-with-remainder.nf
 :language: groovy
@@ -740,16 +755,18 @@ The `join` operator can emit all the pairs that are incomplete, i.e. the items f
 Available options:
 
 `by`
-: The index (zero based) of the element to be used as grouping key. A key composed by multiple elements can be defined specifying a list of indices e.g. `by: [0,2]`.
+: The zero-based index of each item to use as the matching key. Can also be a list of indices, e.g. `by: [0, 2]` (default: `[0]`).
 
 `failOnDuplicate`
-: An error is reported when the same key is found more than once.
+: When `true`, an error is reported when the operator receives multiple items from the same channel with the same key (default: `true` if {ref}`strict mode <config-feature-flags>` is enabled, `false` otherwise).
 
 `failOnMismatch`
-: An error is reported when a channel emits a value for which there isn't a corresponding element in the joining channel. This option cannot be used with `remainder`.
+: When `true`, an error is reported when the operator receives an item from one channel for which there no matching item from the other channel (default: `true` if {ref}`strict mode <config-feature-flags>` is enabled, `false` otherwise). This option cannot be used with `remainder`.
 
 `remainder`
-: When `false` incomplete tuples (i.e. with less than `size` grouped items) are discarded (default). When `true` incomplete tuples are emitted as the ending emission.
+: When `true`, unmatched items are emitted at the end, otherwise they are discarded (default: `false`). 
+
+See also: [combine](#combine), [cross](#cross)
 
 (operator-last)=
 
@@ -757,7 +774,7 @@ Available options:
 
 *Returns: value channel*
 
-The `last` operator creates a channel that only returns the last item emitted by the source channel. For example:
+The `last` operator emits the last item from a source channel:
 
 ```{literalinclude} snippets/last.nf
 :language: groovy
@@ -773,7 +790,7 @@ The `last` operator creates a channel that only returns the last item emitted by
 
 *Returns: queue channel*
 
-The `map` operator applies a function of your choosing to every item emitted by a channel, and returns the items so obtained as a new channel. The function applied is called the mapping function and is expressed with a {ref}`closure <script-closure>` as shown in the example below:
+The `map` operator applies a *mapping function* to each item from a source channel:
 
 ```{literalinclude} snippets/map.nf
 :language: groovy
@@ -789,7 +806,7 @@ The `map` operator applies a function of your choosing to every item emitted by
 
 *Returns: value channel*
 
-The `max` operator waits until the source channel completes, and then emits the item that has the greatest value. For example:
+The `max` operator emits the item with the greatest value from a source channel:
 
 ```{literalinclude} snippets/max.nf
 :language: groovy
@@ -799,7 +816,9 @@ The `max` operator waits until the source channel completes, and then emits the
 :language: console
 ```
 
-An optional {ref}`closure <script-closure>` parameter can be specified in order to provide a function that returns the value to be compared. The example below shows how to find the string item that has the maximum length:
+An optional {ref}`closure <script-closure>` can be used to control how the items are compared. The closure can be a *mapping function*, which transforms each item before it is compared, or a *comparator function*, which defines how to compare two items more generally.
+
+The following examples show how to find the longest string in a channel:
 
 ```{literalinclude} snippets/max-with-mapper.nf
 :language: groovy
@@ -809,8 +828,6 @@ An optional {ref}`closure <script-closure>` parameter can be specified in order
 :language: console
 ```
 
-Alternatively it is possible to specify a comparator function i.e. a {ref}`closure <script-closure>` taking two parameters that represent two emitted items to be compared. For example:
-
 ```{literalinclude} snippets/max-with-comparator.nf
 :language: groovy
 ```
@@ -825,9 +842,7 @@ Alternatively it is possible to specify a comparator function i.e. a {ref}`closu
 
 *Returns: queue channel*
 
-The `merge` operator lets you join items emitted by two (or more) channels into a new channel.
-
-For example, the following code merges two channels together: one which emits a series of odd integers and the other which emits a series of even integers:
+The `merge` operator joins the items from two or more channels into a new channel:
 
 ```{literalinclude} snippets/merge.nf
 :language: groovy
@@ -837,7 +852,7 @@ For example, the following code merges two channels together: one which emits a
 :language: console
 ```
 
-An optional closure can be provided to customise the items emitted by the resulting merged channel. For example:
+An optional closure can be used to control how two items are merged:
 
 ```{literalinclude} snippets/merge-with-mapper.nf
 :language: groovy
@@ -859,7 +874,7 @@ You should always use a matching key (e.g. sample ID) to merge multiple channels
 
 *Returns: value channel*
 
-The `min` operator waits until the source channel completes, and then emits the item that has the lowest value. For example:
+The `min` operator emits the item with the lowest value from a source channel:
 
 ```{literalinclude} snippets/min.nf
 :language: groovy
@@ -869,7 +884,9 @@ The `min` operator waits until the source channel completes, and then emits the
 :language: console
 ```
 
-An optional {ref}`closure <script-closure>` parameter can be specified in order to provide a function that returns the value to be compared. The example below shows how to find the string item that has the minimum length:
+An optional {ref}`closure <script-closure>` can be used to control how the items are compared. The closure can be a *mapping function*, which transforms each item before it is compared, or a *comparator function*, which defines how to compare two items more generally.
+
+The following examples show how to find the shortest string in a channel:
 
 ```{literalinclude} snippets/min-with-mapper.nf
 :language: groovy
@@ -879,8 +896,6 @@ An optional {ref}`closure <script-closure>` parameter can be specified in order
 :language: console
 ```
 
-Alternatively it is possible to specify a comparator function i.e. a {ref}`closure <script-closure>` taking two parameters that represent two emitted items to be compared. For example:
-
 ```{literalinclude} snippets/min-with-comparator.nf
 :language: groovy
 ```
@@ -895,9 +910,7 @@ Alternatively it is possible to specify a comparator function i.e. a {ref}`closu
 
 *Returns: queue channel*
 
-The `mix` operator combines the items emitted by two (or more) channels into a single channel.
-
-For example:
+The `mix` operator emits the items from two or more source channels into a single output channel:
 
 ```{literalinclude} snippets/mix.nf
 :language: groovy
@@ -907,18 +920,18 @@ For example:
 :language: console
 ```
 
-:::{note}
-The items emitted by the resulting mixed channel may appear in any order, regardless of which source channel they came from. Thus, the following example could also be a possible result of the above example:
+The items in the mixed output channel may appear in any order, regardless of which source channel they came from. Thus, the previous example could also output the following:
 
-```
-'z'
+```console
+z
 1
-'a'
+a
 2
-'b'
+b
 3
 ```
-:::
+
+See also: [concat](#concat)
 
 (operator-multimap)=
 
@@ -929,9 +942,9 @@ The items emitted by the resulting mixed channel may appear in any order, regard
 
 *Returns: map of queue channels*
 
-The `multiMap` operator allows you to forward the items emitted by a source channel to two or more output channels, mapping each input value as a separate element.
+The `multiMap` operator applies a set of mapping functions to a source channel, producing a separate output channel for each mapping function.
 
-The mapping criteria is defined with a {ref}`closure <script-closure>` that specifies the target channels (labelled with a unique identifier) followed by an expression that maps each item from the input channel to the target channel.
+The multi-map criteria is a {ref}`closure <script-closure>` that defines, for each output channel, a label followed by a mapping expression.
 
 For example:
 
@@ -943,7 +956,7 @@ For example:
 :language: console
 ```
 
-The mapping expression can be omitted when the value to be emitted is the same as the following one. If you just need to forward the same value to multiple channels, you can use the following shorthand:
+Multiple labels can share the same mapping expression using the following shorthand:
 
 ```{literalinclude} snippets/multimap-shared.nf
 :language: groovy
@@ -953,16 +966,16 @@ The mapping expression can be omitted when the value to be emitted is the same a
 :language: console
 ```
 
-As before, this creates two channels, but now both of them receive the same source items.
+The above example creates two channels as before, but now they both receive the same items.
 
-You can use the `multiMapCriteria` method to create a multi-map criteria as a variable that can be passed as an argument to one or more `multiMap` operations, as shown below:
+You can use the `multiMapCriteria()` method to create a multi-map criteria as a variable that can be passed as an argument to any number of `multiMap` operations, as shown below:
 
 ```{literalinclude} snippets/multimap-criteria.nf
 :language: groovy
 ```
 
 :::{note}
-If you use `multiMap` to split a tuple or map into multiple channels, it is recommended that you retain a matching key (e.g. sample ID) with *each* new channel, so that you can re-combine these channels later on if needed. In general, you should not expect to be able to merge channels correctly without a matching key, due to the parallel and asynchronous nature of Nextflow pipelines.
+If you use `multiMap` to split a tuple or map into multiple channels, it is recommended that you retain a matching key (e.g. sample ID) with *each* new channel, so that you can re-combine these channels later on if needed. In general, you should not expect to be able to merge channels correctly without a matching key, due to the concurrent nature of Nextflow pipelines.
 :::
 
 (operator-randomsample)=
@@ -971,21 +984,21 @@ If you use `multiMap` to split a tuple or map into multiple channels, it is reco
 
 *Returns: queue channel*
 
-The `randomSample` operator allows you to create a channel emitting the specified number of items randomly taken from the channel to which is applied. For example:
+The `randomSample` operator emits a randomly-selected subset of items from a source channel:
 
 ```{literalinclude} snippets/random-sample.nf
 :language: groovy
 ```
 
-The above snippet will print 10 numbers in the range from 1 to 100.
+The above snippet will print 10 randomly-selected numbers between 1 and 100 (without replacement).
 
-The operator supports a second parameter that allows you to set the initial `seed` for the random number generator. By setting it, the `randomSample` operator will always return the same pseudo-random sequence. For example:
+An optional second parameter can be used to set the initial *seed* for the random number generator, which ensures that the `randomSample` operator produces the same pseudo-random sequence across runs:
 
 ```{literalinclude} snippets/random-sample-with-seed.nf
 :language: groovy
 ```
 
-The above example will print 10 random numbers in the range between 1 and 100. At each run of the script, the same sequence will be returned.
+The above example will print 10 randomly-selected numbers between 1 and 100 (without replacement). Each subsequent script execution will produce the same sequence.
 
 (operator-reduce)=
 
@@ -993,9 +1006,7 @@ The above example will print 10 random numbers in the range between 1 and 100. A
 
 *Returns: value channel*
 
-The `reduce` operator applies a function of your choosing to every item emitted by a channel. Each time this function is invoked it takes two parameters: the accumulated value and the *i-th* emitted item. The result is passed as the accumulated value to the next function call, along with the *i+1 th* item, until all the items are processed.
-
-Finally, the `reduce` operator emits the result of the last invocation of your function as the sole output.
+The `reduce` operator applies an *accumulator function* sequentially to each item in a source channel, and emits the final accumulated value. The accumulator function takes two parameters -- the accumulated value and the *i*-th emitted item -- and it should return the accumulated result, which is passed to the next invocation with the *i+1*-th item. This process is repeated for each item in the source channel.
 
 For example:
 
@@ -1007,11 +1018,7 @@ For example:
 :language: console
 ```
 
-:::{tip}
-A common use case for this operator is to use the first parameter as an accumulator and the second parameter as the `i-th` item to be processed.
-:::
-
-Optionally you can specify an initial value for the accumulator as shown below:
+By default, the first item is used as the initial accumulated value. You can optionally specify a different initial value as shown below:
 
 ```{literalinclude} snippets/reduce-with-initial-value.nf
 :language: groovy
@@ -1027,19 +1034,19 @@ Optionally you can specify an initial value for the accumulator as shown below:
 
 *Returns: nothing*
 
-The `set` operator assigns the channel to a variable whose name is specified as a closure parameter. For example:
+The `set` operator assigns a source channel to a variable, whose name is specified as a closure parameter:
 
 ```groovy
 Channel.of(10, 20, 30).set { my_channel }
 ```
 
-This is semantically equivalent to the following assignment:
+Using `set` is semantically equivalent to assigning a variable:
 
 ```groovy
 my_channel = Channel.of(10, 20, 30)
 ```
 
-However the `set` operator is more idiomatic in Nextflow scripting, since it can be used at the end of a chain of operator transformations, thus resulting in a more fluent and readable operation.
+See also: [tap](#tap)
 
 (operator-splitcsv)=
 
@@ -1047,9 +1054,9 @@ However the `set` operator is more idiomatic in Nextflow scripting, since it can
 
 *Returns: queue channel*
 
-The `splitCsv` operator allows you to parse text items emitted by a channel, that are formatted using the [CSV format](http://en.wikipedia.org/wiki/Comma-separated_values), and split them into records or group them into list of records with a specified length.
+The `splitCsv` operator parses and splits [CSV-formatted](http://en.wikipedia.org/wiki/Comma-separated_values) text from a source channel into records, or groups of records with a given size.
 
-In the simplest case just apply the `splitCsv` operator to a channel emitting a CSV formatted text files or text entries. For example:
+For example:
 
 ```{literalinclude} snippets/splitcsv.nf
 :language: groovy
@@ -1059,9 +1066,9 @@ In the simplest case just apply the `splitCsv` operator to a channel emitting a
 :language: console
 ```
 
-The above example shows hows CSV text is parsed and is split into single rows. Values can be accessed by its column index in the row object.
+The above example shows hows CSV text is parsed and split into individual rows, where each row is simply a list of columns.
 
-When the CSV begins with a header line defining the column names, you can specify the parameter `header: true` which allows you to reference each value by its name, as shown in the following example:
+When the CSV begins with a header line defining the column names, and the `header` option is `true`, each row is returned as a map instead:
 
 ```{literalinclude} snippets/splitcsv-with-header.nf
 :language: groovy
@@ -1071,7 +1078,7 @@ When the CSV begins with a header line defining the column names, you can specif
 :language: console
 ```
 
-Alternatively you can provide custom header names by specifying a the list of strings in the `header` parameter as shown below:
+The `header` option can also just be a list of columns:
 
 ```{literalinclude} snippets/splitcsv-with-columns.nf
 :language: groovy
@@ -1081,42 +1088,37 @@ Alternatively you can provide custom header names by specifying a the list of st
 :language: console
 ```
 
-:::{note}
-- By default, the `splitCsv` operator returns each row as a *list* object. Items are accessed by using the 0-based column index.
-- When the `header` is specified each row is returned as a *map* object (also known as dictionary). Items are accessed via the corresponding column name. 
-:::
-
 Available options:
 
 `by`
-: The number of rows in each `chunk`
+: When specified, group rows into *chunks* with the given size (default: none).
 
 `charset`
-: Parse the content by using the specified charset e.g. `UTF-8`
+: Parse the content with the specified charset, e.g. `UTF-8`. See the list of [standard charsets](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/nio/charset/StandardCharsets.html) for available options.
 
 `decompress`
-: When `true` decompress the content using the GZIP format before processing it (note: files whose name ends with `.gz` extension are decompressed automatically)
+: When `true`, decompress the content using the GZIP format before processing it (default: `false`). Files with the `.gz` extension are decompressed automatically.
 
 `elem`
-: The index of the element to split when the operator is applied to a channel emitting list/tuple objects (default: first file object or first element)
+: The index of the element to split when the source items are lists or tuples (default: first file object or first element).
 
 `header`
-: When `true` the first line is used as columns names. Alternatively it can be used to provide the list of columns names.
+: When `true`, the first line is used as the columns names (default: `false`). Can also be a list of columns names.
 
 `limit`
-: Limits the number of retrieved records for each file to the specified value.
+: Limits the number of records to retrieve for each source item (default: no limit).
 
 `quote`
-: Values may be quoted by single or double quote characters.
+: The character used to quote values (default: `''` or `""`).
 
 `sep`
-: The character used to separate the values (default: `,`)
+: The character used to separate values (default: `,`)
 
 `skip`
-: Number of lines since the file beginning to ignore when parsing the CSV content.
+: Number of lines to ignore from the beginning when parsing the CSV text (default: `0`).
 
 `strip`
-: Removes leading and trailing blanks from values (default: `false`)
+: When `true`, remove leading and trailing blanks from values (default: `false`).
 
 (operator-splitfasta)=
 
@@ -1124,9 +1126,9 @@ Available options:
 
 *Returns: queue channel*
 
-The `splitFasta` operator allows you to split the entries emitted by a channel, that are formatted using the [FASTA format](http://en.wikipedia.org/wiki/FASTA_format). It returns a channel which emits text item for each sequence in the received FASTA content.
+The `splitFasta` operator splits [FASTA-formatted](http://en.wikipedia.org/wiki/FASTA_format) text from a source channel into individual sequences.
 
-The number of sequences in each text chunk produced by the `splitFasta` operator can be set by using the `by` parameter. The following example shows how to read a FASTA file and split it into chunks containing 10 sequences each:
+The `by` option can be used to group sequences into chunks of a given size. The following example shows how to read a FASTA file and split it into chunks of 10 sequences each:
 
 ```groovy
 Channel
@@ -1136,59 +1138,57 @@ Channel
 ```
 
 :::{warning}
-Chunks are stored in memory by default. When splitting large files, specify the parameter `file: true` to save the chunks into files in order to avoid an `OutOfMemoryException`. See the parameter table below for details.
+Chunks are stored in memory by default. When splitting large files, specify `file: true` to save the chunks into files in order to avoid running out of memory. See the list of options below for details.
 :::
 
-A second version of the `splitFasta` operator allows you to split a FASTA content into record objects, instead of text chunks. A record object contains a set of fields that let you access and manipulate the FASTA sequence information with ease.
-
-In order to split a FASTA content into record objects, simply use the `record` parameter specifying the map of required the fields, as shown in the example below:
+The `record` option can be used to split FASTA content into *records* instead of text chunks. Each record is a map that allows you to access the FASTA sequence data with ease. For example:
 
 ```groovy
 Channel
      .fromPath('misc/sample.fa')
-     .splitFasta( record: [id: true, seqString: true ])
+     .splitFasta( record: [id: true, seqString: true] )
      .filter { record -> record.id =~ /^ENST0.*/ }
      .view { record -> record.seqString }
 ```
 
-In this example, the file `misc/sample.fa` is split into records containing the `id` and the `seqString` fields (i.e. the sequence id and the sequence data). The following `filter` operator only keeps the sequences whose ID starts with the `ENST0` prefix, finally the sequence content is printed by using the `subscribe` operator.
+The above example loads the `misc/sample.fa` file, splits it into records containing the `id` and `seqString` fields (i.e. the sequence id and the sequence data), filters records by their ID, and finally prints the sequence string of each record.
 
 Available options:
 
 `by`
-: Defines the number of sequences in each `chunk` (default: `1`)
+: Defines the number of sequences in each chunk (default: `1`).
 
 `charset`
-: Parse the content by using the specified charset e.g. `UTF-8`.
+: Parse the content with the specified charset, e.g. `UTF-8`. See the list of [standard charsets](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/nio/charset/StandardCharsets.html) for available options.
 
 `compress`
-: When `true` resulting file chunks are GZIP compressed. The `.gz` suffix is automatically added to chunk file names.
+: When `true`, resulting file chunks are GZIP compressed (default: `false`). The `.gz` suffix is automatically added to chunk file names.
 
 `decompress`
-: When `true`, decompress the content using the GZIP format before processing it (note: files whose name ends with `.gz` extension are decompressed automatically).
+: When `true`, decompress the content using the GZIP format before processing it (default: `false`). Files with the `.gz` extension are decompressed automatically.
 
 `elem`
-: The index of the element to split when the operator is applied to a channel emitting list/tuple objects (default: first file object or first element).
+: The index of the element to split when the source items are lists or tuples (default: first file object or first element).
 
 `file`
-: When `true` saves each split to a file. Use a string instead of `true` value to create split files with a specific name (split index number is automatically added). Finally, set this attribute to an existing directory, in order to save the split files into the specified folder.
+: When `true`, saves each split to a file. Use a string instead of `true` value to create split files with a specific name (split index number is automatically added). Finally, set this attribute to an existing directory, in order to save the split files into the specified directory.
 
 `limit`
-: Limits the number of retrieved sequences for each file to the specified value.
+: Limits the number of sequences to retrieve for each source item (default: no limit).
 
 `record`
-: Parse each entry in the FASTA file as record objects. The following fields are available:
+: Parse each entry in the FASTA file into a record. The following fields are available:
 
-  - `id`: The FASTA sequence identifier i.e. the word following the `>` symbol up to the first `blank` or `newline` character
+  - `id`: The FASTA sequence identifier, i.e. the word following the `>` symbol up to the first blank or newline character
   - `header`: The first line in a FASTA sequence without the `>` character
   - `desc`: The text in the FASTA header following the ID value
   - `text`: The complete FASTA sequence including the header
-  - `seqString`: The sequence data as a single line string i.e. containing no `newline` characters
-  - `sequence`: The sequence data as a multi-line string (always ending with a `newline` character)
-  - `width`: Define the length of a single line when the `sequence` field is used, after that the sequence data continues on a new line.
+  - `seqString`: The sequence data as a single-line string, i.e. containing no newline characters
+  - `sequence`: The sequence data as a multi-line string, i.e. always ending with a newline character
+  - `width`: Define the length of a single line when the `sequence` field is used, after which the sequence data continues on a new line.
 
 `size`
-: Defines the size in memory units of the expected chunks e.g. `1.MB`.
+: Defines the size of the expected chunks as a memory unit, e.g. `1.MB`.
 
 See also: [countFasta](#countfasta)
 
@@ -1198,9 +1198,9 @@ See also: [countFasta](#countfasta)
 
 *Returns: queue channel*
 
-The `splitFastq` operator allows you to split the entries emitted by a channel, that are formatted using the [FASTQ format](http://en.wikipedia.org/wiki/FASTQ_format). It returns a channel which emits a text chunk for each sequence in the received item.
+The `splitFasta` operator splits [FASTQ formatted](http://en.wikipedia.org/wiki/FASTQ_format) text from a source channel into individual sequences.
 
-The number of sequences in each text chunk produced by the `splitFastq` operator is defined by the parameter `by`. The following example shows you how to read a FASTQ file and split it into chunks containing 10 sequences each:
+The `by` option can be used to group sequences into chunks of a given size. The following example shows how to read a FASTQ file and split it into chunks of 10 sequences each:
 
 ```groovy
 Channel
@@ -1210,12 +1210,10 @@ Channel
 ```
 
 :::{warning}
-Chunks are stored in memory by default. When splitting large files, specify the parameter `file: true` to save the chunks into files in order to avoid an `OutOfMemoryException`. See the parameter table below for details.
+Chunks are stored in memory by default. When splitting large files, specify `file: true` to save the chunks into files in order to avoid running out of memory. See the list of options below for details.
 :::
 
-A second version of the `splitFastq` operator allows you to split a FASTQ formatted content into record objects, instead of text chunks. A record object contains a set of fields that let you access and manipulate the FASTQ sequence data with ease.
-
-In order to split FASTQ sequences into record objects simply use the `record` parameter specifying the map of the required fields, or just specify `record: true` as in the example shown below:
+The `record` option can be used to split FASTQ content into *records* instead of text chunks. Each record is a map that allows you to access the FASTQ sequence data with ease. For example:
 
 ```groovy
 Channel
@@ -1224,7 +1222,7 @@ Channel
     .view { record -> record.readHeader }
 ```
 
-Finally the `splitFastq` operator is able to split paired-end read pair FASTQ files. It must be applied to a channel which emits tuples containing at least two elements that are the files to be split. For example:
+The `pe` option can be used to split paired-end FASTQ files. The source channel must emit tuples containing the file pairs. For example:
 
 ```groovy
 Channel
@@ -1234,41 +1232,41 @@ Channel
 ```
 
 :::{note}
-The `fromFilePairs` requires the `flat: true` option in order to emit the file pairs as separate elements in the produced tuples.
+`Channel.fromFilePairs()` requires the `flat: true` option in order to emit the file pairs as separate elements in the produced tuples.
 :::
 
 :::{note}
-This operator assumes that the order of the paired-end reads correspond with each other and both files contain the same number of reads.
+This operator assumes that the order of the paired-end reads correspond with each other and that both files contain the same number of reads.
 :::
 
 Available options:
 
 `by`
-: Defines the number of *reads* in each `chunk` (default: `1`)
+: Defines the number of sequences in each chunk (default: `1`).
 
 `charset`
-: Parse the content by using the specified charset e.g. `UTF-8`
+: Parse the content with the specified charset, e.g. `UTF-8`. See the list of [standard charsets](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/nio/charset/StandardCharsets.html) for available options.
 
 `compress`
-: When `true` resulting file chunks are GZIP compressed. The `.gz` suffix is automatically added to chunk file names.
+: When `true`, resulting file chunks are GZIP compressed (default: `false`). The `.gz` suffix is automatically added to chunk file names.
 
 `decompress`
-: When `true` decompress the content using the GZIP format before processing it (note: files whose name ends with `.gz` extension are decompressed automatically)
+: When `true`, decompress the content using the GZIP format before processing it (default: `false`). Files with the `.gz` extension are decompressed automatically.
 
 `elem`
-: The index of the element to split when the operator is applied to a channel emitting list/tuple objects (default: first file object or first element)
+: The index of the element to split when the source items are lists or tuples (default: first file object or first element).
 
 `file`
-: When `true` saves each split to a file. Use a string instead of `true` value to create split files with a specific name (split index number is automatically added). Finally, set this attribute to an existing directory, in order to save the split files into the specified folder.
+: When `true`, saves each split to a file. Use a string instead of `true` value to create split files with a specific name (split index number is automatically added). Finally, set this attribute to an existing directory, in order to save the split files into the specified directory.
 
 `limit`
-: Limits the number of retrieved *reads* for each file to the specified value.
+: Limits the number of sequences to retrieve for each source item (default: no limit).
 
 `pe`
-: When `true` splits paired-end read files, therefore items emitted by the source channel must be tuples in which at least two elements are the read-pair files to be split.
+: When `true`, splits paired-end read files. Items emitted by the source channel must be tuples with the file pairs.
 
 `record`
-: Parse each entry in the FASTQ file as record objects. The following fields are available:
+: Parse each entry in the FASTQ file into a record. The following fields are available:
 
   - `readHeader`: Sequence header (without the `@` prefix)
   - `readString`: The raw sequence data
@@ -1283,9 +1281,9 @@ See also: [countFastq](#countfastq)
 
 *Returns: queue channel*
 
-The `splitJson` operator allows you to split a JSON document from a source channel into individual records. If the document is a JSON array, each element of the array will be emitted. If the document is a JSON object, each key-value pair will be emitted as a map with the properties `key`  and `value`.
+The `splitJson` operator splits [JSON formatted](https://en.wikipedia.org/wiki/JSON) text from a source channel into individual records.
 
-An example with a JSON array:
+If the source item is a JSON array, each element of the array will be emitted:
 
 ```{literalinclude} snippets/splitjson-array.nf
 :language: groovy
@@ -1295,7 +1293,7 @@ An example with a JSON array:
 :language: console
 ```
 
-An example with a JSON object:
+If the source item is a JSON object, each key-value pair will be emitted as a map with the properties `key`  and `value`:
 
 ```{literalinclude} snippets/splitjson-object.nf
 :language: groovy
@@ -1305,7 +1303,7 @@ An example with a JSON object:
 :language: console
 ```
 
-You can optionally query a section of the JSON document to parse and split, using the `path` option:
+The `path` option can be used to query a section of the JSON document to parse and split:
 
 ```{literalinclude} snippets/splitjson-with-path.nf
 :language: groovy
@@ -1318,10 +1316,10 @@ You can optionally query a section of the JSON document to parse and split, usin
 Available options:
 
 `limit`
-: Limits the number of retrieved lines for each file to the specified value.
+: Limits the number of records to retrieve for each source item (default: no limit).
 
 `path`
-: Define the section of the JSON document that you want to extract. The expression is a set of paths separated by a dot, similar to [JSONPath](https://goessner.net/articles/JsonPath/). The empty string is the document root (default). An integer in brackets is the 0-based index in a JSON array. A string preceded by a dot `.` is the key in a JSON object.
+: Defines a query for a section of each source item to parse and split. The expression should be a path similar to [JSONPath](https://goessner.net/articles/JsonPath/). The empty string is the document root (default). An integer in brackets is a zero-based index in a JSON array. A string preceded by a dot `.` is a key in a JSON object.
 
 See also: [countJson](#countjson)
 
@@ -1331,9 +1329,7 @@ See also: [countJson](#countjson)
 
 *Returns: queue channel*
 
-The `splitText` operator allows you to split multi-line strings or text file items, emitted by a source channel into chunks containing `n` lines, which will be emitted by the resulting channel.
-
-For example:
+The `splitText` operator splits multi-line text content from a source channel into chunks of *N* lines:
 
 ```groovy
 Channel
@@ -1342,9 +1338,9 @@ Channel
     .view()
 ```
 
-It splits the content of the files with suffix `.txt`, and prints it line by line.
+The above example loads a collection of text files, splits the content of each file into individual lines, and prints each line.
 
-By default the `splitText` operator splits each item into chunks of one line. You can define the number of lines in each chunk by using the parameter `by`, as shown in the following example:
+The `by` option can be used to emit chunks of *N* lines:
 
 ```groovy
 Channel
@@ -1356,7 +1352,7 @@ Channel
     }
 ```
 
-An optional {ref}`closure <script-closure>` can be specified in order to transform the text chunks produced by the operator. The following example shows how to split text files into chunks of 10 lines and transform them to capital letters:
+An optional {ref}`closure <script-closure>` can be used to transform each text chunk produced by the operator. The following example shows how to split text files into chunks of 10 lines and transform them to uppercase letters:
 
 ```groovy
 Channel
@@ -1375,25 +1371,25 @@ Available options:
 : Defines the number of lines in each `chunk` (default: `1`).
 
 `charset`
-: Parse the content by using the specified charset e.g. `UTF-8`.
+: Parse the content with the specified charset, e.g. `UTF-8`. See the list of [standard charsets](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/nio/charset/StandardCharsets.html) for available options.
 
 `compress`
-: When `true` resulting file chunks are GZIP compressed. The `.gz` suffix is automatically added to chunk file names.
+: When `true`, resulting file chunks are GZIP compressed (default: `false`). The `.gz` suffix is automatically added to chunk file names.
 
 `decompress`
-: When `true`, decompress the content using the GZIP format before processing it (note: files whose name ends with `.gz` extension are decompressed automatically).
+: When `true`, decompresses the content using the GZIP format before processing it (default: `false`). Files with the `.gz` extension are decompressed automatically.
 
 `elem`
-: The index of the element to split when the operator is applied to a channel emitting list/tuple objects (default: first file object or first element).
+: The index of the element to split when the source items are lists or tuples (default: first file object or first element).
 
 `file`
-: When `true` saves each split to a file. Use a string instead of `true` value to create split files with a specific name (split index number is automatically added). Finally, set this attribute to an existing directory, in order to save the split files into the specified folder.
+: When `true`, saves each split to a file. Use a string instead of `true` value to create split files with a specific name (split index number is automatically added). Finally, set this attribute to an existing directory, in order to save the split files into the specified directory.
 
 `keepHeader`
-: Parses the first line as header and prepends it to each emitted chunk.
+: Parses the first line as header and prepends it to each emitted chunk (default: `false`).
 
 `limit`
-: Limits the number of retrieved lines for each file to the specified value.
+: Limits the number of lines to retrieve for each source item (default: no limit).
 
 See also: [countLines](#countlines)
 
@@ -1403,9 +1399,7 @@ See also: [countLines](#countlines)
 
 *Returns: nothing*
 
-The `subscribe` operator allows you to execute a user defined function each time a new value is emitted by the source channel.
-
-The emitted value is passed implicitly to the specified function. For example:
+The `subscribe` operator invokes a custom function for each item from a source channel:
 
 ```{literalinclude} snippets/subscribe.nf
 :language: groovy
@@ -1415,11 +1409,7 @@ The emitted value is passed implicitly to the specified function. For example:
 :language: console
 ```
 
-:::{note}
-In Groovy, the language on which Nextflow is based, the user defined function is called a **closure**. Read the {ref}`script-closure` section to learn more about closures.
-:::
-
-If needed the closure parameter can be defined explicitly, using a name other than `it` and, optionally, specifying the expected value type, as shown in the following example:
+The closure parameter can be defined explicitly if needed, using a name other than `it` and, optionally, the expected type:
 
 ```{literalinclude} snippets/subscribe-with-param.nf
 :language: groovy
@@ -1429,16 +1419,7 @@ If needed the closure parameter can be defined explicitly, using a name other th
 :language: console
 ```
 
-```
-```
-
-The `subscribe` operator may accept one or more of the following event handlers:
-
-- `onNext`: function that is invoked whenever the channel emits a value. Equivalent to using the `subscribe` with a plain closure as described in the examples above.
-- `onComplete`: function that is invoked after the last value is emitted by the channel.
-- `onError`: function that it is invoked when an exception is raised while handling the `onNext` event. It will not make further calls to `onNext` or `onComplete`. The `onError` method takes as its parameter the `Throwable` that caused the error.
-
-For example:
+The `subscribe` operator supports multiple types of event handlers:
 
 ```{literalinclude} snippets/subscribe-with-on-complete.nf
 :language: groovy
@@ -1448,13 +1429,24 @@ For example:
 :language: console
 ```
 
+Available options:
+
+`onNext`
+: Closure that is invoked when an item is emitted. Equivalent to providing a closure as the first argument.
+
+`onComplete`
+: Closure that is invoked after the last item is emitted by the channel.
+
+`onError`
+: Closure that is invoked when an exception is raised while handling the `onNext` event. It will not make further calls to `onNext` or `onComplete`. The `onError` method takes as its parameter the `Throwable` that caused the error.
+
 (operator-sum)=
 
 ## sum
 
 *Returns: value channel*
 
-The `sum` operator creates a channel that emits the sum of all the items emitted by the channel itself. For example:
+The `sum` operator emits the sum of all items in a source channel:
 
 ```{literalinclude} snippets/sum.nf
 :language: groovy
@@ -1464,7 +1456,7 @@ The `sum` operator creates a channel that emits the sum of all the items emitted
 :language: console
 ```
 
-An optional {ref}`closure <script-closure>` parameter can be specified in order to provide a function that, given an item, returns the value to be summed. For example:
+An optional {ref}`closure <script-closure>` can be used to transform each item before it is added to the sum:
 
 ```{literalinclude} snippets/sum-with-mapper.nf
 :language: groovy
@@ -1478,7 +1470,7 @@ An optional {ref}`closure <script-closure>` parameter can be specified in order
 
 *Returns: queue channel*
 
-The `take` operator allows you to filter only the first `n` items emitted by a channel. For example:
+The `take` operator takes the first *N* items from a source channel:
 
 ```{literalinclude} snippets/take.nf
 :language: groovy
@@ -1492,15 +1484,13 @@ The `take` operator allows you to filter only the first `n` items emitted by a c
 Specifying a size of `-1` causes the operator to take all values.
 :::
 
-See also [until](#until).
+See also: [until](#until)
 
 ## tap
 
 *Returns: queue channel*
 
-The `tap` operator is like the [set](#set) operator in that it assigns a source channel to a new target channel.
-but it also emits the source channel for downstream use. This operator is a useful way to extract intermediate
-output channels from a chain of operators. For example:
+The `tap` operator assigns a source channel to a variable, and emits the source channel. It is a useful way to extract intermediate output channels from a chain of operators. For example:
 
 ```{literalinclude} snippets/tap.nf
 :language: groovy
@@ -1510,11 +1500,13 @@ output channels from a chain of operators. For example:
 :language: console
 ```
 
+See also: [set](#set)
+
 ## toInteger
 
 *Returns: queue channel*
 
-The `toInteger` operator allows you to convert the string values emitted by a channel to `Integer` values. For example:
+The `toInteger` operator converts string values from a source channel to integer values:
 
 ```{literalinclude} snippets/tointeger.nf
 :language: groovy
@@ -1524,7 +1516,15 @@ The `toInteger` operator allows you to convert the string values emitted by a ch
 :language: console
 ```
 
-:::{tip}
+:::{note}
+`toInteger` is equivalent to:
+
+```groovy
+map { it -> it as Integer }
+```
+:::
+
+:::{note}
 You can also use `toLong`, `toFloat`, and `toDouble` to convert to other numerical types.
 :::
 
@@ -1532,7 +1532,7 @@ You can also use `toLong`, `toFloat`, and `toDouble` to convert to other numeric
 
 *Returns: value channel*
 
-The `toList` operator collects all the items emitted by a channel to a `List` object and emits the resulting collection as a single item. For example:
+The `toList` operator collects all the items from a source channel into a list and emits the list as a single item:
 
 ```{literalinclude} snippets/tolist.nf
 :language: groovy
@@ -1543,7 +1543,7 @@ The `toList` operator collects all the items emitted by a channel to a `List` ob
 ```
 
 :::{note}
-There are two differences between `toList` and `collect`:
+There are two main differences between `toList` and `collect`:
 
 - When there is no input, `toList` emits an empty list whereas `collect` emits nothing.
 - By default, `collect` flattens list items by one level.
@@ -1555,13 +1555,13 @@ collect(flat: false).ifEmpty([])
 ```
 :::
 
-See also: [collect](#collect) operator.
+See also: [collect](#collect)
 
 ## toSortedList
 
 *Returns: value channel*
 
-The `toSortedList` operator collects all the items emitted by a channel to a `List` object where they are sorted and emits the resulting collection as a single item. For example:
+The `toSortedList` operator collects all the items from a source channel into a sorted list and emits the list as a single item:
 
 ```{literalinclude} snippets/tosortedlist.nf
 :language: groovy
@@ -1571,8 +1571,7 @@ The `toSortedList` operator collects all the items emitted by a channel to a `Li
 :language: console
 ```
 
-You may also pass a comparator closure as an argument to the `toSortedList` operator to customize the sorting criteria. For example, to sort by the second element of a tuple in descending order:
-
+An optional closure can be used to control how items are compared when sorting. For example, to sort tuples by their second element in descending order:
 
 ```{literalinclude} snippets/tosortedlist-with-comparator.nf
 :language: groovy
@@ -1582,78 +1581,69 @@ You may also pass a comparator closure as an argument to the `toSortedList` oper
 :language: console
 ```
 
-See also: [collect](#collect) operator.
+:::{note}
+`toSortedList` is equivalent to:
+
+```groovy
+collect(flat: false, sort: true).ifEmpty([])
+```
+:::
+
+See also: [collect](#collect)
 
 ## transpose
 
 *Returns: queue channel*
 
-The `transpose` operator transforms a channel in such a way that the emitted items are the result of a transposition of all tuple elements in each item. For example:
+The `transpose` operator "transposes" each tuple from a source channel by flattening any nested list in each tuple, emitting each nested item separately.
+
+To be more precise, the operator transforms a sequence of tuples like *(K, list(V), list(W), ..)* into a sequence of tuples like *(K, V, W, ..)*.
 
-```{literalinclude} snippets/transpose.nf
+For example:
+
+```{literalinclude} snippets/transpose-1.nf
 :language: groovy
 ```
 
-```{literalinclude} snippets/transpose.out
+```{literalinclude} snippets/transpose-1.out
 :language: console
 ```
 
-If each element of the channel has more than 2 items, these will be flattened by the first item in the element and only emit an element when the element is complete:
+If each source item has more than two elements, these will be flattened by the first element in the item, and a new item will be emitted only when it is complete:
 
-```groovy
-Channel.of(
-        [1, [1], ['A']],
-        [2, [1, 2], ['B', 'C']],
-        [3, [1, 2, 3], ['D', 'E']]
-    )
-    .transpose()
-    .view()
+```{literalinclude} snippets/transpose-2.nf
+:language: groovy
 ```
 
-```
-[1, 1, A]
-[2, 1, B]
-[2, 2, C]
-[3, 1, D]
-[3, 2, E]
+```{literalinclude} snippets/transpose-2.out
+:language: console
 ```
 
-To emit all elements, use `remainder: true`:
+The `remainder` option can be used to emit any incomplete items:
 
-```groovy
-Channel.of(
-        [1, [1], ['A']],
-        [2, [1, 2], ['B', 'C']],
-        [3, [1, 2, 3], ['D', 'E']]
-    )
-    .transpose(remainder: true)
-    .view()
+```{literalinclude} snippets/transpose-2-with-remainder.nf
+:language: groovy
 ```
 
-```
-[1, 1, A]
-[2, 1, B]
-[2, 2, C]
-[3, 1, D]
-[3, 2, E]
-[3, 3, null]
+```{literalinclude} snippets/transpose-2-with-remainder.out
+:language: console
 ```
 
 Available options:
 
-` by`
-: The index (zero based) of the element to be transposed. Multiple elements can be defined specifying as list of indices e.g. `by: [0,2]`
+`by`
+: The zero-based index of the element to be transposed. Can also be a list of indices, e.g. `by: [0,2]`. By default, every list element is transposed.
+
+`remainder`
+: When `true`, incomplete tuples are emitted with `null` values for missing elements, otherwise they are discarded (default: `false`). 
 
-` remainder`
-: When `false` incomplete tuples are discarded (default). When `true` incomplete tuples are emitted containing a `null` in place of a missing element.
+See also: [groupTuple](#grouptuple)
 
 ## unique
 
 *Returns: queue channel*
 
-The `unique` operator allows you to remove duplicate items from a channel and only emit single items with no repetition.
-
-For example:
+The `unique` operator emits the unique items from a source channel:
 
 ```{literalinclude} snippets/unique.nf
 :language: groovy
@@ -1663,7 +1653,7 @@ For example:
 :language: console
 ```
 
-You can also specify an optional {ref}`closure <script-closure>` that customizes the way it distinguishes between unique items. For example:
+An optional {ref}`closure <script-closure>` can be used to transform each item before it is evaluated for uniqueness:
 
 ```{literalinclude} snippets/unique-with-mapper.nf
 :language: groovy
@@ -1673,11 +1663,17 @@ You can also specify an optional {ref}`closure <script-closure>` that customizes
 :language: console
 ```
 
+:::{note}
+The difference between `unique` and `distinct` is that `unique` removes *all* duplicate values, whereas `distinct` removes only *consecutive* duplicate values. As a result, `unique` must process the entire source channel before it can emit anything, whereas `distinct` can emit each value immediately.
+:::
+
+See also: [distinct](#distinct)
+
 ## until
 
 *Returns: queue channel*
 
-The `until` operator creates a channel that returns the items emitted by the source channel and stop when the condition specified is verified. For example:
+The `until` operator emits each item from a source channel until a stopping condition is satisfied:
 
 ```{literalinclude} snippets/until.nf
 :language: groovy
@@ -1687,7 +1683,7 @@ The `until` operator creates a channel that returns the items emitted by the sou
 :language: console
 ```
 
-See also [take](#take).
+See also: [take](#take)
 
 (operator-view)=
 
@@ -1695,7 +1691,7 @@ See also [take](#take).
 
 *Returns: queue channel*
 
-The `view` operator prints the items emitted by a channel to the console standard output. For example:
+The `view` operator prints each item from a source channel to standard output:
 
 ```{literalinclude} snippets/view.nf
 :language: groovy
@@ -1705,9 +1701,7 @@ The `view` operator prints the items emitted by a channel to the console standar
 :language: console
 ```
 
-Each item is printed on a separate line unless otherwise specified by using the `newLine: false` optional parameter.
-
-How the channel items are printed can be controlled by using an optional closure parameter. The closure must return the actual value of the item to be printed:
+An optional closure can be used to transform each item before it is printed:
 
 ```{literalinclude} snippets/view-with-mapper.nf
 :language: groovy
@@ -1718,3 +1712,8 @@ How the channel items are printed can be controlled by using an optional closure
 ```
 
 The `view` operator also emits every item that it receives, allowing it to be chained with other operators.
+
+Available options:
+
+`newLine`
+: Print each item to a separate line (default: `true`).
diff --git a/docs/process.md b/docs/process.md
index 73d6dec191..af245312cf 100644
--- a/docs/process.md
+++ b/docs/process.md
@@ -2005,7 +2005,7 @@ process your_task {
 
 The above snippet defines an environment variable named `FOO` whose value is `bar`.
 
-When defined in the Nextflow configuration file, pod settings should be defined as maps. For example:
+When defined in the Nextflow configuration file, a pod setting can be defined as a map:
 
 ```groovy
 process {
@@ -2013,13 +2013,13 @@ process {
 }
 ```
 
-Multiple pod settings can be provided as a list of maps:
+Or as a list of maps:
 
 ```groovy
 process {
   pod = [
-      [env: 'FOO', value: 'bar'],
-      [secret: 'my-secret/key1', mountPath: '/etc/file.txt']
+    [env: 'FOO', value: 'bar'],
+    [secret: 'my-secret/key1', mountPath: '/etc/file.txt']
   ]
 }
 ```
diff --git a/docs/script.md b/docs/script.md
index 071675e103..f8471f76d4 100644
--- a/docs/script.md
+++ b/docs/script.md
@@ -86,7 +86,7 @@ Learn more about lists:
 Maps are used to store *associative arrays* (also known as *dictionaries*). They are unordered collections of heterogeneous, named data:
 
 ```groovy
-scores = [ "Brett":100, "Pete":"Did not finish", "Andrew":86.87934 ]
+scores = ["Brett": 100, "Pete": "Did not finish", "Andrew": 86.87934]
 ```
 
 Note that each of the values stored in the map can be of a different type. `Brett` is an integer, `Pete` is a string, and `Andrew` is a floating-point number.
@@ -454,6 +454,50 @@ Local variables should be declared using a qualifier such as `def` or a type nam
 
 Learn more about closures in the [Groovy documentation](http://groovy-lang.org/closures.html)
 
+### Syntax sugar
+
+Groovy provides several forms of "syntax sugar", or shorthands that can make your code easier to read.
+
+Some programming languages require every statement to be terminated by a semi-colon. In Groovy, semi-colons are optional, but they can still be used to write multiple statements on the same line:
+
+```groovy
+println 'Hello!' ; println 'Hello again!'
+```
+
+When calling a function, the parentheses around the function arguments are optional:
+
+```groovy
+// full syntax
+printf('Hello %s!\n', 'World')
+
+// shorthand
+printf 'Hello %s!\n', 'World'
+```
+
+It is especially useful when calling a function with a closure parameter:
+
+```groovy
+// full syntax
+[1, 2, 3].each({ println it })
+
+// shorthand
+[1, 2, 3].each { println it }
+```
+
+If the last argument is a closure, the closure can be written outside of the parentheses:
+
+```groovy
+// full syntax
+[1, 2, 3].inject('result:', { accum, v -> accum + ' ' + v })
+
+// shorthand
+[1, 2, 3].inject('result:') { accum, v -> accum + ' ' + v }
+```
+
+:::{note}
+In some cases, you might not be able to omit the parentheses because it would be syntactically ambiguous. You can use the `groovysh` REPL console to play around with Groovy and figure out what works.
+:::
+
 (implicit-variables)=
 
 ## Implicit variables
diff --git a/docs/snippets/transpose.nf b/docs/snippets/transpose-1.nf
similarity index 100%
rename from docs/snippets/transpose.nf
rename to docs/snippets/transpose-1.nf
diff --git a/docs/snippets/transpose.out b/docs/snippets/transpose-1.out
similarity index 100%
rename from docs/snippets/transpose.out
rename to docs/snippets/transpose-1.out
diff --git a/docs/snippets/transpose-2-with-remainder.nf b/docs/snippets/transpose-2-with-remainder.nf
new file mode 100644
index 0000000000..2b90726abe
--- /dev/null
+++ b/docs/snippets/transpose-2-with-remainder.nf
@@ -0,0 +1,7 @@
+Channel.of(
+        [1, [1], ['A']],
+        [2, [1, 2], ['B', 'C']],
+        [3, [1, 2, 3], ['D', 'E']]
+    )
+    .transpose(remainder: true)
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/transpose-2-with-remainder.out b/docs/snippets/transpose-2-with-remainder.out
new file mode 100644
index 0000000000..c156136ee6
--- /dev/null
+++ b/docs/snippets/transpose-2-with-remainder.out
@@ -0,0 +1,6 @@
+[1, 1, A]
+[2, 1, B]
+[2, 2, C]
+[3, 1, D]
+[3, 2, E]
+[3, 3, null]
\ No newline at end of file
diff --git a/docs/snippets/transpose-2.nf b/docs/snippets/transpose-2.nf
new file mode 100644
index 0000000000..822c7bf45e
--- /dev/null
+++ b/docs/snippets/transpose-2.nf
@@ -0,0 +1,7 @@
+Channel.of(
+        [1, [1], ['A']],
+        [2, [1, 2], ['B', 'C']],
+        [3, [1, 2, 3], ['D', 'E']]
+    )
+    .transpose()
+    .view()
\ No newline at end of file
diff --git a/docs/snippets/transpose-2.out b/docs/snippets/transpose-2.out
new file mode 100644
index 0000000000..6c9ede99ac
--- /dev/null
+++ b/docs/snippets/transpose-2.out
@@ -0,0 +1,5 @@
+[1, 1, A]
+[2, 1, B]
+[2, 2, C]
+[3, 1, D]
+[3, 2, E]
\ No newline at end of file

From 3fb29f78bc68c98e1973b04ec91955eab086a3f8 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Tue, 21 Nov 2023 13:39:39 -0600
Subject: [PATCH 274/350] Add docs section on container requirements (#4501)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/aws.md       | 27 ++++++++++++---------------
 docs/container.md |  2 +-
 2 files changed, 13 insertions(+), 16 deletions(-)

diff --git a/docs/aws.md b/docs/aws.md
index 4cd2488f1b..d9179c186c 100644
--- a/docs/aws.md
+++ b/docs/aws.md
@@ -138,24 +138,18 @@ Nextflow provides built-in support for AWS Batch, allowing the seamless deployme
 
 Read the {ref}`AWS Batch executor <awsbatch-executor>` section to learn more about the `awsbatch` executor in Nextflow.
 
-(aws-batch-config)=
+(aws-batch-cli)=
 
 ### AWS CLI
 
-Nextflow needs the [AWS command line tool](https://aws.amazon.com/cli/) (`aws`) to be available in the container in which tasks are executed, in order to stage input files and output files to and from S3 storage.
-
 :::{tip}
-When using {ref}`wave-page` and {ref}`fusion-page`, the AWS command line tool is not needed for task containers or the underlying EC2 instances when running Nextflow on AWS Batch. See the {ref}`fusion-page` documentation for more details.
+The need for the AWS CLI is considered a legacy requirement for the deployment of Nextflow pipelines with AWS Batch.
+Instead, consider using {ref}`wave-page` and {ref}`fusion-page` to facilitate access to S3 without using the AWS CLI.
 :::
 
-The `aws` command can be made available in the container in two ways:
-
-1. Installed in the Docker image(s) used during the pipeline execution,
-2. Installed in a custom [AMI (Amazon Machine Image)](https://docs.aws.amazon.com/AWSEC2/latest/UserGuide/AMIs.html) to use in place of the default AMI when configuring AWS Batch (see next section).
+Nextflow uses the [AWS command line tool](https://aws.amazon.com/cli/) (`aws`) to stage input files and output files between S3 and the task containers.
 
-The latter approach is preferred because it allows the use of existing Docker images without having to add the AWS CLI to each one.
-
-See the sections below to learn how to create a custom AMI and install the AWS CLI tool in it.
+The `aws` command can be made available by either (1) installing it in the container image(s) or (2) installing it in a {ref}`custom AMI <aws-custom-ami>` to be used instead of the default AMI when configuring AWS Batch.
 
 ### Get started
 
@@ -194,7 +188,7 @@ process {
 
 aws {
     batch {
-        // NOTE: this setting is only required if the AWS CLI tool is installed in a custom AMI
+        // NOTE: this setting is only required if the AWS CLI is installed in a custom AMI
         cliPath = '/home/ec2-user/miniconda/bin/aws'
     }
     region = 'us-east-1'
@@ -249,6 +243,8 @@ containerOptions '--ulimit nofile=1280:2560 --ulimit nproc=16:32 --privileged'
 
 Check the [AWS documentation](https://docs.aws.amazon.com/batch/latest/APIReference/API_ContainerProperties.html) for further details.
 
+(aws-custom-ami)=
+
 ## Custom AMI
 
 There are several reasons why you might need to create your own [AMI (Amazon Machine Image)](https://docs.aws.amazon.com/AWSEC2/latest/UserGuide/AMIs.html) to use in your Compute Environments:
@@ -282,10 +278,11 @@ Any additional software must be installed on the EC2 instance *before* creating
 ### AWS CLI installation
 
 :::{tip}
-When using {ref}`wave-page` and {ref}`fusion-page`, the AWS command line tool is not needed for task containers or the underlying EC2 instances when running Nextflow on AWS Batch. See the {ref}`fusion-page` documentation for more details.
+The need for the AWS CLI is considered a legacy requirement for the deployment of Nextflow pipelines with AWS Batch.
+Instead, consider using {ref}`wave-page` and {ref}`fusion-page` to facilitate access to S3 without using the AWS CLI.
 :::
 
-The [AWS CLI tool](https://aws.amazon.com/cli) should be installed in your custom AMI using a self-contained package manager such as [Conda](https://conda.io). That way, you can control which version of Python is used by the AWS CLI (which is written in Python).
+The [AWS CLI](https://aws.amazon.com/cli) should be installed in your custom AMI using a self-contained package manager such as [Conda](https://conda.io). That way, you can control which version of Python is used by the AWS CLI (which is written in Python).
 
 If you don't use Conda, the `aws` command will attempt to use the version of Python that is installed in the container, and it won't be able to find the necessary dependencies.
 
@@ -410,7 +407,7 @@ The bucket path should include at least a top level directory name, e.g. `s3://m
 
 Nextflow allows the use of multiple executors in the same workflow application. This feature enables the deployment of hybrid workloads in which some jobs are executed in the local computer or local computing cluster and some jobs are offloaded to AWS Batch.
 
-To enable this feature, use one or more {ref}`config-process-selectors` in your Nextflow configuration to apply the AWS Batch {ref}`configuration <aws-batch-config>` to the subset of processes that you want to offload. For example:
+To enable this feature, use one or more {ref}`config-process-selectors` in your Nextflow configuration to apply the AWS Batch configuration to the subset of processes that you want to offload. For example:
 
 ```groovy
 aws {
diff --git a/docs/container.md b/docs/container.md
index a1f3799693..cb5d50547d 100644
--- a/docs/container.md
+++ b/docs/container.md
@@ -5,7 +5,7 @@
 Nextflow supports a variety of container runtimes. Containerization allows you to write self-contained and truly reproducible computational pipelines, by packaging the binary dependencies of a script into a standard and portable format that can be executed on any platform that supports a container runtime. Furthermore, the same pipeline can be transparently executed with any of the supported container runtimes, depending on which runtimes are available in the target compute environment.
 
 :::{note}
-When creating your container image to use with Nextflow, make sure that Bash (3.x or later) and `ps` are installed in your image, along with other tools required for collecting metrics (See  {ref}`this section <execution-report-tasks>`). Also, Bash should be available on the path `/bin/bash` and it should be the container entrypoint.
+When creating a container image to use with Nextflow, make sure that Bash (3.x or later) and `ps` are installed in the image, along with other tools required for collecting metrics (See {ref}`this section <execution-report-tasks>`). Bash should be available on the path `/bin/bash` and it should be the container entrypoint.
 :::
 
 (container-apptainer)=

From c271bb188b7f4ce37689db584f56d5b7dc2aa179 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Tue, 21 Nov 2023 20:44:31 +0100
Subject: [PATCH 275/350] Add Retry policy to Google Storage (#4524)

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Co-authored-by: Ben Sherman <bentshermann@gmail.com>
---
 docs/config.md                                | 56 ++++++++++++++++---
 .../nextflow/cloud/google/GoogleOpts.groovy   | 19 +++++--
 .../google/config/GoogleRetryOpts.groovy      | 44 +++++++++++++++
 .../google/config/GoogleStorageOpts.groovy    | 32 +++++++++++
 .../cloud/google/util/GsPathFactory.groovy    | 23 ++++++--
 .../google/config/GoogleRetryOptsTest.groovy  | 44 +++++++++++++++
 .../google/util/GsPathFactoryTest.groovy      | 25 +++++++++
 .../io/seqera/wave/plugin/WaveClient.groovy   |  2 +
 .../seqera/wave/plugin/WaveClientTest.groovy  |  2 +-
 9 files changed, 225 insertions(+), 22 deletions(-)
 create mode 100644 plugins/nf-google/src/main/nextflow/cloud/google/config/GoogleRetryOpts.groovy
 create mode 100644 plugins/nf-google/src/main/nextflow/cloud/google/config/GoogleStorageOpts.groovy
 create mode 100644 plugins/nf-google/src/test/nextflow/cloud/google/config/GoogleRetryOptsTest.groovy

diff --git a/docs/config.md b/docs/config.md
index d9641dbcb1..4a49e668c7 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -755,7 +755,9 @@ The `google` scope allows you to configure the interactions with Google Cloud, i
 
 Read the {ref}`google-page` page for more information.
 
-The following settings are available:
+#### Cloud Batch
+
+The following settings are available for Google Cloud Batch:
 
 `google.enableRequesterPaysBuckets`
 : When `true` uses the given Google Cloud project ID as the billing project for storage access. This is required when accessing data from *requester pays enabled* buckets. See [Requester Pays on Google Cloud Storage documentation](https://cloud.google.com/storage/docs/requester-pays) (default: `false`).
@@ -776,14 +778,6 @@ The following settings are available:
 `google.project`
 : The Google Cloud project ID to use for pipeline execution
 
-`google.region`
-: *Available only for Google Life Sciences*
-: The Google Cloud region where jobs are executed. Multiple regions can be provided as a comma-separated list. Cannot be used with the `google.zone` option. See the [Google Cloud documentation](https://cloud.google.com/compute/docs/regions-zones/) for a list of available regions and zones.
-
-`google.zone`
-: *Available only for Google Life Sciences*
-: The Google Cloud zone where jobs are executed. Multiple zones can be provided as a comma-separated list. Cannot be used with the `google.region` option. See the [Google Cloud documentation](https://cloud.google.com/compute/docs/regions-zones/) for a list of available regions and zones.
-
 `google.batch.allowedLocations`
 : :::{versionadded} 22.12.0-edge
   :::
@@ -822,6 +816,50 @@ The following settings are available:
 `google.batch.usePrivateAddress`
 : When `true` the VM will NOT be provided with a public IP address, and only contain an internal IP. If this option is enabled, the associated job can only load docker images from Google Container Registry, and the job executable cannot use external services other than Google APIs (default: `false`).
 
+`google.storage.maxAttempts`
+: :::{versionadded} 23.11.0-edge
+  :::
+: Max attempts when retrying failed API requests to Cloud Storage (default: `10`).
+
+`google.storage.maxDelay`
+: :::{versionadded} 23.11.0-edge
+  :::
+: Max delay when retrying failed API requests to Cloud Storage (default: `'90s'`).
+
+`google.storage.multiplier`
+: :::{versionadded} 23.11.0-edge
+  :::
+: Delay multiplier when retrying failed API requests to Cloud Storage (default: `2.0`).
+
+#### Cloud Life Sciences
+
+The following settings are available for Cloud Life Sciences:
+
+`google.enableRequesterPaysBuckets`
+: When `true` uses the given Google Cloud project ID as the billing project for storage access. This is required when accessing data from *requester pays enabled* buckets. See [Requester Pays on Google Cloud Storage documentation](https://cloud.google.com/storage/docs/requester-pays) (default: `false`).
+
+`google.httpConnectTimeout`
+: :::{versionadded} 23.06.0-edge
+  :::
+: Defines the HTTP connection timeout for Cloud Storage API requests (default: `'60s'`).
+
+`google.httpReadTimeout`
+: :::{versionadded} 23.06.0-edge
+  :::
+: Defines the HTTP read timeout for Cloud Storage API requests (default: `'60s'`).
+
+`google.location`
+: The Google Cloud location where jobs are executed (default: `us-central1`).
+
+`google.project`
+: The Google Cloud project ID to use for pipeline execution
+
+`google.region`
+: The Google Cloud region where jobs are executed. Multiple regions can be provided as a comma-separated list. Cannot be used with the `google.zone` option. See the [Google Cloud documentation](https://cloud.google.com/compute/docs/regions-zones/) for a list of available regions and zones.
+
+`google.zone`
+: The Google Cloud zone where jobs are executed. Multiple zones can be provided as a comma-separated list. Cannot be used with the `google.region` option. See the [Google Cloud documentation](https://cloud.google.com/compute/docs/regions-zones/) for a list of available regions and zones.
+
 `google.lifeSciences.bootDiskSize`
 : Set the size of the virtual machine boot disk e.g `50.GB` (default: none).
 
diff --git a/plugins/nf-google/src/main/nextflow/cloud/google/GoogleOpts.groovy b/plugins/nf-google/src/main/nextflow/cloud/google/GoogleOpts.groovy
index 3250870ff6..99de01e499 100644
--- a/plugins/nf-google/src/main/nextflow/cloud/google/GoogleOpts.groovy
+++ b/plugins/nf-google/src/main/nextflow/cloud/google/GoogleOpts.groovy
@@ -24,6 +24,7 @@ import groovy.transform.Memoized
 import groovy.transform.ToString
 import groovy.util.logging.Slf4j
 import nextflow.Session
+import nextflow.cloud.google.config.GoogleStorageOpts
 import nextflow.exception.AbortOperationException
 import nextflow.util.Duration
 /**
@@ -46,6 +47,7 @@ class GoogleOpts {
     private boolean enableRequesterPaysBuckets
     private Duration httpConnectTimeout
     private Duration httpReadTimeout
+    private GoogleStorageOpts storageOpts
 
     String getProjectId() { projectId }
     File getCredsFile() { credsFile }
@@ -53,6 +55,16 @@ class GoogleOpts {
     boolean getEnableRequesterPaysBuckets() { enableRequesterPaysBuckets }
     Duration getHttpConnectTimeout() { httpConnectTimeout }
     Duration getHttpReadTimeout() { httpReadTimeout }
+    GoogleStorageOpts getStorageOpts() { storageOpts }
+
+    GoogleOpts(Map opts) {
+        projectId = opts.project as String
+        location = opts.location as String
+        enableRequesterPaysBuckets = opts.enableRequesterPaysBuckets as boolean
+        httpConnectTimeout = opts.httpConnectTimeout ? opts.httpConnectTimeout as Duration : Duration.of('60s')
+        httpReadTimeout = opts.httpReadTimeout ? opts.httpReadTimeout as Duration : Duration.of('60s')
+        storageOpts = new GoogleStorageOpts( opts.storage as Map ?: Map.of() )
+    }
 
     @Memoized
     static GoogleOpts fromSession(Session session) {
@@ -66,12 +78,7 @@ class GoogleOpts {
     }
 
     protected static GoogleOpts fromSession0(Map config) {
-        final result = new GoogleOpts()
-        result.projectId = config.navigate("google.project") as String
-        result.location = config.navigate("google.location") as String
-        result.enableRequesterPaysBuckets = config.navigate('google.enableRequesterPaysBuckets') as boolean
-        result.httpConnectTimeout = config.navigate('google.httpConnectTimeout', '60s') as Duration
-        result.httpReadTimeout = config.navigate('google.httpReadTimeout', '60s') as Duration
+        final result = new GoogleOpts( config.google as Map ?: Map.of() )
 
         if( result.enableRequesterPaysBuckets && !result.projectId )
             throw new IllegalArgumentException("Config option 'google.enableRequesterPaysBuckets' cannot be honoured because the Google project Id has not been specified - Provide it by adding the option 'google.project' in the nextflow.config file")
diff --git a/plugins/nf-google/src/main/nextflow/cloud/google/config/GoogleRetryOpts.groovy b/plugins/nf-google/src/main/nextflow/cloud/google/config/GoogleRetryOpts.groovy
new file mode 100644
index 0000000000..de071069c0
--- /dev/null
+++ b/plugins/nf-google/src/main/nextflow/cloud/google/config/GoogleRetryOpts.groovy
@@ -0,0 +1,44 @@
+/*
+ * Copyright 2013-2023, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package nextflow.cloud.google.config
+
+import groovy.transform.CompileStatic
+import nextflow.util.Duration
+
+/**
+ * Model Google storage retry settings
+ *
+ * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
+ */
+@CompileStatic
+class GoogleRetryOpts {
+
+    final int maxAttempts
+    final double multiplier
+    final Duration maxDelay
+
+    GoogleRetryOpts(Map opts) {
+        maxAttempts = opts.maxAttempts ? opts.maxAttempts as int : 10
+        multiplier = opts.multiplier ? opts.multiplier as double : 2d
+        maxDelay = opts.maxDelay ? opts.maxDelay as Duration : Duration.of('90s')
+    }
+
+    long maxDelaySecs() {
+        return maxDelay.seconds
+    }
+}
diff --git a/plugins/nf-google/src/main/nextflow/cloud/google/config/GoogleStorageOpts.groovy b/plugins/nf-google/src/main/nextflow/cloud/google/config/GoogleStorageOpts.groovy
new file mode 100644
index 0000000000..80a8c8a580
--- /dev/null
+++ b/plugins/nf-google/src/main/nextflow/cloud/google/config/GoogleStorageOpts.groovy
@@ -0,0 +1,32 @@
+/*
+ * Copyright 2013-2023, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package nextflow.cloud.google.config
+
+/**
+ *
+ * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
+ */
+class GoogleStorageOpts {
+
+    final GoogleRetryOpts retryPolicy
+
+    GoogleStorageOpts(Map opts) {
+        retryPolicy = new GoogleRetryOpts( opts.retryPolicy as Map ?: Map.of()  )
+    }
+
+}
diff --git a/plugins/nf-google/src/main/nextflow/cloud/google/util/GsPathFactory.groovy b/plugins/nf-google/src/main/nextflow/cloud/google/util/GsPathFactory.groovy
index f550d404e7..1924432e4a 100644
--- a/plugins/nf-google/src/main/nextflow/cloud/google/util/GsPathFactory.groovy
+++ b/plugins/nf-google/src/main/nextflow/cloud/google/util/GsPathFactory.groovy
@@ -18,6 +18,7 @@ package nextflow.cloud.google.util
 
 import java.nio.file.Path
 
+import com.google.api.gax.retrying.RetrySettings
 import com.google.cloud.storage.StorageOptions
 import com.google.cloud.storage.contrib.nio.CloudStorageConfiguration
 import com.google.cloud.storage.contrib.nio.CloudStorageFileSystem
@@ -57,15 +58,25 @@ class GsPathFactory extends FileSystemPathFactory {
         return builder.build()
     }
 
-    static protected StorageOptions getCloudStorageOptions(GoogleOpts googleOpts) {
+    static protected StorageOptions getCloudStorageOptions(GoogleOpts opts) {
         final transportOptions = StorageOptions.getDefaultHttpTransportOptions().toBuilder()
-        if( googleOpts.httpConnectTimeout )
-            transportOptions.setConnectTimeout( (int)googleOpts.httpConnectTimeout.toMillis() )
-        if( googleOpts.httpReadTimeout )
-            transportOptions.setReadTimeout( (int)googleOpts.httpReadTimeout.toMillis() )
+        if( opts.httpConnectTimeout )
+            transportOptions.setConnectTimeout( (int)opts.httpConnectTimeout.toMillis() )
+        if( opts.httpReadTimeout )
+            transportOptions.setReadTimeout( (int)opts.httpReadTimeout.toMillis() )
 
-        return StorageOptions.getDefaultInstance().toBuilder()
+        RetrySettings retrySettings =
+            StorageOptions.getDefaultRetrySettings()
+                .toBuilder()
+                .setMaxAttempts(opts.storageOpts.retryPolicy.maxAttempts)
+                .setRetryDelayMultiplier(opts.storageOpts.retryPolicy.multiplier)
+                .setTotalTimeout(org.threeten.bp.Duration.ofSeconds(opts.storageOpts.retryPolicy.maxDelaySecs()))
+                .build()
+
+        return StorageOptions.getDefaultInstance()
+            .toBuilder()
             .setTransportOptions(transportOptions.build())
+            .setRetrySettings(retrySettings)
             .build()
     }
 
diff --git a/plugins/nf-google/src/test/nextflow/cloud/google/config/GoogleRetryOptsTest.groovy b/plugins/nf-google/src/test/nextflow/cloud/google/config/GoogleRetryOptsTest.groovy
new file mode 100644
index 0000000000..69685472c8
--- /dev/null
+++ b/plugins/nf-google/src/test/nextflow/cloud/google/config/GoogleRetryOptsTest.groovy
@@ -0,0 +1,44 @@
+/*
+ * Copyright 2013-2023, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package nextflow.cloud.google.config
+
+import nextflow.util.Duration
+import spock.lang.Specification
+
+/**
+ *
+ * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
+ */
+class GoogleRetryOptsTest extends Specification {
+
+    def 'should get retry opts' () {
+        when:
+        def opts1 = new GoogleRetryOpts([:])
+        then:
+        opts1.maxAttempts == 10
+        opts1.multiplier == 2.0d
+        opts1.maxDelay ==  Duration.of('90s')
+
+        when:
+        def opts2 = new GoogleRetryOpts([maxAttempts: 5, maxDelay: '5s', multiplier: 10])
+        then:
+        opts2.maxAttempts == 5
+        opts2.multiplier == 10d
+        opts2.maxDelay ==  Duration.of('5s')
+    }
+}
diff --git a/plugins/nf-google/src/test/nextflow/cloud/google/util/GsPathFactoryTest.groovy b/plugins/nf-google/src/test/nextflow/cloud/google/util/GsPathFactoryTest.groovy
index e00bf8bd99..8dd6bde8f4 100644
--- a/plugins/nf-google/src/test/nextflow/cloud/google/util/GsPathFactoryTest.groovy
+++ b/plugins/nf-google/src/test/nextflow/cloud/google/util/GsPathFactoryTest.groovy
@@ -20,6 +20,7 @@ import com.google.cloud.storage.StorageOptions
 import nextflow.Global
 import nextflow.Session
 import nextflow.cloud.google.GoogleOpts
+import nextflow.cloud.google.config.GoogleRetryOpts
 import spock.lang.Specification
 import spock.lang.Unroll
 
@@ -87,6 +88,14 @@ class GsPathFactoryTest extends Specification {
             getConfig() >> [google:[httpConnectTimeout: CONNECT, httpReadTimeout: READ]]
         }
         and:
+        def policy = new GoogleRetryOpts([:])
+        def retrySettings = StorageOptions.getDefaultRetrySettings()
+            .toBuilder()
+            .setMaxAttempts(policy.maxAttempts)
+            .setRetryDelayMultiplier(policy.multiplier)
+            .setTotalTimeout(org.threeten.bp.Duration.ofSeconds(policy.maxDelaySecs()))
+            .build()
+        and:
         def opts = GoogleOpts.fromSession(session)
         and:
         def storageOptions = GsPathFactory.getCloudStorageOptions(opts)
@@ -98,6 +107,7 @@ class GsPathFactoryTest extends Specification {
         expect:
         storageOptions == StorageOptions.getDefaultInstance().toBuilder()
             .setTransportOptions(transportOptions.build())
+            .setRetrySettings(retrySettings)
             .build()
 
         where:
@@ -106,4 +116,19 @@ class GsPathFactoryTest extends Specification {
         '30s'   | 30000          | '30s' | 30000
         '60s'   | 60000          | '60s' | 60000
     }
+
+    def 'should apply retry settings' () {
+        given:
+        def session = Mock(Session) {
+            getConfig() >> [google:[storage:[retryPolicy: [maxAttempts: 5, maxDelay:'50s', multiplier: 500]]]]
+        }
+
+        when:
+        def opts = GoogleOpts.fromSession(session)
+        then:
+        opts.storageOpts.retryPolicy.maxAttempts == 5
+        opts.storageOpts.retryPolicy.maxDelaySecs() == 50
+        opts.storageOpts.retryPolicy.multiplier == 500d
+
+    }
 }
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
index 7e4b4f7487..6966f5a780 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
@@ -567,6 +567,8 @@ class WaveClient {
             return false
         if( value.startsWith('http://') || value.startsWith('https://') )
             return false
+        if( value.startsWith('/') && !value.contains('/n') )
+            return true
         return value.endsWith('.yaml') || value.endsWith('.yml') || value.endsWith('.txt')
     }
 
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
index 6842819bb2..c85f89ad63 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
@@ -33,7 +33,6 @@ import groovy.util.logging.Slf4j
 import nextflow.Session
 import nextflow.SysEnv
 import nextflow.container.inspect.ContainerInspectMode
-import nextflow.container.inspect.ContainersInspector
 import nextflow.extension.FilesEx
 import nextflow.file.FileHelper
 import nextflow.processor.TaskRun
@@ -1215,6 +1214,7 @@ class WaveClientTest extends Specification {
         'foo'               | false
         'foo.yml'           | true
         'foo.txt'           | true
+        '/foo/bar'          | true
         'foo\nbar.yml'      | false
         'http://foo.com'    | false
     }

From ea1c1b70da7a9b8c90de445b8aee1ee7a7148c9b Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Tue, 21 Nov 2023 14:07:39 -0600
Subject: [PATCH 276/350] Add Google Batch native retry on spot termination
 (#4500)

This commit adds the automatic retry made by Google Batch when
a spot reclaim terminates a job.

This feature can be controlled by the setting:

```
google.batch.maxSpotAttempts = <number>
```

By default, the execution is attempted 5 times. When 0 is specified,
no attempt is made on a spot reclaim.

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/config.md                                 |  5 +++++
 .../google/batch/GoogleBatchTaskHandler.groovy | 18 ++++++++++++++++++
 .../google/batch/client/BatchConfig.groovy     |  7 +++++--
 .../batch/GoogleBatchTaskHandlerTest.groovy    | 17 +++++++++++------
 4 files changed, 39 insertions(+), 8 deletions(-)

diff --git a/docs/config.md b/docs/config.md
index 4a49e668c7..b22e2601f7 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -775,6 +775,11 @@ The following settings are available for Google Cloud Batch:
 `google.location`
 : The Google Cloud location where jobs are executed (default: `us-central1`).
 
+`google.batch.maxSpotAttempts`
+: :::{versionadded} 23.11.0-edge
+  :::
+: Max number of execution attempts of a job interrupted by a Compute Engine spot reclaim event (default: `5`).
+
 `google.project`
 : The Google Cloud project ID to use for pipeline execution
 
diff --git a/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchTaskHandler.groovy b/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchTaskHandler.groovy
index 7bd4e1367f..827eb1e483 100644
--- a/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchTaskHandler.groovy
+++ b/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchTaskHandler.groovy
@@ -24,6 +24,7 @@ import com.google.cloud.batch.v1.AllocationPolicy
 import com.google.cloud.batch.v1.ComputeResource
 import com.google.cloud.batch.v1.Environment
 import com.google.cloud.batch.v1.Job
+import com.google.cloud.batch.v1.LifecyclePolicy
 import com.google.cloud.batch.v1.LogsPolicy
 import com.google.cloud.batch.v1.Runnable
 import com.google.cloud.batch.v1.ServiceAccount
@@ -207,6 +208,23 @@ class GoogleBatchTaskHandler extends TaskHandler implements FusionAwareTask {
             )
             .addAllVolumes( launcher.getVolumes() )
 
+        // retry on spot reclaim
+        if( executor.config.maxSpotAttempts ) {
+            // Note: Google Batch uses the special exit status 50001 to signal
+            // the execution was terminated due a spot reclaim. When this happens
+            // The policy re-execute the jobs automatically up to `maxSpotAttempts` times
+            taskSpec
+                .setMaxRetryCount( executor.config.maxSpotAttempts )
+                .addLifecyclePolicies(
+                    LifecyclePolicy.newBuilder()
+                        .setActionCondition(
+                            LifecyclePolicy.ActionCondition.newBuilder()
+                                .addExitCodes(50001)
+                        )
+                        .setAction(LifecyclePolicy.Action.RETRY_TASK)
+                )
+        }
+
         // instance policy
         final allocationPolicy = AllocationPolicy.newBuilder()
         final instancePolicyOrTemplate = AllocationPolicy.InstancePolicyOrTemplate.newBuilder()
diff --git a/plugins/nf-google/src/main/nextflow/cloud/google/batch/client/BatchConfig.groovy b/plugins/nf-google/src/main/nextflow/cloud/google/batch/client/BatchConfig.groovy
index dae9b35805..a1dcc07a1e 100644
--- a/plugins/nf-google/src/main/nextflow/cloud/google/batch/client/BatchConfig.groovy
+++ b/plugins/nf-google/src/main/nextflow/cloud/google/batch/client/BatchConfig.groovy
@@ -37,8 +37,9 @@ class BatchConfig {
     private List<String> allowedLocations
     private MemoryUnit bootDiskSize
     private String cpuPlatform
-    private boolean spot
+    private int maxSpotAttempts
     private boolean preemptible
+    private boolean spot
     private boolean usePrivateAddress
     private String network
     private String subnetwork
@@ -49,6 +50,7 @@ class BatchConfig {
     List<String> getAllowedLocations() { allowedLocations }
     MemoryUnit getBootDiskSize() { bootDiskSize }
     String getCpuPlatform() { cpuPlatform }
+    int getMaxSpotAttempts() { maxSpotAttempts }
     boolean getPreemptible() { preemptible }
     boolean getSpot() { spot }
     boolean getUsePrivateAddress() { usePrivateAddress }
@@ -63,8 +65,9 @@ class BatchConfig {
         result.allowedLocations = session.config.navigate('google.batch.allowedLocations', List.of()) as List<String>
         result.bootDiskSize = session.config.navigate('google.batch.bootDiskSize') as MemoryUnit
         result.cpuPlatform = session.config.navigate('google.batch.cpuPlatform')
-        result.spot = session.config.navigate('google.batch.spot',false)
+        result.maxSpotAttempts = session.config.navigate('google.batch.maxSpotAttempts',5) as int
         result.preemptible = session.config.navigate('google.batch.preemptible',false)
+        result.spot = session.config.navigate('google.batch.spot',false)
         result.usePrivateAddress = session.config.navigate('google.batch.usePrivateAddress',false)
         result.network = session.config.navigate('google.batch.network')
         result.subnetwork = session.config.navigate('google.batch.subnetwork')
diff --git a/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchTaskHandlerTest.groovy b/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchTaskHandlerTest.groovy
index 4d0d36c6f1..48b523ed75 100644
--- a/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchTaskHandlerTest.groovy
+++ b/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchTaskHandlerTest.groovy
@@ -130,6 +130,7 @@ class GoogleBatchTaskHandlerTest extends Specification {
                 getAllowedLocations() >> ['zones/us-central1-a', 'zones/us-central1-c']
                 getBootDiskSize() >> BOOT_DISK
                 getCpuPlatform() >> CPU_PLATFORM
+                getMaxSpotAttempts() >> 5
                 getSpot() >> true
                 getNetwork() >> 'net-1'
                 getServiceAccountEmail() >> 'foo@bar.baz'
@@ -170,16 +171,20 @@ class GoogleBatchTaskHandlerTest extends Specification {
 
         and:
         def taskGroup = req.getTaskGroups(0)
-        def runnable = taskGroup.getTaskSpec().getRunnables(0)
+        def taskSpec = taskGroup.getTaskSpec()
+        def runnable = taskSpec.getRunnables(0)
         def allocationPolicy = req.getAllocationPolicy()
         def instancePolicy = allocationPolicy.getInstances(0).getPolicy()
         def networkInterface = allocationPolicy.getNetwork().getNetworkInterfaces(0)
         and:
-        taskGroup.getTaskSpec().getComputeResource().getBootDiskMib() == BOOT_DISK.toMega()
-        taskGroup.getTaskSpec().getComputeResource().getCpuMilli() == CPUS * 1_000
-        taskGroup.getTaskSpec().getComputeResource().getMemoryMib() == MEM.toMega()
-        taskGroup.getTaskSpec().getMaxRunDuration().getSeconds() == TIMEOUT.seconds
-        taskGroup.getTaskSpec().getVolumes(0).getMountPath() == '/tmp'
+        taskSpec.getComputeResource().getBootDiskMib() == BOOT_DISK.toMega()
+        taskSpec.getComputeResource().getCpuMilli() == CPUS * 1_000
+        taskSpec.getComputeResource().getMemoryMib() == MEM.toMega()
+        taskSpec.getMaxRunDuration().getSeconds() == TIMEOUT.seconds
+        taskSpec.getVolumes(0).getMountPath() == '/tmp'
+        taskSpec.getMaxRetryCount() == 5
+        taskSpec.getLifecyclePolicies(0).getActionCondition().getExitCodes(0) == 50001
+        taskSpec.getLifecyclePolicies(0).getAction().toString() == 'RETRY_TASK'
         and:
         runnable.getContainer().getCommandsList().join(' ') == '/bin/bash -o pipefail -c bash .command.run'
         runnable.getContainer().getImageUri() == CONTAINER_IMAGE

From 4d5bc21670c8faffb1d9fd336113c75bc60fecde Mon Sep 17 00:00:00 2001
From: Dr Marco Claudio De La Pierre <marco.delapierre@gmail.com>
Date: Wed, 22 Nov 2023 21:10:01 +0800
Subject: [PATCH 277/350] Fix detection of Conda local path made by Wave client
 [ci fast] (#4532)

Signed-off-by: Dr Marco Claudio De La Pierre <marco.delapierre@gmail.com>
---
 .../nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
index 6966f5a780..0559e8c411 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
@@ -567,7 +567,7 @@ class WaveClient {
             return false
         if( value.startsWith('http://') || value.startsWith('https://') )
             return false
-        if( value.startsWith('/') && !value.contains('/n') )
+        if( value.startsWith('/') && !value.contains('\n') )
             return true
         return value.endsWith('.yaml') || value.endsWith('.yml') || value.endsWith('.txt')
     }

From b480ee0e8b937f9b112e46882d58b9fc08d22134 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Thu, 23 Nov 2023 12:00:59 -0600
Subject: [PATCH 278/350] Fix ParamsMap copyWith param aliases (#4188)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../groovy/nextflow/script/ScriptBinding.groovy  |   6 +++++-
 .../nextflow/script/ScriptBindingTest.groovy     |  10 +++++++++-
 validation/google_credentials.gpg                | Bin 1726 -> 0 bytes
 3 files changed, 14 insertions(+), 2 deletions(-)
 delete mode 100644 validation/google_credentials.gpg

diff --git a/modules/nextflow/src/main/groovy/nextflow/script/ScriptBinding.groovy b/modules/nextflow/src/main/groovy/nextflow/script/ScriptBinding.groovy
index 09293c144b..a95bbd5328 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/ScriptBinding.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/ScriptBinding.groovy
@@ -239,7 +239,11 @@ class ScriptBinding extends WorkflowBinding {
         }
 
         private ParamsMap allowNames(Set names) {
-            readOnlyNames.removeAll(names)
+            for( String name : names ) {
+                final name2 = name.contains('-') ? hyphenToCamelCase(name) : camelCaseToHyphen(name)
+                readOnlyNames.remove(name)
+                readOnlyNames.remove(name2)
+            }
             return this
         }
 
diff --git a/modules/nextflow/src/test/groovy/nextflow/script/ScriptBindingTest.groovy b/modules/nextflow/src/test/groovy/nextflow/script/ScriptBindingTest.groovy
index 57089deafb..c86b2a36dd 100644
--- a/modules/nextflow/src/test/groovy/nextflow/script/ScriptBindingTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/script/ScriptBindingTest.groovy
@@ -144,23 +144,31 @@ class ScriptBindingTest extends Specification {
         def map = new ScriptBinding.ParamsMap()
         map['alpha'] = 0
         map['alpha'] = 1
+        map['alphaBeta'] = 0
+        map['alphaBeta'] = 1
         map['delta'] = 2
         map['gamma'] = 3
         then:
         map.alpha == 0
+        map.alphaBeta == 0
+        map.'alpha-beta' == 0
         map.delta == 2
         map.gamma == 3
 
         when:
-        def copy = map.copyWith(foo:1, omega: 9)
+        def copy = map.copyWith(foo:1, alphaBeta: 4, omega: 9)
         then:
         copy.foo == 1
+        copy.alphaBeta == 4
+        copy.'alpha-beta' == 4
         copy.delta == 2
         copy.gamma == 3
         copy.omega == 9
         and:
         // source does not change
         map.alpha == 0
+        map.alphaBeta == 0
+        map.'alpha-beta' == 0
         map.delta == 2
         map.gamma == 3
         !map.containsKey('omega')
diff --git a/validation/google_credentials.gpg b/validation/google_credentials.gpg
deleted file mode 100644
index b0dfd31a26150fda8afee59ba09389dc0f353239..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 1726
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zMLs+pltI<3&pX+HsP8iE<=Vaygaf!oQ0f6JqxcmjpQA3gfh@Ly%oHtghHeq81b9Su
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From b641d67791f1089a87bbf499ec52335b4aaa2d37 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Fri, 24 Nov 2023 19:22:20 +0100
Subject: [PATCH 279/350] Normalise channel docs

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/channel.md | 116 ++++++++++++++++++++++++++----------------------
 1 file changed, 64 insertions(+), 52 deletions(-)

diff --git a/docs/channel.md b/docs/channel.md
index 754d48c4ad..ab58b8a1b5 100644
--- a/docs/channel.md
+++ b/docs/channel.md
@@ -70,7 +70,7 @@ Channels may be created explicitly using the following channel factory methods.
 
 ### empty
 
-The `empty` factory method, by definition, creates a channel that doesn't emit any value.
+The `channel.empty` factory method, by definition, creates a channel that doesn't emit any value.
 
 See also: {ref}`operator-ifempty`.
 
@@ -79,13 +79,13 @@ See also: {ref}`operator-ifempty`.
 ### from
 
 :::{deprecated} 19.09.0-edge
-Use [of](#of) or [fromList](#fromlist) instead.
+Use [channel.of](#of) or [channel.fromList](#fromlist) instead.
 :::
 
-The `from` method allows you to create a channel emitting any sequence of values that are specified as the method argument, for example:
+The `channel.from` method allows you to create a channel emitting any sequence of values that are specified as the method argument, for example:
 
 ```groovy
-ch = Channel.from( 1, 3, 5, 7 )
+ch = channel.from( 1, 3, 5, 7 )
 ch.subscribe { println "value: $it" }
 ```
 
@@ -101,25 +101,25 @@ value: 7
 The following example shows how to create a channel from a *range* of numbers or strings:
 
 ```groovy
-zeroToNine = Channel.from( 0..9 )
-strings = Channel.from( 'A'..'Z' )
+zeroToNine = channel.from( 0..9 )
+strings = channel.from( 'A'..'Z' )
 ```
 
 :::{note}
-When the `from` argument is an object implementing the (Java) [Collection](http://docs.oracle.com/javase/7/docs/api/java/util/Collection.html) interface, the resulting channel emits the collection entries as individual items.
+When the `channel.from` argument is an object implementing the (Java) [Collection](http://docs.oracle.com/javase/7/docs/api/java/util/Collection.html) interface, the resulting channel emits the collection entries as individual items.
 :::
 
 Thus the following two declarations produce an identical result even though in the first case the items are specified as multiple arguments while in the second case as a single list object argument:
 
 ```groovy
-Channel.from( 1, 3, 5, 7, 9 )
-Channel.from( [1, 3, 5, 7, 9] )
+channel.from( 1, 3, 5, 7, 9 )
+channel.from( [1, 3, 5, 7, 9] )
 ```
 
 But when more than one argument is provided, they are always managed as *single* emissions. Thus, the following example creates a channel emitting three entries each of which is a list containing two elements:
 
 ```groovy
-Channel.from( [1, 2], [5,6], [7,9] )
+channel.from( [1, 2], [5,6], [7,9] )
 ```
 
 (channel-fromlist)=
@@ -129,10 +129,10 @@ Channel.from( [1, 2], [5,6], [7,9] )
 :::{versionadded} 19.10.0
 :::
 
-The `fromList` method allows you to create a channel emitting the values provided as a list of elements, for example:
+The `channel.fromList` method allows you to create a channel emitting the values provided as a list of elements, for example:
 
 ```groovy
-Channel
+channel
     .fromList( ['a', 'b', 'c', 'd'] )
     .view { "value: $it" }
 ```
@@ -146,28 +146,31 @@ value: c
 value: d
 ```
 
-See also: [of](#of) factory method.
+See also: [channel.of](#of) factory method.
 
 (channel-path)=
 
 ### fromPath
 
-You can create a channel emitting one or more file paths by using the `fromPath` method and specifying a path string as an argument. For example:
+You can create a channel emitting one or more file paths by using the `channel.fromPath` method and specifying a path
+string as an argument. For example:
 
 ```groovy
-myFileChannel = Channel.fromPath( '/data/some/bigfile.txt' )
+myFileChannel = channel.fromPath( '/data/some/bigfile.txt' )
 ```
 
-The above line creates a channel and binds it to a [Path](http://docs.oracle.com/javase/7/docs/api/java/nio/file/Path.html) object for the specified file.
+The above line creates a channel and binds it to a [Path](http://docs.oracle.com/javase/7/docs/api/java/nio/file/Path.html)
+object for the specified file.
 
 :::{note}
-`fromPath` does not check whether the file exists.
+`channel.fromPath` does not check whether the file exists.
 :::
 
-Whenever the `fromPath` argument contains a `*` or `?` wildcard character it is interpreted as a [glob][glob] path matcher. For example:
+Whenever the `channel.fromPath` argument contains a `*` or `?` wildcard character it is interpreted as a [glob][glob] path matcher.
+For example:
 
 ```groovy
-myFileChannel = Channel.fromPath( '/data/big/*.txt' )
+myFileChannel = channel.fromPath( '/data/big/*.txt' )
 ```
 
 This example creates a channel and emits as many `Path` items as there are files with `txt` extension in the `/data/big` folder.
@@ -179,9 +182,9 @@ Two asterisks, i.e. `**`, works like `*` but crosses directory boundaries. This
 For example:
 
 ```groovy
-files = Channel.fromPath( 'data/**.fa' )
-moreFiles = Channel.fromPath( 'data/**/*.fa' )
-pairFiles = Channel.fromPath( 'data/file_{1,2}.fq' )
+files = channel.fromPath( 'data/**.fa' )
+moreFiles = channel.fromPath( 'data/**/*.fa' )
+pairFiles = channel.fromPath( 'data/file_{1,2}.fq' )
 ```
 
 The first line returns a channel emitting the files ending with the suffix `.fa` in the `data` folder *and* recursively in all its sub-folders. While the second one only emits the files which have the same suffix in *any* sub-folder in the `data` path. Finally the last example emits two files: `data/file_1.fq` and `data/file_2.fq`.
@@ -193,15 +196,15 @@ As in Linux Bash, the `*` wildcard does not catch hidden files (i.e. files whose
 Multiple paths or glob patterns can be specified using a list:
 
 ```groovy
-Channel.fromPath( ['/some/path/*.fq', '/other/path/*.fastq'] )
+channel.fromPath( ['/some/path/*.fq', '/other/path/*.fastq'] )
 ```
 
 In order to include hidden files, you need to start your pattern with a period character or specify the `hidden: true` option. For example:
 
 ```groovy
-expl1 = Channel.fromPath( '/path/.*' )
-expl2 = Channel.fromPath( '/path/.*.fa' )
-expl3 = Channel.fromPath( '/path/*', hidden: true )
+expl1 = channel.fromPath( '/path/.*' )
+expl2 = channel.fromPath( '/path/.*.fa' )
+expl3 = channel.fromPath( '/path/*', hidden: true )
 ```
 
 The first example returns all hidden files in the specified path. The second one returns all hidden files ending with the `.fa` suffix. Finally the last example returns all files (hidden and non-hidden) in that path.
@@ -211,8 +214,8 @@ By default a [glob][glob] pattern only looks for regular file paths that match t
 You can use the `type` option specifying the value `file`, `dir` or `any` in order to define what kind of paths you want. For example:
 
 ```groovy
-myFileChannel = Channel.fromPath( '/path/*b', type: 'dir' )
-myFileChannel = Channel.fromPath( '/path/a*', type: 'any' )
+myFileChannel = channel.fromPath( '/path/*b', type: 'dir' )
+myFileChannel = channel.fromPath( '/path/a*', type: 'any' )
 ```
 
 The first example will return all *directory* paths ending with the `b` suffix, while the second will return any file or directory starting with a `a` prefix.
@@ -244,10 +247,11 @@ Available options:
 
 ### fromFilePairs
 
-The `fromFilePairs` method creates a channel emitting the file pairs matching a [glob][glob] pattern provided by the user. The matching files are emitted as tuples in which the first element is the grouping key of the matching pair and the second element is the list of files (sorted in lexicographical order). For example:
+The `channel.fromFilePairs` method creates a channel emitting the file pairs matching a [glob][glob] pattern provided
+by the user. The matching files are emitted as tuples in which the first element is the grouping key of the matching pair and the second element is the list of files (sorted in lexicographical order). For example:
 
 ```groovy
-Channel
+channel
     .fromFilePairs('/my/data/SRR*_{1,2}.fastq')
     .view()
 ```
@@ -270,13 +274,13 @@ The glob pattern must contain at least one `*` wildcard character.
 Multiple glob patterns can be specified using a list:
 
 ```groovy
-Channel.fromFilePairs( ['/some/data/SRR*_{1,2}.fastq', '/other/data/QFF*_{1,2}.fastq'] )
+channel.fromFilePairs( ['/some/data/SRR*_{1,2}.fastq', '/other/data/QFF*_{1,2}.fastq'] )
 ```
 
 Alternatively, it is possible to implement a custom file pair grouping strategy providing a closure which, given the current file as parameter, returns the grouping key. For example:
 
 ```groovy
-Channel
+channel
     .fromFilePairs('/some/data/*', size: -1) { file -> file.extension }
     .view { ext, files -> "Files with the extension $ext are $files" }
 ```
@@ -311,10 +315,10 @@ Available options:
 :::{versionadded} 19.04.0
 :::
 
-The `fromSRA` method queries the [NCBI SRA](https://www.ncbi.nlm.nih.gov/sra) database and returns a channel emitting the FASTQ files matching the specified criteria i.e project or accession number(s). For example:
+The `channel.fromSRA` method queries the [NCBI SRA](https://www.ncbi.nlm.nih.gov/sra) database and returns a channel emitting the FASTQ files matching the specified criteria i.e project or accession number(s). For example:
 
 ```groovy
-Channel
+channel
     .fromSRA('SRP043510')
     .view()
 ```
@@ -335,7 +339,7 @@ Multiple accession IDs can be specified using a list object:
 
 ```groovy
 ids = ['ERR908507', 'ERR908506', 'ERR908505']
-Channel
+channel
     .fromSRA(ids)
     .view()
 ```
@@ -356,7 +360,7 @@ To access the ESearch API, you must provide your [NCBI API keys](https://ncbiins
 
 - The `apiKey` option:
   ```groovy
-  Channel.fromSRA(ids, apiKey:'0123456789abcdef')
+  channel.fromSRA(ids, apiKey:'0123456789abcdef')
   ```
 
 - The `NCBI_API_KEY` variable in your environment:
@@ -385,14 +389,15 @@ Available options:
 :::{versionadded} 19.10.0
 :::
 
-The `of` method allows you to create a channel that emits the arguments provided to it, for example:
+The `channel.of` method allows you to create a channel that emits the arguments provided to it, for example:
 
 ```groovy
-ch = Channel.of( 1, 3, 5, 7 )
+ch = channel.of( 1, 3, 5, 7 )
 ch.view { "value: $it" }
 ```
 
-The first line in this example creates a variable `ch` which holds a channel object. This channel emits the arguments supplied to the `of` method. Thus the second line prints the following:
+The first line in this example creates a variable `ch` which holds a channel object. This channel emits the arguments
+supplied to the `of` method. Thus the second line prints the following:
 
 ```
 value: 1
@@ -404,7 +409,7 @@ value: 7
 Ranges of values are expanded accordingly:
 
 ```groovy
-Channel
+channel
     .of(1..23, 'X', 'Y')
     .view()
 ```
@@ -422,37 +427,42 @@ X
 Y
 ```
 
-See also: [fromList](#fromlist) factory method.
+See also: [channel.fromList](#fromlist) factory method.
 
 (channel-value)=
 
 ### value
 
-The `value` method is used to create a value channel. An optional (not `null`) argument can be specified to bind the channel to a specific value. For example:
+The `channel.value` method is used to create a value channel. An optional (not `null`) argument can be specified to bind
+the channel to a specific value. For example:
 
 ```groovy
-expl1 = Channel.value()
-expl2 = Channel.value( 'Hello there' )
-expl3 = Channel.value( [1,2,3,4,5] )
+expl1 = channel.value()
+expl2 = channel.value( 'Hello there' )
+expl3 = channel.value( [1,2,3,4,5] )
 ```
 
-The first line in the example creates an 'empty' variable. The second line creates a channel and binds a string to it. The third line creates a channel and binds a list object to it that will be emitted as a single value.
+The first line in the example creates an 'empty' variable. The second line creates a channel and binds a string to it.
+The third line creates a channel and binds a list object to it that will be emitted as a single value.
 
 (channel-watchpath)=
 
 ### watchPath
 
-The `watchPath` method watches a folder for one or more files matching a specified pattern. As soon as there is a file that meets the specified condition, it is emitted over the channel that is returned by the `watchPath` method. The condition on files to watch can be specified by using `*` or `?` wildcard characters i.e. by specifying a [glob][glob] path matching criteria.
+The `channel.watchPath` method watches a folder for one or more files matching a specified pattern. As soon as there
+is a file that meets the specified condition, it is emitted over the channel that is returned by the `watchPath` method.
+The condition on files to watch can be specified by using `*` or `?` wildcard characters i.e. by specifying a [glob][glob] path matching criteria.
 
 For example:
 
 ```groovy
-Channel
+channel
     .watchPath( '/path/*.fa' )
     .subscribe { println "Fasta file: $it" }
 ```
 
-By default it watches only for new files created in the specified folder. Optionally, it is possible to provide a second argument that specifies what event(s) to watch. The supported events are:
+By default it watches only for new files created in the specified folder. Optionally, it is possible to provide a second
+argument that specifies what event(s) to watch. The supported events are:
 
 - `create`: A new file is created (default)
 - `modify`: A file is modified
@@ -461,15 +471,17 @@ By default it watches only for new files created in the specified folder. Option
 You can specify more than one of these events by using a comma separated string as shown below:
 
 ```groovy
-Channel
+channel
     .watchPath( '/path/*.fa', 'create,modify' )
     .subscribe { println "File created or modified: $it" }
 ```
 
 :::{warning}
-The `watchPath` factory waits endlessly for files that match the specified pattern and event(s), which means that it will cause your pipeline to run forever. Consider using the `take` or `until` operator to close the channel when a certain condition is met (e.g. after receiving 10 files, receiving a file named `DONE`).
+The `channel.watchPath` factory waits endlessly for files that match the specified pattern and event(s), which means
+that it will cause your pipeline to run forever. Consider using the `take` or `until` operator to close the channel when
+a certain condition is met (e.g. after receiving 10 files, receiving a file named `DONE`).
 :::
 
-See also: [fromPath](#frompath) factory method.
+See also: [channel.fromPath](#frompath) factory method.
 
 [glob]: http://docs.oracle.com/javase/tutorial/essential/io/fileOps.html#glob

From 921313d1441e352fe4e14e15a693eed8ac57e537 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Fri, 24 Nov 2023 20:04:02 +0100
Subject: [PATCH 280/350] Add "topic" channel  (#4459)

This commit adds experimental support for topic channel.

A topic channel allows multiple processes to write over the same
channel identified by a shared topic name.


Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Co-authored-by: Ben Sherman <bentshermann@gmail.com>
---
 docs/channel.md                               | 118 +++++++++++++++++-
 docs/config.md                                |   9 ++
 docs/process.md                               |  81 ++++++------
 docs/workflow.md                              |   4 +-
 .../src/main/groovy/nextflow/Channel.groovy   |   5 +
 .../src/main/groovy/nextflow/NF.groovy        |   4 +
 .../main/groovy/nextflow/NextflowMeta.groovy  |   7 ++
 .../nextflow/ast/NextflowDSLImpl.groovy       |  10 +-
 .../main/groovy/nextflow/extension/CH.groovy  |  67 +++++++++-
 .../groovy/nextflow/extension/MixOp.groovy    |  16 ++-
 .../groovy/nextflow/script/ProcessDef.groovy  |  10 +-
 .../script/params/BaseOutParam.groovy         |  16 +++
 .../nextflow/script/params/OutParam.groovy    |   2 +
 .../script/params/ParamsOutTest.groovy        |  83 +++++++++++-
 tests/checks/topic-channel.nf/.checks         |  15 +++
 tests/checks/topic-channel.nf/.expected       |   2 +
 tests/topic-channel.nf                        |  37 ++++++
 17 files changed, 426 insertions(+), 60 deletions(-)
 create mode 100644 tests/checks/topic-channel.nf/.checks
 create mode 100644 tests/checks/topic-channel.nf/.expected
 create mode 100644 tests/topic-channel.nf

diff --git a/docs/channel.md b/docs/channel.md
index ab58b8a1b5..157ae08534 100644
--- a/docs/channel.md
+++ b/docs/channel.md
@@ -19,7 +19,8 @@ In Nextflow there are two kinds of channels: *queue channels* and *value channel
 
 ### Queue channel
 
-A *queue channel* is a non-blocking unidirectional FIFO queue which connects two processes, channel factories, or operators.
+A *queue channel* is a non-blocking unidirectional FIFO queue connecting a *producer* process (i.e. outputting a value)
+to a consumer process, or an operators.
 
 A queue channel can be created by factory methods ([of](#of), [fromPath](#frompath), etc), operators ({ref}`operator-map`, {ref}`operator-flatmap`, etc), and processes (see {ref}`Process outputs <process-output>`).
 
@@ -27,9 +28,12 @@ A queue channel can be created by factory methods ([of](#of), [fromPath](#frompa
 
 ### Value channel
 
-A *value channel* contains a single value and can be consumed any number of times by a process or operator.
+A *value channel* can be bound (i.e. assigned) with one and only one value, and can be consumed any number of times by
+a process or an operator.
 
-A value channel can be created with the [value](#value) factory method or by any operator that produces a single value ({ref}`operator-first`, {ref}`operator-collect`, {ref}`operator-reduce`, etc). Additionally, a process will emit value channels if it is invoked with all value channels, including simple values which are implicitly wrapped in a value channel.
+A value channel can be created with the [value](#value) factory method or by any operator that produces a single value
+({ref}`operator-first`, {ref}`operator-collect`, {ref}`operator-reduce`, etc). Additionally, a process will emit value
+channels if it is invoked with all value channels, including simple values which are implicitly wrapped in a value channel.
 
 For example:
 
@@ -52,7 +56,8 @@ workflow {
 }
 ```
 
-In the above example, since the `foo` process is invoked with a simple value instead of a channel, the input is implicitly wrapped in a value channel, and the output is also emitted as a value channel.
+In the above example, since the `foo` process is invoked with a simple value instead of a channel, the input is implicitly
+wrapped in a value channel, and the output is also emitted as a value channel.
 
 See also: {ref}`process-multiple-input-channels`.
 
@@ -63,7 +68,8 @@ See also: {ref}`process-multiple-input-channels`.
 Channels may be created explicitly using the following channel factory methods.
 
 :::{versionadded} 20.07.0
-`channel` was introduced as an alias of `Channel`, allowing factory methods to be specified as `channel.of()` or `Channel.of()`, and so on.
+`channel` was introduced as an alias of `Channel`, allowing factory methods to be specified as `channel.of()` or
+`Channel.of()`, and so on.
 :::
 
 (channel-empty)=
@@ -429,6 +435,108 @@ Y
 
 See also: [channel.fromList](#fromlist) factory method.
 
+(channel-topic)=
+
+### topic
+
+:::{versionadded} 23.11.0-edge
+:::
+
+:::{note}
+This feature requires the `nextflow.preview.topic` feature flag to be enabled.
+:::
+
+A *topic* is a channel type introduced as of Nextflow 23.11.0-edge along with {ref}`channel-type-value` and
+{ref}`channel-type-queue`.
+
+A *topic channel*, similarly to a *queue channel*, is non-blocking unidirectional FIFO queue, however it connects
+multiple *producer* processes with multiple *consumer* processes or operators.
+
+:::{tip}
+You can think about it as a channel that is shared across many different process using the same *topic name*.
+:::
+
+A process output can be assigned to a topic using the `topic` option on an output, for example:
+
+```groovy
+process foo {
+  output:
+  val('foo'), topic: my_topic
+}
+
+process bar {
+  output:
+  val('bar'), topic: my_topic
+}
+```
+
+The `channel.topic` method allows referencing the topic channel with the specified name, which can be used as a process
+input or operator composition as any other Nextflow channel:
+
+```groovy
+channel.topic('my-topic').view()
+```
+
+This approach is a convenient way to collect related items from many different sources without explicitly defining
+the logic connecting many different queue channels altogether, commonly using the `mix` operator.
+
+:::{warning}
+Any process that consumes a channel topic should not send any outputs to that topic, or else the pipeline will hang forever.
+:::
+
+See also: {ref}`process-additional-options` for process outputs.
+
+(channel-topic)=
+
+### topic
+
+:::{versionadded} 23.11.0-edge
+:::
+
+:::{note}
+This feature requires the `nextflow.preview.topic` feature flag to be enabled.
+:::
+
+A *topic* is a channel type introduced as of Nextflow 23.11.0-edge along with {ref}`channel-type-value` and
+{ref}`channel-type-queue`.
+
+A *topic channel*, similarly to a *queue channel*, is non-blocking unidirectional FIFO queue, however it connects
+multiple *producer* processes with multiple *consumer* processes or operators.
+
+:::{tip}
+You can think about it as a channel that is shared across many different process using the same *topic name*.
+:::
+
+A process output can be assigned to a topic using the `topic` option on an output, for example:
+
+```groovy
+process foo {
+  output:
+  val('foo'), topic: my_topic
+}
+
+process bar {
+  output:
+  val('bar'), topic: my_topic
+}
+```
+
+The `channel.topic` method allows referencing the topic channel with the specified name, which can be used as a process
+input or operator composition as any other Nextflow channel:
+
+```groovy
+Channel.topic('my-topic').view()
+```
+
+This approach is a convenient way to collect related items from many different sources without explicitly defining
+the logic connecting many different queue channels altogether, commonly using the `mix` operator.
+
+:::{warning}
+Any process that consumes a channel topic should not send any outputs to that topic, or else the pipeline will hang forever.
+:::
+
+See also: {ref}`process-additional-options` for process outputs.
+
 (channel-value)=
 
 ### value
diff --git a/docs/config.md b/docs/config.md
index b22e2601f7..2848954d5f 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -1856,3 +1856,12 @@ Some features can be enabled using the `nextflow.enable` and `nextflow.preview`
 : *Experimental: may change in a future release.*
 
 : When `true`, enables process and workflow recursion. See [this GitHub discussion](https://github.com/nextflow-io/nextflow/discussions/2521) for more information.
+
+`nextflow.preview.topic`
+
+: :::{versionadded} 23.11.0-edge
+  :::
+
+: *Experimental: may change in a future release.*
+
+: When `true`, enables {ref}`topic channels <channel-topic>` feature.
diff --git a/docs/process.md b/docs/process.md
index af245312cf..57062d19f1 100644
--- a/docs/process.md
+++ b/docs/process.md
@@ -1166,62 +1166,59 @@ process foo {
 ```
 :::
 
-### Optional outputs
+(process-additional-options)=
 
-In most cases, a process is expected to produce an output for each output definition. However, there are situations where it is valid for a process to not generate output. In these cases, `optional: true` may be added to the output definition, which tells Nextflow not to fail the process if the declared output is not produced:
+### Additional options
 
-```groovy
-output:
-    path("output.txt"), optional: true
-```
+The following options are available for all process outputs:
 
-In this example, the process is normally expected to produce an `output.txt` file, but in the cases where the file is legitimately missing, the process does not fail. The output channel will only contain values for those processes that produce `output.txt`.
+`emit: <name>`
 
-(process-multiple-outputs)=
+: Defines the name of the output channel, which can be used to access the channel by name from the process output:
 
-### Multiple outputs
+  ```groovy
+  process FOO {
+      output:
+      path 'hello.txt', emit: hello
+      path 'bye.txt', emit: bye
+
+      """
+      echo "hello" > hello.txt
+      echo "bye" > bye.txt
+      """
+  }
 
-When a process declares multiple outputs, each output can be accessed by index. The following example prints the second process output (indexes start at zero):
+  workflow {
+      FOO()
+      FOO.out.hello.view()
+  }
+  ```
 
-```groovy
-process FOO {
-    output:
-    path 'bye_file.txt'
-    path 'hi_file.txt'
+  See {ref}`workflow-process-invocation` for more details.
 
-    """
-    echo "bye" > bye_file.txt
-    echo "hi" > hi_file.txt
-    """
-}
+`optional: true | false`
 
-workflow {
-    FOO()
-    FOO.out[1].view()
-}
-```
+: Normally, if a specified output is not produced by the task, the task will fail. Setting `optional: true` will cause the task to not fail, and instead emit nothing to the given output channel.
 
-You can also use the `emit` option to assign a name to each output and access them by name:
+  ```groovy
+  output:
+  path("output.txt"), optional: true
+  ```
 
-```groovy
-process FOO {
-    output:
-    path 'bye_file.txt', emit: bye_file
-    path 'hi_file.txt',  emit: hi_file
+  In this example, the process is normally expected to produce an `output.txt` file, but in the cases where the file is missing, the task will not fail. The output channel will only contain values for those tasks that produced `output.txt`.
 
-    """
-    echo "bye" > bye_file.txt
-    echo "hi" > hi_file.txt
-    """
-}
+: :::{note}
+  While this option can be used with any process output, it cannot be applied to individual elements of a [tuple](#output-type-tuple) output. The entire tuple must be optional or not optional.
+  :::
 
-workflow {
-    FOO()
-    FOO.out.hi_file.view()
-}
-```
+`topic: <name>`
+
+: :::{versionadded} 23.11.0-edge
+  :::
+
+: *Experimental: may change in a future release.*
 
-See {ref}`workflow-process-invocation` for more details.
+: Defines the {ref}`channel topic <channel-topic>` to which the output will be sent.
 
 ## When
 
diff --git a/docs/workflow.md b/docs/workflow.md
index 260ebeb37e..6bc45f1015 100644
--- a/docs/workflow.md
+++ b/docs/workflow.md
@@ -104,7 +104,7 @@ workflow {
 }
 ```
 
-When a process defines multiple output channels, each output can be accessed using the array element operator (`out[0]`, `out[1]`, etc.) or using *named outputs* (see below).
+When a process defines multiple output channels, each output can be accessed by index (`out[0]`, `out[1]`, etc.) or by name (see below).
 
 The process output(s) can also be accessed like the return value of a function:
 
@@ -144,7 +144,7 @@ workflow {
 }
 ```
 
-See {ref}`process-multiple-outputs` for more details.
+See {ref}`process outputs <process-additional-options>` for more details.
 
 ### Process named stdout
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/Channel.groovy b/modules/nextflow/src/main/groovy/nextflow/Channel.groovy
index 822ce03537..84c0d2bf0e 100644
--- a/modules/nextflow/src/main/groovy/nextflow/Channel.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/Channel.groovy
@@ -121,6 +121,11 @@ class Channel  {
         return CH.queue()
     }
 
+    static DataflowWriteChannel topic(String name) {
+        if( !NF.topicChannelEnabled ) throw new MissingMethodException('topic', Channel.class, InvokerHelper.EMPTY_ARGS)
+        return CH.topic(name)
+    }
+
     /**
      * Create a empty channel i.e. only emits a STOP signal
      *
diff --git a/modules/nextflow/src/main/groovy/nextflow/NF.groovy b/modules/nextflow/src/main/groovy/nextflow/NF.groovy
index df8b592b31..3f13630088 100644
--- a/modules/nextflow/src/main/groovy/nextflow/NF.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/NF.groovy
@@ -67,4 +67,8 @@ class NF {
     static boolean isRecurseEnabled() {
         NextflowMeta.instance.preview.recursion
     }
+
+    static boolean isTopicChannelEnabled() {
+        NextflowMeta.instance.preview.topic
+    }
 }
diff --git a/modules/nextflow/src/main/groovy/nextflow/NextflowMeta.groovy b/modules/nextflow/src/main/groovy/nextflow/NextflowMeta.groovy
index b9b279fb87..bd350b945d 100644
--- a/modules/nextflow/src/main/groovy/nextflow/NextflowMeta.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/NextflowMeta.groovy
@@ -43,6 +43,7 @@ class NextflowMeta {
         volatile float dsl
         boolean strict
         boolean recursion
+        boolean topic
 
         void setDsl( float num ) {
             if( num == 1 )
@@ -59,6 +60,12 @@ class NextflowMeta {
                 log.warn "NEXTFLOW RECURSION IS A PREVIEW FEATURE - SYNTAX AND FUNCTIONALITY CAN CHANGE IN FUTURE RELEASES"
             this.recursion = recurse
         }
+
+        void setTopic(Boolean value) {
+            if( topic )
+                log.warn "CHANNEL TOPICS ARE A PREVIEW FEATURE - SYNTAX AND FUNCTIONALITY CAN CHANGE IN FUTURE RELEASES"
+            this.topic = value
+        }
     }
 
     static class Features implements Flags {
diff --git a/modules/nextflow/src/main/groovy/nextflow/ast/NextflowDSLImpl.groovy b/modules/nextflow/src/main/groovy/nextflow/ast/NextflowDSLImpl.groovy
index a278fdd8f6..0586019d7a 100644
--- a/modules/nextflow/src/main/groovy/nextflow/ast/NextflowDSLImpl.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/ast/NextflowDSLImpl.groovy
@@ -915,15 +915,16 @@ class NextflowDSLImpl implements ASTTransformation {
 
         /**
          * Transform a map entry `emit: something` into `emit: 'something'
+         * and `topic: something` into `topic: 'something'
          * (ie. as a constant) in a map expression passed as argument to
          * a method call. This allow the syntax
          *
          *   output:
-         *   path 'foo', emit: bar
+         *   path 'foo', emit: bar, topic: baz
          *
          * @param call
          */
-        protected void fixOutEmitOption(MethodCallExpression call) {
+        protected void fixOutEmitAndTopicOptions(MethodCallExpression call) {
             List<Expression> args = isTupleX(call.arguments)?.expressions
             if( !args ) return
             if( args.size()<2 && (args.size()!=1 || call.methodAsString!='_out_stdout')) return
@@ -936,6 +937,9 @@ class NextflowDSLImpl implements ASTTransformation {
                 if( key?.text == 'emit' && val ) {
                     map.mapEntryExpressions[i] = new MapEntryExpression(key, constX(val.text))
                 }
+                else if( key?.text == 'topic' && val ) {
+                    map.mapEntryExpressions[i] = new MapEntryExpression(key, constX(val.text))
+                }
             }
         }
 
@@ -955,7 +959,7 @@ class NextflowDSLImpl implements ASTTransformation {
                 // prefix the method name with the string '_out_'
                 methodCall.setMethod( new ConstantExpression('_out_' + methodName) )
                 fixMethodCall(methodCall)
-                fixOutEmitOption(methodCall)
+                fixOutEmitAndTopicOptions(methodCall)
             }
 
             else if( methodName in ['into','mode'] ) {
diff --git a/modules/nextflow/src/main/groovy/nextflow/extension/CH.groovy b/modules/nextflow/src/main/groovy/nextflow/extension/CH.groovy
index ba8727808e..6069317f86 100644
--- a/modules/nextflow/src/main/groovy/nextflow/extension/CH.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/extension/CH.groovy
@@ -1,5 +1,7 @@
 package nextflow.extension
 
+import static nextflow.Channel.*
+
 import groovy.transform.CompileStatic
 import groovy.transform.PackageScope
 import groovy.util.logging.Slf4j
@@ -15,8 +17,6 @@ import nextflow.Channel
 import nextflow.Global
 import nextflow.NF
 import nextflow.Session
-import static nextflow.Channel.STOP
-
 /**
  * Helper class to handle channel internal api ops
  *
@@ -30,7 +30,14 @@ class CH {
         return (Session) Global.session
     }
 
-    static private Map<DataflowQueue, DataflowBroadcast> bridges = new HashMap<>(10)
+    static class Topic {
+        DataflowBroadcast broadcaster = new DataflowBroadcast()
+        List<DataflowWriteChannel> sources = new ArrayList<>(10)
+    }
+
+    static final private Map<String, Topic> allTopics = new HashMap<>(10)
+
+    static final private Map<DataflowQueue, DataflowBroadcast> bridges = new HashMap<>(10)
 
     static DataflowReadChannel getReadChannel(channel) {
         if (channel instanceof DataflowQueue)
@@ -66,7 +73,15 @@ class CH {
     }
 
     static void broadcast() {
-        // connect all dataflow queue variables to associated broadcast channel 
+        // connect all broadcast topics, note this must be before the following
+        // "bridging" step because it can modify the final network topology
+        connectTopics()
+        // bridge together all broadcast channels
+        bridgeChannels()
+    }
+
+    static private void bridgeChannels() {
+        // connect all dataflow queue variables to associated broadcast channel
         for( DataflowQueue queue : bridges.keySet() ) {
             log.trace "Bridging dataflow queue=$queue"
             def broadcast = bridges.get(queue)
@@ -74,6 +89,25 @@ class CH {
         }
     }
 
+    static private void connectTopics() {
+        for( Topic topic : allTopics.values() ) {
+            if( topic.sources ) {
+                // get the list of source channels for this topic
+                final ch = new ArrayList(topic.sources)
+                // the mix operator requires at least two sources, add an empty channel if needed
+                if( ch.size()==1 )
+                    ch.add(empty())
+                // map write channels to read channels
+                final sources = ch.collect(it -> getReadChannel(it))
+                // mix all of them 
+                new MixOp(sources).withTarget(topic.broadcaster).apply()
+            }
+            else {
+                topic.broadcaster.bind(STOP)
+            }
+        }
+    }
+
     static void init() { bridges.clear() }
 
     @PackageScope
@@ -102,6 +136,31 @@ class CH {
         return new DataflowQueue()
     }
 
+    static DataflowBroadcast topic(String name) {
+        synchronized (allTopics) {
+            def topic = allTopics[name]
+            if( topic!=null )
+                return topic.broadcaster
+            // create a new topic
+            topic = new Topic()
+            allTopics[name] = topic
+            return topic.broadcaster
+        }
+    }
+
+    static DataflowWriteChannel createTopicSource(String name) {
+        synchronized (allTopics) {
+            def topic = allTopics.get(name)
+            if( topic==null ) {
+                topic = new Topic()
+                allTopics.put(name, topic)
+            }
+            final result = CH.create()
+            topic.sources.add(result)
+            return result
+        }
+    }
+
     static boolean isChannel(obj) {
         obj instanceof DataflowReadChannel || obj instanceof DataflowWriteChannel
     }
diff --git a/modules/nextflow/src/main/groovy/nextflow/extension/MixOp.groovy b/modules/nextflow/src/main/groovy/nextflow/extension/MixOp.groovy
index f8e0aed304..62ba37d5f2 100644
--- a/modules/nextflow/src/main/groovy/nextflow/extension/MixOp.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/extension/MixOp.groovy
@@ -36,6 +36,7 @@ class MixOp {
 
     private DataflowReadChannel source
     private List<DataflowReadChannel> others
+    private DataflowWriteChannel target
 
     MixOp(DataflowReadChannel source, DataflowReadChannel other) {
         this.source = source
@@ -47,8 +48,21 @@ class MixOp {
         this.others = others.toList()
     }
 
+    MixOp(List<DataflowReadChannel> channels) {
+        if( channels.size()<2 )
+            throw new IllegalArgumentException("Mix operator requires at least 2 source channels")
+        this.source = channels.get(0)
+        this.others = channels.subList(1, channels.size())
+    }
+
+    MixOp withTarget(DataflowWriteChannel target) {
+        this.target = target
+        return this
+    }
+
     DataflowWriteChannel apply() {
-        def target = CH.create()
+        if( target == null )
+            target = CH.create()
         def count = new AtomicInteger( others.size()+1 )
         def handlers = [
                 onNext: { target << it },
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/ProcessDef.groovy b/modules/nextflow/src/main/groovy/nextflow/script/ProcessDef.groovy
index 7cfc6309cc..caac95d11d 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/ProcessDef.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/ProcessDef.groovy
@@ -194,8 +194,14 @@ class ProcessDef extends BindableDef implements IterableDef, ChainableDef {
                 throw new ScriptRuntimeException("Process `$processName` inputs and outputs do not have the same cardinality - Feedback loop is not supported"  )
 
             for(int i=0; i<declaredOutputs.size(); i++ ) {
-                final ch = feedbackChannels ? feedbackChannels[i] : CH.create(singleton)
-                (declaredOutputs[i] as BaseOutParam).setInto(ch)
+                final param = (declaredOutputs[i] as BaseOutParam)
+                final topicName = param.channelTopicName
+                if( topicName && feedbackChannels )
+                    throw new IllegalArgumentException("Output topic conflicts with recursion feature - process `$processName` should not declare any output topic" )
+                final ch = feedbackChannels
+                        ? feedbackChannels[i]
+                        : ( topicName ? CH.createTopicSource(topicName) : CH.create(singleton) )
+                param.setInto(ch)
             }
         }
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/params/BaseOutParam.groovy b/modules/nextflow/src/main/groovy/nextflow/script/params/BaseOutParam.groovy
index 366110ded4..8cf9408175 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/params/BaseOutParam.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/params/BaseOutParam.groovy
@@ -44,6 +44,8 @@ abstract class BaseOutParam extends BaseParam implements OutParam {
 
     String channelEmitName
 
+    String channelTopicName
+
     BaseOutParam( Binding binding, List list, short ownerIndex = -1) {
         super(binding,list,ownerIndex)
     }
@@ -182,4 +184,18 @@ abstract class BaseOutParam extends BaseParam implements OutParam {
         this.channelEmitName = value
         return this
     }
+
+    BaseOutParam setTopic( String name ) {
+        if( isNestedParam() )
+            throw new IllegalArgumentException("Output `topic` option it not allowed in tuple components")
+        if( !name )
+            throw new IllegalArgumentException("Missing output `topic` name")
+        if( !ConfigHelper.isValidIdentifier(name) ) {
+            final msg = "Output topic '$name' is not a valid name -- Make sure it starts with an alphabetic or underscore character and it does not contain any blank, dot or other special characters"
+            throw new IllegalArgumentException(msg)
+        }
+
+        this.channelTopicName = name
+        return this
+    }
 }
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/params/OutParam.groovy b/modules/nextflow/src/main/groovy/nextflow/script/params/OutParam.groovy
index 3f4977974d..e145beec56 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/params/OutParam.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/params/OutParam.groovy
@@ -40,4 +40,6 @@ interface OutParam extends Cloneable {
 
     String getChannelEmitName()
 
+    String getChannelTopicName()
+
 }
diff --git a/modules/nextflow/src/test/groovy/nextflow/script/params/ParamsOutTest.groovy b/modules/nextflow/src/test/groovy/nextflow/script/params/ParamsOutTest.groovy
index d19820f4f6..f907d61e11 100644
--- a/modules/nextflow/src/test/groovy/nextflow/script/params/ParamsOutTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/script/params/ParamsOutTest.groovy
@@ -811,7 +811,7 @@ class ParamsOutTest extends Dsl2Spec {
 
             process hola {
               output:
-              path "${x}_name", emit: aaa
+              path "${x}_name", emit: aaa, topic: 'foo'
               path "${x}_${y}.fa", emit: bbb 
               path "simple.txt", emit: ccc 
               path "data/sub/dir/file:${x}.fa", emit: ddd 
@@ -840,6 +840,7 @@ class ParamsOutTest extends Dsl2Spec {
         out0.isDynamic()
         out0.isPathQualifier()
         out0.channelEmitName == 'aaa'
+        out0.channelTopicName == 'foo'
 
         out1.name == null
         out1.getFilePatterns(ctx,null) == ['hola_99.fa']
@@ -1196,4 +1197,84 @@ class ParamsOutTest extends Dsl2Spec {
         outs[2].inner[1].name == 'bar'
 
     }
+
+
+    def 'should define out with topic' () {
+        setup:
+        def text = '''
+            process hola {
+              output:
+              val x,     topic: ch0
+              env FOO,   topic: ch1
+              path '-',  topic: ch2
+              stdout     topic: ch3    
+              /return/
+            }
+            
+            workflow { hola() }
+            '''
+
+        def binding = [:]
+        def process = parseAndReturnProcess(text, binding)
+
+        when:
+        def outs = process.config.getOutputs() as List<OutParam>
+        then:
+        outs[0].name == 'x'
+        outs[0].channelTopicName == 'ch0'
+        and:
+        outs[1].name == 'FOO'
+        outs[1].channelTopicName == 'ch1'
+        and:
+        outs[2] instanceof StdOutParam  // <-- note: declared as `path`, turned into a `stdout`
+        outs[2].name == '-'
+        outs[2].channelTopicName == 'ch2'
+        and:
+        outs[3] instanceof StdOutParam
+        outs[3].name == '-'
+        outs[3].channelTopicName == 'ch3'
+    }
+
+    def 'should define out tuple with topic'() {
+
+        setup:
+        def text = '''
+            process hola {
+              output:
+                tuple val(x), val(y),   topic: ch1
+                tuple path('foo'),      topic: ch2
+                tuple stdout,env(bar),  topic: ch3
+
+              /return/
+            }
+            
+            workflow { hola() }
+            '''
+
+        def binding = [:]
+        def process = parseAndReturnProcess(text, binding)
+
+        when:
+        def outs = process.config.getOutputs() as List<TupleOutParam>
+
+        then:
+        outs[0].name == 'tupleoutparam<0>'
+        outs[0].channelTopicName == 'ch1'
+        outs[0].inner[0] instanceof ValueOutParam
+        outs[0].inner[0].name == 'x'
+        outs[0].inner[1] instanceof ValueOutParam
+        outs[0].inner[1].name == 'y'
+        and:
+        outs[1].name == 'tupleoutparam<1>'
+        outs[1].channelTopicName == 'ch2'
+        outs[1].inner[0] instanceof FileOutParam
+        and:
+        outs[2].name == 'tupleoutparam<2>'
+        outs[2].channelTopicName == 'ch3'
+        outs[2].inner[0] instanceof StdOutParam
+        outs[2].inner[0].name == '-'
+        outs[2].inner[1] instanceof EnvOutParam
+        outs[2].inner[1].name == 'bar'
+
+    }
 }
diff --git a/tests/checks/topic-channel.nf/.checks b/tests/checks/topic-channel.nf/.checks
new file mode 100644
index 0000000000..425cb15ae2
--- /dev/null
+++ b/tests/checks/topic-channel.nf/.checks
@@ -0,0 +1,15 @@
+#
+# initial run
+#
+echo Initial run
+$NXF_RUN
+
+cmp versions.txt .expected || false
+
+#
+# Resumed run
+#
+echo Resumed run
+$NXF_RUN -resume
+
+cmp versions.txt .expected || false
diff --git a/tests/checks/topic-channel.nf/.expected b/tests/checks/topic-channel.nf/.expected
new file mode 100644
index 0000000000..1bb4d6b958
--- /dev/null
+++ b/tests/checks/topic-channel.nf/.expected
@@ -0,0 +1,2 @@
+bar: 0.9.0
+foo: 0.1.0
diff --git a/tests/topic-channel.nf b/tests/topic-channel.nf
new file mode 100644
index 0000000000..c5eb17bc97
--- /dev/null
+++ b/tests/topic-channel.nf
@@ -0,0 +1,37 @@
+
+nextflow.preview.topic = true
+
+process foo {
+  input:
+  val(index)
+
+  output:
+  stdout emit: versions, topic: versions
+
+  script:
+  """
+  echo 'foo: 0.1.0'
+  """
+}
+
+process bar {
+  input:
+  val(index)
+
+  output:
+  stdout emit: versions, topic: versions
+
+  script:
+  """
+  echo 'bar: 0.9.0'
+  """
+}
+
+workflow {
+  Channel.of( 1..3 ) | foo
+  Channel.of( 1..3 ) | bar
+
+  Channel.topic('versions')
+  | unique
+  | collectFile(name: 'versions.txt', sort: true, storeDir: '.')
+}

From 627c595ec496fd86b650dd047dbf2a34fc33ece5 Mon Sep 17 00:00:00 2001
From: zetxqx <118311804+zetxqx@users.noreply.github.com>
Date: Fri, 24 Nov 2023 11:06:23 -0800
Subject: [PATCH 281/350] Add labels field in Job request for Google Batch
 (#4538)

Signed-off-by: Bob Tian <bobzetian@google.com>
---
 .../nextflow/cloud/google/batch/GoogleBatchTaskHandler.groovy  | 1 +
 .../cloud/google/batch/GoogleBatchTaskHandlerTest.groovy       | 3 +++
 2 files changed, 4 insertions(+)

diff --git a/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchTaskHandler.groovy b/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchTaskHandler.groovy
index 827eb1e483..c7cbd17dc6 100644
--- a/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchTaskHandler.groovy
+++ b/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchTaskHandler.groovy
@@ -347,6 +347,7 @@ class GoogleBatchTaskHandler extends TaskHandler implements FusionAwareTask {
                 LogsPolicy.newBuilder()
                     .setDestination(LogsPolicy.Destination.CLOUD_LOGGING)
             )
+            .putAllLabels(task.config.getResourceLabels())
             .build()
     }
 
diff --git a/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchTaskHandlerTest.groovy b/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchTaskHandlerTest.groovy
index 48b523ed75..ec648112cb 100644
--- a/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchTaskHandlerTest.groovy
+++ b/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchTaskHandlerTest.groovy
@@ -217,6 +217,9 @@ class GoogleBatchTaskHandlerTest extends Specification {
         networkInterface.getNoExternalIpAddress() == true
         and:
         req.getLogsPolicy().getDestination().toString() == 'CLOUD_LOGGING'
+        and:
+        req.getLabelsMap() == [foo: 'bar']
+
 
         when:
         req = handler.newSubmitRequest(task, launcher)

From 8e2d7879858dfb442cce980495afc7b83d7284d4 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Fri, 24 Nov 2023 21:13:28 +0100
Subject: [PATCH 282/350] Bump nf-amazon@2.2.0

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-amazon/changelog.txt                      | 6 ++++++
 plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF | 4 ++--
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/plugins/nf-amazon/changelog.txt b/plugins/nf-amazon/changelog.txt
index 8696d88720..f8d898430c 100644
--- a/plugins/nf-amazon/changelog.txt
+++ b/plugins/nf-amazon/changelog.txt
@@ -1,5 +1,11 @@
 nf-amazon changelog
 ===================
+2.2.0 - 24 Nov 2023
+- Add support for FUSION_AWS_REGION (#4481) [8f8b09fa]
+- Fix security vulnerabilities (#4513) [a310c777]
+- Fix typos (#4519) [ci fast] [6b1ea726]
+- Fix Fusion symlinks when publishing files (#4348) [89f09fe0]
+
 2.1.4 - 10 Oct 2023
 - Improve S3 endpoint validation [2b9ae6aa]
 - Add -cloudcache CLI option (#4385) [73fda582]
diff --git a/plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF b/plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF
index f206656eb2..41788507b1 100644
--- a/plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: nextflow.cloud.aws.AmazonPlugin
 Plugin-Id: nf-amazon
-Plugin-Version: 2.1.4
+Plugin-Version: 2.2.0
 Plugin-Provider: Seqera Labs
-Plugin-Requires: >=23.05.0-edge
+Plugin-Requires: >=23.11.0-edge

From 7c47d0907b1447d3fdcc60b09e8f1733807f14a3 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Fri, 24 Nov 2023 21:14:02 +0100
Subject: [PATCH 283/350] Bump nf-azure@1.4.0

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-azure/changelog.txt                      | 4 ++++
 plugins/nf-azure/src/resources/META-INF/MANIFEST.MF | 4 ++--
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/plugins/nf-azure/changelog.txt b/plugins/nf-azure/changelog.txt
index cc42b1938b..409ba65056 100644
--- a/plugins/nf-azure/changelog.txt
+++ b/plugins/nf-azure/changelog.txt
@@ -1,5 +1,9 @@
 nf-azure changelog
 ===================
+1.4.0 - 24 Nov 2023
+- Fix security vulnerabilities (#4513) [a310c777]
+- Add support for Azure low-priority pool (#4527) [8320ea10]
+
 1.3.2 - 28 Sep 2023
 - Retry TimeoutException in azure file system (#4295) [79248355]
 
diff --git a/plugins/nf-azure/src/resources/META-INF/MANIFEST.MF b/plugins/nf-azure/src/resources/META-INF/MANIFEST.MF
index d9273f2629..46261512b7 100644
--- a/plugins/nf-azure/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-azure/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: nextflow.cloud.azure.AzurePlugin
 Plugin-Id: nf-azure
-Plugin-Version: 1.3.2
+Plugin-Version: 1.4.0
 Plugin-Provider: Seqera Labs
-Plugin-Requires: >=23.01.0-edge
+Plugin-Requires: >=23.11.0-edge

From 65240b755fbc01b3cae8d7072baf8165d794aa74 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Fri, 24 Nov 2023 21:14:29 +0100
Subject: [PATCH 284/350] Bump nf-cloudcache@0.3.1

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-cloudcache/changelog.txt                      | 3 +++
 plugins/nf-cloudcache/src/resources/META-INF/MANIFEST.MF | 4 ++--
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/plugins/nf-cloudcache/changelog.txt b/plugins/nf-cloudcache/changelog.txt
index 05fd5fad8e..20dbd6679a 100644
--- a/plugins/nf-cloudcache/changelog.txt
+++ b/plugins/nf-cloudcache/changelog.txt
@@ -1,5 +1,8 @@
 nf-cloudcache changelog
 =======================
+0.3.1 - 24 Nov 2023
+- Fix security vulnerabilities (#4513) [a310c777]
+
 0.3.0 - 10 Oct 2023
 - Add -cloudcache CLI option (#4385) [73fda582]
 
diff --git a/plugins/nf-cloudcache/src/resources/META-INF/MANIFEST.MF b/plugins/nf-cloudcache/src/resources/META-INF/MANIFEST.MF
index b4267c3b61..2d9e60d1d7 100644
--- a/plugins/nf-cloudcache/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-cloudcache/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: nextflow.CloudCachePlugin
 Plugin-Id: nf-cloudcache
-Plugin-Version: 0.3.0
+Plugin-Version: 0.3.1
 Plugin-Provider: Seqera Labs
-Plugin-Requires: >=23.04.0
+Plugin-Requires: >=23.11.0-edge

From 725f0510a003cf7decbd36b8c8a3b3fc54cb6a30 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Fri, 24 Nov 2023 21:15:19 +0100
Subject: [PATCH 285/350] Bump nf-codecommit@0.1.6

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-codecommit/changelog.txt                      | 3 +++
 plugins/nf-codecommit/src/resources/META-INF/MANIFEST.MF | 4 ++--
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/plugins/nf-codecommit/changelog.txt b/plugins/nf-codecommit/changelog.txt
index 9c732b5bdd..065cbcaa1a 100644
--- a/plugins/nf-codecommit/changelog.txt
+++ b/plugins/nf-codecommit/changelog.txt
@@ -1,5 +1,8 @@
 nf-amazon changelog
 ===================
+0.1.6 - 24 Nov 2023
+- Fix security vulnerabilities (#4513) [a310c777]
+
 0.1.5 - 15 May 2023
 - Update logging libraries [d7eae86e]
 
diff --git a/plugins/nf-codecommit/src/resources/META-INF/MANIFEST.MF b/plugins/nf-codecommit/src/resources/META-INF/MANIFEST.MF
index c7b679a478..1c15084500 100644
--- a/plugins/nf-codecommit/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-codecommit/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: nextflow.cloud.aws.codecommit.AwsCodeCommitPlugin
 Plugin-Id: nf-codecommit
-Plugin-Version: 0.1.5
+Plugin-Version: 0.1.6
 Plugin-Provider: Seqera Labs
-Plugin-Requires: >=22.06.1-edge
+Plugin-Requires: >=23.11.0-edge

From a307686c6f5a5fe5b46b69ef53ed2b18f3bdbaea Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Fri, 24 Nov 2023 21:15:38 +0100
Subject: [PATCH 286/350] Bump nf-console@1.0.7

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-console/src/resources/META-INF/MANIFEST.MF | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/plugins/nf-console/src/resources/META-INF/MANIFEST.MF b/plugins/nf-console/src/resources/META-INF/MANIFEST.MF
index c29012ba0b..e8ee9c2869 100644
--- a/plugins/nf-console/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-console/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: nextflow.ui.console.ConsolePlugin
 Plugin-Id: nf-console
-Plugin-Version: 1.0.6
+Plugin-Version: 1.0.7
 Plugin-Provider: Seqera Labs
-Plugin-Requires: >=23.04.0
+Plugin-Requires: >=23.11.0-edge

From e54ea00704bb34aa185113c62cf379863ae8573a Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Fri, 24 Nov 2023 21:15:51 +0100
Subject: [PATCH 287/350] Bump nf-ga4gh@1.1.1

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-ga4gh/src/resources/META-INF/MANIFEST.MF | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/plugins/nf-ga4gh/src/resources/META-INF/MANIFEST.MF b/plugins/nf-ga4gh/src/resources/META-INF/MANIFEST.MF
index 2835d79c84..69568da5ea 100644
--- a/plugins/nf-ga4gh/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-ga4gh/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: nextflow.ga4gh.Ga4ghPlugin
 Plugin-Id: nf-ga4gh
-Plugin-Version: 1.1.0
+Plugin-Version: 1.1.1
 Plugin-Provider: Seqera Labs
-Plugin-Requires: >=23.05.0-edge
+Plugin-Requires: >=23.11.0-edge

From 033ec92c9d6c7c2bf4f29383ed166d8c666e8166 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Fri, 24 Nov 2023 21:16:15 +0100
Subject: [PATCH 288/350] Bump nf-google@1.9.0

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-google/changelog.txt                      | 9 +++++++++
 plugins/nf-google/src/resources/META-INF/MANIFEST.MF | 4 ++--
 2 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/plugins/nf-google/changelog.txt b/plugins/nf-google/changelog.txt
index 1637822ae4..30440b654a 100644
--- a/plugins/nf-google/changelog.txt
+++ b/plugins/nf-google/changelog.txt
@@ -1,5 +1,14 @@
 nf-google changelog
 ===================
+1.9.0 - 24 Nov 2023
+- Add labels field in Job request for Google Batch (#4538) [627c595e]
+- Add Google Batch native retry on spot termination (#4500) [ea1c1b70]
+- Add ability detect Google Batch spot interruption (#4462) [d49f02ae]
+- Add Retry policy to Google Storage (#4524) [c271bb18]
+- Fix security vulnerabilities (#4513) [a310c777]
+- Fix Bypass Google Batch Price query if task cpus and memory are defined (#4521) [7f8f20d3]
+- Update logging filter for Google Batch provider. (#4488) [66a3ed19]
+
 1.8.3 - 10 Oct 2023
 - Add setting to enable the use of sync command [f0d5cc5c]
 - Fix Google Batch do not stop running jobs (#4381) [3d6b7358]
diff --git a/plugins/nf-google/src/resources/META-INF/MANIFEST.MF b/plugins/nf-google/src/resources/META-INF/MANIFEST.MF
index 8522585c8e..aa04d212ae 100644
--- a/plugins/nf-google/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-google/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: nextflow.cloud.google.GoogleCloudPlugin
 Plugin-Id: nf-google
-Plugin-Version: 1.8.3
+Plugin-Version: 1.9.0
 Plugin-Provider: Seqera Labs
-Plugin-Requires: >=23.02.0-edge
+Plugin-Requires: >=23.11.0-edge

From 836a44a52c8e343e32edd802eb82ef2a8f25eae8 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Fri, 24 Nov 2023 21:16:34 +0100
Subject: [PATCH 289/350] Bump nf-tower@1.7.0

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-tower/changelog.txt                      | 4 ++++
 plugins/nf-tower/src/resources/META-INF/MANIFEST.MF | 4 ++--
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/plugins/nf-tower/changelog.txt b/plugins/nf-tower/changelog.txt
index 897aa3f12a..9bf2dedd72 100644
--- a/plugins/nf-tower/changelog.txt
+++ b/plugins/nf-tower/changelog.txt
@@ -1,5 +1,9 @@
 nf-tower changelog
 ===================
+1.7.0 - 24 Nov 2023
+- Fix security vulnerabilities (#4513) [a310c777]
+- Remove deprecated TowerArchiver feature [ff8e06a3]
+
 1.6.3 - 10 Oct 2023
 - Add -cloudcache CLI option (#4385) [73fda582]
 
diff --git a/plugins/nf-tower/src/resources/META-INF/MANIFEST.MF b/plugins/nf-tower/src/resources/META-INF/MANIFEST.MF
index 58bd2aa7d9..6522d288d7 100644
--- a/plugins/nf-tower/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-tower/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: io.seqera.tower.plugin.TowerPlugin
 Plugin-Id: nf-tower
-Plugin-Version: 1.6.3
+Plugin-Version: 1.7.0
 Plugin-Provider: Seqera Labs
-Plugin-Requires: >=23.05.0-edge
+Plugin-Requires: >=23.11.0-edge

From 620523efc732e51fc236b380d0cd882bb2e4311c Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Fri, 24 Nov 2023 21:16:54 +0100
Subject: [PATCH 290/350] Bump nf-wave@1.1.0

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-wave/changelog.txt                      | 9 +++++++++
 plugins/nf-wave/src/resources/META-INF/MANIFEST.MF | 4 ++--
 2 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/plugins/nf-wave/changelog.txt b/plugins/nf-wave/changelog.txt
index 5886b9be8a..eb3a22bf38 100644
--- a/plugins/nf-wave/changelog.txt
+++ b/plugins/nf-wave/changelog.txt
@@ -1,5 +1,14 @@
 nf-wave changelog
 ==================
+1.1.0 - 24 Nov 2023
+- Add Retry policy to Google Storage (#4524) [c271bb18]
+- Add support for Singularity OCI mode (#4440) [f5362a7b]
+- Fix detection of Conda local path made by Wave client (#4532) [4d5bc216]
+- Fix security vulnerabilities (#4513) [a310c777]
+- Fix container hashing for Singularity + Wave containers [4c6f2e85]
+- Use consistently NXF_TASK_WORKDIR (#4484) [48ee3c64]
+- Fix Inspect command fails with Singularity [f5bb829f]
+
 1.0.0 - 15 Oct 2023
 - Fix conda channels order [ci fast] [6672c6d7]
 - Bump nf-wave@1.0.0 [795849d7]
diff --git a/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF b/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF
index c45b973508..10bc31538d 100644
--- a/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: io.seqera.wave.plugin.WavePlugin
 Plugin-Id: nf-wave
-Plugin-Version: 1.0.0
+Plugin-Version: 1.1.0
 Plugin-Provider: Seqera Labs
-Plugin-Requires: >=23.05.0-edge
+Plugin-Requires: >=23.11.0-edge

From 4ddbb01963cbcad8dac25524898cebfbb56814ff Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Fri, 24 Nov 2023 21:24:46 +0100
Subject: [PATCH 291/350] Update changelog

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 changelog.txt | 59 +++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 59 insertions(+)

diff --git a/changelog.txt b/changelog.txt
index ac135b9f76..57aae56f06 100644
--- a/changelog.txt
+++ b/changelog.txt
@@ -1,5 +1,64 @@
 NEXTFLOW CHANGE-LOG
 ===================
+23.11.0-edge - 24 Nov 2023
+- Add `fusion.cacheSize` config option (#4518) [2faadc22]
+- Add Topic channel type (experimental) (#4459) [921313d1]
+- Add Google Batch native retry on spot termination (#4500) [ea1c1b70]
+- Add Retry policy to Google Storage (#4524) [c271bb18]
+- Add ability detect Google Batch spot interruption (#4462) [d49f02ae]
+- Add doc tests, move some snippets to separate files (#3959) [0ff3b305]
+- Add docs section on container requirements (#4501) [3fb29f78]
+- Add labels field in Job request for Google Batch (#4538) [627c595e]
+- Add note about limitations of glacier auto retrieval (#4514) [82e56799]
+- Add note about local executor and enforcing resource limits (#4468) [6a0626f7]
+- Add section about sharing modules (#4482) [3e66fba4]
+- Add section on process directives to plugin docs (#4477) [d9ee9870]
+- Add support for Azure low-priority pool (#4527) [8320ea10]
+- Add support for FUSION_AWS_REGION (#4481) [8f8b09fa]
+- Add support for Fusion when using Singularity OCI mode (#4508) [4f3aa631]
+- Add support for K8s schedulerName pod spec (#4485) [ci fast] [dfc7b7c8]
+- Add support for Singularity OCI mode (#4440) [f5362a7b]
+- Allow the use of error build-in function in onComplete handler (#4458) [ci fast] [35a4424b]
+- Fix Bug in JsonSplitter ordering [ci fast] [8ec14dd2]
+- Fix Bypass Google Batch Price query if task cpus and memory are defined (#4521) [7f8f20d3]
+- Fix Checkout remote tag if checkout remote branch fails (#4247) [b8907ccb]
+- Fix Fusion symlinks when publishing files (#4348) [89f09fe0]
+- Fix Inspect command fails with Singularity [f5bb829f]
+- Fix ParamsMap copyWith param aliases (#4188) [b480ee0e]
+- Fix Singularity docs [e952299f]
+- Fix container hashing for Singularity + Wave containers [4c6f2e85]
+- Fix detection of Conda local path made by Wave client [ci fast] (#4532) [4d5bc216]
+- Fix doc tests to fail on test failure (#4505) [4d326551]
+- Fix errors when NXF_HOME contains spaces (#4456) [ci fast] [fe5bea99]
+- Fix Google Batch network/subnetwork docs (#4475) [27d132f3]
+- Fix rounding error with long durations (#4496) [ci fast] [0356178b]
+- Fix security vulnerabilities (#4513) [a310c777]
+- Fix Use consistently NXF_TASK_WORKDIR (#4484) [48ee3c64]
+- Improve error details for AbortOperationException [35609cb0]
+- Improve operator docs (#4502) [38210e11]
+- Makefile clean to also remove buildSrc/build (#4517) [2ccb05d0]
+- Minor test improvements [ci fast] [171831ea]
+- Minor types improvement for mix operator [ci fast] [91c1ab15]
+- Normalise channel docs [b641d677]
+- Remove deprecated TowerArchiver feature [ff8e06a3]
+- Remove dsl1 deprecated code (part 2) [159effb1]
+- Remove dsl1 deprecated code [2b433a52]
+- Remove incorrect note about workflow inputs (#4509) [54bc0b7d]
+- Return error if plugin version is not specified in offline mode (#4487) [f5d7246e]
+- Update README.md with new branding color for Nextflow (#4412) [7a13b18b]
+- Update background color of docs status badges (#4411) [3cb1c53c]
+- Update logging filter for Google Batch provider. (#4488) [66a3ed19]
+- Bump Gradle 8.4 and test vs Java 21 (#4450) [8cb2702c]
+- Bump nf-amazon@2.2.0 [8e2d7879]
+- Bump nf-azure@1.4.0 [7c47d090]
+- Bump nf-cloudcache@0.3.1 [65240b75]
+- Bump nf-codecommit@0.1.6 [725f0510]
+- Bump nf-console@1.0.7 [a307686c]
+- Bump nf-ga4gh@1.1.1 [e54ea007]
+- Bump nf-google@1.9.0 [033ec92c]
+- Bump nf-tower@1.7.0 [836a44a5]
+- Bump nf-wave@1.1.0 [620523ef]
+
 23.10.0 - 15 Oct 2023
 - Add support for K8s hostPath [10c32325]
 - Add AWS SES docs [b83e7148]

From 1715dd29b242901f9167f7186ed4a0dd09e75ef7 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Fri, 24 Nov 2023 21:34:17 +0100
Subject: [PATCH 292/350] Bump jaxb-api:2.4.0-b180830.0359

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-amazon/build.gradle      | 2 +-
 plugins/nf-amazon/changelog.txt     | 1 +
 plugins/nf-codecommit/build.gradle  | 2 +-
 plugins/nf-codecommit/changelog.txt | 1 +
 4 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/plugins/nf-amazon/build.gradle b/plugins/nf-amazon/build.gradle
index de082b0fc2..93a07e40be 100644
--- a/plugins/nf-amazon/build.gradle
+++ b/plugins/nf-amazon/build.gradle
@@ -37,7 +37,7 @@ dependencies {
     compileOnly 'org.slf4j:slf4j-api:2.0.7'
     compileOnly 'org.pf4j:pf4j:3.10.0'
 
-    api ('javax.xml.bind:jaxb-api:2.3.1')
+    api ('javax.xml.bind:jaxb-api:2.4.0-b180830.0359')
     api ('com.amazonaws:aws-java-sdk-s3:1.12.429')
     api ('com.amazonaws:aws-java-sdk-ec2:1.12.429')
     api ('com.amazonaws:aws-java-sdk-batch:1.12.429')
diff --git a/plugins/nf-amazon/changelog.txt b/plugins/nf-amazon/changelog.txt
index f8d898430c..0ec2acf6c0 100644
--- a/plugins/nf-amazon/changelog.txt
+++ b/plugins/nf-amazon/changelog.txt
@@ -5,6 +5,7 @@ nf-amazon changelog
 - Fix security vulnerabilities (#4513) [a310c777]
 - Fix typos (#4519) [ci fast] [6b1ea726]
 - Fix Fusion symlinks when publishing files (#4348) [89f09fe0]
+- Bump javax.xml.bind:jaxb-api:2.4.0-b180830.0359
 
 2.1.4 - 10 Oct 2023
 - Improve S3 endpoint validation [2b9ae6aa]
diff --git a/plugins/nf-codecommit/build.gradle b/plugins/nf-codecommit/build.gradle
index c2b9dabaf7..b7402d77a3 100644
--- a/plugins/nf-codecommit/build.gradle
+++ b/plugins/nf-codecommit/build.gradle
@@ -37,7 +37,7 @@ dependencies {
     compileOnly 'org.slf4j:slf4j-api:2.0.7'
     compileOnly 'org.pf4j:pf4j:3.10.0'
 
-    api ('javax.xml.bind:jaxb-api:2.3.1')
+    api ('javax.xml.bind:jaxb-api:2.4.0-b180830.0359')
     api ('com.amazonaws:aws-java-sdk-codecommit:1.12.429')
         
     testImplementation(testFixtures(project(":nextflow")))
diff --git a/plugins/nf-codecommit/changelog.txt b/plugins/nf-codecommit/changelog.txt
index 065cbcaa1a..19bcc2f655 100644
--- a/plugins/nf-codecommit/changelog.txt
+++ b/plugins/nf-codecommit/changelog.txt
@@ -2,6 +2,7 @@ nf-amazon changelog
 ===================
 0.1.6 - 24 Nov 2023
 - Fix security vulnerabilities (#4513) [a310c777]
+- Bump javax.xml.bind:jaxb-api:2.4.0-b180830.0359
 
 0.1.5 - 15 May 2023
 - Update logging libraries [d7eae86e]

From 19d2ccb60ae7d281e6cb43769216a0384cb27313 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Fri, 24 Nov 2023 21:35:34 +0100
Subject: [PATCH 293/350] [release 23.11.0-edge] Update timestamp and build
 number

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 VERSION                                        |  2 +-
 changelog.txt                                  |  2 +-
 docs/conf.py                                   |  4 ++--
 .../main/resources/META-INF/plugins-info.txt   | 18 +++++++++---------
 .../nf-commons/src/main/nextflow/Const.groovy  |  6 +++---
 nextflow                                       |  2 +-
 nextflow.md5                                   |  2 +-
 nextflow.sha1                                  |  2 +-
 nextflow.sha256                                |  2 +-
 9 files changed, 20 insertions(+), 20 deletions(-)

diff --git a/VERSION b/VERSION
index 7d7a070243..c412fc2d77 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-23.10.0
+23.11.0-edge
diff --git a/changelog.txt b/changelog.txt
index 57aae56f06..5ce78b9124 100644
--- a/changelog.txt
+++ b/changelog.txt
@@ -18,7 +18,7 @@ NEXTFLOW CHANGE-LOG
 - Add support for Fusion when using Singularity OCI mode (#4508) [4f3aa631]
 - Add support for K8s schedulerName pod spec (#4485) [ci fast] [dfc7b7c8]
 - Add support for Singularity OCI mode (#4440) [f5362a7b]
-- Allow the use of error build-in function in onComplete handler (#4458) [ci fast] [35a4424b]
+- Allow the use of error built-in function in onComplete handler (#4458) [ci fast] [35a4424b]
 - Fix Bug in JsonSplitter ordering [ci fast] [8ec14dd2]
 - Fix Bypass Google Batch Price query if task cpus and memory are defined (#4521) [7f8f20d3]
 - Fix Checkout remote tag if checkout remote branch fails (#4247) [b8907ccb]
diff --git a/docs/conf.py b/docs/conf.py
index 7a9f214174..80b1ac70b2 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -64,9 +64,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '23.10'
+version = '23.11'
 # The full version, including alpha/beta/rc tags.
-release = '23.10.0'
+release = '23.11.0-edge'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
diff --git a/modules/nextflow/src/main/resources/META-INF/plugins-info.txt b/modules/nextflow/src/main/resources/META-INF/plugins-info.txt
index 4f2d453db3..74e02769f1 100644
--- a/modules/nextflow/src/main/resources/META-INF/plugins-info.txt
+++ b/modules/nextflow/src/main/resources/META-INF/plugins-info.txt
@@ -1,9 +1,9 @@
-nf-amazon@2.1.4
-nf-azure@1.3.2
-nf-cloudcache@0.3.0
-nf-codecommit@0.1.5
-nf-console@1.0.6
-nf-ga4gh@1.1.0
-nf-google@1.8.3
-nf-tower@1.6.3
-nf-wave@1.0.0
\ No newline at end of file
+nf-amazon@2.2.0
+nf-azure@1.4.0
+nf-cloudcache@0.3.1
+nf-codecommit@0.1.6
+nf-console@1.0.7
+nf-ga4gh@1.1.1
+nf-google@1.9.0
+nf-tower@1.7.0
+nf-wave@1.1.0
\ No newline at end of file
diff --git a/modules/nf-commons/src/main/nextflow/Const.groovy b/modules/nf-commons/src/main/nextflow/Const.groovy
index 6ad8318823..6f39ccd143 100644
--- a/modules/nf-commons/src/main/nextflow/Const.groovy
+++ b/modules/nf-commons/src/main/nextflow/Const.groovy
@@ -52,17 +52,17 @@ class Const {
     /**
      * The application version
      */
-    static public final String APP_VER = "23.10.0"
+    static public final String APP_VER = "23.11.0-edge"
 
     /**
      * The app build time as linux/unix timestamp
      */
-    static public final long APP_TIMESTAMP = 1697382483238
+    static public final long APP_TIMESTAMP = 1700857448507
 
     /**
      * The app build number
      */
-    static public final int APP_BUILDNUM = 5890
+    static public final int APP_BUILDNUM = 5891
 
     /**
      * The app build time string relative to UTC timezone
diff --git a/nextflow b/nextflow
index fdbdedccd3..7906c2aa67 100755
--- a/nextflow
+++ b/nextflow
@@ -15,7 +15,7 @@
 #  limitations under the License.
 
 [[ "$NXF_DEBUG" == 'x' ]] && set -x
-NXF_VER=${NXF_VER:-'23.10.0'}
+NXF_VER=${NXF_VER:-'23.11.0-edge'}
 NXF_ORG=${NXF_ORG:-'nextflow-io'}
 NXF_HOME=${NXF_HOME:-$HOME/.nextflow}
 NXF_PROT=${NXF_PROT:-'https'}
diff --git a/nextflow.md5 b/nextflow.md5
index ca1fedf1bf..574adce9f0 100644
--- a/nextflow.md5
+++ b/nextflow.md5
@@ -1 +1 @@
-72d4fc9e2c3d8cf2d1232690b7ea0121
+8a4583bb84d6e8304cc0b1ff5446f21f
diff --git a/nextflow.sha1 b/nextflow.sha1
index 0e653c427c..5214121c92 100644
--- a/nextflow.sha1
+++ b/nextflow.sha1
@@ -1 +1 @@
-9ff8060a99bad698d5ad9316ea3a4acfe2ae51c1
+965e377c383f399cb01e2c109ed2edd8335671e6
diff --git a/nextflow.sha256 b/nextflow.sha256
index 9c595903d8..5fd857dc00 100644
--- a/nextflow.sha256
+++ b/nextflow.sha256
@@ -1 +1 @@
-4b7fba61ecc6d53a6850390bb435455a54ae4d0c3108199f88b16b49e555afdd
+ddb037f134a8289215fa41b45f85e678e4bd45b8da2a3379caf326a99dfbbeeb

From 5a3a0fa2cc6236ff94e427cf02dfee5609bcf3bc Mon Sep 17 00:00:00 2001
From: Dr Marco Claudio De La Pierre <marco.delapierre@gmail.com>
Date: Mon, 27 Nov 2023 17:30:27 +0800
Subject: [PATCH 294/350] [ci fast] update config doc for Singularity OCI mode
 (#4544)

Signed-off-by: Dr Marco Claudio De La Pierre <marco.delapierre@gmail.com>
---
 docs/config.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/config.md b/docs/config.md
index 2848954d5f..e4dd9cffa9 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -1400,7 +1400,7 @@ The following settings are available:
 `singularity.oci`
 : :::{versionadded} 23.11.0-edge
   :::
-: Enable OCI-mode the allows the use of native OCI-compatible containers with Singularity. See [Singularity documentation](https://docs.sylabs.io/guides/4.0/user-guide/oci_runtime.html#oci-mode) for more details and requirements (default: `false`).
+: Enable OCI-mode, that allows running native OCI-compatible containers with Singularity using `crun` or `runc` as low-level runtime. See `--oci` flag in the [Singularity documentation](https://docs.sylabs.io/guides/4.0/user-guide/oci_runtime.html#oci-mode) for more details and requirements (default: `false`).
 
 
 `singularity.pullTimeout`

From 0e009ef75b2fea6547a345ea0c3b9f7edfc6a3d0 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Fri, 1 Dec 2023 18:28:44 -0500
Subject: [PATCH 295/350] Remove deprecated Wave observer [ci fast]

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../io/seqera/wave/plugin/WaveFactory.groovy  |  5 +-
 .../io/seqera/wave/plugin/WaveObserver.groovy | 85 -------------------
 .../wave/plugin/WaveObserverTest.groovy       | 47 ----------
 3 files changed, 1 insertion(+), 136 deletions(-)
 delete mode 100644 plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveObserver.groovy
 delete mode 100644 plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveObserverTest.groovy

diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveFactory.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveFactory.groovy
index 48ae1b974e..29f1699b9b 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveFactory.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveFactory.groovy
@@ -56,9 +56,6 @@ class WaveFactory implements TraceObserverFactory {
             }
         }
 
-        final observer = new WaveObserver(session)
-        return wave.enabled && observer.reportOpts().enabled()
-                ? List.<TraceObserver>of(observer)
-                : List.<TraceObserver>of()
+        return List.<TraceObserver>of()
     }
 }
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveObserver.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveObserver.groovy
deleted file mode 100644
index 7e8a3e6e1d..0000000000
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveObserver.groovy
+++ /dev/null
@@ -1,85 +0,0 @@
-/*
- * Copyright 2013-2023, Seqera Labs
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package io.seqera.wave.plugin
-
-import java.util.concurrent.ConcurrentHashMap
-
-import groovy.transform.CompileStatic
-import groovy.util.logging.Slf4j
-import io.seqera.wave.plugin.config.ReportOpts
-import nextflow.Session
-import nextflow.file.FileHelper
-import nextflow.processor.TaskHandler
-import nextflow.trace.TraceObserver
-import nextflow.trace.TraceRecord
-/**
- *
- * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
- */
-@Slf4j
-@CompileStatic
-@Deprecated
-class WaveObserver implements TraceObserver {
-
-    private WaveClient client
-
-    private ConcurrentHashMap<String,String> containers = new ConcurrentHashMap<>()
-
-    WaveObserver(Session session) {
-        this.client = new WaveClient(session)
-    }
-
-    @Override
-    void onFlowCreate(Session session) {
-        log.warn "Wave report feature has been deprecated in favour of the new 'nextflow inspect' command"
-    }
-
-    protected void apply(TaskHandler handler) {
-        final process = handler.task.getProcessor().getName()
-        containers.computeIfAbsent(process, (String it) -> handler.task.getContainer())
-    }
-
-    void onProcessComplete(TaskHandler handler, TraceRecord trace){
-        apply(handler)
-    }
-
-    void onProcessCached(TaskHandler handler, TraceRecord trace){
-        apply(handler)
-    }
-
-    @Override
-    void onFlowComplete() {
-        final result = renderContainersConfig(containers)
-        // save the report file
-        FileHelper
-                .asPath(reportOpts().file())
-                .text = result.toString()
-    }
-
-    protected String renderContainersConfig(Map<String,String> containers) {
-        final result = new StringBuilder()
-        for( Map.Entry<String,String> entry : containers ) {
-            result.append("process { withName: '${entry.key}' { container='$entry.value' }}\n")
-        }
-        return result.toString()
-    }
-
-    ReportOpts reportOpts() {
-        client.config().reportOpts()
-    }
-}
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveObserverTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveObserverTest.groovy
deleted file mode 100644
index 69be66d69e..0000000000
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveObserverTest.groovy
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * Copyright 2013-2023, Seqera Labs
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package io.seqera.wave.plugin
-
-import nextflow.Session
-import spock.lang.Specification
-
-/**
- *
- * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
- */
-class WaveObserverTest extends Specification {
-
-    def 'should render containers config' () {
-        given:
-        def sess = Mock(Session) {getConfig() >> [:] }
-        def observer = new WaveObserver(sess)
-        and:
-        Map<String,String> containers = [:]
-        containers.foo = 'quay.io/ubuntu:latest'
-        containers.bar = 'quay.io/alpine:latest'
-
-        when:
-        def result = observer.renderContainersConfig(containers)
-        then:
-        result == '''\
-            process { withName: 'foo' { container='quay.io/ubuntu:latest' }}
-            process { withName: 'bar' { container='quay.io/alpine:latest' }}
-            '''.stripIndent(true)
-    }
-
-}

From c9993dabf89a05137aed9878bcdb6a468a526529 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Fri, 1 Dec 2023 18:58:50 -0500
Subject: [PATCH 296/350] Fix typo [ci skip]

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
index ac66878d64..8f3edf8b06 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
@@ -412,7 +412,7 @@ class CmdRun extends CmdBase implements HubOptions {
         // -- script can still override the DSL version
         final scriptDsl = NextflowMeta.checkDslMode(scriptText)
         if( scriptDsl ) {
-            log.debug("Applied DSL=$scriptDsl from script declararion")
+            log.debug("Applied DSL=$scriptDsl from script declaration")
             return scriptDsl
         }
         else if( dsl ) {

From 687e2e967bf32dcadd1a6dc5950f2e1b2ee309a4 Mon Sep 17 00:00:00 2001
From: Jordi Deu-Pons <jordi@jordeu.net>
Date: Sat, 2 Dec 2023 14:57:01 +0100
Subject: [PATCH 297/350] Fix Fusion tags documentation (#4551)

Signed-off-by: Jordi Deu-Pons <jordi@jordeu.net>
---
 docs/fusion.md | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/docs/fusion.md b/docs/fusion.md
index 2479e097e3..04a07e7928 100644
--- a/docs/fusion.md
+++ b/docs/fusion.md
@@ -212,8 +212,6 @@ The following configuration options are available:
   executor which requires the use the [k8s-fuse-plugin](https://github.com/nextflow-io/k8s-fuse-plugin) to be installed
   in the target cluster (default: `true`).
 
-`fusion.tagsEnabled`
-: Enable/disable the tagging of files created in the underlying object storage via the Fusion client (default: `true`).
-
-`fusion.tagsPattern`
-: The pattern that determines how tags are applied to files created via the Fusion client (default: `[.command.*|.exitcode|.fusion.*](nextflow.io/metadata=true),[*](nextflow.io/temporary=true)`)
+`fusion.tags`
+: The pattern that determines how tags are applied to files created via the Fusion client. To disable tags
+  set it to `false`. (default: `[.command.*|.exitcode|.fusion.*](nextflow.io/metadata=true),[*](nextflow.io/temporary=true)`)

From da93e2a28a066408b5f592e0972cfd8f79beb7f4 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 2 Dec 2023 09:11:18 -0500
Subject: [PATCH 298/350] Docs Rename Amazon to AWS

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/amazons3.md | 12 ++++++------
 docs/aws.md      |  4 ++--
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/docs/amazons3.md b/docs/amazons3.md
index bfcabb23c9..41bcb407fa 100644
--- a/docs/amazons3.md
+++ b/docs/amazons3.md
@@ -1,8 +1,8 @@
 (amazons3-page)=
 
-# Amazon S3 storage
+# AWS S3 storage
 
-Nextflow includes support for Amazon S3 storage. Files stored in an S3 bucket can be accessed transparently in your pipeline script like any other file in the local file system.
+Nextflow includes support for AWS S3 storage. Files stored in an S3 bucket can be accessed transparently in your pipeline script like any other file in the local file system.
 
 ## S3 path
 
@@ -24,10 +24,10 @@ See the {ref}`script-file-io` section to learn more about available file operati
 
 ## Security credentials
 
-Amazon access credentials can be provided in two ways:
+AWS access credentials can be provided in two ways:
 
 1. Using AWS access and secret keys in your pipeline configuration.
-2. Using IAM roles to grant access to S3 storage on Amazon EC2 instances.
+2. Using IAM roles to grant access to S3 storage on AWS EC2 instances.
 
 ### AWS access and secret keys
 
@@ -52,13 +52,13 @@ If the access credentials are not found in the above file, Nextflow looks for AW
 
 More information regarding [AWS Security Credentials](http://docs.aws.amazon.com/general/latest/gr/aws-security-credentials.html) are available in the AWS documentation.
 
-### IAM roles with Amazon EC2 instances
+### IAM roles with AWS EC2 instances
 
 When running your pipeline in an EC2 instance, IAM roles can be used to grant access to AWS resources.
 
 In this scenario, you only need to launch the EC2 instance with an IAM role which includes the `AmazonS3FullAccess` policy. Nextflow will detect and automatically acquire the permission to access S3 storage, without any further configuration.
 
-Learn more about [Using IAM Roles to Delegate Permissions to Applications that Run on Amazon EC2](http://docs.aws.amazon.com/IAM/latest/UserGuide/roles-usingrole-ec2instance.html) in the Amazon documentation.
+Learn more about [Using IAM Roles to Delegate Permissions to Applications that Run on AWS EC2](http://docs.aws.amazon.com/IAM/latest/UserGuide/roles-usingrole-ec2instance.html) in the AWS documentation.
 
 ## China regions
 
diff --git a/docs/aws.md b/docs/aws.md
index d9179c186c..96de486c0b 100644
--- a/docs/aws.md
+++ b/docs/aws.md
@@ -1,6 +1,6 @@
 (aws-page)=
 
-# Amazon Web Services
+# AWS Cloud
 
 ## AWS security credentials
 
@@ -132,7 +132,7 @@ See the [bucket policy documentation](https://docs.aws.amazon.com/config/latest/
 
 ## AWS Batch
 
-[AWS Batch](https://aws.amazon.com/batch/) is a managed computing service that allows the execution of containerised workloads in the Amazon cloud infrastructure. It dynamically provisions the optimal quantity and type of compute resources (e.g., CPU or memory optimized compute resources) based on the volume and specific resource requirements of the jobs submitted.
+[AWS Batch](https://aws.amazon.com/batch/) is a managed computing service that allows the execution of containerised workloads in the AWS cloud infrastructure. It dynamically provisions the optimal quantity and type of compute resources (e.g., CPU or memory optimized compute resources) based on the volume and specific resource requirements of the jobs submitted.
 
 Nextflow provides built-in support for AWS Batch, allowing the seamless deployment of Nextflow pipelines in the cloud, in which tasks are offloaded as Batch jobs.
 

From 47cf335bd79b9d95dc414647e96f3ce9892a8261 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 2 Dec 2023 10:41:16 -0500
Subject: [PATCH 299/350] Add experimental support for Fargate compute type for
 AWS Batch  (#3474)

This commit adds experimental support for the execution of Nextflow pipelines
using AWS Batch API and AWS Fargate compute platform type.

To enable this feature the following setting should be added to the classic nextflow
configuration for AWS Batch

```
aws.batch.platformType = 'fargate'
aws.batch.jobRole = '<your job role arn>'
aws.batch.executionRole = '<your execution role arn>'
```

Moreover, this feature uses the s5cmd command line to stage and unstage
data from S3 work directly.

The `s5cmd` is automatically provisioned in the pipeline containers via Wave
containerisation service, which is required to be enabled to use this feature.


Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/aws.md                                   |  29 +++
 docs/config.md                                |  12 +-
 docs/executor.md                              |   2 +
 plugins/nf-amazon/build.gradle                |  18 +-
 .../cloud/aws/batch/AwsBatchExecutor.groovy   |   2 +-
 .../aws/batch/AwsBatchTaskHandler.groovy      | 124 +++++++++---
 .../cloud/aws/batch/AwsOptions.groovy         |  13 ++
 .../cloud/aws/config/AwsBatchConfig.groovy    |  29 ++-
 .../nextflow/cloud/aws/util/S3BashLib.groovy  |  57 +++++-
 .../aws/batch/AwsBatchTaskHandlerTest.groovy  | 178 ++++++++++++++++--
 .../cloud/aws/batch/AwsOptionsTest.groovy     |  21 +++
 .../aws/config/AwsBatchConfigTest.groovy      |  27 +++
 .../cloud/aws/util/S3BashLibTest.groovy       |  76 ++++++++
 .../io/seqera/wave/plugin/WaveClient.groovy   |  20 ++
 .../io/seqera/wave/plugin/WaveFactory.groovy  |  27 ++-
 .../seqera/wave/plugin/WaveClientTest.groovy  |  19 ++
 .../seqera/wave/plugin/WaveFactoryTest.groovy |  16 ++
 validation/awsbatch.sh                        |   7 +
 validation/awsfargate.config                  |  14 ++
 19 files changed, 631 insertions(+), 60 deletions(-)
 create mode 100644 validation/awsfargate.config

diff --git a/docs/aws.md b/docs/aws.md
index 96de486c0b..acd6bbd01b 100644
--- a/docs/aws.md
+++ b/docs/aws.md
@@ -496,6 +496,35 @@ There are multiple reasons why this can happen. They are mainly related to the C
 
 This [AWS page](https://aws.amazon.com/premiumsupport/knowledge-center/batch-job-stuck-runnable-status/) provides several resolutions and tips to investigate and work around the issue.
 
+## AWS Fargate
+
+:::{versionadded} 23.12.0-edge
+:::
+
+Nextflow provides experimental support for the execution of [AWS Batch jobs with Fargate resources](https://docs.aws.amazon.com/batch/latest/userguide/fargate.html).
+
+AWS Fargate is a technology that you can use with AWS Batch to run containers without having to manage servers or  EC2 instances.
+With AWS Fargate, you no longer have to provision, configure, or scale clusters of virtual machines to run containers.
+
+To enable the use of AWS Fargate in your pipeline use the following settings in your `nextflow.config` file:
+
+```groovy
+process.executor = 'awsbatch'
+process.queue = '<AWS BATCH QUEUE>'
+aws.region = '<AWS REGION>'
+aws.batch.platformType = 'fargate'
+aws.batch.jobRole = 'JOB ROLE ARN'
+aws.batch.executionRole = 'EXECUTION ROLE ARN'
+wave.enabled = true
+```
+
+See the AWS documentation for details how to create the required AWS Batch queue for Fargate, the Batch Job Role
+and the Batch Execution Role.
+
+:::{note}
+This feature requires the use {ref}`Wave <wave-page>` container provisioning service.
+:::
+
 ## Advanced configuration
 
 Read the {ref}`AWS configuration<config-aws>` section to learn more about advanced configuration options.
diff --git a/docs/config.md b/docs/config.md
index e4dd9cffa9..01e879bd5a 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -169,8 +169,13 @@ The following settings are available:
 `aws.batch.delayBetweenAttempts`
 : Delay between download attempts from S3 (default: `10 sec`).
 
+`aws.batch.executionRole`
+: :::{versionadded} 23.12.0-edge
+  :::
+: The AWS Batch Execution Role ARN that needs to be used to execute the Batch Job. This is mandatory when using AWS Fargate platform type. See [AWS documentation](https://docs.aws.amazon.com/batch/latest/userguide/execution-IAM-role.html) for more details.
+
 `aws.batch.jobRole`
-: The AWS Job Role ARN that needs to be used to execute the Batch Job.
+: The AWS Batch Job Role ARN that needs to be used to execute the Batch Job.
 
 `aws.batch.logsGroup`
 : :::{versionadded} 22.09.0-edge
@@ -188,6 +193,11 @@ The following settings are available:
 `aws.batch.maxTransferAttempts`
 : Max number of downloads attempts from S3 (default: `1`).
 
+`aws.batch.platformType`
+: :::{versionadded} 23.12.0-edge
+  :::
+: Allow specifying the compute platform type used by AWS Batch, that can be either `ec2` or `fargate`. See AWS documentation to learn more about [AWS Fargate platform type](https://docs.aws.amazon.com/batch/latest/userguide/fargate.html) for AWS Batch.
+
 `aws.batch.retryMode`
 : The retry mode configuration setting, to accommodate rate-limiting on [AWS services](https://docs.aws.amazon.com/cli/latest/userguide/cli-configure-retries.html) (default: `standard`, other options: `legacy`, `adaptive`); this handling is delegated to AWS. To have Nextflow handle retries instead, use `built-in`.
 
diff --git a/docs/executor.md b/docs/executor.md
index 0f50eff6ae..08aba7bc2d 100644
--- a/docs/executor.md
+++ b/docs/executor.md
@@ -23,9 +23,11 @@ The pipeline can be launched either in a local computer, or an EC2 instance. EC2
 Resource requests and other job characteristics can be controlled via the following process directives:
 
 - {ref}`process-accelerator`
+- {ref}`process-arch` (only when using Fargate platform type for AWS Batch)
 - {ref}`process-container`
 - {ref}`process-containerOptions`
 - {ref}`process-cpus`
+- {ref}`process-disk` (only when using Fargate platform type for AWS Batch)
 - {ref}`process-memory`
 - {ref}`process-queue`
 - {ref}`process-resourcelabels`
diff --git a/plugins/nf-amazon/build.gradle b/plugins/nf-amazon/build.gradle
index 93a07e40be..51ae9d7b27 100644
--- a/plugins/nf-amazon/build.gradle
+++ b/plugins/nf-amazon/build.gradle
@@ -38,15 +38,15 @@ dependencies {
     compileOnly 'org.pf4j:pf4j:3.10.0'
 
     api ('javax.xml.bind:jaxb-api:2.4.0-b180830.0359')
-    api ('com.amazonaws:aws-java-sdk-s3:1.12.429')
-    api ('com.amazonaws:aws-java-sdk-ec2:1.12.429')
-    api ('com.amazonaws:aws-java-sdk-batch:1.12.429')
-    api ('com.amazonaws:aws-java-sdk-iam:1.12.429')
-    api ('com.amazonaws:aws-java-sdk-ecs:1.12.429')
-    api ('com.amazonaws:aws-java-sdk-logs:1.12.429')
-    api ('com.amazonaws:aws-java-sdk-codecommit:1.12.429')
-    api ('com.amazonaws:aws-java-sdk-sts:1.12.429')
-    api ('com.amazonaws:aws-java-sdk-ses:1.12.429')
+    api ('com.amazonaws:aws-java-sdk-s3:1.12.604')
+    api ('com.amazonaws:aws-java-sdk-ec2:1.12.604')
+    api ('com.amazonaws:aws-java-sdk-batch:1.12.604')
+    api ('com.amazonaws:aws-java-sdk-iam:1.12.604')
+    api ('com.amazonaws:aws-java-sdk-ecs:1.12.604')
+    api ('com.amazonaws:aws-java-sdk-logs:1.12.604')
+    api ('com.amazonaws:aws-java-sdk-codecommit:1.12.604')
+    api ('com.amazonaws:aws-java-sdk-sts:1.12.604')
+    api ('com.amazonaws:aws-java-sdk-ses:1.12.604')
     api ('software.amazon.awssdk:sso:2.20.89')
     api ('software.amazon.awssdk:ssooidc:2.20.89')
 
diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsBatchExecutor.groovy b/plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsBatchExecutor.groovy
index ed04eefefa..70b67f496d 100644
--- a/plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsBatchExecutor.groovy
+++ b/plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsBatchExecutor.groovy
@@ -151,7 +151,7 @@ class AwsBatchExecutor extends Executor implements ExtensionPoint {
         helper = new AwsBatchHelper(client, driver)
         // create the options object
         awsOptions = new AwsOptions(this)
-        log.debug "[AWS BATCH] Executor options=$awsOptions"
+        log.debug "[AWS BATCH] Executor ${awsOptions.fargateMode ? '(FARGATE mode) ' : ''}options=$awsOptions"
     }
 
     /**
diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsBatchTaskHandler.groovy b/plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsBatchTaskHandler.groovy
index b200246ad7..08c175dd9d 100644
--- a/plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsBatchTaskHandler.groovy
+++ b/plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsBatchTaskHandler.groovy
@@ -24,6 +24,7 @@ import java.time.Instant
 
 import com.amazonaws.services.batch.AWSBatch
 import com.amazonaws.services.batch.model.AWSBatchException
+import com.amazonaws.services.batch.model.AssignPublicIp
 import com.amazonaws.services.batch.model.AttemptContainerDetail
 import com.amazonaws.services.batch.model.ClientException
 import com.amazonaws.services.batch.model.ContainerOverrides
@@ -32,6 +33,7 @@ import com.amazonaws.services.batch.model.DescribeJobDefinitionsRequest
 import com.amazonaws.services.batch.model.DescribeJobDefinitionsResult
 import com.amazonaws.services.batch.model.DescribeJobsRequest
 import com.amazonaws.services.batch.model.DescribeJobsResult
+import com.amazonaws.services.batch.model.EphemeralStorage
 import com.amazonaws.services.batch.model.EvaluateOnExit
 import com.amazonaws.services.batch.model.Host
 import com.amazonaws.services.batch.model.JobDefinition
@@ -41,15 +43,18 @@ import com.amazonaws.services.batch.model.JobTimeout
 import com.amazonaws.services.batch.model.KeyValuePair
 import com.amazonaws.services.batch.model.LogConfiguration
 import com.amazonaws.services.batch.model.MountPoint
+import com.amazonaws.services.batch.model.NetworkConfiguration
 import com.amazonaws.services.batch.model.RegisterJobDefinitionRequest
 import com.amazonaws.services.batch.model.RegisterJobDefinitionResult
 import com.amazonaws.services.batch.model.ResourceRequirement
 import com.amazonaws.services.batch.model.ResourceType
 import com.amazonaws.services.batch.model.RetryStrategy
+import com.amazonaws.services.batch.model.RuntimePlatform
 import com.amazonaws.services.batch.model.SubmitJobRequest
 import com.amazonaws.services.batch.model.SubmitJobResult
 import com.amazonaws.services.batch.model.TerminateJobRequest
 import com.amazonaws.services.batch.model.Volume
+import groovy.transform.Canonical
 import groovy.transform.CompileStatic
 import groovy.transform.Memoized
 import groovy.util.logging.Slf4j
@@ -67,6 +72,7 @@ import nextflow.processor.TaskRun
 import nextflow.processor.TaskStatus
 import nextflow.trace.TraceRecord
 import nextflow.util.CacheHelper
+import nextflow.util.MemoryUnit
 /**
  * Implements a task handler for AWS Batch jobs
  */
@@ -204,6 +210,9 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
         if( !result ) {
             log.debug "[AWS BATCH] cannot find running status for job=$jobId"
         }
+        else {
+            log.trace "[AWS BATCH] Job id=$jobId details=$result"
+        }
 
         return result
     }
@@ -255,7 +264,7 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
             task.exitStatus = job.container.exitCode ?: readExitFile()
             // finalize the task
             task.stdout = outputFile
-            if( job?.status == 'FAILED' ) {
+            if( job?.status == 'FAILED' || task.exitStatus==Integer.MAX_VALUE ) {
                 task.error = new ProcessUnrecoverableException(errReason(job))
                 task.stderr = executor.getJobOutputStream(jobId) ?: errorFile
             }
@@ -369,7 +378,7 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
             return container.substring(17)
         }
 
-        resolveJobDefinition(container)
+        return resolveJobDefinition(task)
     }
 
     /**
@@ -379,14 +388,14 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
      * @return The Batch Job Definition name associated with the specified container
      */
     @CompileStatic
-    protected String resolveJobDefinition(String container) {
+    protected String resolveJobDefinition(TaskRun task) {
         final int DEFAULT_BACK_OFF_BASE = 3
         final int DEFAULT_BACK_OFF_DELAY = 250
         final int MAX_ATTEMPTS = 5
         int attempt=0
         while( true ) {
             try {
-                return resolveJobDefinition0(container)
+                return resolveJobDefinition0(task)
             }
             catch (ClientException e) {
                 if( e.statusCode != 404 || attempt++ > MAX_ATTEMPTS)
@@ -399,8 +408,10 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
         }
     }
 
-    protected String resolveJobDefinition0(String container) {
-        final req = makeJobDefRequest(container)
+    @CompileStatic
+    protected String resolveJobDefinition0(TaskRun task) {
+        final req = makeJobDefRequest(task)
+        final container = task.getContainer()
         final token = req.getParameters().get('nf-token')
         final jobKey = "$container:$token".toString()
         if( jobDefinitions.containsKey(jobKey) )
@@ -436,9 +447,9 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
      * @param image The Docker container image for which is required to create a Batch job definition
      * @return An instance of {@link com.amazonaws.services.batch.model.RegisterJobDefinitionRequest} for the specified Docker image
      */
-    protected RegisterJobDefinitionRequest makeJobDefRequest(String image) {
+    protected RegisterJobDefinitionRequest makeJobDefRequest(TaskRun task) {
         final uniq = new ArrayList()
-        final result = configJobDefRequest(image, uniq)
+        final result = configJobDefRequest(task, uniq)
 
         // create a job marker uuid
         def hash = computeUniqueToken(uniq)
@@ -462,7 +473,8 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
      * @return
      *      An instance of {@link com.amazonaws.services.batch.model.RegisterJobDefinitionRequest} for the specified Docker image
      */
-    protected RegisterJobDefinitionRequest configJobDefRequest(String image, List hashingTokens) {
+    protected RegisterJobDefinitionRequest configJobDefRequest(TaskRun task, List hashingTokens) {
+        final image = task.getContainer()
         final name = normalizeJobDefinitionName(image)
         final opts = getAwsOptions()
 
@@ -470,23 +482,27 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
         result.setJobDefinitionName(name)
         result.setType(JobDefinitionType.Container)
 
-        // create the container opts based on task config 
+        // create the container opts based on task config
         final containerOpts = task.getConfig().getContainerOptionsMap()
         final container = createContainerProperties(containerOpts)
 
         // container definition
-        final _1_cpus = new ResourceRequirement().withType(ResourceType.VCPU).withValue('1')
-        final _1_gb = new ResourceRequirement().withType(ResourceType.MEMORY).withValue('1024')
+        // https://docs.aws.amazon.com/AmazonECS/latest/developerguide/task-cpu-memory-error.html
+        final reqCpus = new ResourceRequirement().withType(ResourceType.VCPU).withValue('1')
+        final reqMem = new ResourceRequirement().withType(ResourceType.MEMORY).withValue( opts.fargateMode ? '2048' : '1024')
         container
                 .withImage(image)
                 .withCommand('true')
                 // note the actual command, memory and cpus are overridden when the job is executed
-                .withResourceRequirements( _1_cpus, _1_gb )
+                .withResourceRequirements( reqCpus, reqMem )
 
         final jobRole = opts.getJobRole()
         if( jobRole )
             container.setJobRoleArn(jobRole)
 
+        if( opts.executionRole )
+            container.setExecutionRoleArn(opts.executionRole)
+        
         final logsGroup = opts.getLogsGroup()
         if( logsGroup )
             container.setLogConfiguration(getLogConfiguration(logsGroup, opts.getRegion()))
@@ -496,7 +512,7 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
 
         final mountsMap = new LinkedHashMap( 10)
         final awscli = opts.cliPath
-        if( awscli ) {
+        if( awscli && !opts.fargateMode ) {
             def path = Paths.get(awscli).parent.parent.toString()
             mountsMap.put('aws-cli', "$path:$path:ro")
         }
@@ -510,6 +526,18 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
         if( mountsMap )
             addVolumeMountsToContainer(mountsMap, container)
 
+        // Fargate specific settings
+        if( opts.isFargateMode() ) {
+            result.setPlatformCapabilities(List.of('FARGATE'))
+            container.withNetworkConfiguration( new NetworkConfiguration().withAssignPublicIp(AssignPublicIp.ENABLED) )
+            // use at least 50 GB as disk local storage
+            final diskGb = task.config.getDisk()?.toGiga()?.toInteger() ?: 50
+            container.withEphemeralStorage( new EphemeralStorage().withSizeInGiB(diskGb) )
+            // check for arm64 cpu architecture
+            if( task.config.getArchitecture()?.arch == 'arm64' )
+                container.withRuntimePlatform(new RuntimePlatform().withCpuArchitecture('ARM64'))
+        }
+
         // finally set the container options
         result.setContainerProperties(container)
 
@@ -625,13 +653,26 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
     protected List<String> classicSubmitCli() {
         // the cmd list to launch it
         final opts = getAwsOptions()
+        final cmd = opts.s5cmdPath ? s5Cmd(opts) : s3Cmd(opts)
+        return ['bash','-o','pipefail','-c', cmd.toString()]
+    }
+
+    protected String s3Cmd(AwsOptions opts) {
         final cli = opts.getAwsCli()
         final debug = opts.debug ? ' --debug' : ''
         final sse = opts.storageEncryption ? " --sse $opts.storageEncryption" : ''
         final kms = opts.storageKmsKeyId ? " --sse-kms-key-id $opts.storageKmsKeyId" : ''
         final aws = "$cli s3 cp --only-show-errors${sse}${kms}${debug}"
         final cmd = "trap \"{ ret=\$?; $aws ${TaskRun.CMD_LOG} s3:/${getLogFile()}||true; exit \$ret; }\" EXIT; $aws s3:/${getWrapperFile()} - | bash 2>&1 | tee ${TaskRun.CMD_LOG}"
-        return ['bash','-o','pipefail','-c', cmd.toString()]
+        return cmd
+    }
+
+    protected String s5Cmd(AwsOptions opts) {
+        final cli = opts.getS5cmdPath()
+        final sse = opts.storageEncryption ? " --sse $opts.storageEncryption" : ''
+        final kms = opts.storageKmsKeyId ? " --sse-kms-key-id $opts.storageKmsKeyId" : ''
+        final cmd = "trap \"{ ret=\$?; $cli cp${sse}${kms} ${TaskRun.CMD_LOG} s3:/${getLogFile()}||true; exit \$ret; }\" EXIT; $cli cat s3:/${getWrapperFile()} | bash 2>&1 | tee ${TaskRun.CMD_LOG}"
+        return cmd
     }
 
     protected List<String> getSubmitCommand() {
@@ -656,6 +697,7 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
         /*
          * create the request object
          */
+        final opts = getAwsOptions()
         final labels = task.config.getResourceLabels()
         final result = new SubmitJobRequest()
         result.setJobName(normalizeJobName(task.name))
@@ -666,9 +708,9 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
             result.setPropagateTags(true)
         }
         // set the share identifier
-        if( this.getAwsOptions().shareIdentifier ) {
-            result.setShareIdentifier(this.getAwsOptions().shareIdentifier)
-            result.setSchedulingPriorityOverride(this.getAwsOptions().schedulingPriority)
+        if( opts.shareIdentifier ) {
+            result.setShareIdentifier(opts.shareIdentifier)
+            result.setSchedulingPriorityOverride(opts.schedulingPriority)
         }
 
         /*
@@ -700,18 +742,20 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
 
         // set the actual command
         final resources = new ArrayList<ResourceRequirement>(5)
-        def container = new ContainerOverrides()
+        final container = new ContainerOverrides()
         container.command = getSubmitCommand()
         // set the task memory
-        if( task.config.getMemory() ) {
-            final mega = (int)task.config.getMemory().toMega()
+        final cpus = task.config.getCpus()
+        final mem = task.config.getMemory()
+        if( mem ) {
+            final mega = opts.fargateMode ? normaliseFargateMem(cpus, mem) : mem.toMega()
             if( mega >= 4 )
                 resources << new ResourceRequirement().withType(ResourceType.MEMORY).withValue(mega.toString())
             else
                 log.warn "Ignoring task ${task.lazyName()} memory directive: ${task.config.getMemory()} -- AWS Batch job memory request cannot be lower than 4 MB"
         }
         // set the task cpus
-        if( task.config.getCpus() > 1 )
+        if( cpus > 1 )
             resources << new ResourceRequirement().withType(ResourceType.VCPU).withValue(task.config.getCpus().toString())
 
         final accelerator = task.config.getAccelerator()
@@ -838,5 +882,41 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
         }
     }
 
+    @Canonical
+    static class MemSlot {
+        int min
+        int max
+        int step
+
+        static ofGiga(int min, int max, int step) {
+            new MemSlot(min *1024, max *1024, step *1024)
+        }
+    }
+
+    static final Map<Integer, MemSlot> FARGATE_MEM = [1 : MemSlot.ofGiga(2,8,1),
+                                                      2 : MemSlot.ofGiga(4, 16, 1),
+                                                      4 : MemSlot.ofGiga(8, 30, 1),
+                                                      8 : MemSlot.ofGiga(16,60, 4),
+                                                      16: MemSlot.ofGiga(32, 120, 8) ]
+
+    protected long normaliseFargateMem(Integer cpus, MemoryUnit mem) {
+        final mega = mem.toMega()
+        final slot = FARGATE_MEM.get(cpus)
+        if( slot==null )
+            new ProcessUnrecoverableException("Requirement of $cpus CPUs is not allowed by Fargate -- Check process with name '${task.lazyName()}'")
+        if( mega <=slot.min ) {
+            log.warn "Process '${task.lazyName()}' memory requirement of ${mem} is below the minimum allowed by Fargate of ${MemoryUnit.of(mega+'MB')}"
+            return slot.min
+        }
+        if( mega >slot.max ) {
+            log.warn "Process '${task.lazyName()}' memory requirement of ${mem} is above the maximum allowed by Fargate of ${MemoryUnit.of(mega+'MB')}"
+            return slot.max
+        }
+        return ceilDiv(mega, slot.step) * slot.step
+    }
+
+    static private long ceilDiv(long x, long y){
+        return -Math.floorDiv(-x,y);
+    }
 }
 
diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsOptions.groovy b/plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsOptions.groovy
index 525da3b8c5..0e9028f433 100644
--- a/plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsOptions.groovy
+++ b/plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsOptions.groovy
@@ -144,4 +144,17 @@ class AwsOptions implements CloudTransferOptions {
         awsConfig.batchConfig.addVolume(path)
         return this
     }
+
+    boolean isFargateMode() {
+        return awsConfig.batchConfig.fargateMode
+    }
+
+    String getS5cmdPath() {
+        return awsConfig.batchConfig.s5cmdPath
+    }
+
+    String getExecutionRole() {
+        return awsConfig.batchConfig.getExecutionRole()
+    }
+
 }
diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/config/AwsBatchConfig.groovy b/plugins/nf-amazon/src/main/nextflow/cloud/aws/config/AwsBatchConfig.groovy
index 6a9552904f..94d5ccad55 100644
--- a/plugins/nf-amazon/src/main/nextflow/cloud/aws/config/AwsBatchConfig.groovy
+++ b/plugins/nf-amazon/src/main/nextflow/cloud/aws/config/AwsBatchConfig.groovy
@@ -79,13 +79,30 @@ class AwsBatchConfig implements CloudTransferOptions {
      */
     private Integer schedulingPriority
 
+    /**
+     * The container execution role
+     */
+    String executionRole
+
+    /**
+     * The path for the `s5cmd` tool as an alternative to `aws s3` CLI to upload/download files
+     */
+    String s5cmdPath
+
+    /**
+     * Whenever it should use Fargate API
+     */
+    boolean fargateMode
+
     /*
      * only for testing
      */
     protected AwsBatchConfig() {}
 
     AwsBatchConfig(Map opts) {
-        cliPath = parseCliPath(opts.cliPath as String)
+        fargateMode = opts.platformType == 'fargate'
+        cliPath = !fargateMode ? parseCliPath(opts.cliPath as String) : null
+        s5cmdPath = fargateMode ? parses5cmdPath(opts.cliPath as String) : null
         maxParallelTransfers = opts.maxParallelTransfers as Integer ?: MAX_TRANSFER
         maxTransferAttempts = opts.maxTransferAttempts as Integer ?: defaultMaxTransferAttempts()
         delayBetweenAttempts = opts.delayBetweenAttempts as Duration ?: DEFAULT_DELAY_BETWEEN_ATTEMPTS
@@ -96,6 +113,7 @@ class AwsBatchConfig implements CloudTransferOptions {
         retryMode = opts.retryMode ?: 'standard'
         shareIdentifier = opts.shareIdentifier
         schedulingPriority = opts.schedulingPriority as Integer ?: 0
+        executionRole = opts.executionRole
         if( retryMode == 'built-in' )
             retryMode = null // this force falling back on NF built-in retry mode instead of delegating to AWS CLI tool
         if( retryMode && retryMode !in AwsOptions.VALID_RETRY_MODES )
@@ -161,6 +179,8 @@ class AwsBatchConfig implements CloudTransferOptions {
     private String parseCliPath(String value) {
         if( !value )
             return null
+        if( value.tokenize('/ ').contains('s5cmd') )
+            return null
         if( !value.startsWith('/') )
             throw new ProcessUnrecoverableException("Not a valid aws-cli tools path: $value -- it must be an absolute path")
         if( !value.endsWith('/bin/aws'))
@@ -195,4 +215,11 @@ class AwsBatchConfig implements CloudTransferOptions {
         return this
     }
 
+    protected String parses5cmdPath(String value) {
+        if( !value )
+            return 's5cmd'
+        if( value.tokenize('/ ').contains('s5cmd') )
+            return value
+        return 's5cmd'
+    }
 }
diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/util/S3BashLib.groovy b/plugins/nf-amazon/src/main/nextflow/cloud/aws/util/S3BashLib.groovy
index d203650d50..e203ce0411 100644
--- a/plugins/nf-amazon/src/main/nextflow/cloud/aws/util/S3BashLib.groovy
+++ b/plugins/nf-amazon/src/main/nextflow/cloud/aws/util/S3BashLib.groovy
@@ -17,6 +17,7 @@
 package nextflow.cloud.aws.util
 
 import com.amazonaws.services.s3.model.CannedAccessControlList
+import groovy.transform.CompileStatic
 import nextflow.Global
 import nextflow.Session
 import nextflow.cloud.aws.batch.AwsOptions
@@ -25,6 +26,7 @@ import nextflow.executor.BashFunLib
 /**
  * AWS S3 helper class
  */
+@CompileStatic
 class S3BashLib extends BashFunLib<S3BashLib> {
 
     private String storageClass = 'STANDARD'
@@ -33,6 +35,7 @@ class S3BashLib extends BashFunLib<S3BashLib> {
     private String debug = ''
     private String cli = 'aws'
     private String retryMode
+    private String s5cmdPath
     private String acl = ''
 
     S3BashLib withCliPath(String cliPath) {
@@ -70,6 +73,11 @@ class S3BashLib extends BashFunLib<S3BashLib> {
         return this
     }
 
+    S3BashLib withS5cmdPath(String value) {
+        this.s5cmdPath = value
+        return this
+    }
+    
     S3BashLib withAcl(CannedAccessControlList value) {
         if( value )
             this.acl = "--acl $value "
@@ -86,6 +94,11 @@ class S3BashLib extends BashFunLib<S3BashLib> {
         """.stripIndent().rightTrim()
     }
 
+    /**
+     * Implement S3 upload/download helper using `aws s3` CLI tool
+     *
+     * @return The Bash script implementing the S3 helper functions
+     */
     protected String s3Lib() {
         """
         # aws helper
@@ -115,8 +128,49 @@ class S3BashLib extends BashFunLib<S3BashLib> {
         """.stripIndent(true)
     }
 
+    /**
+     * Implement S3 upload/download helper using s3cmd CLI tool
+     * https://github.com/peak/s5cmd
+     *
+     * @return The Bash script implementing the S3 helper functions
+     */
+    protected String s5cmdLib() {
+        final cli = s5cmdPath
+        """
+        # aws helper for s5cmd
+        nxf_s3_upload() {
+            local name=\$1
+            local s3path=\$2
+            if [[ "\$name" == - ]]; then
+              local tmp=\$(nxf_mktemp)
+              cp /dev/stdin \$tmp/\$name
+              $cli cp ${acl}${storageEncryption}${storageKmsKeyId}--storage-class $storageClass \$tmp/\$name "\$s3path"
+            elif [[ -d "\$name" ]]; then
+              $cli cp ${acl}${storageEncryption}${storageKmsKeyId}--storage-class $storageClass "\$name/" "\$s3path/\$name/"
+            else
+              $cli cp ${acl}${storageEncryption}${storageKmsKeyId}--storage-class $storageClass "\$name" "\$s3path/\$name"
+            fi
+        }
+        
+        nxf_s3_download() {
+            local source=\$1
+            local target=\$2
+            local file_name=\$(basename \$1)
+            local is_dir=\$($cli ls \$source | grep -F "DIR \${file_name}/" -c)
+            if [[ \$is_dir == 1 ]]; then
+                $cli cp "\$source/*" "\$target"
+            else 
+                $cli cp "\$source" "\$target"
+            fi
+        }
+        """.stripIndent()
+    }
+
+    @Override
     String render() {
-        super.render() + retryEnv() + s3Lib()
+        return s5cmdPath
+                ? super.render() + s5cmdLib()
+                : super.render() + retryEnv() + s3Lib()
     }
 
     static private S3BashLib lib0(AwsOptions opts, boolean includeCore) {
@@ -131,6 +185,7 @@ class S3BashLib extends BashFunLib<S3BashLib> {
                 .withStorageKmsKeyId( opts.storageKmsKeyId )
                 .withRetryMode( opts.retryMode )
                 .withDebug( opts.debug )
+                .withS5cmdPath( opts.s5cmdPath )
                 .withAcl( opts.s3Acl )
     }
 
diff --git a/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchTaskHandlerTest.groovy b/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchTaskHandlerTest.groovy
index 2f55259b93..c9568016d4 100644
--- a/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchTaskHandlerTest.groovy
+++ b/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchTaskHandlerTest.groovy
@@ -35,14 +35,16 @@ import com.amazonaws.services.batch.model.RetryStrategy
 import com.amazonaws.services.batch.model.SubmitJobRequest
 import com.amazonaws.services.batch.model.SubmitJobResult
 import com.amazonaws.services.batch.model.TerminateJobRequest
-import nextflow.cloud.aws.config.AwsConfig
 import nextflow.Const
+import nextflow.Session
+import nextflow.cloud.aws.config.AwsConfig
 import nextflow.cloud.aws.util.S3PathFactory
 import nextflow.cloud.types.CloudMachineInfo
 import nextflow.cloud.types.PriceModel
 import nextflow.exception.ProcessUnrecoverableException
 import nextflow.executor.Executor
 import nextflow.fusion.FusionScriptLauncher
+import nextflow.processor.Architecture
 import nextflow.processor.BatchContext
 import nextflow.processor.TaskConfig
 import nextflow.processor.TaskProcessor
@@ -50,7 +52,9 @@ import nextflow.processor.TaskRun
 import nextflow.processor.TaskStatus
 import nextflow.script.BaseScript
 import nextflow.script.ProcessConfig
+import nextflow.util.MemoryUnit
 import spock.lang.Specification
+import spock.lang.Unroll
 /**
  *
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
@@ -333,7 +337,7 @@ class AwsBatchTaskHandlerTest extends Specification {
         result = handler.getJobDefinition(task)
         then:
         1 * task.getContainer() >> IMAGE
-        1 * handler.resolveJobDefinition(IMAGE) >> JOB_NAME
+        1 * handler.resolveJobDefinition(task) >> JOB_NAME
         result == JOB_NAME
 
     }
@@ -405,6 +409,7 @@ class AwsBatchTaskHandlerTest extends Specification {
         def JOB_NAME = 'nf-foo-bar-1-0'
         def JOB_ID= '123'
         def handler = Spy(AwsBatchTaskHandler)
+        def task = Mock(TaskRun) { getContainer()>>IMAGE }
 
         def req = Mock(RegisterJobDefinitionRequest) {
             getJobDefinitionName() >> JOB_NAME
@@ -412,17 +417,17 @@ class AwsBatchTaskHandlerTest extends Specification {
         }
 
         when:
-        handler.resolveJobDefinition(IMAGE)
+        handler.resolveJobDefinition(task)
         then:
-        1 * handler.makeJobDefRequest(IMAGE) >> req
+        1 * handler.makeJobDefRequest(task) >> req
         1 * handler.findJobDef(JOB_NAME, JOB_ID) >> null
         1 * handler.createJobDef(req) >> null
 
         when:
-        handler.resolveJobDefinition(IMAGE)
+        handler.resolveJobDefinition(task)
         then:
         // second time are not invoked for the same image
-        1 * handler.makeJobDefRequest(IMAGE) >> req
+        1 * handler.makeJobDefRequest(task) >> req
         0 * handler.findJobDef(JOB_NAME, JOB_ID) >> null
         0 * handler.createJobDef(req) >> null
 
@@ -550,14 +555,15 @@ class AwsBatchTaskHandlerTest extends Specification {
         given:
         def IMAGE = 'foo/bar:1.0'
         def JOB_NAME = 'nf-foo-bar-1-0'
+        def task = Mock(TaskRun) { getContainer()>>IMAGE; getConfig() >> Mock(TaskConfig) }
         def handler = Spy(AwsBatchTaskHandler) {
-            getTask() >> Mock(TaskRun) { getConfig() >> Mock(TaskConfig)  }
+            getTask() >> task
             fusionEnabled() >> false
         }
         handler.@executor = Mock(AwsBatchExecutor)
 
         when:
-        def result = handler.makeJobDefRequest(IMAGE)
+        def result = handler.makeJobDefRequest(task)
         then:
         1 * handler.normalizeJobDefinitionName(IMAGE) >> JOB_NAME
         1 * handler.getAwsOptions() >> new AwsOptions()
@@ -569,7 +575,7 @@ class AwsBatchTaskHandlerTest extends Specification {
         !result.containerProperties.privileged
         
         when:
-        result = handler.makeJobDefRequest(IMAGE)
+        result = handler.makeJobDefRequest(task)
         then:
         1 * handler.normalizeJobDefinitionName(IMAGE) >> JOB_NAME
         1 * handler.getAwsOptions() >> new AwsOptions(awsConfig: new AwsConfig(batch: [cliPath: '/home/conda/bin/aws', logsGroup: '/aws/batch'], region: 'us-east-1'))
@@ -587,18 +593,77 @@ class AwsBatchTaskHandlerTest extends Specification {
 
     }
 
+    def 'should create a fargate job definition' () {
+        given:
+        def ARM64 = new Architecture('linux/arm64')
+        def _100GB = MemoryUnit.of('100GB')
+        def IMAGE = 'foo/bar:1.0'
+        def JOB_NAME = 'nf-foo-bar-1-0'
+        def task = Mock(TaskRun) { getContainer()>>IMAGE }
+        def handler = Spy(AwsBatchTaskHandler) {
+            getTask() >> task
+            fusionEnabled() >> false
+        }
+        handler.@executor = Mock(AwsBatchExecutor)
+        and:
+        def session =  Mock(Session) {
+            getConfig() >> [aws:[batch:[platformType:'fargate', jobRole: 'the-job-role', executionRole: 'the-exec-role']]]
+        }
+        def opts = new AwsOptions(session)
+
+        when:
+        def result = handler.makeJobDefRequest(task)
+        then:
+        task.getConfig() >> Mock(TaskConfig)
+        and:
+        1 * handler.normalizeJobDefinitionName(IMAGE) >> JOB_NAME
+        1 * handler.getAwsOptions() >> opts
+        and:
+        result.jobDefinitionName == JOB_NAME
+        result.type == 'container'
+        result.getPlatformCapabilities() == ['FARGATE']
+        result.containerProperties.getJobRoleArn() == 'the-job-role'
+        result.containerProperties.getExecutionRoleArn() == 'the-exec-role'
+        result.containerProperties.getResourceRequirements().find { it.type=='VCPU'}.getValue() == '1'
+        result.containerProperties.getResourceRequirements().find { it.type=='MEMORY'}.getValue() == '2048'
+        and:
+        result.containerProperties.getEphemeralStorage().sizeInGiB == 50
+        result.containerProperties.getRuntimePlatform() == null
+
+        when:
+        result = handler.makeJobDefRequest(task)
+        then:
+        task.getConfig() >> Mock(TaskConfig) { getDisk()>>_100GB ; getArchitecture()>>ARM64 }
+        and:
+        1 * handler.normalizeJobDefinitionName(IMAGE) >> JOB_NAME
+        1 * handler.getAwsOptions() >> opts
+        and:
+        result.jobDefinitionName == JOB_NAME
+        result.type == 'container'
+        result.getPlatformCapabilities() == ['FARGATE']
+        result.containerProperties.getJobRoleArn() == 'the-job-role'
+        result.containerProperties.getExecutionRoleArn() == 'the-exec-role'
+        result.containerProperties.getResourceRequirements().find { it.type=='VCPU'}.getValue() == '1'
+        result.containerProperties.getResourceRequirements().find { it.type=='MEMORY'}.getValue() == '2048'
+        and:
+        result.containerProperties.getEphemeralStorage().sizeInGiB == 100
+        result.containerProperties.getRuntimePlatform().getCpuArchitecture() == 'ARM64'
+    }
+
     def 'should create a job definition request object for fusion' () {
         given:
         def IMAGE = 'foo/bar:1.0'
         def JOB_NAME = 'nf-foo-bar-1-0'
+        def task = Mock(TaskRun) { getContainer()>>IMAGE; getConfig()>>Mock(TaskConfig)  }
+        and:
         AwsBatchTaskHandler handler = Spy(AwsBatchTaskHandler) {
-            getTask() >> Mock(TaskRun) { getConfig() >> Mock(TaskConfig)  }
+            getTask() >> task
             fusionEnabled() >> true
         }
         handler.@executor = Mock(AwsBatchExecutor) {}
 
         when:
-        def result = handler.makeJobDefRequest(IMAGE)
+        def result = handler.makeJobDefRequest(task)
         then:
         1 * handler.normalizeJobDefinitionName(IMAGE) >> JOB_NAME
         1 * handler.getAwsOptions() >> new AwsOptions()
@@ -615,14 +680,16 @@ class AwsBatchTaskHandlerTest extends Specification {
         def JOB_NAME = 'nf-foo-bar-1-0'
         def executor = Mock(AwsBatchExecutor)
         def opts = Mock(AwsOptions)
+        def task = Mock(TaskRun) { getContainer()>>IMAGE; getConfig()>>Mock(TaskConfig)  }
+        and:
         def handler = Spy(AwsBatchTaskHandler) {
-            getTask() >> Mock(TaskRun) { getConfig() >> Mock(TaskConfig)  }
+            getTask() >> task
             fusionEnabled() >> false
         }
         handler.@executor = executor
 
         when:
-        def result = handler.makeJobDefRequest(IMAGE)
+        def result = handler.makeJobDefRequest(task)
         then:
         1 * handler.normalizeJobDefinitionName(IMAGE) >> JOB_NAME
         1 * handler.getAwsOptions() >> opts
@@ -647,14 +714,16 @@ class AwsBatchTaskHandlerTest extends Specification {
         def JOB_NAME = 'nf-foo-bar-1-0'
         def opts = Mock(AwsOptions)
         def executor = Mock(AwsBatchExecutor)
+        def task = Mock(TaskRun) { getContainer()>>IMAGE; getConfig()>>Mock(TaskConfig) }
+        and:
         def handler = Spy(AwsBatchTaskHandler) {
-            getTask() >> Mock(TaskRun) { getConfig() >> Mock(TaskConfig) }
+            getTask() >> task
             fusionEnabled() >> false
         }
         handler.@executor = executor
 
         when:
-        def result = handler.makeJobDefRequest(IMAGE)
+        def result = handler.makeJobDefRequest(task)
         then:
         1 * handler.normalizeJobDefinitionName(IMAGE) >> JOB_NAME
         1 * handler.getAwsOptions() >> opts
@@ -672,14 +741,16 @@ class AwsBatchTaskHandlerTest extends Specification {
         def opts = Mock(AwsOptions)
         def taskConfig = new TaskConfig(containerOptions: '--privileged --user foo')
         def executor = Mock(AwsBatchExecutor)
+        def task = Mock(TaskRun) { getContainer()>>IMAGE; getConfig()>>taskConfig }
+        and:
         def handler = Spy(AwsBatchTaskHandler) {
-            getTask() >> Mock(TaskRun) { getConfig() >> taskConfig }
+            getTask() >> task
             fusionEnabled() >> false
         }
         handler.@executor = executor
 
         when:
-        def result = handler.makeJobDefRequest(IMAGE)
+        def result = handler.makeJobDefRequest(task)
         then:
         1 * handler.normalizeJobDefinitionName(IMAGE) >> JOB_NAME
         1 * handler.getAwsOptions() >> opts
@@ -872,6 +943,36 @@ class AwsBatchTaskHandlerTest extends Specification {
 
     }
 
+    def 'should render submit command with s5cmd' () {
+        given:
+        def handler = Spy(AwsBatchTaskHandler) {
+            fusionEnabled() >> false
+        }
+
+        when:
+        def result =  handler.getSubmitCommand()
+        then:
+        handler.getAwsOptions() >> Mock(AwsOptions)  { getS5cmdPath() >> 's5cmd' }
+        handler.getLogFile() >> Paths.get('/work/log')
+        handler.getWrapperFile() >> Paths.get('/work/run')
+        then:
+        result.join(' ') == 'bash -o pipefail -c trap "{ ret=$?; s5cmd cp .command.log s3://work/log||true; exit $ret; }" EXIT; s5cmd cat s3://work/run | bash 2>&1 | tee .command.log'
+
+        when:
+        result =  handler.getSubmitCommand()
+        then:
+        handler.getAwsOptions() >> Mock(AwsOptions)  {
+            getS5cmdPath() >> 's5cmd --debug'
+            getStorageEncryption() >> 'aws:kms'
+            getStorageKmsKeyId() >> 'kms-key-123'
+        }
+        handler.getLogFile() >> Paths.get('/work/log')
+        handler.getWrapperFile() >> Paths.get('/work/run')
+        then:
+        result.join(' ') == 'bash -o pipefail -c trap "{ ret=$?; s5cmd --debug cp --sse aws:kms --sse-kms-key-id kms-key-123 .command.log s3://work/log||true; exit $ret; }" EXIT; s5cmd --debug cat s3://work/run | bash 2>&1 | tee .command.log'
+
+    }
+
     def 'should create an aws submit request with labels'() {
 
         given:
@@ -922,4 +1023,47 @@ class AwsBatchTaskHandlerTest extends Specification {
         result.join(' ') == '/usr/bin/fusion bash /fusion/s3/my-bucket/work/dir/.command.run'
     }
 
+    @Unroll
+    def 'should normalise fargate mem' () {
+        given:
+        def handler = Spy(AwsBatchTaskHandler) {
+            getTask() >> Mock(TaskRun) { lazyName() >> 'foo' }
+        }
+        expect:
+        handler.normaliseFargateMem(CPUS, MemoryUnit.of( MEM * 1024L*1024L )) == EXPECTED
+
+        where:
+        CPUS    | MEM       | EXPECTED
+        1       | 100       | 2048
+        1       | 1000      | 2048
+        1       | 2000      | 2048
+        1       | 3000      | 3072
+        1       | 7000      | 7168
+        1       | 8000      | 8192
+        1       | 10000     | 8192
+        and:
+        2       | 1000      | 4096
+        2       | 6000      | 6144
+        2       | 16000     | 16384
+        2       | 20000     | 16384
+        and:
+        4       | 1000      | 8192
+        4       | 8000      | 8192
+        4       | 16000     | 16384
+        4       | 30000     | 30720
+        4       | 40000     | 30720
+        and:
+        8       | 1000      | 16384
+        8       | 10000     | 16384
+        8       | 20000     | 20480
+        8       | 30000     | 32768
+        8       | 100000    | 61440
+        and:
+        16      | 1000      | 32768
+        16      | 30000     | 32768
+        16      | 40000     | 40960
+        16      | 60000     | 65536
+        16      | 100000    | 106496
+        16      | 200000    | 122880
+    }
 }
diff --git a/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsOptionsTest.groovy b/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsOptionsTest.groovy
index de843c1700..8d7a743ebe 100644
--- a/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsOptionsTest.groovy
+++ b/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsOptionsTest.groovy
@@ -222,6 +222,27 @@ class AwsOptionsTest extends Specification {
         opts.volumes == ['/some/dir', '/other/dir']
     }
 
+    @Unroll
+    def 'should get aws cli path' () {
+        def session = new Session(CONFIG)
+
+        when:
+        def opts = new AwsOptions(session)
+        then:
+        opts.cliPath == S3CLI_PATH
+        opts.s5cmdPath == S5CMD_PATH
+
+        where:
+        CONFIG                                                                      | S3CLI_PATH        | S5CMD_PATH
+        [aws:[batch:[:]]]                                                           | null              | null
+        [aws:[batch:[cliPath: '/usr/bin/aws']]]                                     | '/usr/bin/aws'    | null
+        [aws:[batch:[cliPath: 's5cmd']]]                                            | null              | null
+        [aws:[batch:[platformType: 'fargate', cliPath: 's5cmd']]]                   | null              | 's5cmd'
+        [aws:[batch:[platformType: 'fargate', cliPath: '/some/path/s5cmd']]]        | null              | '/some/path/s5cmd'
+        [aws:[batch:[platformType: 'fargate', cliPath: 's5cmd --foo']]]             | null              | 's5cmd --foo'
+        [aws:[batch:[platformType: 'fargate', cliPath: '/some/path/s5cmd --foo']]]  | null              | '/some/path/s5cmd --foo'
+    }
+    
     def 'should parse s3 acl' ( ) {
         when:
         def opts = new AwsOptions(new Session(aws:[client:[s3Acl: 'PublicRead']]))
diff --git a/plugins/nf-amazon/src/test/nextflow/cloud/aws/config/AwsBatchConfigTest.groovy b/plugins/nf-amazon/src/test/nextflow/cloud/aws/config/AwsBatchConfigTest.groovy
index a86fc5b3b5..18a1c6b71a 100644
--- a/plugins/nf-amazon/src/test/nextflow/cloud/aws/config/AwsBatchConfigTest.groovy
+++ b/plugins/nf-amazon/src/test/nextflow/cloud/aws/config/AwsBatchConfigTest.groovy
@@ -40,8 +40,11 @@ class AwsBatchConfigTest extends Specification {
         !batch.cliPath
         !batch.volumes
         !batch.jobRole
+        !batch.executionRole
         !batch.logsGroup
         !batch.shareIdentifier
+        !batch.isFargateMode()
+        !batch.s5cmdPath
         batch.schedulingPriority == 0
     }
 
@@ -55,6 +58,7 @@ class AwsBatchConfigTest extends Specification {
                 maxSpotAttempts: 4,
                 volumes: '/some/path:/mnt/path,/other/path',
                 jobRole: 'xyz',
+                executionRole: 'some:exec:role',
                 logsGroup: 'group-name-123',
                 retryMode: 'legacy',
                 shareIdentifier: 'id-x1',
@@ -71,10 +75,12 @@ class AwsBatchConfigTest extends Specification {
         batch.maxSpotAttempts == 4
         batch.volumes == ['/some/path:/mnt/path', '/other/path']
         batch.jobRole == 'xyz'
+        batch.executionRole == 'some:exec:role'
         batch.logsGroup == 'group-name-123'
         batch.retryMode == 'legacy'
         batch.shareIdentifier == 'id-x1'
         batch.schedulingPriority == 100
+        !batch.isFargateMode()
     }
 
     def 'should parse volumes list' () {
@@ -112,4 +118,25 @@ class AwsBatchConfigTest extends Specification {
         opts.volumes == ['/some/dir', '/other/dir']
     }
 
+    def 'should parse cli path' () {
+        given:
+        def opts = new AwsBatchConfig(OPTS)
+
+        expect:
+        opts.cliPath == S3_CLI_PATH
+        opts.s5cmdPath == S5_CLI_PATH
+        opts.isFargateMode() == FARGATE
+        
+        where:
+        OPTS                                                        | S3_CLI_PATH       | S5_CLI_PATH       | FARGATE
+        [:]                                                         | null              | null              | false
+        [cliPath: "/opt/bin/aws"]                                   | '/opt/bin/aws'    | null              | false
+        [cliPath: "/s5cmd"]                                         | null              | null              | false
+        [cliPath: "/opt/s5cmd --foo"]                               | null              | null              | false
+        and:
+        [platformType: 'fargate', cliPath: "/opt/bin/aws"]          | null              | 's5cmd'           | true
+        [platformType: 'fargate', cliPath: "/opt/s5cmd"]            | null              | '/opt/s5cmd'      | true
+        [platformType: 'fargate', cliPath: "/opt/s5cmd --foo"]      | null              | '/opt/s5cmd --foo'| true
+    }
+
 }
diff --git a/plugins/nf-amazon/src/test/nextflow/cloud/aws/util/S3BashLibTest.groovy b/plugins/nf-amazon/src/test/nextflow/cloud/aws/util/S3BashLibTest.groovy
index f3c3608a18..524dda71ee 100644
--- a/plugins/nf-amazon/src/test/nextflow/cloud/aws/util/S3BashLibTest.groovy
+++ b/plugins/nf-amazon/src/test/nextflow/cloud/aws/util/S3BashLibTest.groovy
@@ -742,4 +742,80 @@ class S3BashLibTest extends Specification {
             }
             '''.stripIndent(true)
     }
+
+    def 'should create s5cmd script' () {
+        given:
+        Global.session = Mock(Session) {
+            getConfig() >> [aws:[batch:[platformType: 'fargate', cliPath: 's5cmd']]]
+        }
+
+        expect:
+        S3BashLib.script()  == '''
+            # aws helper for s5cmd
+            nxf_s3_upload() {
+                local name=$1
+                local s3path=$2
+                if [[ "$name" == - ]]; then
+                  local tmp=$(nxf_mktemp)
+                  cp /dev/stdin $tmp/$name
+                  s5cmd cp --storage-class STANDARD $tmp/$name "$s3path"
+                elif [[ -d "$name" ]]; then
+                  s5cmd cp --storage-class STANDARD "$name/" "$s3path/$name/"
+                else
+                  s5cmd cp --storage-class STANDARD "$name" "$s3path/$name"
+                fi
+            }
+            
+            nxf_s3_download() {
+                local source=$1
+                local target=$2
+                local file_name=$(basename $1)
+                local is_dir=$(s5cmd ls $source | grep -F "DIR ${file_name}/" -c)
+                if [[ $is_dir == 1 ]]; then
+                    s5cmd cp "$source/*" "$target"
+                else 
+                    s5cmd cp "$source" "$target"
+                fi
+            }
+            '''.stripIndent(true)
+    }
+
+    def 'should create s5cmd script with acl' () {
+        given:
+        Global.session = Mock(Session) {
+            getConfig() >> [aws:[batch:[platformType: 'fargate', cliPath: 's5cmd'], client:[ s3Acl: 'PublicRead']]]
+        }
+
+        expect:
+        S3BashLib.script()  == '''
+            # aws helper for s5cmd
+            nxf_s3_upload() {
+                local name=$1
+                local s3path=$2
+                if [[ "$name" == - ]]; then
+                  local tmp=$(nxf_mktemp)
+                  cp /dev/stdin $tmp/$name
+                  s5cmd cp --acl public-read --storage-class STANDARD $tmp/$name "$s3path"
+                elif [[ -d "$name" ]]; then
+                  s5cmd cp --acl public-read --storage-class STANDARD "$name/" "$s3path/$name/"
+                else
+                  s5cmd cp --acl public-read --storage-class STANDARD "$name" "$s3path/$name"
+                fi
+            }
+            
+            nxf_s3_download() {
+                local source=$1
+                local target=$2
+                local file_name=$(basename $1)
+                local is_dir=$(s5cmd ls $source | grep -F "DIR ${file_name}/" -c)
+                if [[ $is_dir == 1 ]]; then
+                    s5cmd cp "$source/*" "$target"
+                else 
+                    s5cmd cp "$source" "$target"
+                fi
+            }
+            '''.stripIndent(true)
+    }
+    
+
 }
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
index 0559e8c411..367ac8d4be 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
@@ -69,6 +69,9 @@ import org.slf4j.LoggerFactory
 @CompileStatic
 class WaveClient {
 
+    final static public String DEFAULT_S5CMD_AMD64_URL = 'https://nf-xpack.seqera.io/s5cmd/linux_amd64_2.0.0.json'
+    final static public String DEFAULT_S5CMD_ARM64_URL = 'https://nf-xpack.seqera.io/s5cmd/linux_arm64_2.0.0.json'
+
     private static Logger log = LoggerFactory.getLogger(WaveClient)
 
     final static private String[] REQUEST_HEADERS =  new String[]{
@@ -112,11 +115,17 @@ class WaveClient {
 
     final private String waveRegistry
 
+    final private boolean awsFargate
+
+    final private URL s5cmdConfigUrl
+
     WaveClient(Session session) {
         this.session = session
         this.config = new WaveConfig(session.config.wave as Map ?: Collections.emptyMap(), SysEnv.get())
         this.fusion = new FusionConfig(session.config.fusion as Map ?: Collections.emptyMap(), SysEnv.get())
         this.tower = new TowerConfig(session.config.tower as Map ?: Collections.emptyMap(), SysEnv.get())
+        this.awsFargate = WaveFactory.isAwsBatchFargateMode(session.config)
+        this.s5cmdConfigUrl = session.config.navigate('wave.s5cmdConfigUrl') as URL
         this.endpoint = config.endpoint()
         this.condaChannels = session.getCondaConfig()?.getChannels() ?: DEFAULT_CONDA_CHANNELS
         log.debug "Wave config: $config"
@@ -280,12 +289,23 @@ class WaveClient {
                 : new URL(FusionConfig.DEFAULT_FUSION_AMD64_URL)
     }
 
+    protected URL defaultS5cmdUrl(String platform) {
+        final isArm = platform.tokenize('/')?.contains('arm64')
+        return isArm
+            ? new URL(DEFAULT_S5CMD_ARM64_URL)
+            : new URL(DEFAULT_S5CMD_AMD64_URL)
+    }
+
     ContainerConfig resolveContainerConfig(String platform = DEFAULT_DOCKER_PLATFORM) {
         final urls = new ArrayList<URL>(config.containerConfigUrl())
         if( fusion.enabled() ) {
             final fusionUrl = fusion.containerConfigUrl() ?: defaultFusionUrl(platform)
             urls.add(fusionUrl)
         }
+        if( awsFargate ) {
+            final s5cmdUrl = s5cmdConfigUrl ?: defaultS5cmdUrl(platform)
+            urls.add(s5cmdUrl)
+        }
         if( !urls )
             return null
         def result = new ContainerConfig()
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveFactory.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveFactory.groovy
index 29f1699b9b..6e16e301fb 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveFactory.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveFactory.groovy
@@ -46,16 +46,27 @@ class WaveFactory implements TraceObserverFactory {
         }
         
         if( fusion.enabled ) {
-            if( !wave.enabled ) {
-                throw new AbortOperationException("Fusion feature requires enabling Wave service")
-            }
-            else {
-                log.debug "Detected Fusion enabled -- Enabling bundle project resources -- Disabling upload of remote bin directory"
-                wave.bundleProjectResources = true
-                session.disableRemoteBinDir = true
-            }
+            checkWaveRequirement(session, wave, 'Fusion')
+        }
+        if( isAwsBatchFargateMode(config) ) {
+            checkWaveRequirement(session, wave, 'Fargate')
         }
 
         return List.<TraceObserver>of()
     }
+
+    protected void checkWaveRequirement(Session session, Map wave, String feature) {
+        if( !wave.enabled ) {
+            throw new AbortOperationException("$feature feature requires enabling Wave service")
+        }
+        else {
+            log.debug "Detected $feature enabled -- Enabling bundle project resources -- Disabling upload of remote bin directory"
+            wave.bundleProjectResources = true
+            session.disableRemoteBinDir = true
+        }
+    }
+
+    static boolean isAwsBatchFargateMode(Map config) {
+        return 'fargate'.equalsIgnoreCase(config.navigate('aws.batch.platformType') as String)
+    }
 }
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
index c85f89ad63..a15c8cc2bb 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
@@ -1205,6 +1205,25 @@ class WaveClientTest extends Specification {
         'linux/arm64/v8'    | 'https://fusionfs.seqera.io/releases/v2.2-arm64.json'
     }
 
+    @Unroll
+    def 'should get s5cmd default url' () {
+        given:
+        def sess = Mock(Session) {getConfig() >> [:] }
+        and:
+        def wave = Spy(new WaveClient(sess))
+
+        expect:
+        wave.defaultS5cmdUrl(ARCH).toURI().toString() == EXPECTED
+
+        where:
+        ARCH                | EXPECTED
+        'linux/amd64'       | 'https://nf-xpack.seqera.io/s5cmd/linux_amd64_2.0.0.json'
+        'linux/x86_64'      | 'https://nf-xpack.seqera.io/s5cmd/linux_amd64_2.0.0.json'
+        'arm64'             | 'https://nf-xpack.seqera.io/s5cmd/linux_arm64_2.0.0.json'
+        'linux/arm64'       | 'https://nf-xpack.seqera.io/s5cmd/linux_arm64_2.0.0.json'
+        'linux/arm64/v8'    | 'https://nf-xpack.seqera.io/s5cmd/linux_arm64_2.0.0.json'
+    }
+
     def 'should check is local conda file' () {
         expect:
         WaveClient.isCondaLocalFile(CONTENT) == EXPECTED
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveFactoryTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveFactoryTest.groovy
index 980c9c9c9d..482c24e453 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveFactoryTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveFactoryTest.groovy
@@ -49,6 +49,22 @@ class WaveFactoryTest extends Specification {
         [wave:[enabled:true], fusion:[enabled:true]]     | [wave:[enabled:true,bundleProjectResources:true], fusion:[enabled:true]] | 1
     }
 
+    @Unroll
+    def 'should check s5cmd is enabled' () {
+        given:
+        def factory = new WaveFactory()
+
+        expect:
+        factory.isAwsBatchFargateMode(CONFIG) == EXPECTED
+        
+        where:
+        CONFIG                                  | EXPECTED
+        [:]                                     | false
+        [aws:[batch:[platformType:'foo']]]       | false
+        [aws:[batch:[platformType:'fargate']]]   | true
+        [aws:[batch:[platformType:'Fargate']]]   | true
+
+    }
     def 'should fail when wave is disabled' () {
         given:
         def CONFIG = [wave:[:], fusion:[enabled:true]]
diff --git a/validation/awsbatch.sh b/validation/awsbatch.sh
index 504e0a8b63..6b0298756b 100644
--- a/validation/awsbatch.sh
+++ b/validation/awsbatch.sh
@@ -53,3 +53,10 @@ $NXF_CMD run nextflow-io/rnaseq-nf \
     -resume
 [[ `grep -c 'Using Nextflow cache factory: nextflow.cache.CloudCacheFactory' .nextflow.log` == 1 ]] || false
 [[ `grep -c 'Cached process > ' .nextflow.log` == 4 ]] || false
+
+## run with fargate + wave
+NXF_CLOUDCACHE_PATH=s3://nextflow-ci/cache \
+$NXF_CMD run nextflow-io/rnaseq-nf \
+    -profile batch \
+    -plugins nf-cloudcache,nf-wave \
+    -c awsfargate.config
diff --git a/validation/awsfargate.config b/validation/awsfargate.config
new file mode 100644
index 0000000000..d05ba3a17e
--- /dev/null
+++ b/validation/awsfargate.config
@@ -0,0 +1,14 @@
+/*
+ * do not include plugin requirements otherwise latest
+ * published version will be downloaded instead of using local build
+ */
+
+workDir = 's3://nextflow-ci/work'
+process.executor = 'awsbatch'
+process.queue = 'nextflow-fg'
+process.container = 'quay.io/nextflow/rnaseq-nf:latest'
+aws.region = 'eu-west-1'
+aws.batch.platformType = 'fargate'
+aws.batch.jobRole = 'arn:aws:iam::195996028523:role/nf-batchjobrole'
+aws.batch.executionRole = 'arn:aws:iam::195996028523:role/nf-batchexecutionrole'
+wave.enabled = true

From f7662e6877937768da3275d3c46922ad2fa33071 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 2 Dec 2023 21:09:56 -0500
Subject: [PATCH 300/350] Replace each iterator with class for

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 modules/nextflow/src/main/groovy/nextflow/Session.groovy | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/Session.groovy b/modules/nextflow/src/main/groovy/nextflow/Session.groovy
index 668b1166ad..c23e6c8c7b 100644
--- a/modules/nextflow/src/main/groovy/nextflow/Session.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/Session.groovy
@@ -1080,11 +1080,15 @@ class Session implements ISession {
     }
 
     void notifyFlowBegin() {
-        observers.each { trace -> trace.onFlowBegin() }
+        for( TraceObserver trace : observers ) {
+            trace.onFlowBegin()
+        }
     }
 
     void notifyFlowCreate() {
-        observers.each { trace -> trace.onFlowCreate(this) }
+        for( TraceObserver trace : observers ) {
+            trace.onFlowCreate(this)
+        }
     }
 
     void notifyFilePublish(Path destination, Path source=null) {

From e9ee3b2c4e1d8a904f8e0a0a0dd9aa31990f51cd Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 2 Dec 2023 21:36:50 -0500
Subject: [PATCH 301/350] Remove unused dsl2 check

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 modules/nextflow/src/main/groovy/nextflow/Session.groovy | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/Session.groovy b/modules/nextflow/src/main/groovy/nextflow/Session.groovy
index c23e6c8c7b..c4471baaf4 100644
--- a/modules/nextflow/src/main/groovy/nextflow/Session.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/Session.groovy
@@ -489,10 +489,6 @@ class Session implements ISession {
         checkConfig()
         notifyFlowBegin()
 
-        if( !NextflowMeta.instance.isDsl2() ) {
-            return
-        }
-
         // bridge any dataflow queue into a broadcast channel
         CH.broadcast()
 

From 58590b1c9f5904b04dac8decfbed4513f9e0043e Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 2 Dec 2023 22:16:21 -0500
Subject: [PATCH 302/350] Improve GLS tests [ci fast]

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../GoogleLifeSciencesHelperTest.groovy       |  6 ++---
 .../GoogleLifeSciencesTaskHandlerTest.groovy  | 22 +++++++++----------
 2 files changed, 13 insertions(+), 15 deletions(-)

diff --git a/plugins/nf-google/src/test/nextflow/cloud/google/lifesciences/GoogleLifeSciencesHelperTest.groovy b/plugins/nf-google/src/test/nextflow/cloud/google/lifesciences/GoogleLifeSciencesHelperTest.groovy
index b66ee3d6d2..1b0eb7cbe6 100644
--- a/plugins/nf-google/src/test/nextflow/cloud/google/lifesciences/GoogleLifeSciencesHelperTest.groovy
+++ b/plugins/nf-google/src/test/nextflow/cloud/google/lifesciences/GoogleLifeSciencesHelperTest.groovy
@@ -440,10 +440,8 @@ class GoogleLifeSciencesHelperTest extends GoogleSpecification {
 
     def 'should create pipeline actions with keepalive' () {
         given:
-        def helper = Spy(GoogleLifeSciencesHelper)
-        helper.config = Mock(GoogleLifeSciencesConfig) {
-            getKeepAliveOnFailure() >> true
-        }
+        def config = new GoogleLifeSciencesConfig(keepAliveOnFailure: true)
+        def helper = Spy(new GoogleLifeSciencesHelper(config: config))
         and:
         def req = Mock(GoogleLifeSciencesSubmitRequest)
 
diff --git a/plugins/nf-google/src/test/nextflow/cloud/google/lifesciences/GoogleLifeSciencesTaskHandlerTest.groovy b/plugins/nf-google/src/test/nextflow/cloud/google/lifesciences/GoogleLifeSciencesTaskHandlerTest.groovy
index 72d3b8eedf..73ea282be4 100644
--- a/plugins/nf-google/src/test/nextflow/cloud/google/lifesciences/GoogleLifeSciencesTaskHandlerTest.groovy
+++ b/plugins/nf-google/src/test/nextflow/cloud/google/lifesciences/GoogleLifeSciencesTaskHandlerTest.groovy
@@ -198,19 +198,19 @@ class GoogleLifeSciencesTaskHandlerTest extends GoogleSpecification {
         given:
         def workDir = mockGsPath('gs://my-bucket/work/dir')
         and:
+        def config = new GoogleLifeSciencesConfig(
+            project: 'my-project',
+            zones: ['my-zone'],
+            regions: ['my-region'],
+            preemptible: true,
+            bootDiskSize: MemoryUnit.of('20 GB'),
+            usePrivateAddress: true,
+            cpuPlatform: 'Intel Skylake'
+        )
+        and:
         def executor = Mock(GoogleLifeSciencesExecutor) {
             getHelper() >> Mock(GoogleLifeSciencesHelper)
-            getConfig() >> {
-                Mock(GoogleLifeSciencesConfig) {
-                    getProject() >> 'my-project'
-                    getZones() >> ['my-zone']
-                    getRegions() >> ['my-region']
-                    getPreemptible() >> true
-                    getBootDiskSize() >> MemoryUnit.of('20 GB')
-                    getUsePrivateAddress() >> true
-                    getCpuPlatform() >> 'Intel Skylake'
-                }
-            }
+            getConfig() >> config
         }
         and:
         def task = Mock(TaskRun)

From d3c2f330994ab93dd4e0932911928b3c70e09ce5 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Tue, 5 Dec 2023 10:46:33 +0000
Subject: [PATCH 303/350] Fix smoke tests [ci fast]

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../nextflow/src/test/groovy/nextflow/cli/CmdCloneTest.groovy   | 2 ++
 .../test/groovy/nextflow/scm/GiteaRepositoryProviderTest.groovy | 2 ++
 2 files changed, 4 insertions(+)

diff --git a/modules/nextflow/src/test/groovy/nextflow/cli/CmdCloneTest.groovy b/modules/nextflow/src/test/groovy/nextflow/cli/CmdCloneTest.groovy
index 5ecbcda749..a65e1cb1e6 100644
--- a/modules/nextflow/src/test/groovy/nextflow/cli/CmdCloneTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/cli/CmdCloneTest.groovy
@@ -18,6 +18,7 @@ package nextflow.cli
 import java.nio.file.Files
 
 import nextflow.plugin.Plugins
+import spock.lang.IgnoreIf
 import spock.lang.Requires
 import spock.lang.Specification
 /**
@@ -26,6 +27,7 @@ import spock.lang.Specification
  */
 class CmdCloneTest extends Specification {
 
+    @IgnoreIf({System.getenv('NXF_SMOKE')})
     @Requires({System.getenv('NXF_GITHUB_ACCESS_TOKEN')})
     def testClone() {
 
diff --git a/modules/nextflow/src/test/groovy/nextflow/scm/GiteaRepositoryProviderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/scm/GiteaRepositoryProviderTest.groovy
index f933b469d2..bdfea1d0f8 100644
--- a/modules/nextflow/src/test/groovy/nextflow/scm/GiteaRepositoryProviderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/scm/GiteaRepositoryProviderTest.groovy
@@ -16,6 +16,7 @@
 
 package nextflow.scm
 
+import spock.lang.IgnoreIf
 import spock.lang.Requires
 import spock.lang.Specification
 
@@ -76,6 +77,7 @@ class GiteaRepositoryProviderTest extends Specification {
 
     }
 
+    @IgnoreIf({System.getenv('NXF_SMOKE')})
     @Requires({System.getenv('NXF_GITEA_ACCESS_TOKEN')})
     def 'should read file content'() {
 

From 832bff241f64cc3ce9b4cdc794a58d1664c0933c Mon Sep 17 00:00:00 2001
From: Robert Syme <rob.syme@gmail.com>
Date: Sat, 9 Dec 2023 03:04:14 -0500
Subject: [PATCH 304/350] Fix Harden regular expression to used to strip
 secrets in logs (#4563) [ci fast]

Include option to strip secrets from single-quoted strings

Signed-off-by: Rob Syme <rob.syme@gmail.com>
---
 .../src/main/nextflow/util/StringUtils.groovy    |  2 +-
 .../test/nextflow/util/StringUtilsTest.groovy    | 16 +++++++++-------
 2 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/modules/nf-commons/src/main/nextflow/util/StringUtils.groovy b/modules/nf-commons/src/main/nextflow/util/StringUtils.groovy
index 73480b1a5f..8e43acbcaa 100644
--- a/modules/nf-commons/src/main/nextflow/util/StringUtils.groovy
+++ b/modules/nf-commons/src/main/nextflow/util/StringUtils.groovy
@@ -56,7 +56,7 @@ class StringUtils {
         return m.matches() ? m.group(1).toLowerCase() : null
     }
 
-    static private Pattern multilinePattern = ~/"?(password|token|secret|license)"?\s?[:=]\s?"?(\w+)"?/
+    static private Pattern multilinePattern = ~/["']?(password|token|secret|license)["']?\s?[:=]\s?["']?(\w+)["']?/
 
     static String stripSecrets(String message) {
         if (message == null) {
diff --git a/modules/nf-commons/src/test/nextflow/util/StringUtilsTest.groovy b/modules/nf-commons/src/test/nextflow/util/StringUtilsTest.groovy
index e1e7522902..7feea08f18 100644
--- a/modules/nf-commons/src/test/nextflow/util/StringUtilsTest.groovy
+++ b/modules/nf-commons/src/test/nextflow/util/StringUtilsTest.groovy
@@ -100,13 +100,15 @@ class StringUtilsTest extends Specification {
         StringUtils.stripSecrets(SECRET) == EXPECTED
 
         where:
-        SECRET                                  | EXPECTED
-        'Hi\n here is the "password" : "1234"'  | 'Hi\n here is the "password" : "********"'
-        'Hi\n here is the password : "1"'       | 'Hi\n here is the password : "********"'
-        'Hi\n here is the password : "1"'       | 'Hi\n here is the password : "********"'
-        'Hi\n "password" :"1" \n "token": "123"'| 'Hi\n "password" :"********" \n "token": "********"'
-        'Hi\n password :"1"\nsecret: "345"'     | 'Hi\n password :"********"\nsecret: "********"'
-        'secret="abc" password:"1" more text'   | 'secret="********" password:"********" more text'
+        SECRET                                          | EXPECTED
+        'Hi\n here is the "password" : "1234"'          | 'Hi\n here is the "password" : "********"'
+        'Hi\n here is the password : "1"'               | 'Hi\n here is the password : "********"'
+        'Hi\n here is the password : \'1\''             | 'Hi\n here is the password : \'********\''
+        'Hi\n "password" :"1" \n "token": "123"'        | 'Hi\n "password" :"********" \n "token": "********"'
+        'Hi\n "password" :\'1\' \n "token": "123"'      | 'Hi\n "password" :\'********\' \n "token": "********"'
+        'Hi\n \'password\' :\'1\' \n \'token\': \'123\''| 'Hi\n \'password\' :\'********\' \n \'token\': \'********\''
+        'Hi\n password :"1"\nsecret: "345"'             | 'Hi\n password :"********"\nsecret: "********"'
+        'secret="abc" password:"1" more text'           | 'secret="********" password:"********" more text'
     }
 
     @Unroll

From ccf4f59e9c6dbc189f7a570304528f4491ada6ea Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Wed, 13 Dec 2023 08:25:50 +0100
Subject: [PATCH 305/350] Fix custom notification template

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/config.md                                |  4 +-
 .../nextflow/script/WorkflowMetadata.groovy   |  8 ++--
 .../nextflow/script/WorkflowNotifier.groovy   | 12 +++---
 .../script/WorkflowNotifierTest.groovy        | 37 ++++++++++++++++++-
 4 files changed, 49 insertions(+), 12 deletions(-)

diff --git a/docs/config.md b/docs/config.md
index 01e879bd5a..20acf2a51c 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -1149,8 +1149,8 @@ Read the {ref}`sharing-page` page to learn how to publish your pipeline to GitHu
 
 The `notification` scope allows you to define the automatic sending of a notification email message when the workflow execution terminates.
 
-`notification.binding`
-: A map modelling the variables in the template file.
+`notification.attributes`
+: A map object modelling the variables that can be used in the template file.
 
 `notification.enabled`
 : Enables the sending of a notification message when the workflow execution completes.
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/WorkflowMetadata.groovy b/modules/nextflow/src/main/groovy/nextflow/script/WorkflowMetadata.groovy
index af00db5be0..745fa7e6a4 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/WorkflowMetadata.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/WorkflowMetadata.groovy
@@ -463,10 +463,10 @@ class WorkflowMetadata {
      */
     protected void safeMailNotification() {
         try {
-            def notifier = new WorkflowNotifier()
-            notifier.workflow = this
-            notifier.config = session.config
-            notifier.variables = NF.binding.variables
+            final notifier = new WorkflowNotifier(
+                workflow: this,
+                config: session.config,
+                variables: NF.binding.variables )
             notifier.sendNotification()
         }
         catch (Exception e) {
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/WorkflowNotifier.groovy b/modules/nextflow/src/main/groovy/nextflow/script/WorkflowNotifier.groovy
index 7cc351048f..13228a2b42 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/WorkflowNotifier.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/WorkflowNotifier.groovy
@@ -110,9 +110,9 @@ class WorkflowNotifier {
         List<File> templates = []
         normaliseTemplate0(notification.template, templates)
         if (templates) {
-            final binding = normaliseBindings0(notification.binding)
+            final binding = normaliseBindings0(notification.attributes)
 
-            templates.each { file ->
+            for( File file : templates ) {
                 def content = loadMailTemplate(file, binding)
                 def plain = file.extension == 'txt'
                 if (plain) {
@@ -135,7 +135,7 @@ class WorkflowNotifier {
     protected Map normaliseBindings0(binding) {
 
         if (binding == null)
-            return null
+            return Map.of()
 
         if (binding instanceof Map)
             return binding
@@ -218,8 +218,10 @@ class WorkflowNotifier {
 
     private String loadMailTemplate0(InputStream source, Map binding) {
         def map = new HashMap()
-        map.putAll(variables)
-        map.putAll(binding)
+        if( variables )
+            map.putAll(variables)
+        if( binding )
+            map.putAll(binding)
 
         def template = new GStringTemplateEngine().createTemplate(new InputStreamReader(source))
         template.make(map).toString()
diff --git a/modules/nextflow/src/test/groovy/nextflow/script/WorkflowNotifierTest.groovy b/modules/nextflow/src/test/groovy/nextflow/script/WorkflowNotifierTest.groovy
index 91bfeb0bc2..e41a4e31cf 100644
--- a/modules/nextflow/src/test/groovy/nextflow/script/WorkflowNotifierTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/script/WorkflowNotifierTest.groovy
@@ -16,6 +16,7 @@
 
 package nextflow.script
 
+import java.nio.file.Files
 import java.nio.file.Paths
 import java.time.Instant
 import java.time.OffsetDateTime
@@ -256,7 +257,7 @@ class WorkflowNotifierTest extends Specification {
         when:
         workflow.success = false
         workflow.runName = 'bar'
-        mail = notifier.createMail([to:'alpha@dot.com', from:'beta@dot.com', template: ['/some/file.txt', '/other/file.html'], binding: [one:1, two:2]])
+        mail = notifier.createMail([to:'alpha@dot.com', from:'beta@dot.com', template: ['/some/file.txt', '/other/file.html'], attributes: [one:1, two:2]])
         then:
         1 * notifier.loadMailTemplate(new File('/some/file.txt'), [one:1, two:2]) >> 'TEXT template'
         1 * notifier.loadMailTemplate(new File('/other/file.html'), [one:1, two:2]) >> 'HTML template'
@@ -268,6 +269,40 @@ class WorkflowNotifierTest extends Specification {
 
     }
 
+    def 'should create notification mail with custom template' () {
+        given:
+        def folder  = Files.createTempDirectory('test')
+        def template = folder.resolve('template.txt').toFile(); template.text = 'Hello world!'
+
+        and:
+        Mail mail
+        def workflow = new WorkflowMetadata()
+        def notifier = Spy(WorkflowNotifier)
+        notifier.@workflow = workflow
+
+        /*
+         * create success completion  *default* notification email
+         */
+        when:
+        workflow.success = true
+        workflow.runName = 'foo'
+        mail = notifier.createMail([to:'paolo@yo.com', from:'bot@nextflow.com', template: template])
+        then:
+        0 * notifier.loadDefaultTextTemplate()
+        0 * notifier.loadDefaultHtmlTemplate()
+        1 * notifier.loadMailTemplate(template, [:])
+        and:
+        mail.to == 'paolo@yo.com'
+        mail.from == 'bot@nextflow.com'
+        mail.subject == 'Workflow completion [foo] - SUCCEED'
+        mail.text == 'Hello world!'
+        !mail.body 
+        !mail.attachments
+
+        cleanup:
+        folder?.deleteDir()
+    }
+
 
     def 'should send notification email' () {
 

From 887f06f4d8e69d7fede6f3d8169e4261ddf3b9ee Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Wed, 13 Dec 2023 08:39:12 +0100
Subject: [PATCH 306/350] Load nf-amazon when AWS SES is enabled

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy b/modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy
index b4320d435e..f3982627c3 100644
--- a/modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy
+++ b/modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy
@@ -397,7 +397,7 @@ class PluginsFacade implements PluginStateListener {
         final bucketDir = config.bucketDir as String
         final executor = Bolts.navigate(config, 'process.executor')
 
-        if( executor == 'awsbatch' || workDir?.startsWith('s3://') || bucketDir?.startsWith('s3://') )
+        if( executor == 'awsbatch' || workDir?.startsWith('s3://') || bucketDir?.startsWith('s3://') || SysEnv.containsKey('NXF_ENABLE_AWS_SES') )
             plugins << defaultPlugins.getPlugin('nf-amazon')
 
         if( executor == 'google-lifesciences' || executor == 'google-batch' || workDir?.startsWith('gs://') || bucketDir?.startsWith('gs://')  )

From 552f29b0a0cf9f689cc2f0b1c3fdda3da317ff14 Mon Sep 17 00:00:00 2001
From: Jordi Deu-Pons <jordi@jordeu.net>
Date: Wed, 13 Dec 2023 11:55:42 +0100
Subject: [PATCH 307/350] Add AWS_SESSION_TOKEN to Fusion environment (#4581)

Signed-off-by: Jordi Deu-Pons <jordi@jordeu.net>
---
 .../cloud/aws/fusion/AwsFusionEnv.groovy      |  7 ++++++
 .../cloud/aws/fusion/AwsFusionEnvTest.groovy  | 24 +++++++++++++++++++
 2 files changed, 31 insertions(+)

diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/fusion/AwsFusionEnv.groovy b/plugins/nf-amazon/src/main/nextflow/cloud/aws/fusion/AwsFusionEnv.groovy
index 4c2bcb82d4..30c8584094 100644
--- a/plugins/nf-amazon/src/main/nextflow/cloud/aws/fusion/AwsFusionEnv.groovy
+++ b/plugins/nf-amazon/src/main/nextflow/cloud/aws/fusion/AwsFusionEnv.groovy
@@ -43,6 +43,9 @@ class AwsFusionEnv implements FusionEnv {
         if( creds ) {
             result.AWS_ACCESS_KEY_ID = creds[0]
             result.AWS_SECRET_ACCESS_KEY = creds[1]
+
+            if( creds.size() > 2 )
+                result.AWS_SESSION_TOKEN = creds[2]
         }
         if( endpoint )
             result.AWS_S3_ENDPOINT = endpoint
@@ -59,6 +62,10 @@ class AwsFusionEnv implements FusionEnv {
         final result = awsConfig.getCredentials()
         if( result )
             return result
+
+        if( SysEnv.get('AWS_ACCESS_KEY_ID') && SysEnv.get('AWS_SECRET_ACCESS_KEY') && SysEnv.get('AWS_SESSION_TOKEN') )
+            return List.<String>of(SysEnv.get('AWS_ACCESS_KEY_ID'), SysEnv.get('AWS_SECRET_ACCESS_KEY'), SysEnv.get('AWS_SESSION_TOKEN'))
+
         if( SysEnv.get('AWS_ACCESS_KEY_ID') && SysEnv.get('AWS_SECRET_ACCESS_KEY') )
             return List.<String>of(SysEnv.get('AWS_ACCESS_KEY_ID'), SysEnv.get('AWS_SECRET_ACCESS_KEY'))
         else
diff --git a/plugins/nf-amazon/src/test/nextflow/cloud/aws/fusion/AwsFusionEnvTest.groovy b/plugins/nf-amazon/src/test/nextflow/cloud/aws/fusion/AwsFusionEnvTest.groovy
index dfa15d661e..feba870298 100644
--- a/plugins/nf-amazon/src/test/nextflow/cloud/aws/fusion/AwsFusionEnvTest.groovy
+++ b/plugins/nf-amazon/src/test/nextflow/cloud/aws/fusion/AwsFusionEnvTest.groovy
@@ -77,4 +77,28 @@ class AwsFusionEnvTest extends Specification {
         cleanup:
         Global.config = null
     }
+
+    def 'should return env environment with session token' () {
+        given:
+        SysEnv.push([AWS_ACCESS_KEY_ID: 'x1', AWS_SECRET_ACCESS_KEY: 'y1', AWS_S3_ENDPOINT: 'http://my-host.com', AWS_SESSION_TOKEN: 'z1'])
+        and:
+
+        when:
+        def config = Mock(FusionConfig)
+        def env = new AwsFusionEnv().getEnvironment('s3', Mock(FusionConfig))
+        then:
+        env == [AWS_S3_ENDPOINT:'http://my-host.com']
+
+        when:
+        config = Mock(FusionConfig) { exportStorageCredentials() >> true }
+        env = new AwsFusionEnv().getEnvironment('s3', config)
+        then:
+        env == [AWS_ACCESS_KEY_ID: 'x1',
+                AWS_SECRET_ACCESS_KEY: 'y1',
+                AWS_S3_ENDPOINT:'http://my-host.com',
+                AWS_SESSION_TOKEN: 'z1']
+
+        cleanup:
+        SysEnv.pop()
+    }
 }

From 08c858417755aad644ea673e308bf04001cbf5d6 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Wed, 13 Dec 2023 20:12:01 +0100
Subject: [PATCH 308/350] Fix failing test

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../src/main/nextflow/plugin/PluginsFacade.groovy   |  2 +-
 .../test/nextflow/plugin/PluginsFacadeTest.groovy   | 13 +++++++++++++
 2 files changed, 14 insertions(+), 1 deletion(-)

diff --git a/modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy b/modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy
index f3982627c3..331181d647 100644
--- a/modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy
+++ b/modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy
@@ -397,7 +397,7 @@ class PluginsFacade implements PluginStateListener {
         final bucketDir = config.bucketDir as String
         final executor = Bolts.navigate(config, 'process.executor')
 
-        if( executor == 'awsbatch' || workDir?.startsWith('s3://') || bucketDir?.startsWith('s3://') || SysEnv.containsKey('NXF_ENABLE_AWS_SES') )
+        if( executor == 'awsbatch' || workDir?.startsWith('s3://') || bucketDir?.startsWith('s3://') || env.containsKey('NXF_ENABLE_AWS_SES') )
             plugins << defaultPlugins.getPlugin('nf-amazon')
 
         if( executor == 'google-lifesciences' || executor == 'google-batch' || workDir?.startsWith('gs://') || bucketDir?.startsWith('gs://')  )
diff --git a/modules/nf-commons/src/test/nextflow/plugin/PluginsFacadeTest.groovy b/modules/nf-commons/src/test/nextflow/plugin/PluginsFacadeTest.groovy
index 20eb74ac32..5bb8aa4bf7 100644
--- a/modules/nf-commons/src/test/nextflow/plugin/PluginsFacadeTest.groovy
+++ b/modules/nf-commons/src/test/nextflow/plugin/PluginsFacadeTest.groovy
@@ -4,6 +4,7 @@ import java.nio.file.Files
 import java.nio.file.Paths
 
 import com.sun.net.httpserver.HttpServer
+import nextflow.SysEnv
 import spock.lang.Specification
 import spock.lang.Unroll
 /**
@@ -149,6 +150,8 @@ class PluginsFacadeTest extends Specification {
 
     def 'should return default plugins given config' () {
         given:
+        SysEnv.push([:])
+        and:
         def defaults = new DefaultPlugins(plugins: [
                 'nf-amazon': new PluginSpec('nf-amazon', '0.1.0'),
                 'nf-google': new PluginSpec('nf-google', '0.1.0'),
@@ -187,10 +190,14 @@ class PluginsFacadeTest extends Specification {
         !plugins.find { it.id == 'nf-google' }
         !plugins.find { it.id == 'nf-azure' }
 
+        cleanup:
+        SysEnv.pop()
     }
 
     def 'should return default plugins given workdir' () {
         given:
+        SysEnv.push([:])
+        and:
         def defaults = new DefaultPlugins(plugins: [
                 'nf-amazon': new PluginSpec('nf-amazon', '0.1.0'),
                 'nf-google': new PluginSpec('nf-google', '0.1.0'),
@@ -228,10 +235,14 @@ class PluginsFacadeTest extends Specification {
         !plugins.find { it.id == 'nf-google' }
         !plugins.find { it.id == 'nf-azure' }
 
+        cleanup:
+        SysEnv.pop()
     }
 
     def 'should return default plugins given bucket dir' () {
         given:
+        SysEnv.push([:])
+        and:
         def defaults = new DefaultPlugins(plugins: [
                 'nf-amazon': new PluginSpec('nf-amazon', '0.1.0'),
                 'nf-google': new PluginSpec('nf-google', '0.1.0'),
@@ -269,6 +280,8 @@ class PluginsFacadeTest extends Specification {
         !plugins.find { it.id == 'nf-google' }
         !plugins.find { it.id == 'nf-azure' }
 
+        cleanup:
+        SysEnv.pop()
     }
 
     def 'should get plugins list from env' () {

From ec8083d4c5fbca1ef38414aaee4ccb90351e0baf Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Wed, 13 Dec 2023 20:28:02 +0100
Subject: [PATCH 309/350] Move build num & timestamp to BuildInfo class

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 build.gradle                                  | 26 ++++--
 .../main/groovy/nextflow/NextflowMeta.groovy  | 10 +--
 .../main/groovy/nextflow/cli/CmdInfo.groovy   |  6 +-
 .../main/groovy/nextflow/cli/Launcher.groovy  | 18 +++-
 .../resources/META-INF/build-info.properties  |  4 +
 .../groovy/nextflow/NextflowMetaTest.groovy   | 10 +--
 .../script/WorkflowMetadataTest.groovy        |  9 +-
 .../src/main/nextflow/BuildInfo.groovy        | 88 +++++++++++++++++++
 .../nf-commons/src/main/nextflow/Const.groovy | 60 +------------
 .../src/test/nextflow/BuildInfoTest.groovy    | 35 ++++++++
 10 files changed, 179 insertions(+), 87 deletions(-)
 create mode 100644 modules/nextflow/src/main/resources/META-INF/build-info.properties
 create mode 100644 modules/nf-commons/src/main/nextflow/BuildInfo.groovy
 create mode 100644 modules/nf-commons/src/test/nextflow/BuildInfoTest.groovy

diff --git a/build.gradle b/build.gradle
index fa5df23a8d..940ab9272b 100644
--- a/build.gradle
+++ b/build.gradle
@@ -48,8 +48,15 @@ def projects(String...args) {
     args.collect {project(it)}
 }
 
+String gitVersion() {
+    def p = new ProcessBuilder() .command('sh','-c','git rev-parse --short HEAD') .start()
+    def r = p.waitFor()
+    return r==0 ? p.text.trim() : '(unknown)'
+}
+
 group = 'io.nextflow'
 version = rootProject.file('VERSION').text.trim()
+ext.commitId = gitVersion()
 
 allprojects {
     apply plugin: 'java'
@@ -190,20 +197,23 @@ jar.enabled = false
  */
 task buildInfo { doLast {
 
-    def file0 = file('./modules/nf-commons/src/main/nextflow/Const.groovy')
+    def file0 = file('modules/nextflow/src/main/resources/META-INF/build-info.properties')
     def buildNum = 0
     def src = file0.text
-    src.find(/APP_BUILDNUM *= *([0-9]*)/) { buildNum = it[1]?.toInteger()+1 }
-    src = src.replaceAll('APP_VER *= *"[0-9a-zA-Z_\\-\\.]+"', "APP_VER = \"${version}\"" as String)
-    src = src.replaceAll('APP_TIMESTAMP *= *[0-9]*', "APP_TIMESTAMP = ${System.currentTimeMillis()}" as String)
-    if( buildNum ) {
-        src = src.replaceAll('APP_BUILDNUM *= *[0-9]*', "APP_BUILDNUM = ${buildNum}" as String)
-    }
-    else {
+    src.find(/build *= *([0-9]*)/) { buildNum = it[1]?.toInteger()+1 }
+    if( !buildNum ) {
         println "WARN: Unable to find current build number"
     }
     file0.text = src
 
+    // -- update build-info file
+    file0.text = """\
+    build=${buildNum}
+    version=${version}
+    timestamp=${System.currentTimeMillis()}
+    commitId=${project.property('commitId')}
+    """.stripIndent()
+    
     // -- update 'nextflow' wrapper
     file0 = file('nextflow')
     src = file0.text
diff --git a/modules/nextflow/src/main/groovy/nextflow/NextflowMeta.groovy b/modules/nextflow/src/main/groovy/nextflow/NextflowMeta.groovy
index bd350b945d..bb836ab61a 100644
--- a/modules/nextflow/src/main/groovy/nextflow/NextflowMeta.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/NextflowMeta.groovy
@@ -1,5 +1,7 @@
 package nextflow
 
+import static nextflow.extension.Bolts.*
+
 import java.text.SimpleDateFormat
 import java.util.regex.Pattern
 
@@ -9,8 +11,6 @@ import groovy.transform.ToString
 import groovy.util.logging.Slf4j
 import nextflow.exception.AbortOperationException
 import nextflow.util.VersionNumber
-import static nextflow.extension.Bolts.DATETIME_FORMAT
-
 /**
  * Models nextflow script properties and metadata
  * 
@@ -87,9 +87,9 @@ class NextflowMeta {
     final Features enable = new Features()
 
     private NextflowMeta() {
-        version = new VersionNumber(Const.APP_VER)
-        build = Const.APP_BUILDNUM
-        timestamp = Const.APP_TIMESTAMP_UTC
+        version = new VersionNumber(BuildInfo.version)
+        build = BuildInfo.buildNum as int
+        timestamp = BuildInfo.timestampUTC
     }
 
     protected NextflowMeta(String ver, int build, String timestamp ) {
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdInfo.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdInfo.groovy
index f2a174b914..e679d1fcd5 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdInfo.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdInfo.groovy
@@ -25,7 +25,7 @@ import com.sun.management.OperatingSystemMXBean
 import groovy.json.JsonOutput
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
-import nextflow.Const
+import nextflow.BuildInfo
 import nextflow.exception.AbortOperationException
 import nextflow.plugin.DefaultPlugins
 import nextflow.plugin.Plugins
@@ -208,8 +208,8 @@ class CmdInfo extends CmdBase {
 
         def props = System.getProperties()
         def result = new StringBuilder()
-        result << BLANK << "Version: ${Const.APP_VER} build ${Const.APP_BUILDNUM}" << NEWLINE
-        result << BLANK << "Created: ${Const.APP_TIMESTAMP_UTC} ${Const.deltaLocal()}" << NEWLINE
+        result << BLANK << "Version: ${BuildInfo.version} build ${BuildInfo.buildNum}" << NEWLINE
+        result << BLANK << "Created: ${BuildInfo.timestampUTC} ${BuildInfo.timestampDelta}" << NEWLINE
         result << BLANK << "System: ${props['os.name']} ${props['os.version']}" << NEWLINE
         result << BLANK << "Runtime: Groovy ${GroovySystem.getVersion()} on ${System.getProperty('java.vm.name')} ${props['java.runtime.version']}" << NEWLINE
         result << BLANK << "Encoding: ${System.getProperty('file.encoding')} (${System.getProperty('sun.jnu.encoding')})" << NEWLINE
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy
index 8ed41196c1..f99702b90a 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy
@@ -29,6 +29,7 @@ import groovy.transform.CompileDynamic
 import groovy.transform.CompileStatic
 import groovy.transform.PackageScope
 import groovy.util.logging.Slf4j
+import nextflow.BuildInfo
 import nextflow.exception.AbortOperationException
 import nextflow.exception.AbortRunException
 import nextflow.exception.ConfigParseException
@@ -685,10 +686,25 @@ class Launcher {
             SPLASH
         }
         else {
-            "${APP_NAME} version ${APP_VER}.${APP_BUILDNUM}"
+            "${APP_NAME} version ${BuildInfo.version}.${BuildInfo.buildNum}"
         }
 
     }
 
+    /*
+     * The application 'logo'
+     */
+    /*
+     * The application 'logo'
+     */
+    static public final String SPLASH =
+
+"""
+      N E X T F L O W
+      version ${BuildInfo.version} build ${BuildInfo.buildNum}
+      created ${BuildInfo.timestampUTC} ${BuildInfo.timestampDelta}
+      cite doi:10.1038/nbt.3820
+      http://nextflow.io
+"""
 
 }
diff --git a/modules/nextflow/src/main/resources/META-INF/build-info.properties b/modules/nextflow/src/main/resources/META-INF/build-info.properties
new file mode 100644
index 0000000000..95836440d9
--- /dev/null
+++ b/modules/nextflow/src/main/resources/META-INF/build-info.properties
@@ -0,0 +1,4 @@
+build=5900
+version=23.11.0-edge
+timestamp=1702494578227
+commitId=887f06f4d
diff --git a/modules/nextflow/src/test/groovy/nextflow/NextflowMetaTest.groovy b/modules/nextflow/src/test/groovy/nextflow/NextflowMetaTest.groovy
index 0abe709dc9..5abaac2ba9 100644
--- a/modules/nextflow/src/test/groovy/nextflow/NextflowMetaTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/NextflowMetaTest.groovy
@@ -1,13 +1,11 @@
 package nextflow
 
-import spock.lang.Specification
+import static nextflow.extension.Bolts.*
 
 import java.text.SimpleDateFormat
 
-import static nextflow.extension.Bolts.DATETIME_FORMAT
-
+import spock.lang.Specification
 import spock.lang.Unroll
-
 /**
  *
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
@@ -23,7 +21,7 @@ class NextflowMetaTest extends Specification {
 
     def 'should convert to map'() {
         given:
-        def meta = new NextflowMeta('10.12.0', 123, Const.APP_TIMESTAMP_UTC)
+        def meta = new NextflowMeta('10.12.0', 123, BuildInfo.timestampUTC)
         meta.enableDsl2()
 
         when:
@@ -32,7 +30,7 @@ class NextflowMetaTest extends Specification {
         map.version == '10.12.0'
         map.build == 123
         map.enable.dsl == 2
-        dateToString((Date) map.timestamp) == Const.APP_TIMESTAMP_UTC
+        dateToString((Date) map.timestamp) == BuildInfo.timestampUTC
 
     }
 
diff --git a/modules/nextflow/src/test/groovy/nextflow/script/WorkflowMetadataTest.groovy b/modules/nextflow/src/test/groovy/nextflow/script/WorkflowMetadataTest.groovy
index 05e370c612..4d05157297 100644
--- a/modules/nextflow/src/test/groovy/nextflow/script/WorkflowMetadataTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/script/WorkflowMetadataTest.groovy
@@ -16,12 +16,11 @@
 
 package nextflow.script
 
-
 import java.nio.file.Paths
 import java.time.OffsetDateTime
 
-import nextflow.Const
 import nextflow.Session
+import nextflow.BuildInfo
 import nextflow.exception.WorkflowScriptErrorException
 import nextflow.trace.TraceRecord
 import nextflow.trace.WorkflowStats
@@ -83,9 +82,9 @@ class WorkflowMetadataTest extends Specification {
         metadata.start <= OffsetDateTime.now()
         metadata.complete == null
         metadata.commandLine == 'nextflow run -this -that'
-        metadata.nextflow.version == new VersionNumber(Const.APP_VER)
-        metadata.nextflow.build == Const.APP_BUILDNUM
-        metadata.nextflow.timestamp == Const.APP_TIMESTAMP_UTC
+        metadata.nextflow.version == new VersionNumber(BuildInfo.version)
+        metadata.nextflow.build == BuildInfo.buildNum as int
+        metadata.nextflow.timestamp == BuildInfo.timestampUTC
         metadata.profile == 'standard'
         metadata.sessionId == session.uniqueId
         metadata.runName == session.runName
diff --git a/modules/nf-commons/src/main/nextflow/BuildInfo.groovy b/modules/nf-commons/src/main/nextflow/BuildInfo.groovy
new file mode 100644
index 0000000000..ad236f4ab1
--- /dev/null
+++ b/modules/nf-commons/src/main/nextflow/BuildInfo.groovy
@@ -0,0 +1,88 @@
+/*
+ * Copyright 2013-2023, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package nextflow
+
+import static nextflow.extension.Bolts.*
+
+import java.text.SimpleDateFormat
+
+import groovy.transform.CompileStatic
+import groovy.util.logging.Slf4j
+/**
+ * Model app build information
+ * 
+ * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
+ */
+@Slf4j
+@CompileStatic
+class BuildInfo {
+
+    private static Properties properties
+
+    static {
+        final BUILD_INFO = '/META-INF/build-info.properties'
+        properties = new Properties()
+        try {
+            properties.load( BuildInfo.getResourceAsStream(BUILD_INFO) )
+        }
+        catch( Exception e ) {
+            log.warn "Unable to parse $BUILD_INFO - Cause ${e.message ?: e}"
+        }
+    }
+
+    static Properties getProperties() { properties }
+
+    static String getVersion() { properties.getProperty('version') }
+
+    static String getCommitId() { properties.getProperty('commitId')}
+
+    static String getBuildNum() { properties.getProperty('build') }
+
+    static long getTimestampMillis() { properties.getProperty('timestamp') as long }
+
+    static String getTimestampUTC() {
+        def tz = TimeZone.getTimeZone('UTC')
+        def fmt = new SimpleDateFormat(DATETIME_FORMAT)
+        fmt.setTimeZone(tz)
+        fmt.format(new Date(getTimestampMillis())) + ' ' + tz.getDisplayName( true, TimeZone.SHORT )
+    }
+
+    static String getTimestampLocal() {
+        def tz = TimeZone.getDefault()
+        def fmt = new SimpleDateFormat(DATETIME_FORMAT)
+        fmt.setTimeZone(tz)
+        fmt.format(new Date(getTimestampMillis())) + ' ' + tz.getDisplayName( true, TimeZone.SHORT )
+    }
+
+    static String getTimestampDelta() {
+        if( getTimestampUTC() == getTimestampLocal() ) {
+            return ''
+        }
+
+        final utc = getTimestampUTC().split(' ')
+        final loc = getTimestampLocal().split(' ')
+
+        final result = utc[0] == loc[0] ? loc[1,-1].join(' ') : loc.join(' ')
+        return "($result)"
+    }
+
+    static String getFullVersion() {
+        "${version}_${commitId}"
+    }
+
+}
diff --git a/modules/nf-commons/src/main/nextflow/Const.groovy b/modules/nf-commons/src/main/nextflow/Const.groovy
index 6f39ccd143..b7965713e9 100644
--- a/modules/nf-commons/src/main/nextflow/Const.groovy
+++ b/modules/nf-commons/src/main/nextflow/Const.groovy
@@ -15,12 +15,9 @@
  */
 
 package nextflow
+
 import java.nio.file.Path
 import java.nio.file.Paths
-import java.text.SimpleDateFormat
-
-import static nextflow.extension.Bolts.DATETIME_FORMAT
-
 /**
  * Application main constants
  *
@@ -59,48 +56,6 @@ class Const {
      */
     static public final long APP_TIMESTAMP = 1700857448507
 
-    /**
-     * The app build number
-     */
-    static public final int APP_BUILDNUM = 5891
-
-    /**
-     * The app build time string relative to UTC timezone
-     */
-    static public final String APP_TIMESTAMP_UTC = {
-
-        def tz = TimeZone.getTimeZone('UTC')
-        def fmt = new SimpleDateFormat(DATETIME_FORMAT)
-        fmt.setTimeZone(tz)
-        fmt.format(new Date(APP_TIMESTAMP)) + ' ' + tz.getDisplayName( true, TimeZone.SHORT )
-
-    } ()
-
-
-    /**
-     * The app build time string relative to local timezone
-     */
-    static public final String APP_TIMESTAMP_LOCAL = {
-
-        def tz = TimeZone.getDefault()
-        def fmt = new SimpleDateFormat(DATETIME_FORMAT)
-        fmt.setTimeZone(tz)
-        fmt.format(new Date(APP_TIMESTAMP)) + ' ' + tz.getDisplayName( true, TimeZone.SHORT )
-
-    } ()
-
-    static String deltaLocal() {
-        def utc = APP_TIMESTAMP_UTC.split(' ')
-        def loc = APP_TIMESTAMP_LOCAL.split(' ')
-
-        if( APP_TIMESTAMP_UTC == APP_TIMESTAMP_LOCAL ) {
-            return ''
-        }
-
-        def result = utc[0] == loc[0] ? loc[1,-1].join(' ') : loc.join(' ')
-        return "($result)"
-    }
-
 
     private static Path getHomeDir(String appname) {
         def home = System.getenv('NXF_HOME')
@@ -113,19 +68,6 @@ class Const {
         return result
     }
 
-    /*
-     * The application 'logo'
-     */
-    static public final String SPLASH =
-
-"""
-      N E X T F L O W
-      version ${APP_VER} build ${APP_BUILDNUM}
-      created ${APP_TIMESTAMP_UTC} ${deltaLocal()}
-      cite doi:10.1038/nbt.3820
-      http://nextflow.io
-"""
-
     static public final String S3_UPLOADER_CLASS = 'nextflow.cloud.aws.nio'
 
     static public final String ROLE_WORKER = 'worker'
diff --git a/modules/nf-commons/src/test/nextflow/BuildInfoTest.groovy b/modules/nf-commons/src/test/nextflow/BuildInfoTest.groovy
new file mode 100644
index 0000000000..5e4ff2d9bc
--- /dev/null
+++ b/modules/nf-commons/src/test/nextflow/BuildInfoTest.groovy
@@ -0,0 +1,35 @@
+/*
+ * Copyright 2013-2023, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package nextflow
+
+import spock.lang.Specification
+
+/**
+ *
+ * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
+ */
+class BuildInfoTest extends Specification {
+
+    def 'should load version and commit id' () {
+        expect:
+        BuildInfo.getVersion()
+        BuildInfo.getBuildNum()
+        BuildInfo.getCommitId()
+        BuildInfo.getTimestampMillis()
+    }
+}

From 5ad41e4463bdf9106038b5637e1afd4010055208 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Thu, 14 Dec 2023 07:55:01 -0600
Subject: [PATCH 310/350] Build optimizations (#4579)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 Makefile     | 2 +-
 build.gradle | 1 -
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/Makefile b/Makefile
index fb508c68a4..bf55192bd3 100644
--- a/Makefile
+++ b/Makefile
@@ -43,7 +43,7 @@ compile:
 	@echo "DONE `date`"
 
 assemble:
-	./gradlew compile assemble
+	./gradlew buildInfo compile assemble
 
 check:
 	./gradlew check
diff --git a/build.gradle b/build.gradle
index 940ab9272b..0c13c17f78 100644
--- a/build.gradle
+++ b/build.gradle
@@ -248,7 +248,6 @@ task buildInfo { doLast {
  * Compile sources and copies all libs to target directory
  */
 task compile {
-    dependsOn buildInfo
     dependsOn allprojects.classes
 }
 

From 09e85582c41653f02202ffb30cc5ad42e20dba1d Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Sun, 17 Dec 2023 09:39:19 -0600
Subject: [PATCH 311/350] Fix bug with Fusion symlink resolution (#4593)

This commit is a supplement to PR https://github.com/nextflow-io/nextflow/pull/4348
to fix the issue https://github.com/nextflow-io/nextflow/issues/4309

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../src/main/groovy/nextflow/processor/PublishDir.groovy       | 3 ++-
 tests/checks/fusion-symlink.nf/.checks                         | 2 ++
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/PublishDir.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/PublishDir.groovy
index 0a503ab920..775fb68f9e 100644
--- a/modules/nextflow/src/main/groovy/nextflow/processor/PublishDir.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/processor/PublishDir.groovy
@@ -134,7 +134,7 @@ class PublishDir {
     }
 
     protected Map<String,Path> getTaskInputs() {
-        return task?.getInputFilesMap()
+        return task ? task.getInputFilesMap() : Map.<String,Path>of()
     }
 
     void setPath( def value ) {
@@ -294,6 +294,7 @@ class PublishDir {
         this.sourceDir = task.targetDir
         this.sourceFileSystem = sourceDir.fileSystem
         this.stageInMode = task.config.stageInMode
+        this.task = task
 
         apply0(files)
     }
diff --git a/tests/checks/fusion-symlink.nf/.checks b/tests/checks/fusion-symlink.nf/.checks
index a28366d245..5d758c6f21 100644
--- a/tests/checks/fusion-symlink.nf/.checks
+++ b/tests/checks/fusion-symlink.nf/.checks
@@ -10,6 +10,7 @@ fi
 # normal run
 #
 echo initial run
+$NXF_CMD fs rm s3://nextflow-ci/work/ci-test/fusion-symlink/data.txt || true
 $NXF_RUN -c .config
 
 $NXF_CMD fs cp s3://nextflow-ci/work/ci-test/fusion-symlink/data.txt data.txt
@@ -19,6 +20,7 @@ cmp data.txt .expected || false
 # resume run
 #
 echo resumed run
+$NXF_CMD fs rm s3://nextflow-ci/work/ci-test/fusion-symlink/data.txt || true
 $NXF_RUN -c .config -resume
 
 $NXF_CMD fs cp s3://nextflow-ci/work/ci-test/fusion-symlink/data.txt data.txt

From e0fe952f0d9ee60dd97ef90b39bec210fd5a8286 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sun, 17 Dec 2023 18:00:04 +0100
Subject: [PATCH 312/350] Fix container environment with special chars (#4594)

This commit fixes the environment exported in the container execution
context when a variable includes special characters such as blanks,
parentheses, etc. These characters do not need to be escaped.

This issue was breaking the PATH variable for projects having a
`bin/` scripts folder and launching in a root path, including special
characters because the project scripts were not accessing, being
the PATH is malformed due to the character escaping.

See also https://stackoverflow.com/a/57622677/395921

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>

---------

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../processor/TaskProcessorTest.groovy        |  2 +-
 .../src/main/nextflow/util/Escape.groovy      |  6 +-
 .../src/test/nextflow/util/EscapeTest.groovy  | 10 +--
 .../.checks                                   | 77 +++++++++++++++++++
 tests/checks/run.sh                           |  4 +-
 tests/env-container-with(special)chars.nf     | 22 ++++++
 6 files changed, 110 insertions(+), 11 deletions(-)
 create mode 100644 tests/checks/env-container-with(special)chars.nf/.checks
 create mode 100644 tests/env-container-with(special)chars.nf

diff --git a/modules/nextflow/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy b/modules/nextflow/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy
index b616669c2e..11fc13f237 100644
--- a/modules/nextflow/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy
@@ -798,7 +798,7 @@ class TaskProcessorTest extends Specification {
         then:
         env == '''\
             export PATH="foo:\\$PATH"
-            export HOLA="one\\|two"
+            export HOLA="one|two"
             '''.stripIndent()
         env.charAt(env.size()-1) == '\n' as char
 
diff --git a/modules/nf-commons/src/main/nextflow/util/Escape.groovy b/modules/nf-commons/src/main/nextflow/util/Escape.groovy
index 5db0682bc6..f2651a81d4 100644
--- a/modules/nf-commons/src/main/nextflow/util/Escape.groovy
+++ b/modules/nf-commons/src/main/nextflow/util/Escape.groovy
@@ -29,11 +29,11 @@ import nextflow.extension.FilesEx
 @CompileStatic
 class Escape {
 
-    private static List<String> SPECIAL_CHARS = ["'", '"', ' ', '(', ')', '\\', '!', '&', '|', '<', '>', '`', ':', ';']
+    final private static List<String> SPECIAL_CHARS = ["'", '"', ' ', '(', ')', '\\', '!', '&', '|', '<', '>', '`', ':', ';']
 
-    private static List<String> VAR_CHARS = ['$', "'", '"', '(', ')', '\\', '&', '|', '<', '>', '`']
+    final private static List<String> VAR_CHARS = ['$']
 
-    private static List<String> WILDCARDS = ["*", "?", "{", "}", "[", "]", "'", '"', ' ', '(', ')', '\\', '!', '&', '|', '<', '>', '`', ':']
+    final private static List<String> WILDCARDS = ["*", "?", "{", "}", "[", "]", "'", '"', ' ', '(', ')', '\\', '!', '&', '|', '<', '>', '`', ':']
 
     private static String replace(List<String> special, String str, boolean doNotEscapeComplement=false) {
         def copy = new StringBuilder(str.size() +10)
diff --git a/modules/nf-commons/src/test/nextflow/util/EscapeTest.groovy b/modules/nf-commons/src/test/nextflow/util/EscapeTest.groovy
index 85f4cf5fb4..93b3053c6c 100644
--- a/modules/nf-commons/src/test/nextflow/util/EscapeTest.groovy
+++ b/modules/nf-commons/src/test/nextflow/util/EscapeTest.groovy
@@ -108,12 +108,12 @@ class EscapeTest extends Specification {
         'foo:bar'   | 'foo:bar'
         'foo!bar'   | 'foo!bar'
         'foo[!x]bar'| 'foo[!x]bar'
+        'foo|bar'   | 'foo|bar'
+        'foo`bar'   | 'foo`bar'
+        'foo&bar'   | 'foo&bar'
+        'foo(x)bar' | 'foo(x)bar'
+        'foo<x>bar' | 'foo<x>bar'
         and:
         '$foo'      | '\\$foo'
-        'foo|bar'   | 'foo\\|bar'
-        'foo`bar'   | 'foo\\`bar'
-        'foo&bar'   | 'foo\\&bar'
-        'foo(x)bar' | 'foo\\(x\\)bar'
-        'foo<x>bar' | 'foo\\<x\\>bar'
     }
 }
diff --git a/tests/checks/env-container-with(special)chars.nf/.checks b/tests/checks/env-container-with(special)chars.nf/.checks
new file mode 100644
index 0000000000..d10f378da2
--- /dev/null
+++ b/tests/checks/env-container-with(special)chars.nf/.checks
@@ -0,0 +1,77 @@
+set -e
+export NXF_ANSI_LOG=false
+
+#
+# create the `hello.sh` executable script
+#
+mkdir -p bin
+echo "echo Hola mundo" > bin/hello.sh
+chmod +x bin/hello.sh
+
+#
+# create the nextflow config file 
+#
+cat << EOF > nextflow.config
+env.FOO = 'HOLA'
+process.container = 'quay.io/nextflow/bash'
+EOF
+
+#
+# create the nextflow script 
+#
+cat << EOF > foo.nf
+process foo {
+  echo true
+  input: 
+  env BAR
+  '''
+  env | sort 
+  hello.sh
+  '''
+}
+
+workflow {
+  channel.value('Hello World!') | foo
+}
+EOF
+
+#
+# not the testing part 
+#
+
+# NF plain run  
+$NXF_CMD run foo.nf | tee stdout
+
+# run tests 
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process'` == 1 ]] || false
+[[ `< stdout grep -c 'FOO=HOLA'` == 1 ]] || false
+[[ `< stdout grep -c 'BAR=Hello World!'` == 1 ]] || false
+[[ `< stdout grep -c 'Hola mundo'` == 1 ]] || false
+
+# NF run with trace
+$NXF_CMD run foo.nf -with-trace | tee stdout
+
+# run tests 
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process'` == 1 ]] || false
+[[ `< stdout grep -c 'FOO=HOLA'` == 1 ]] || false
+[[ `< stdout grep -c 'BAR=Hello World!'` == 1 ]] || false
+[[ `< stdout grep -c 'Hola mundo'` == 1 ]] || false
+
+# NF run with docker
+$NXF_CMD run foo.nf -with-docker | tee stdout
+
+# run tests 
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process'` == 1 ]] || false
+[[ `< stdout grep -c 'FOO=HOLA'` == 1 ]] || false
+[[ `< stdout grep -c 'BAR=Hello World!'` == 1 ]] || false
+[[ `< stdout grep -c 'Hola mundo'` == 1 ]] || false
+
+
+# NF run with docker and trace
+$NXF_CMD run foo.nf -with-trace -with-docker | tee stdout
+
+# run tests 
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process'` == 1 ]] || false
+[[ `< stdout grep -c 'FOO=HOLA'` == 1 ]] || false
+[[ `< stdout grep -c 'BAR=Hello World!'` == 1 ]] || false
+[[ `< stdout grep -c 'Hola mundo'` == 1 ]] || false
diff --git a/tests/checks/run.sh b/tests/checks/run.sh
index 46443587ea..5bcb18f6c6 100644
--- a/tests/checks/run.sh
+++ b/tests/checks/run.sh
@@ -37,7 +37,7 @@ rm -rf $NXF_WORK
 
 function run_checks() {
   NXF_SCRIPT="../../$1"
-  NXF_RUN="$NXF_CMD -q run $NXF_SCRIPT" 
+  NXF_RUN="$NXF_CMD -q run $NXF_SCRIPT"
   export NXF_SCRIPT
   export NXF_CMD
   export NXF_RUN
@@ -50,7 +50,7 @@ function run_checks() {
   else
      mkdir -p $1
      cd $1
-     $NXF_RUN > checks.out 
+     $NXF_RUN > checks.out
   fi
   
   ret=$?
diff --git a/tests/env-container-with(special)chars.nf b/tests/env-container-with(special)chars.nf
new file mode 100644
index 0000000000..a5ec261b91
--- /dev/null
+++ b/tests/env-container-with(special)chars.nf
@@ -0,0 +1,22 @@
+/*
+ * Copyright 2013-2023, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+println """
+  THIS IS JUST A PLACEHOLDER 
+  THE REAL TEST SCRIPT IS CREATED THE `.checks` FILE
+  SEE THE CONTENT OF `env-container-with(special)chars.nf` DIRECTORY 
+"""

From b7f1a192630e19b03938929f7cdb265a2250edb0 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sun, 17 Dec 2023 21:12:16 +0100
Subject: [PATCH 313/350] Add support for Singularity/Apptainer auto pull mode
 for OCI containers

This commit supports Singularity and Apptainer auto pull mode for OCI container images.

When this feature is enabled, the Singularity and Apptainer container engine runs OCI container
images, converting them to the SIF format automatically without requiring the execution of a
separate pull command man aged by the Nextflow runtime.

To enable this capability the following settings should be added to the nextflow.config file
respectively for Apptainer and Singularity:

```
apptainer.ociAutoPull = true|false
singularity.ociAutoPull = true|false
```

Moreover the setting `singularity.oci` is renamed to `singularity.ociMode`.


Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Dr Marco Claudio De La Pierre <marco.delapierre@gmail.com>
Co-authored-by: Jordi Deu-Pons <jordi@jordeu.net>
Co-authored-by: Ben Sherman <bentshermann@gmail.com>
---
 docs/config.md                                | 15 ++++--
 .../nextflow/container/ContainerConfig.groovy | 39 +++++++++++++--
 .../container/ContainerHandler.groovy         |  4 +-
 .../container/SingularityBuilder.groovy       | 17 ++++---
 .../container/ApptainerBuilderTest.groovy     |  5 ++
 .../container/ContainerConfigTest.groovy      | 38 +++++++++-----
 .../container/ContainerHandlerTest.groovy     | 50 ++++++++++++++++++-
 .../container/SingularityBuilderTest.groovy   |  6 +++
 .../resolver/WaveContainerResolver.groovy     |  3 +-
 9 files changed, 147 insertions(+), 30 deletions(-)

diff --git a/docs/config.md b/docs/config.md
index 20acf2a51c..51be41cb9d 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -104,6 +104,11 @@ The following settings are available:
 `apptainer.noHttps`
 : Pull the Apptainer image with http protocol (default: `false`).
 
+`apptainer.ociAutoPull`
+: :::{versionadded} 23.12.0-edge
+  :::
+: When enabled, OCI (and Docker) container images are pulled and converted to the SIF format by the Apptainer run command, instead of Nextflow (default: `false`).
+
 `apptainer.pullTimeout`
 : The amount of time the Apptainer pull can last, exceeding which the process is terminated (default: `20 min`).
 
@@ -1407,11 +1412,15 @@ The following settings are available:
 `singularity.noHttps`
 : Pull the Singularity image with http protocol (default: `false`).
 
-`singularity.oci`
-: :::{versionadded} 23.11.0-edge
+`singularity.ociAutoPull`
+: :::{versionadded} 23.12.0-edge
   :::
-: Enable OCI-mode, that allows running native OCI-compatible containers with Singularity using `crun` or `runc` as low-level runtime. See `--oci` flag in the [Singularity documentation](https://docs.sylabs.io/guides/4.0/user-guide/oci_runtime.html#oci-mode) for more details and requirements (default: `false`).
+: When enabled, OCI (and Docker) container images are pull and converted to a SIF image file format implicitly by the Singularity run command, instead of Nextflow. Requires Singulairty 3.11 or later (default: `false`).
 
+`singularity.ociMode`
+: :::{versionadded} 23.12.0-edge
+  :::
+: Enable OCI-mode, that allows running native OCI compliant container image with Singularity using `crun` or `runc` as low-level runtime. Note: it requires Singulairty 4 or later. See `--oci` flag in the [Singularity documentation](https://docs.sylabs.io/guides/4.0/user-guide/oci_runtime.html#oci-mode) for more details and requirements (default: `false`).
 
 `singularity.pullTimeout`
 : The amount of time the Singularity pull can last, exceeding which the process is terminated (default: `20 min`).
diff --git a/modules/nextflow/src/main/groovy/nextflow/container/ContainerConfig.groovy b/modules/nextflow/src/main/groovy/nextflow/container/ContainerConfig.groovy
index 71fb346713..5a372ed6e8 100644
--- a/modules/nextflow/src/main/groovy/nextflow/container/ContainerConfig.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/container/ContainerConfig.groovy
@@ -17,6 +17,7 @@
 package nextflow.container
 
 import groovy.transform.CompileStatic
+import groovy.transform.Memoized
 import groovy.util.logging.Slf4j
 
 /**
@@ -55,8 +56,40 @@ class ContainerConfig extends LinkedHashMap {
         get('engine')
     }
 
-    boolean singularityOciMode() {
-        getEngine()=='singularity' && get('oci')?.toString() == 'true'
+    /**
+     * Whenever Singularity or Apptainer container engine can a OCI (Docker)
+     * image without requiring a separate OCI to SIF conversion execution (managed by Nextflow via {@link SingularityCache).
+     *
+     * @return
+     *  {@code true} when the OCI container can be run without an explicit OCI to SIF conversion or {@code false}
+     *  otherwise
+     *
+     */
+    boolean canRunOciImage() {
+        if( isSingularityOciMode() )
+            return true
+        if( (getEngine()!='singularity' && getEngine()!='apptainer') )
+            return false
+        return get('ociAutoPull')?.toString()=='true'
+    }
+
+    /**
+     * Whenever the Singularity OCI-mode is enabled
+     *
+     * @return {@code true} when Singularity OCI-mode is enabled or {@code false} otherwise
+     */
+    @Memoized
+    boolean isSingularityOciMode() {
+        if( getEngine()!='singularity' ) {
+            return false
+        }
+        if( get('oci')?.toString()=='true' ) {
+            log.warn "The setting `singularity.oci` is deprecated - use `singularity.ociNative` instead"
+            return true
+        }
+        if( get('ociMode')?.toString()=='true' )
+            return true
+        return false
     }
 
     List<String> getEnvWhitelist() {
@@ -93,7 +126,7 @@ class ContainerConfig extends LinkedHashMap {
             return null
         if( eng=='docker' || eng=='podman' )
             return '--rm --privileged'
-        if( singularityOciMode() )
+        if( isSingularityOciMode() )
             return '-B /dev/fuse'
         if( eng=='singularity' || eng=='apptainer' )
             return null
diff --git a/modules/nextflow/src/main/groovy/nextflow/container/ContainerHandler.groovy b/modules/nextflow/src/main/groovy/nextflow/container/ContainerHandler.groovy
index 524ce6d9e3..ab29fddb72 100644
--- a/modules/nextflow/src/main/groovy/nextflow/container/ContainerHandler.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/container/ContainerHandler.groovy
@@ -67,7 +67,7 @@ class ContainerHandler {
             final normalizedImageName = normalizeSingularityImageName(imageName)
             if( !config.isEnabled() || !normalizedImageName )
                 return normalizedImageName
-            if( normalizedImageName.startsWith('docker://') && config.singularityOciMode() )
+            if( normalizedImageName.startsWith('docker://') && config.canRunOciImage() )
                 return normalizedImageName
             final requiresCaching = normalizedImageName =~ IMAGE_URL_PREFIX
             if( ContainerInspectMode.active() && requiresCaching )
@@ -79,6 +79,8 @@ class ContainerHandler {
             final normalizedImageName = normalizeApptainerImageName(imageName)
             if( !config.isEnabled() || !normalizedImageName )
                 return normalizedImageName
+            if( normalizedImageName.startsWith('docker://') && config.canRunOciImage() )
+                return normalizedImageName
             final requiresCaching = normalizedImageName =~ IMAGE_URL_PREFIX
             if( ContainerInspectMode.active() && requiresCaching )
                 return imageName
diff --git a/modules/nextflow/src/main/groovy/nextflow/container/SingularityBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/container/SingularityBuilder.groovy
index a4829f0f54..9a02b85765 100644
--- a/modules/nextflow/src/main/groovy/nextflow/container/SingularityBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/container/SingularityBuilder.groovy
@@ -39,7 +39,7 @@ class SingularityBuilder extends ContainerBuilder<SingularityBuilder> {
 
     private String runCmd0
 
-    private Boolean oci
+    private Boolean ociMode
 
     SingularityBuilder(String name) {
         this.image = name
@@ -94,8 +94,11 @@ class SingularityBuilder extends ContainerBuilder<SingularityBuilder> {
         if( params.containsKey('readOnlyInputs') )
             this.readOnlyInputs = params.readOnlyInputs?.toString() == 'true'
 
-        if( params.oci!=null )
-            oci = params.oci.toString() == 'true'
+        // note: 'oci' flag should be ignored by Apptainer sub-class
+        if( params.oci!=null && this.class==SingularityBuilder )
+            ociMode = params.oci.toString() == 'true'
+        else if( params.ociMode!=null && this.class==SingularityBuilder )
+            ociMode = params.ociMode.toString() == 'true'
 
         return this
     }
@@ -122,11 +125,11 @@ class SingularityBuilder extends ContainerBuilder<SingularityBuilder> {
         if( !homeMount )
             result << '--no-home '
 
-        if( newPidNamespace && !oci )
+        if( newPidNamespace && !ociMode )
             result << '--pid '
 
-        if( oci != null )
-            result << (oci ? '--oci ' : '--no-oci ')
+        if( ociMode != null )
+            result << (ociMode ? '--oci ' : '--no-oci ')
 
         if( autoMounts ) {
             makeVolumes(mounts, result)
@@ -154,7 +157,7 @@ class SingularityBuilder extends ContainerBuilder<SingularityBuilder> {
         makeEnv('TMP',result) .append(' ')
         makeEnv('TMPDIR',result) .append(' ')
         // add magic variables required by singularity to run in OCI-mode
-        if( oci ) {
+        if( ociMode ) {
             result .append('${XDG_RUNTIME_DIR:+XDG_RUNTIME_DIR="$XDG_RUNTIME_DIR"} ')
             result .append('${DBUS_SESSION_BUS_ADDRESS:+DBUS_SESSION_BUS_ADDRESS="$DBUS_SESSION_BUS_ADDRESS"} ')
         }
diff --git a/modules/nextflow/src/test/groovy/nextflow/container/ApptainerBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/container/ApptainerBuilderTest.groovy
index 0f4404cf95..256aeb93b4 100644
--- a/modules/nextflow/src/test/groovy/nextflow/container/ApptainerBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/container/ApptainerBuilderTest.groovy
@@ -153,6 +153,11 @@ class ApptainerBuilderTest extends Specification {
                 .build()
                 .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home -B "$NXF_TASK_WORKDIR" ubuntu'
 
+        new ApptainerBuilder('ubuntu')
+            .params(oci: true)
+            .build()
+            .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+APPTAINERENV_TMP="$TMP"} ${TMPDIR:+APPTAINERENV_TMPDIR="$TMPDIR"} apptainer exec --no-home --pid -B "$NXF_TASK_WORKDIR" ubuntu'
+
     }
 
     def 'should mount home directory if specified' () {
diff --git a/modules/nextflow/src/test/groovy/nextflow/container/ContainerConfigTest.groovy b/modules/nextflow/src/test/groovy/nextflow/container/ContainerConfigTest.groovy
index 29ce5704e4..294bced198 100644
--- a/modules/nextflow/src/test/groovy/nextflow/container/ContainerConfigTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/container/ContainerConfigTest.groovy
@@ -61,24 +61,34 @@ class ContainerConfigTest extends Specification {
 
     }
 
-
-    def 'should validate oci mode' () {
+    @Unroll
+    def 'should validate oci mode and direct mode' () {
 
         when:
         def cfg = new ContainerConfig(OPTS)
         then:
-        cfg.singularityOciMode() == EXPECTED
+        cfg.isSingularityOciMode() == OCI_MODE
+        cfg.canRunOciImage() == AUTO_PULL
 
         where:
-        OPTS                                | EXPECTED
-        [:]                                 | false
-        [oci:false]                         | false
-        [oci:true]                          | false
-        [engine:'apptainer', oci:true]      | false
-        [engine:'docker', oci:true]         | false
-        [engine:'singularity']              | false
-        [engine:'singularity', oci:false]   | false
-        [engine:'singularity', oci:true]    | true
+        OPTS                                        | OCI_MODE  | AUTO_PULL
+        [:]                                         | false     | false
+        [oci:true]                                  | false     | false
+        [oci:false]                                 | false     | false
+        [ociMode:true]                              | false     | false
+        and:
+        [engine:'docker', oci:true]                 | false     | false
+        [engine:'singularity']                      | false     | false
+        [engine:'singularity', oci:false]           | false     | false
+        [engine:'singularity', ociAutoPull:false]   | false     | false
+        and:
+        [engine:'singularity', oci:true]            | true      | true
+        [engine:'singularity', ociMode:true]        | true      | true
+        [engine:'apptainer', oci:true]              | false     | false
+        [engine:'apptainer', ociMode:true]          | false     | false
+        and:
+        [engine:'singularity', ociAutoPull:true]    | false         | true
+        [engine:'apptainer', ociAutoPull:true]      | false         | true
 
     }
 
@@ -96,7 +106,9 @@ class ContainerConfigTest extends Specification {
         [engine:'podman']                               | '--rm --privileged'
         and:
         [engine: 'singularity']                         | null
-        [engine: 'singularity', oci:true]               | '-B /dev/fuse'
+        [engine: 'singularity', ociMode:true]           | '-B /dev/fuse'
+        [engine: 'singularity', ociAutoPull: true]      | null
+        [engine: 'apptainer', oci:true]                 | null
         and:
         [engine:'docker', fusionOptions:'--cap-add foo']| '--cap-add foo'
         [engine:'podman', fusionOptions:'--cap-add bar']| '--cap-add bar'
diff --git a/modules/nextflow/src/test/groovy/nextflow/container/ContainerHandlerTest.groovy b/modules/nextflow/src/test/groovy/nextflow/container/ContainerHandlerTest.groovy
index 7459c9de21..f3f9a128d2 100644
--- a/modules/nextflow/src/test/groovy/nextflow/container/ContainerHandlerTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/container/ContainerHandlerTest.groovy
@@ -205,7 +205,7 @@ class ContainerHandlerTest extends Specification {
     def 'test normalize method for singularity' () {
         given:
         def BASE = Paths.get('/abs/path/')
-        def handler = Spy(new ContainerHandler(engine: 'singularity', enabled: true, oci:OCI, baseDir: BASE))
+        def handler = Spy(new ContainerHandler(engine: 'singularity', enabled: true, ociMode: OCI, baseDir: BASE))
 
         when:
         def result = handler.normalizeImageName(IMAGE)
@@ -233,6 +233,54 @@ class ContainerHandlerTest extends Specification {
 
     }
 
+    @Unroll
+    def 'test normalize method for OCI direct mode' () {
+        given:
+        def BASE = Paths.get('/abs/path/')
+        def handler = Spy(new ContainerHandler(engine: 'apptainer', enabled: true, ociAutoPull:AUTO, baseDir: BASE))
+
+        when:
+        def result = handler.normalizeImageName(IMAGE)
+
+        then:
+        1 * handler.normalizeApptainerImageName(IMAGE) >> NORMALIZED
+        X * handler.createApptainerCache(handler.config, NORMALIZED) >> EXPECTED
+        result == EXPECTED
+
+        where:
+        IMAGE                                       | NORMALIZED                                        | ENGINE            | AUTO  | X | EXPECTED
+        null                                        | null                                              | 'singularity'     | false |           0 | null
+        ''                                          | null                                              | 'singularity'     | false |           0 | null
+        '/abs/path/bar.img'                         | '/abs/path/bar.img'                               | 'singularity'     | false |           0 | '/abs/path/bar.img'
+        '/abs/path bar.img'                         | '/abs/path bar.img'                               | 'singularity'     | false |           0 | '/abs/path\\ bar.img'
+        'file:///abs/path/bar.img'                  | '/abs/path/bar.img'                               | 'singularity'     | false |           0 | '/abs/path/bar.img'
+        'foo.img'                                   | Paths.get('foo.img').toAbsolutePath().toString()  | 'singularity'     | false |           0 | Paths.get('foo.img').toAbsolutePath().toString()
+        'shub://busybox'                            | 'shub://busybox'                                  | 'singularity'     | false |           1 | '/path/to/busybox'
+        'docker://library/busybox'                  | 'docker://library/busybox'                        | 'singularity'     | false |           1 | '/path/to/busybox'
+        'foo'                                       | 'docker://foo'                                    | 'singularity'     | false |           1 | '/path/to/foo'
+        'library://pditommaso/foo/bar.sif:latest'   | 'library://pditommaso/foo/bar.sif:latest'         | 'singularity'     | false |           1 | '/path/to/foo-bar-latest.img'
+        and:
+        'docker://library/busybox'                  | 'docker://library/busybox'                        | 'singularity'     | true  |           0 | 'docker://library/busybox'
+        'shub://busybox'                            | 'shub://busybox'                                  | 'singularity'     | true  |           1 | '/path/to/busybox'
+
+        and:
+        null                                        | null                                              | 'apptainer'     | false |           0 | null
+        ''                                          | null                                              | 'apptainer'     | false |           0 | null
+        '/abs/path/bar.img'                         | '/abs/path/bar.img'                               | 'apptainer'     | false |           0 | '/abs/path/bar.img'
+        '/abs/path bar.img'                         | '/abs/path bar.img'                               | 'apptainer'     | false |           0 | '/abs/path\\ bar.img'
+        'file:///abs/path/bar.img'                  | '/abs/path/bar.img'                               | 'apptainer'     | false |           0 | '/abs/path/bar.img'
+        'foo.img'                                   | Paths.get('foo.img').toAbsolutePath().toString()  | 'apptainer'     | false |           0 | Paths.get('foo.img').toAbsolutePath().toString()
+        'shub://busybox'                            | 'shub://busybox'                                  | 'apptainer'     | false |           1 | '/path/to/busybox'
+        'docker://library/busybox'                  | 'docker://library/busybox'                        | 'apptainer'     | false |           1 | '/path/to/busybox'
+        'foo'                                       | 'docker://foo'                                    | 'apptainer'     | false |           1 | '/path/to/foo'
+        'library://pditommaso/foo/bar.sif:latest'   | 'library://pditommaso/foo/bar.sif:latest'         | 'apptainer'     | false |           1 | '/path/to/foo-bar-latest.img'
+        and:
+        'docker://library/busybox'                  | 'docker://library/busybox'                        | 'apptainer'     | true  |           0 | 'docker://library/busybox'
+        'shub://busybox'                            | 'shub://busybox'                                  | 'apptainer'     | true  |           1 | '/path/to/busybox'
+
+
+    }
+
     def 'should not invoke caching when engine is disabled' () {
         given:
         final handler = Spy(new ContainerHandler([engine: 'singularity']))
diff --git a/modules/nextflow/src/test/groovy/nextflow/container/SingularityBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/container/SingularityBuilderTest.groovy
index dd475dc80d..724449efa4 100644
--- a/modules/nextflow/src/test/groovy/nextflow/container/SingularityBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/container/SingularityBuilderTest.groovy
@@ -159,6 +159,12 @@ class SingularityBuilderTest extends Specification {
             .build()
             .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} ${XDG_RUNTIME_DIR:+XDG_RUNTIME_DIR="$XDG_RUNTIME_DIR"} ${DBUS_SESSION_BUS_ADDRESS:+DBUS_SESSION_BUS_ADDRESS="$DBUS_SESSION_BUS_ADDRESS"} singularity exec --no-home --oci -B "$NXF_TASK_WORKDIR" ubuntu'
 
+        new SingularityBuilder('ubuntu')
+            .params(ociMode: true)
+            .build()
+            .runCommand == 'set +u; env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} ${XDG_RUNTIME_DIR:+XDG_RUNTIME_DIR="$XDG_RUNTIME_DIR"} ${DBUS_SESSION_BUS_ADDRESS:+DBUS_SESSION_BUS_ADDRESS="$DBUS_SESSION_BUS_ADDRESS"} singularity exec --no-home --oci -B "$NXF_TASK_WORKDIR" ubuntu'
+
+
     }
 
     def 'should mount home directory if specified' () {
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/resolver/WaveContainerResolver.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/resolver/WaveContainerResolver.groovy
index 8049d292da..3dc3d412c3 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/resolver/WaveContainerResolver.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/resolver/WaveContainerResolver.groovy
@@ -70,8 +70,7 @@ class WaveContainerResolver implements ContainerResolver {
         final freeze = client().config().freezeMode()
         final config = task.getContainerConfig()
         final engine = getContainerEngine0(config)
-        final singularityOciMode = config.singularityOciMode()
-        final singularitySpec = freeze && engine in SINGULARITY_LIKE && !singularityOciMode
+        final singularitySpec = freeze && engine in SINGULARITY_LIKE && !config.canRunOciImage()
         if( !imageName ) {
             // when no image name is provided the module bundle should include a
             // Dockerfile or a Conda recipe or a Spack recipe to build

From f6c79788cbf1affcd45a26d08dc58f3de4ac068e Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Mon, 18 Dec 2023 16:27:05 +0100
Subject: [PATCH 314/350] Remove undocumented userEmulation mode (#4596)

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../nextflow/container/DockerBuilder.groovy       | 15 ++++++---------
 .../nextflow/container/DockerBuilderTest.groovy   |  5 -----
 2 files changed, 6 insertions(+), 14 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/container/DockerBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/container/DockerBuilder.groovy
index edc5fc9cb0..ad219a2f26 100644
--- a/modules/nextflow/src/main/groovy/nextflow/container/DockerBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/container/DockerBuilder.groovy
@@ -15,12 +15,16 @@
  */
 
 package nextflow.container
+
+
 import groovy.transform.CompileStatic
+import groovy.util.logging.Slf4j
 /**
  * Helper methods to handle Docker containers
  *
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
  */
+@Slf4j
 @CompileStatic
 class DockerBuilder extends ContainerBuilder<DockerBuilder> {
 
@@ -28,16 +32,12 @@ class DockerBuilder extends ContainerBuilder<DockerBuilder> {
 
     private boolean remove = true
 
-    private boolean userEmulation
-
     private String registry
 
     private String name
 
     private boolean tty
 
-    private static final String USER_AND_HOME_EMULATION = '-u $(id -u) -e "HOME=${HOME}" -v /etc/passwd:/etc/passwd:ro -v /etc/shadow:/etc/shadow:ro -v /etc/group:/etc/group:ro -v $HOME:$HOME'
-
     private String removeCommand
 
     private String killCommand
@@ -69,8 +69,8 @@ class DockerBuilder extends ContainerBuilder<DockerBuilder> {
         if( params.containsKey('runOptions') )
             addRunOptions(params.runOptions.toString())
 
-        if ( params.containsKey('userEmulation') )
-            this.userEmulation = params.userEmulation?.toString() == 'true'
+        if ( params.userEmulation?.toString() == 'true' )
+            log.warn1("Undocumented setting `docker.userEmulation` is not supported any more - consider to remove it from your config")
 
         if ( params.containsKey('remove') )
             this.remove = params.remove?.toString() == 'true'
@@ -150,9 +150,6 @@ class DockerBuilder extends ContainerBuilder<DockerBuilder> {
         if( temp )
             result << "-v $temp:/tmp "
 
-        if( userEmulation )
-            result << USER_AND_HOME_EMULATION << ' '
-
         // mount the input folders
         result << makeVolumes(mounts)
         result << '-w "$NXF_TASK_WORKDIR" '
diff --git a/modules/nextflow/src/test/groovy/nextflow/container/DockerBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/container/DockerBuilderTest.groovy
index 3a18743f3a..4265591326 100644
--- a/modules/nextflow/src/test/groovy/nextflow/container/DockerBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/container/DockerBuilderTest.groovy
@@ -97,11 +97,6 @@ class DockerBuilderTest extends Specification {
                 .build()
                 .runCommand == 'docker run -i -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" -x --zeta busybox'
 
-        new DockerBuilder('busybox')
-                .params(userEmulation:true)
-                .build()
-                .runCommand == 'docker run -i -u $(id -u) -e "HOME=${HOME}" -v /etc/passwd:/etc/passwd:ro -v /etc/shadow:/etc/shadow:ro -v /etc/group:/etc/group:ro -v $HOME:$HOME -v "$NXF_TASK_WORKDIR":"$NXF_TASK_WORKDIR" -w "$NXF_TASK_WORKDIR" busybox'
-
         new DockerBuilder('busybox')
                 .setName('hola')
                 .build()

From 58937831ee789c32160c79c94ace97ff89e322ce Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Tue, 19 Dec 2023 14:47:18 +0100
Subject: [PATCH 315/350] Fix BitBucket get source API with custom branch

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../scm/BitbucketRepositoryProvider.groovy    |  7 +++-
 .../BitbucketRepositoryProviderTest.groovy    | 39 +++++++++++--------
 2 files changed, 28 insertions(+), 18 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/scm/BitbucketRepositoryProvider.groovy b/modules/nextflow/src/main/groovy/nextflow/scm/BitbucketRepositoryProvider.groovy
index 8ee2223926..2e0392b21d 100644
--- a/modules/nextflow/src/main/groovy/nextflow/scm/BitbucketRepositoryProvider.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/scm/BitbucketRepositoryProvider.groovy
@@ -50,7 +50,7 @@ final class BitbucketRepositoryProvider extends RepositoryProvider {
 
     @Override
     String getContentUrl( String path ) {
-        final ref = revision ?: getMainBranch()
+        final ref = revision ? getRefForRevision(revision) : getMainBranch()
         return "${config.endpoint}/api/2.0/repositories/$project/src/$ref/$path"
     }
 
@@ -62,6 +62,11 @@ final class BitbucketRepositoryProvider extends RepositoryProvider {
         invokeAndParseResponse(getMainBranchUrl()) ?. mainbranch ?. name
     }
 
+    private String getRefForRevision(String revision){
+        final resp = invokeAndParseResponse("${config.endpoint}/api/2.0/repositories/$project/refs/branches/$revision")
+        return resp?.target?.hash
+    }
+
     @Memoized
     protected <T> List<T> invokeAndResponseWithPaging(String url, Closure<T> parse) {
         final result = new ArrayList<T>(50)
diff --git a/modules/nextflow/src/test/groovy/nextflow/scm/BitbucketRepositoryProviderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/scm/BitbucketRepositoryProviderTest.groovy
index f32f124e08..8fb8f51b21 100644
--- a/modules/nextflow/src/test/groovy/nextflow/scm/BitbucketRepositoryProviderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/scm/BitbucketRepositoryProviderTest.groovy
@@ -91,27 +91,32 @@ class BitbucketRepositoryProviderTest extends Specification {
         result.contains( new RepositoryProvider.BranchInfo('test-branch', '755ba829cbc4f28dcb3c16b9dcc1c49c7ee47ff5') )
     }
 
+    @Requires( { System.getenv('NXF_BITBUCKET_ACCESS_TOKEN') } )
     def 'should return content URL' () {
         given:
-        String CONFIG = '''
-        providers {
-            mybitbucket {
-                server = 'https://bitbucket.org'
-                endpoint = 'https://bitbucket.org'
-                platform = 'bitbucket'
-                user = 'myname'
-                password = 'mypassword'
-            }
-        }
-        '''
-
-        def config = new ConfigSlurper().parse(CONFIG)
-        def obj = new ProviderConfig('bitbucket', config.providers.mybitbucket as ConfigObject)
+        def token = System.getenv('NXF_BITBUCKET_ACCESS_TOKEN')
+        def config = new ProviderConfig('bitbucket').setAuth(token)
 
         expect:
-        new BitbucketRepositoryProvider('pditommaso/hello', obj)
-                .setRevision('foo')
-                .getContentUrl('main.nf') == 'https://bitbucket.org/api/2.0/repositories/pditommaso/hello/src/foo/main.nf'
+        new BitbucketRepositoryProvider('pditommaso/tutorial', config)
+                .setRevision('test-branch')
+                .getContentUrl('main.nf') == 'https://bitbucket.org/api/2.0/repositories/pditommaso/tutorial/src/755ba829cbc4f28dcb3c16b9dcc1c49c7ee47ff5/main.nf'
+    }
 
+    @Requires( { System.getenv('NXF_BITBUCKET_ACCESS_TOKEN') } )
+    def 'should read content on main and on separate branch' () {
+        given:
+        def token = System.getenv('NXF_BITBUCKET_ACCESS_TOKEN')
+        def config = new ProviderConfig('bitbucket').setAuth(token)
+        and:
+        def repo = new BitbucketRepositoryProvider('pditommaso/tutorial', config)
+
+        expect:
+        repo.readText('main.nf').contains('world')
+        !repo.readText('main.nf').contains('WORLD')
+        and:
+        repo.setRevision('feature/with-slash')
+        !repo.readText('main.nf').contains('world')
+        repo.readText('main.nf').contains('WORLD')
     }
 }

From 681ace86e81039a95864ebeb7ee13126f0765b10 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Tue, 19 Dec 2023 11:32:21 -0600
Subject: [PATCH 316/350] Fix fusion symlink test (#4604) [ci fast]

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 tests/checks/fusion-symlink.nf/.checks | 2 --
 1 file changed, 2 deletions(-)

diff --git a/tests/checks/fusion-symlink.nf/.checks b/tests/checks/fusion-symlink.nf/.checks
index 5d758c6f21..a28366d245 100644
--- a/tests/checks/fusion-symlink.nf/.checks
+++ b/tests/checks/fusion-symlink.nf/.checks
@@ -10,7 +10,6 @@ fi
 # normal run
 #
 echo initial run
-$NXF_CMD fs rm s3://nextflow-ci/work/ci-test/fusion-symlink/data.txt || true
 $NXF_RUN -c .config
 
 $NXF_CMD fs cp s3://nextflow-ci/work/ci-test/fusion-symlink/data.txt data.txt
@@ -20,7 +19,6 @@ cmp data.txt .expected || false
 # resume run
 #
 echo resumed run
-$NXF_CMD fs rm s3://nextflow-ci/work/ci-test/fusion-symlink/data.txt || true
 $NXF_RUN -c .config -resume
 
 $NXF_CMD fs cp s3://nextflow-ci/work/ci-test/fusion-symlink/data.txt data.txt

From df7ed294520ad2bfc9ad091114ae347c1e26ae96 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Tue, 19 Dec 2023 21:32:27 +0100
Subject: [PATCH 317/350] Add support for Instance template to Google Batch

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/config.md                                |  31 ++++
 docs/google.md                                |  63 +++++--
 .../batch/GoogleBatchTaskHandler.groovy       | 157 ++++++++++--------
 .../google/batch/client/BatchConfig.groovy    |   3 +
 .../batch/GoogleBatchTaskHandlerTest.groovy   |  80 ++++++++-
 5 files changed, 250 insertions(+), 84 deletions(-)

diff --git a/docs/config.md b/docs/config.md
index 51be41cb9d..f85e8c7977 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -880,6 +880,37 @@ The following settings are available for Cloud Life Sciences:
 `google.zone`
 : The Google Cloud zone where jobs are executed. Multiple zones can be provided as a comma-separated list. Cannot be used with the `google.region` option. See the [Google Cloud documentation](https://cloud.google.com/compute/docs/regions-zones/) for a list of available regions and zones.
 
+`google.batch.allowedLocations`
+: :::{versionadded} 22.12.0-edge
+  :::
+: Define the set of allowed locations for VMs to be provisioned. See [Google documentation](https://cloud.google.com/batch/docs/reference/rest/v1/projects.locations.jobs#locationpolicy) for details (default: no restriction).
+
+`google.batch.bootDiskSize`
+: Set the size of the virtual machine boot disk, e.g `50.GB` (default: none).
+
+`google.batch.cpuPlatform`
+: Set the minimum CPU Platform, e.g. `'Intel Skylake'`. See [Specifying a minimum CPU Platform for VM instances](https://cloud.google.com/compute/docs/instances/specify-min-cpu-platform#specifications) (default: none).
+
+`google.batch.installGpuDrivers`
+: :::{versionadded} 23.08.0-edge
+  :::
+: When `true` automatically installs the appropriate GPU drivers to the VM when a GPU is requested (default: `false`). Only needed when using an instance template.
+
+`google.batch.network`
+: Set network name to attach the VM's network interface to. The value will be prefixed with `global/networks/` unless it contains a `/`, in which case it is assumed to be a fully specified network resource URL. If unspecified, the global default network is used.
+
+`google.batch.serviceAccountEmail`
+: Define the Google service account email to use for the pipeline execution. If not specified, the default Compute Engine service account for the project will be used.
+
+`google.batch.spot`
+: When `true` enables the usage of *spot* virtual machines or `false` otherwise (default: `false`).
+
+`google.batch.subnetwork`
+: Define the name of the subnetwork to attach the instance to must be specified here, when the specified network is configured for custom subnet creation. The value is prefixed with `regions/subnetworks/` unless it contains a `/`, in which case it is assumed to be a fully specified subnetwork resource URL.
+
+`google.batch.usePrivateAddress`
+: When `true` the VM will NOT be provided with a public IP address, and only contain an internal IP. If this option is enabled, the associated job can only load docker images from Google Container Registry, and the job executable cannot use external services other than Google APIs (default: `false`).
+
 `google.lifeSciences.bootDiskSize`
 : Set the size of the virtual machine boot disk e.g `50.GB` (default: none).
 
diff --git a/docs/google.md b/docs/google.md
index 1dcddfc2d8..39cabf5722 100644
--- a/docs/google.md
+++ b/docs/google.md
@@ -90,45 +90,78 @@ Read the {ref}`Google configuration<config-google>` section to learn more about
 
 ### Process definition
 
-Processes can be defined as usual and by default the `cpus` and `memory` directives are used to find the cheapest machine type available at current location that fits the requested resources. If `memory` is not specified, 1GB of memory is allocated per cpu.
+By default, the `cpus` and `memory` directives are used to find the cheapest machine type that is available at the current
+location and that fits the requested resources. If `memory` is not specified, 1 GB of memory is allocated per CPU.
 
-:::{versionadded} 23.02.0-edge
-The `machineType` directive can be a list of patterns separated by comma. The pattern can contain a `*` to match any number of characters and `?` to match any single character. Examples of valid patterns: `c2-*`, `m?-standard*`, `n*`.
-
-Alternatively it can also be used to define a specific predefined Google Compute Platform [machine type](https://cloud.google.com/compute/docs/machine-types) or a custom machine type.
-:::
-
-Examples:
+The `machineType` directive can be used to request a specific VM instance type. It can be any predefined Google Compute
+Platform [machine type](https://cloud.google.com/compute/docs/machine-types) or [custom machine type](https://cloud.google.com/compute/docs/instances/creating-instance-with-custom-machine-type).
 
 ```groovy
-process automatic_resources_task {
+process myTask {
     cpus 8
     memory '40 GB'
 
     """
-    <Your script here>
+    your_command --here
+    """
+}
+
+process anotherTask {
+    machineType 'n1-highmem-8'
+
+    """
+    your_command --here
     """
 }
+```
 
-process allowing_some_series {
+:::{versionadded} 23.02.0-edge
+:::
+
+The `machineType` directive can also be a comma-separated list of patterns. The pattern can contain a `*` to match any
+number of characters and `?` to match any single character. Examples of valid patterns: `c2-*`, `m?-standard*`, `n*`.
+
+```groovy
+process myTask {
     cpus 8
     memory '20 GB'
     machineType 'n2-*,c2-*,m3-*'
 
     """
-    <Your script here>
+    your_command --here
     """
 }
+```
 
-process predefined_resources_task {
-    machineType 'n1-highmem-8'
+:::{versionadded} 23.12.0-edge
+:::
+
+The `machineType` directive can also be an [Instance Template](https://cloud.google.com/compute/docs/instance-templates),
+specified as `template://<instance-template>`. For example:
+
+```groovy
+process myTask {
+    cpus 8
+    memory '20 GB'
+    machineType 'template://my-template'
 
     """
-    <Your script here>
+    your_command --here
     """
 }
 ```
 
+:::{note}
+Using an instance template will overwrite the `accelerator` and `disk` directives, as well as the following Google Batch
+config options: `cpuPlatform`, `preemptible`, and `spot`.
+:::
+
+To use an instance template with GPUs, you must also set the `google.batch.installGpuDrivers` config option to `true`.
+
+To use an instance template with Fusion, the instance template must include a `local-ssd` disk named `fusion` with 375 GB.
+See the [Google Batch documentation](https://cloud.google.com/compute/docs/disks/local-ssd) for more details about local SSDs.
+
+
 :::{versionadded} 23.06.0-edge
 :::
 
diff --git a/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchTaskHandler.groovy b/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchTaskHandler.groovy
index c7cbd17dc6..8e35fc1c43 100644
--- a/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchTaskHandler.groovy
+++ b/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchTaskHandler.groovy
@@ -176,16 +176,16 @@ class GoogleBatchTaskHandler extends TaskHandler implements FusionAwareTask {
         final accel = task.config.getAccelerator()
         // add nvidia specific driver paths
         // see https://cloud.google.com/batch/docs/create-run-job#create-job-gpu
-        if(  accel && accel.type.toLowerCase().startsWith('nvidia-') ) {
+        if( accel && accel.type.toLowerCase().startsWith('nvidia-') ) {
             container
                 .addVolumes('/var/lib/nvidia/lib64:/usr/local/nvidia/lib64')
                 .addVolumes('/var/lib/nvidia/bin:/usr/local/nvidia/bin')
         }
 
-        def containerOptions= task.config.getContainerOptions() ?: ''
+        def containerOptions = task.config.getContainerOptions() ?: ''
         // accelerator requires privileged option
         // https://cloud.google.com/batch/docs/create-run-job#create-job-gpu
-        if( task.config.getAccelerator() || fusionEnabled()) {
+        if( task.config.getAccelerator() || fusionEnabled() ) {
             if( containerOptions ) containerOptions += ' '
             containerOptions += '--privileged'
         }
@@ -226,9 +226,9 @@ class GoogleBatchTaskHandler extends TaskHandler implements FusionAwareTask {
         }
 
         // instance policy
+        // allocation policy
         final allocationPolicy = AllocationPolicy.newBuilder()
         final instancePolicyOrTemplate = AllocationPolicy.InstancePolicyOrTemplate.newBuilder()
-        final instancePolicy = AllocationPolicy.InstancePolicy.newBuilder()
 
         if( executor.config.getAllowedLocations() )
             allocationPolicy.setLocation(
@@ -236,80 +236,107 @@ class GoogleBatchTaskHandler extends TaskHandler implements FusionAwareTask {
                     .addAllAllowedLocations( executor.config.getAllowedLocations() )
             )
 
-        if( task.config.getAccelerator() ) {
-            final accelerator = AllocationPolicy.Accelerator.newBuilder()
-                .setCount( task.config.getAccelerator().getRequest() )
+        if( executor.config.serviceAccountEmail )
+            allocationPolicy.setServiceAccount(
+                ServiceAccount.newBuilder()
+                    .setEmail( executor.config.serviceAccountEmail )
+            )
 
-            if( task.config.getAccelerator().getType() )
-                accelerator.setType( task.config.getAccelerator().getType() )
+        allocationPolicy.putAllLabels( task.config.getResourceLabels() )
 
-            instancePolicy.addAccelerators(accelerator)
-            instancePolicyOrTemplate.setInstallGpuDrivers(true)
-        }
+        // use instance template if specified
+        if( task.config.getMachineType()?.startsWith('template://') ) {
+            if( task.config.getAccelerator() )
+                log.warn1 'Process directive `accelerator` ignored because an instance template was specified'
 
-        if( fusionEnabled() && !disk ) {
-            disk = new DiskResource(request: '375 GB', type: 'local-ssd')
-            log.debug "[GOOGLE BATCH] Process `${task.lazyName()}` - adding local volume as fusion scratch: $disk"
-        }
+            if( task.config.getDisk() )
+                log.warn1 'Process directive `disk` ignored because an instance template was specified'
 
-        if( executor.config.cpuPlatform ) {
-            instancePolicy.setMinCpuPlatform( executor.config.cpuPlatform )
-        }
+            if( executor.config.cpuPlatform )
+                log.warn1 'Config option `google.batch.cpuPlatform` ignored because an instance template was specified'
 
-        final machineType = findBestMachineType(task.config, disk?.type == 'local-ssd')
-        if( machineType ) {
-            instancePolicy.setMachineType(machineType.type)
-            machineInfo = new CloudMachineInfo(
-                    type: machineType.type,
-                    zone: machineType.location,
-                    priceModel: machineType.priceModel
-            )
+            if( executor.config.preemptible )
+                log.warn1 'Config option `google.batch.premptible` ignored because an instance template was specified'
+
+            if( executor.config.spot )
+                log.warn1 'Config option `google.batch.spot` ignored because an instance template was specified'
+
+            instancePolicyOrTemplate
+                .setInstallGpuDrivers( executor.config.getInstallGpuDrivers() )
+                .setInstanceTemplate( task.config.getMachineType().minus('template://') )
         }
 
-        // When using local SSD not all the disk sizes are valid and depends on the machine type
-        if( disk?.type == 'local-ssd' && machineType ) {
-            final validSize = GoogleBatchMachineTypeSelector.INSTANCE.findValidLocalSSDSize(disk.request, machineType)
-            if( validSize != disk.request ) {
-                disk = new DiskResource(request: validSize, type: 'local-ssd')
-                log.debug "[GOOGLE BATCH] Process `${task.lazyName()}` - adjusting local disk size to: $validSize"
+        // otherwise create instance policy
+        else {
+            final instancePolicy = AllocationPolicy.InstancePolicy.newBuilder()
+
+            if( task.config.getAccelerator() ) {
+                final accelerator = AllocationPolicy.Accelerator.newBuilder()
+                    .setCount( task.config.getAccelerator().getRequest() )
+
+                if( task.config.getAccelerator().getType() )
+                    accelerator.setType( task.config.getAccelerator().getType() )
+
+                instancePolicy.addAccelerators(accelerator)
+                instancePolicyOrTemplate.setInstallGpuDrivers(true)
             }
-        }
 
-        // use disk directive for an attached disk if type is specified
-        if( disk?.type ) {
-            instancePolicy.addDisks(
-                AllocationPolicy.AttachedDisk.newBuilder()
-                    .setNewDisk(
-                        AllocationPolicy.Disk.newBuilder()
-                            .setType(disk.type)
-                            .setSizeGb(disk.request.toGiga())
-                    )
-                    .setDeviceName('scratch')
-            )
+            if( fusionEnabled() && !disk ) {
+                disk = new DiskResource(request: '375 GB', type: 'local-ssd')
+                log.debug "[GOOGLE BATCH] Process `${task.lazyName()}` - adding local volume as fusion scratch: $disk"
+            }
 
-            taskSpec.addVolumes(
-                Volume.newBuilder()
-                    .setDeviceName('scratch')
-                    .setMountPath('/tmp')
-            )
-        }
+            final machineType = findBestMachineType(task.config, disk?.type == 'local-ssd')
+            if( machineType ) {
+                instancePolicy.setMachineType(machineType.type)
+                machineInfo = new CloudMachineInfo(
+                        type: machineType.type,
+                        zone: machineType.location,
+                        priceModel: machineType.priceModel
+                )
+            }
 
-        if( executor.config.serviceAccountEmail )
-            allocationPolicy.setServiceAccount(
-                ServiceAccount.newBuilder()
-                    .setEmail(executor.config.serviceAccountEmail)
-            )
+            // When using local SSD not all the disk sizes are valid and depends on the machine type
+            if( disk?.type == 'local-ssd' && machineType ) {
+                final validSize = GoogleBatchMachineTypeSelector.INSTANCE.findValidLocalSSDSize(disk.request, machineType)
+                if( validSize != disk.request ) {
+                    disk = new DiskResource(request: validSize, type: 'local-ssd')
+                    log.debug "[GOOGLE BATCH] Process `${task.lazyName()}` - adjusting local disk size to: $validSize"
+                }
+            }
 
-        if( executor.config.preemptible )
-            instancePolicy.setProvisioningModel( AllocationPolicy.ProvisioningModel.PREEMPTIBLE )
+            // use disk directive for an attached disk if type is specified
+            if( disk?.type ) {
+                instancePolicy.addDisks(
+                    AllocationPolicy.AttachedDisk.newBuilder()
+                        .setNewDisk(
+                            AllocationPolicy.Disk.newBuilder()
+                                .setType(disk.type)
+                                .setSizeGb(disk.request.toGiga())
+                        )
+                        .setDeviceName('scratch')
+                )
 
-        if( executor.config.spot )
-            instancePolicy.setProvisioningModel( AllocationPolicy.ProvisioningModel.SPOT )
+                taskSpec.addVolumes(
+                    Volume.newBuilder()
+                        .setDeviceName('scratch')
+                        .setMountPath('/tmp')
+                )
+            }
 
-        allocationPolicy.addInstances(
-            instancePolicyOrTemplate
-                .setPolicy(instancePolicy)
-        )
+            if( executor.config.cpuPlatform )
+                instancePolicy.setMinCpuPlatform( executor.config.cpuPlatform )
+
+            if( executor.config.preemptible )
+                instancePolicy.setProvisioningModel( AllocationPolicy.ProvisioningModel.PREEMPTIBLE )
+
+            if( executor.config.spot )
+                instancePolicy.setProvisioningModel( AllocationPolicy.ProvisioningModel.SPOT )
+
+            instancePolicyOrTemplate.setPolicy( instancePolicy )
+        }
+
+        allocationPolicy.addInstances(instancePolicyOrTemplate)
 
         // network policy
         final networkInterface = AllocationPolicy.NetworkInterface.newBuilder()
@@ -334,8 +361,6 @@ class GoogleBatchTaskHandler extends TaskHandler implements FusionAwareTask {
                     .addNetworkInterfaces(networkInterface)
             )
 
-        allocationPolicy.putAllLabels(task.config.getResourceLabels())
-
         // create the job
         return Job.newBuilder()
             .addTaskGroups(
diff --git a/plugins/nf-google/src/main/nextflow/cloud/google/batch/client/BatchConfig.groovy b/plugins/nf-google/src/main/nextflow/cloud/google/batch/client/BatchConfig.groovy
index a1dcc07a1e..e1894d20b2 100644
--- a/plugins/nf-google/src/main/nextflow/cloud/google/batch/client/BatchConfig.groovy
+++ b/plugins/nf-google/src/main/nextflow/cloud/google/batch/client/BatchConfig.groovy
@@ -38,6 +38,7 @@ class BatchConfig {
     private MemoryUnit bootDiskSize
     private String cpuPlatform
     private int maxSpotAttempts
+    private boolean installGpuDrivers
     private boolean preemptible
     private boolean spot
     private boolean usePrivateAddress
@@ -51,6 +52,7 @@ class BatchConfig {
     MemoryUnit getBootDiskSize() { bootDiskSize }
     String getCpuPlatform() { cpuPlatform }
     int getMaxSpotAttempts() { maxSpotAttempts }
+    boolean getInstallGpuDrivers() { installGpuDrivers }
     boolean getPreemptible() { preemptible }
     boolean getSpot() { spot }
     boolean getUsePrivateAddress() { usePrivateAddress }
@@ -66,6 +68,7 @@ class BatchConfig {
         result.bootDiskSize = session.config.navigate('google.batch.bootDiskSize') as MemoryUnit
         result.cpuPlatform = session.config.navigate('google.batch.cpuPlatform')
         result.maxSpotAttempts = session.config.navigate('google.batch.maxSpotAttempts',5) as int
+        result.installGpuDrivers = session.config.navigate('google.batch.installGpuDrivers',false)
         result.preemptible = session.config.navigate('google.batch.preemptible',false)
         result.spot = session.config.navigate('google.batch.spot',false)
         result.usePrivateAddress = session.config.navigate('google.batch.usePrivateAddress',false)
diff --git a/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchTaskHandlerTest.groovy b/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchTaskHandlerTest.groovy
index ec648112cb..69b28a2c2d 100644
--- a/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchTaskHandlerTest.groovy
+++ b/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchTaskHandlerTest.groovy
@@ -83,6 +83,7 @@ class GoogleBatchTaskHandlerTest extends Specification {
         def taskGroup = req.getTaskGroups(0)
         def runnable = taskGroup.getTaskSpec().getRunnables(0)
         def allocationPolicy = req.getAllocationPolicy()
+        def instancePolicyOrTemplate = allocationPolicy.getInstances(0)
         def instancePolicy = allocationPolicy.getInstances(0).getPolicy()
         and:
         taskGroup.getTaskSpec().getComputeResource().getBootDiskMib() == 0
@@ -92,13 +93,15 @@ class GoogleBatchTaskHandlerTest extends Specification {
         and:
         runnable.getContainer().getCommandsList().join(' ') == '/bin/bash -o pipefail -c bash .command.run'
         runnable.getContainer().getImageUri() == CONTAINER_IMAGE
-        runnable.getContainer().getOptions() == ''
+        !runnable.getContainer().getOptions()
         runnable.getContainer().getVolumesList() == ['/mnt/disks/foo/scratch:/mnt/disks/foo/scratch:rw']
         and:
+        !instancePolicyOrTemplate.getInstanceTemplate()
+        and:
         instancePolicy.getAcceleratorsCount() == 0
         instancePolicy.getDisksCount() == 0
-        instancePolicy.getMachineType() == ''
-        instancePolicy.getMinCpuPlatform() == ''
+        !instancePolicy.getMachineType()
+        !instancePolicy.getMinCpuPlatform()
         instancePolicy.getProvisioningModel().toString() == 'PROVISIONING_MODEL_UNSPECIFIED'
         and:
         allocationPolicy.getLocation().getAllowedLocationsCount() == 0
@@ -221,6 +224,7 @@ class GoogleBatchTaskHandlerTest extends Specification {
         req.getLabelsMap() == [foo: 'bar']
 
 
+        // with custom disk type
         when:
         req = handler.newSubmitRequest(task, launcher)
         then:
@@ -231,6 +235,67 @@ class GoogleBatchTaskHandlerTest extends Specification {
         req.getTaskGroups(0).getTaskSpec().getComputeResource().getBootDiskMib() == 100 * 1024
     }
 
+    def 'should use instance template' () {
+        given:
+        def GCS_VOL = Volume.newBuilder().setGcs(GCS.newBuilder().setRemotePath('foo').build() ).build()
+        def WORK_DIR = CloudStorageFileSystem.forBucket('foo').getPath('/scratch')
+        def CONTAINER_IMAGE = 'debian:latest'
+        def INSTANCE_TEMPLATE = 'instance-template'
+        def exec = Mock(GoogleBatchExecutor) {
+            getConfig() >> Mock(BatchConfig) {
+                getInstallGpuDrivers() >> true
+            }
+        }
+        and:
+        def bean = new TaskBean(workDir: WORK_DIR, inputFiles: [:])
+        def task = Mock(TaskRun) {
+            toTaskBean() >> bean
+            getHashLog() >> 'abcd1234'
+            getWorkDir() >> WORK_DIR
+            getContainer() >> CONTAINER_IMAGE
+            getConfig() >> Mock(TaskConfig) {
+                getCpus() >> 2
+                getMachineType() >> "template://${INSTANCE_TEMPLATE}"
+                getResourceLabels() >> [:]
+            }
+        }
+        and:
+        def mounts = ['/mnt/disks/foo/scratch:/mnt/disks/foo/scratch:rw']
+        def volumes = [GCS_VOL]
+        def launcher = new GoogleBatchLauncherSpecMock('bash .command.run', mounts, volumes)
+
+        and:
+        def handler = Spy(new GoogleBatchTaskHandler(task, exec))
+
+        when:
+        def req = handler.newSubmitRequest(task, launcher)
+        then:
+        handler.fusionEnabled() >> false
+        handler.findBestMachineType(_, false) >> null
+
+        and:
+        def taskGroup = req.getTaskGroups(0)
+        def runnable = taskGroup.getTaskSpec().getRunnables(0)
+        def allocationPolicy = req.getAllocationPolicy()
+        def instancePolicyOrTemplate = allocationPolicy.getInstances(0)
+        and:
+        taskGroup.getTaskSpec().getComputeResource().getBootDiskMib() == 0
+        taskGroup.getTaskSpec().getComputeResource().getCpuMilli() == 2_000
+        taskGroup.getTaskSpec().getComputeResource().getMemoryMib() == 0
+        taskGroup.getTaskSpec().getMaxRunDuration().getSeconds() == 0
+        and:
+        runnable.getContainer().getCommandsList().join(' ') == '/bin/bash -o pipefail -c bash .command.run'
+        runnable.getContainer().getImageUri() == CONTAINER_IMAGE
+        !runnable.getContainer().getOptions()
+        runnable.getContainer().getVolumesList() == ['/mnt/disks/foo/scratch:/mnt/disks/foo/scratch:rw']
+        and:
+        instancePolicyOrTemplate.getInstallGpuDrivers() == true
+        instancePolicyOrTemplate.getInstanceTemplate() == INSTANCE_TEMPLATE
+        and:
+        taskGroup.getTaskSpec().getVolumesCount() == 1
+        taskGroup.getTaskSpec().getVolumes(0) == GCS_VOL
+    }
+
     def 'should create the trace record' () {
         given:
         def exec = Mock(Executor) { getName() >> 'google-batch' }
@@ -305,8 +370,17 @@ class GoogleBatchTaskHandlerTest extends Specification {
         and:
         runnable.getEnvironment().getVariablesMap() == env
         and:
+        instancePolicy.getAcceleratorsCount() == 0
         instancePolicy.getDisks(0).getNewDisk().getSizeGb() == 375
         instancePolicy.getDisks(0).getNewDisk().getType() == 'local-ssd'
+        !instancePolicy.getMachineType()
+        !instancePolicy.getMinCpuPlatform()
+        instancePolicy.getProvisioningModel().toString() == 'PROVISIONING_MODEL_UNSPECIFIED'
+        and:
+        allocationPolicy.getLocation().getAllowedLocationsCount() == 0
+        allocationPolicy.getNetwork().getNetworkInterfacesCount() == 0
+        and:
+        req.getLogsPolicy().getDestination().toString() == 'CLOUD_LOGGING'
     }
 
     def 'should not set wildcard expressions as machine type'() {

From f72518955a9834f763cf10773df70dfb9e7dcdae Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Wed, 20 Dec 2023 08:30:50 +0100
Subject: [PATCH 318/350] Add ability to disable Cloudinfo service (#4606)

This commit adds the ability to disable the use of Cloudinfo service to
fetch the available matching types made by Google Cloud Batch, by setting
the following env variable:

```
export NXF_CLOUDINFO_ENABLED =false
```

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../google/batch/GoogleBatchExecutor.groovy   |  5 ++
 .../batch/GoogleBatchTaskHandler.groovy       | 36 ++++++-----
 .../batch/GoogleBatchExecutorTest.groovy      | 23 ++++++-
 .../batch/GoogleBatchTaskHandlerTest.groovy   | 61 ++++++++++++++++++-
 4 files changed, 107 insertions(+), 18 deletions(-)

diff --git a/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchExecutor.groovy b/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchExecutor.groovy
index 267be03efc..8ce631f00d 100644
--- a/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchExecutor.groovy
+++ b/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchExecutor.groovy
@@ -21,6 +21,7 @@ import java.nio.file.Path
 
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
+import nextflow.SysEnv
 import nextflow.cloud.google.batch.client.BatchConfig
 import nextflow.cloud.google.batch.client.BatchClient
 import nextflow.cloud.google.batch.logging.BatchLogging
@@ -124,4 +125,8 @@ class GoogleBatchExecutor extends Executor implements ExtensionPoint {
     boolean isFusionEnabled() {
         return FusionHelper.isFusionEnabled(session)
     }
+
+    boolean isCloudinfoEnabled() {
+        return Boolean.parseBoolean(SysEnv.get('NXF_CLOUDINFO_ENABLED', 'true') )
+    }
 }
diff --git a/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchTaskHandler.groovy b/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchTaskHandler.groovy
index 8e35fc1c43..b6057cb67e 100644
--- a/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchTaskHandler.groovy
+++ b/plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchTaskHandler.groovy
@@ -17,7 +17,6 @@
 
 package nextflow.cloud.google.batch
 
-
 import java.nio.file.Path
 
 import com.google.cloud.batch.v1.AllocationPolicy
@@ -287,6 +286,7 @@ class GoogleBatchTaskHandler extends TaskHandler implements FusionAwareTask {
             }
 
             final machineType = findBestMachineType(task.config, disk?.type == 'local-ssd')
+
             if( machineType ) {
                 instancePolicy.setMachineType(machineType.type)
                 machineInfo = new CloudMachineInfo(
@@ -494,32 +494,38 @@ class GoogleBatchTaskHandler extends TaskHandler implements FusionAwareTask {
         return result
     }
 
+    protected GoogleBatchMachineTypeSelector.MachineType bestMachineType0(int cpus, int memory, String location, boolean spot, boolean localSSD, List<String> families) {
+        return GoogleBatchMachineTypeSelector.INSTANCE.bestMachineType(cpus, memory, location, spot, localSSD, families)
+    }
+
     protected GoogleBatchMachineTypeSelector.MachineType findBestMachineType(TaskConfig config, boolean localSSD) {
         final location = client.location
         final cpus = config.getCpus()
         final memory = config.getMemory() ? config.getMemory().toMega().toInteger() : 1024
         final spot = executor.config.spot ?: executor.config.preemptible
-        final families = config.getMachineType() ? config.getMachineType().tokenize(',') : []
+        final machineType = config.getMachineType()
+        final families = machineType ? machineType.tokenize(',') : List.<String>of()
         final priceModel = spot ? PriceModel.spot : PriceModel.standard
 
         try {
-            return GoogleBatchMachineTypeSelector.INSTANCE.bestMachineType(cpus, memory, location, spot, localSSD, families)
+            if( executor.isCloudinfoEnabled() ) {
+                return bestMachineType0(cpus, memory, location, spot, localSSD, families)
+            }
         }
         catch (Exception e) {
-            log.debug "[GOOGLE BATCH] Cannot select machine type using cloud info for task: `${task.lazyName()}` - ${e.message}"
-
-            // Check if a specific machine type was provided by the user
-            if( config.getMachineType() && !config.getMachineType().contains(',') && !config.getMachineType().contains('*') )
-                return new GoogleBatchMachineTypeSelector.MachineType(
-                        type: config.getMachineType(),
-                        location: location,
-                        priceModel: priceModel
-                )
-
-            // Fallback to Google Batch automatically deduce from requested resources
-            return null
+            log.debug "[GOOGLE BATCH] Cannot select machine type using Seqera Cloudinfo for task: `${task.lazyName()}` - ${e.message}"
         }
 
+        // Check if a specific machine type was provided by the user
+        if( machineType && !machineType.contains(',') && !machineType.contains('*') )
+            return new GoogleBatchMachineTypeSelector.MachineType(
+                type: machineType,
+                location: location,
+                priceModel: priceModel
+            )
+
+        // Fallback to Google Batch automatically deduce from requested resources
+        return null
     }
 
 }
diff --git a/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchExecutorTest.groovy b/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchExecutorTest.groovy
index 9e0c803bac..f1ab831680 100644
--- a/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchExecutorTest.groovy
+++ b/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchExecutorTest.groovy
@@ -10,6 +10,8 @@ package nextflow.cloud.google.batch
 import nextflow.Session
 import nextflow.SysEnv
 import spock.lang.Specification
+import spock.lang.Unroll
+
 /**
  *
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
@@ -38,7 +40,26 @@ class GoogleBatchExecutorTest extends Specification {
         [fusion:[enabled: false]]   | [FUSION_ENABLED:'true']   | false     // <-- config has priority
         [:]                         | [FUSION_ENABLED:'true']   | true
         [:]                         | [FUSION_ENABLED:'false']  | false
-
     }
 
+    @Unroll
+    def 'should check cloudinfo enabled' () {
+        given:
+        SysEnv.push(ENV)
+        and:
+        def sess = Mock(Session) { getConfig() >> [:] }
+        def executor = new GoogleBatchExecutor(session: sess)
+
+        expect:
+        executor.isCloudinfoEnabled() == EXPECTED
+
+        cleanup:
+        SysEnv.pop()
+
+        where:
+        ENV                             | EXPECTED
+        [:]                             | true
+        [NXF_CLOUDINFO_ENABLED:'true']  | true
+        [NXF_CLOUDINFO_ENABLED:'false'] | false
+    }
 }
diff --git a/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchTaskHandlerTest.groovy b/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchTaskHandlerTest.groovy
index 69b28a2c2d..044822d874 100644
--- a/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchTaskHandlerTest.groovy
+++ b/plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchTaskHandlerTest.groovy
@@ -17,15 +17,16 @@
 
 package nextflow.cloud.google.batch
 
+import java.nio.file.Path
+
 import com.google.cloud.batch.v1.GCS
 import com.google.cloud.batch.v1.JobStatus
 import com.google.cloud.batch.v1.StatusEvent
-import com.google.cloud.batch.v1.TaskExecution
 import com.google.cloud.batch.v1.Volume
 import com.google.cloud.storage.contrib.nio.CloudStorageFileSystem
+import nextflow.SysEnv
 import nextflow.cloud.google.batch.client.BatchClient
 import nextflow.cloud.google.batch.client.BatchConfig
-import nextflow.cloud.types.CloudMachineInfo
 import nextflow.cloud.types.PriceModel
 import nextflow.executor.Executor
 import nextflow.executor.res.AcceleratorResource
@@ -443,4 +444,60 @@ class GoogleBatchTaskHandlerTest extends Specification {
         handler.getJobExitCode() == 50001
         handler.getJobExitCode() == null
     }
+
+    def 'should find best instance type' () {
+        given:
+        def workDir = Path.of('/work/dir')
+        def client = Mock(BatchClient)
+        def task = Mock(TaskRun) {
+             hashLog >> '1234567890'
+             getWorkDir() >> workDir
+        }
+        def exec = Mock(GoogleBatchExecutor) {
+            getClient() >> client
+            getConfig() >> Mock(BatchConfig) { getSpot()>>false }
+            isCloudinfoEnabled() >> true
+        }
+        def handler = Spy(new GoogleBatchTaskHandler(task, exec))
+        and:
+        def config = Mock(TaskConfig)
+        def machineType = GroovyMock(GoogleBatchMachineTypeSelector.MachineType)
+
+        when:
+        def result = handler.findBestMachineType(config, false)
+        then:
+        1 * handler.bestMachineType0(_,_,_,_,_,_) >> machineType
+        and:
+        result == machineType
+    }
+
+    def 'should disable cloudinfo' () {
+        given:
+        SysEnv.push(NXF_CLOUDINFO_ENABLED: 'false')
+
+        def workDir = Path.of('/work/dir')
+        def client = Mock(BatchClient)
+        def task = Mock(TaskRun) {
+            hashLog >> '1234567890'
+            getWorkDir() >> workDir
+        }
+        def exec = Mock(GoogleBatchExecutor) {
+            getClient() >> client
+            getConfig() >> Mock(BatchConfig) { getSpot()>>false }
+            isCloudinfoEnabled() >> false
+        }
+        def handler = Spy(new GoogleBatchTaskHandler(task, exec))
+        and:
+        def config = Mock(TaskConfig)
+
+        when:
+        def result = handler.findBestMachineType(config, false)
+        then:
+        0 * handler.bestMachineType0(_,_,_,_,_,_) >> null
+        and:
+        result == null
+
+        cleanup:
+        SysEnv.pop()
+    }
 }

From 0b40b7b9f183476cfc6ebbcb8bbcef80617f49e4 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Wed, 20 Dec 2023 08:38:44 +0100
Subject: [PATCH 319/350] Bump nf-amazon@2.3.0

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-amazon/changelog.txt                      | 4 ++++
 plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/plugins/nf-amazon/changelog.txt b/plugins/nf-amazon/changelog.txt
index 0ec2acf6c0..dd65d7638d 100644
--- a/plugins/nf-amazon/changelog.txt
+++ b/plugins/nf-amazon/changelog.txt
@@ -1,5 +1,9 @@
 nf-amazon changelog
 ===================
+2.3.0 - 20 Dec 2023
+- Add AWS_SESSION_TOKEN to Fusion environment (#4581) [552f29b0]
+- Add experimental support for Fargate compute type for AWS Batch (#3474) [47cf335b]
+
 2.2.0 - 24 Nov 2023
 - Add support for FUSION_AWS_REGION (#4481) [8f8b09fa]
 - Fix security vulnerabilities (#4513) [a310c777]
diff --git a/plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF b/plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF
index 41788507b1..e77069ebe8 100644
--- a/plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: nextflow.cloud.aws.AmazonPlugin
 Plugin-Id: nf-amazon
-Plugin-Version: 2.2.0
+Plugin-Version: 2.3.0
 Plugin-Provider: Seqera Labs
 Plugin-Requires: >=23.11.0-edge

From bcb20fcf066d008e9d0754813933f5b4a52641af Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Wed, 20 Dec 2023 08:40:44 +0100
Subject: [PATCH 320/350] Bump nf-google@1.10.0

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-google/changelog.txt                      | 5 +++++
 plugins/nf-google/src/resources/META-INF/MANIFEST.MF | 2 +-
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/plugins/nf-google/changelog.txt b/plugins/nf-google/changelog.txt
index 30440b654a..3deea2da74 100644
--- a/plugins/nf-google/changelog.txt
+++ b/plugins/nf-google/changelog.txt
@@ -1,5 +1,10 @@
 nf-google changelog
 ===================
+1.10.0 - 20 Dec 2023
+- Add ability to disable Cloudinfo service (#4606) [f7251895]
+- Add support for Instance template to Google Batch [df7ed294]
+- Improve GLS tests [ci fast] [58590b1c]
+
 1.9.0 - 24 Nov 2023
 - Add labels field in Job request for Google Batch (#4538) [627c595e]
 - Add Google Batch native retry on spot termination (#4500) [ea1c1b70]
diff --git a/plugins/nf-google/src/resources/META-INF/MANIFEST.MF b/plugins/nf-google/src/resources/META-INF/MANIFEST.MF
index aa04d212ae..638f05f9d4 100644
--- a/plugins/nf-google/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-google/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: nextflow.cloud.google.GoogleCloudPlugin
 Plugin-Id: nf-google
-Plugin-Version: 1.9.0
+Plugin-Version: 1.10.0
 Plugin-Provider: Seqera Labs
 Plugin-Requires: >=23.11.0-edge

From 9cb500354655edc7bb3f6968851f272f39428c4e Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Wed, 20 Dec 2023 08:50:30 +0100
Subject: [PATCH 321/350] Bump wave-utils@0.8.1 and micromamba@1.5.5

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-wave/build.gradle                         |  2 +-
 .../test/io/seqera/wave/plugin/WaveClientTest.groovy | 12 ++++++------
 .../seqera/wave/plugin/config/WaveConfigTest.groovy  |  4 ++--
 3 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/plugins/nf-wave/build.gradle b/plugins/nf-wave/build.gradle
index ed170126a5..c4964f9edc 100644
--- a/plugins/nf-wave/build.gradle
+++ b/plugins/nf-wave/build.gradle
@@ -36,7 +36,7 @@ dependencies {
     api 'org.apache.commons:commons-lang3:3.12.0'
     api 'com.google.code.gson:gson:2.10.1'
     api 'org.yaml:snakeyaml:2.0'
-    api 'io.seqera:wave-utils:0.8.0'
+    api 'io.seqera:wave-utils:0.8.1'
 
     testImplementation(testFixtures(project(":nextflow")))
     testImplementation "org.codehaus.groovy:groovy:3.0.19"
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
index a15c8cc2bb..07e0635442 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
@@ -527,7 +527,7 @@ class WaveClientTest extends Specification {
         def assets = client.resolveAssets(task, null, false)
         then:
         assets.containerFile == '''\
-                FROM mambaorg/micromamba:1.5.1
+                FROM mambaorg/micromamba:1.5.5
                 COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml
                 RUN micromamba install -y -n base -f /tmp/conda.yml \\
                     && micromamba install -y -n base conda-forge::procps-ng \\
@@ -566,7 +566,7 @@ class WaveClientTest extends Specification {
         def assets = client.resolveAssets(task, null, false)
         then:
         assets.containerFile == '''\
-                FROM mambaorg/micromamba:1.5.1
+                FROM mambaorg/micromamba:1.5.5
                 RUN \\
                     micromamba install -y -n base -c seqera -c conda-forge -c bioconda -c defaults -f https://host.com/conda-lock.yml \\
                     && micromamba install -y -n base conda-forge::procps-ng \\
@@ -642,7 +642,7 @@ class WaveClientTest extends Specification {
         def assets = client.resolveAssets(task, null, false)
         then:
         assets.containerFile == '''\
-                FROM mambaorg/micromamba:1.5.1
+                FROM mambaorg/micromamba:1.5.5
                 COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml
                 RUN micromamba install -y -n base -f /tmp/conda.yml \\
                     && micromamba install -y -n base conda-forge::procps-ng \\
@@ -723,7 +723,7 @@ class WaveClientTest extends Specification {
         then:
         assets.containerFile == '''\
                 BootStrap: docker
-                From: mambaorg/micromamba:1.5.1
+                From: mambaorg/micromamba:1.5.5
                 %files
                     {{wave_context_dir}}/conda.yml /scratch/conda.yml
                 %post
@@ -766,7 +766,7 @@ class WaveClientTest extends Specification {
         then:
         assets.containerFile == '''\
                 BootStrap: docker
-                From: mambaorg/micromamba:1.5.1
+                From: mambaorg/micromamba:1.5.5
                 %post
                     micromamba install -y -n base -c seqera -c conda-forge -c bioconda -c defaults -f https://host.com/lock-file.yaml
                     micromamba install -y -n base conda-forge::procps-ng
@@ -800,7 +800,7 @@ class WaveClientTest extends Specification {
         then:
         assets.containerFile == '''\
                 BootStrap: docker
-                From: mambaorg/micromamba:1.5.1
+                From: mambaorg/micromamba:1.5.5
                 %files
                     {{wave_context_dir}}/conda.yml /scratch/conda.yml
                 %post
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy
index a904258b2f..16e8dd6aa8 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy
@@ -86,7 +86,7 @@ class WaveConfigTest extends Specification {
         when:
         def opts = new WaveConfig([:])
         then:
-        opts.condaOpts().mambaImage == 'mambaorg/micromamba:1.5.1'
+        opts.condaOpts().mambaImage == 'mambaorg/micromamba:1.5.5'
         opts.condaOpts().commands == null
 
         when:
@@ -199,7 +199,7 @@ class WaveConfigTest extends Specification {
         given:
         def config = new WaveConfig([enabled: true])
         expect:
-        config.toString() == 'WaveConfig(enabled:true, endpoint:https://wave.seqera.io, containerConfigUrl:[], tokensCacheMaxDuration:30m, condaOpts:CondaOpts(mambaImage=mambaorg/micromamba:1.5.1; basePackages=conda-forge::procps-ng, commands=null), spackOpts:SpackOpts(basePackages=null, commands=null), strategy:[container, dockerfile, conda, spack], bundleProjectResources:null, buildRepository:null, cacheRepository:null, retryOpts:RetryOpts(delay:450ms, maxDelay:1m 30s, maxAttempts:10, jitter:0.25), httpClientOpts:HttpOpts(), freezeMode:null)'
+        config.toString() == 'WaveConfig(enabled:true, endpoint:https://wave.seqera.io, containerConfigUrl:[], tokensCacheMaxDuration:30m, condaOpts:CondaOpts(mambaImage=mambaorg/micromamba:1.5.5; basePackages=conda-forge::procps-ng, commands=null), spackOpts:SpackOpts(basePackages=null, commands=null), strategy:[container, dockerfile, conda, spack], bundleProjectResources:null, buildRepository:null, cacheRepository:null, retryOpts:RetryOpts(delay:450ms, maxDelay:1m 30s, maxAttempts:10, jitter:0.25), httpClientOpts:HttpOpts(), freezeMode:null)'
     }
 
     def 'should not allow invalid settinga' () {

From aa981814a14c4c1bf12701e0495719bb8cffa315 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Wed, 20 Dec 2023 08:52:31 +0100
Subject: [PATCH 322/350] Bump nf-wave@1.2.0

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-wave/changelog.txt                      | 6 ++++++
 plugins/nf-wave/src/resources/META-INF/MANIFEST.MF | 4 ++--
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/plugins/nf-wave/changelog.txt b/plugins/nf-wave/changelog.txt
index eb3a22bf38..ba4c802faf 100644
--- a/plugins/nf-wave/changelog.txt
+++ b/plugins/nf-wave/changelog.txt
@@ -1,5 +1,11 @@
 nf-wave changelog
 ==================
+1.2.0 - 20 Dec 2023
+- Add support for Singularity/Apptainer auto pull mode for OCI containers [b7f1a192]
+- Add experimental support for Fargate compute type for AWS Batch (#3474) [47cf335b]
+- Remove deprecated Wave observer [ci fast] [0e009ef7]
+- Bump wave-utils@0.8.1 and micromamba@1.5.5 [9cb50035]
+
 1.1.0 - 24 Nov 2023
 - Add Retry policy to Google Storage (#4524) [c271bb18]
 - Add support for Singularity OCI mode (#4440) [f5362a7b]
diff --git a/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF b/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF
index 10bc31538d..101cbc38ab 100644
--- a/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-wave/src/resources/META-INF/MANIFEST.MF
@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Class: io.seqera.wave.plugin.WavePlugin
 Plugin-Id: nf-wave
-Plugin-Version: 1.1.0
+Plugin-Version: 1.2.0
 Plugin-Provider: Seqera Labs
-Plugin-Requires: >=23.11.0-edge
+Plugin-Requires: >=23.12.0-edge

From 1c4f0e49823e80deef110695fbf7a810bf0513e3 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Wed, 20 Dec 2023 08:54:58 +0100
Subject: [PATCH 323/350] Update changelog

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 changelog.txt | 43 +++++++++++++++++++++++++++++++++++--------
 1 file changed, 35 insertions(+), 8 deletions(-)

diff --git a/changelog.txt b/changelog.txt
index 5ce78b9124..68a871571f 100644
--- a/changelog.txt
+++ b/changelog.txt
@@ -1,5 +1,32 @@
 NEXTFLOW CHANGE-LOG
 ===================
+23.12.0-edge - 20 Dec 2023 
+- Add AWS_SESSION_TOKEN to Fusion environment (#4581) [552f29b0]
+- Add ability to disable Cloudinfo service (#4606) [f7251895]
+- Add experimental support for Fargate compute type for AWS Batch  (#3474) [47cf335b]
+- Add support for Instance template to Google Batch [df7ed294]
+- Add support for Singularity/Apptainer auto pull mode for OCI containers [b7f1a192]
+- Fix BitBucket get source API with custom branch [58937831]
+- Fix Fusion tags documentation (#4551) [687e2e96]
+- Fix Harden regular expression to used to strip secrets in logs (#4563) [832bff24]
+- Fix bug with Fusion symlink resolution (#4593) [09e85582]
+- Fix container environment with special chars (#4594) [e0fe952f]
+- Fix custom notification template [ccf4f59e]
+- Fix fusion symlink test (#4604) [681ace86]
+- Fix smoke tests [d3c2f330]
+- Improve GLS tests [58590b1c]
+- Load nf-amazon when AWS SES is enabled [887f06f4]
+- Move build num & timestamp to BuildInfo class [ec8083d4]
+- Remove deprecated Wave observer [0e009ef7]
+- Remove undocumented userEmulation mode (#4596) [f6c79788]
+- Remove unused DSL2 check [e9ee3b2c]
+- Replace each iterator with class for [f7662e68]
+- Bump nf-amazon@2.3.0 [0b40b7b9]
+- Bump nf-google@1.10.0 [bcb20fcf]
+- Bump nf-wave@1.2.0 [aa981814]
+- Bump wave-utils@0.8.1 and micromamba@1.5.5 [9cb50035]
+- Build optimizations (#4579) [5ad41e44]
+
 23.11.0-edge - 24 Nov 2023
 - Add `fusion.cacheSize` config option (#4518) [2faadc22]
 - Add Topic channel type (experimental) (#4459) [921313d1]
@@ -16,10 +43,10 @@ NEXTFLOW CHANGE-LOG
 - Add support for Azure low-priority pool (#4527) [8320ea10]
 - Add support for FUSION_AWS_REGION (#4481) [8f8b09fa]
 - Add support for Fusion when using Singularity OCI mode (#4508) [4f3aa631]
-- Add support for K8s schedulerName pod spec (#4485) [ci fast] [dfc7b7c8]
+- Add support for K8s schedulerName pod spec (#4485) [dfc7b7c8]
 - Add support for Singularity OCI mode (#4440) [f5362a7b]
-- Allow the use of error built-in function in onComplete handler (#4458) [ci fast] [35a4424b]
-- Fix Bug in JsonSplitter ordering [ci fast] [8ec14dd2]
+- Allow the use of error built-in function in onComplete handler (#4458) [35a4424b]
+- Fix Bug in JsonSplitter ordering [8ec14dd2]
 - Fix Bypass Google Batch Price query if task cpus and memory are defined (#4521) [7f8f20d3]
 - Fix Checkout remote tag if checkout remote branch fails (#4247) [b8907ccb]
 - Fix Fusion symlinks when publishing files (#4348) [89f09fe0]
@@ -27,18 +54,18 @@ NEXTFLOW CHANGE-LOG
 - Fix ParamsMap copyWith param aliases (#4188) [b480ee0e]
 - Fix Singularity docs [e952299f]
 - Fix container hashing for Singularity + Wave containers [4c6f2e85]
-- Fix detection of Conda local path made by Wave client [ci fast] (#4532) [4d5bc216]
+- Fix detection of Conda local path made by Wave client (#4532) [4d5bc216]
 - Fix doc tests to fail on test failure (#4505) [4d326551]
-- Fix errors when NXF_HOME contains spaces (#4456) [ci fast] [fe5bea99]
+- Fix errors when NXF_HOME contains spaces (#4456) [fe5bea99]
 - Fix Google Batch network/subnetwork docs (#4475) [27d132f3]
-- Fix rounding error with long durations (#4496) [ci fast] [0356178b]
+- Fix rounding error with long durations (#4496) [0356178b]
 - Fix security vulnerabilities (#4513) [a310c777]
 - Fix Use consistently NXF_TASK_WORKDIR (#4484) [48ee3c64]
 - Improve error details for AbortOperationException [35609cb0]
 - Improve operator docs (#4502) [38210e11]
 - Makefile clean to also remove buildSrc/build (#4517) [2ccb05d0]
-- Minor test improvements [ci fast] [171831ea]
-- Minor types improvement for mix operator [ci fast] [91c1ab15]
+- Minor test improvements [171831ea]
+- Minor types improvement for mix operator [91c1ab15]
 - Normalise channel docs [b641d677]
 - Remove deprecated TowerArchiver feature [ff8e06a3]
 - Remove dsl1 deprecated code (part 2) [159effb1]

From c7d749e8f1ca9b3b9cd806eb908bb064549eda78 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Wed, 20 Dec 2023 10:41:23 +0100
Subject: [PATCH 324/350] Move app version to BuildInfo class

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../nextflow/src/main/groovy/nextflow/Session.groovy  |  6 +++---
 .../src/main/groovy/nextflow/cli/CmdRun.groovy        |  3 ++-
 .../src/main/groovy/nextflow/k8s/K8sConfig.groovy     |  5 ++---
 .../main/groovy/nextflow/util/SimpleHttpClient.groovy |  5 ++---
 .../src/test/groovy/nextflow/k8s/K8sConfigTest.groovy |  5 ++---
 modules/nf-commons/src/main/nextflow/Const.groovy     | 11 -----------
 .../src/main/nextflow/plugin/BasePlugin.groovy        |  6 +++---
 .../main/nextflow/plugin/CustomPluginManager.groovy   |  5 ++---
 .../src/main/nextflow/plugin/PluginUpdater.groovy     |  3 ++-
 .../nextflow/plugin/CustomPluginManagerTest.groovy    |  5 ++---
 .../src/test/nextflow/plugin/PluginUpdaterTest.groovy |  8 ++++----
 .../cloud/aws/batch/AwsBatchTaskHandler.groovy        |  3 ++-
 .../cloud/aws/batch/AwsBatchTaskHandlerTest.groovy    |  4 ++--
 13 files changed, 28 insertions(+), 41 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/Session.groovy b/modules/nextflow/src/main/groovy/nextflow/Session.groovy
index c4471baaf4..48713ea603 100644
--- a/modules/nextflow/src/main/groovy/nextflow/Session.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/Session.groovy
@@ -854,7 +854,7 @@ class Session implements ISession {
     }
 
     @PackageScope VersionNumber getCurrentVersion() {
-        new VersionNumber(APP_VER)
+        new VersionNumber(BuildInfo.version)
     }
 
     @PackageScope void checkVersion() {
@@ -876,11 +876,11 @@ class Session implements ISession {
     }
 
     @PackageScope void showVersionError(String ver) {
-        throw new AbortOperationException("Nextflow version $Const.APP_VER does not match workflow required version: $ver")
+        throw new AbortOperationException("Nextflow version $BuildInfo.version does not match workflow required version: $ver")
     }
 
     @PackageScope void showVersionWarning(String ver) {
-        log.warn "Nextflow version $Const.APP_VER does not match workflow required version: $ver -- Execution will continue, but things may break!"
+        log.warn "Nextflow version $BuildInfo.version does not match workflow required version: $ver -- Execution will continue, but things may break!"
     }
 
     /**
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
index 8f3edf8b06..b4ca9bccce 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
@@ -29,6 +29,7 @@ import groovy.transform.CompileStatic
 import groovy.transform.Memoized
 import groovy.util.logging.Slf4j
 import groovyx.gpars.GParsConfig
+import nextflow.BuildInfo
 import nextflow.Const
 import nextflow.NF
 import nextflow.NextflowMeta
@@ -310,7 +311,7 @@ class CmdRun extends CmdBase implements HubOptions {
 
         checkRunName()
 
-        log.info "N E X T F L O W  ~  version ${Const.APP_VER}"
+        log.info "N E X T F L O W  ~  version ${BuildInfo.version}"
         Plugins.init()
 
         // -- specify the arguments
diff --git a/modules/nextflow/src/main/groovy/nextflow/k8s/K8sConfig.groovy b/modules/nextflow/src/main/groovy/nextflow/k8s/K8sConfig.groovy
index f0814522d8..0be59bd423 100644
--- a/modules/nextflow/src/main/groovy/nextflow/k8s/K8sConfig.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/k8s/K8sConfig.groovy
@@ -22,7 +22,7 @@ import groovy.transform.CompileStatic
 import groovy.transform.Memoized
 import groovy.transform.PackageScope
 import groovy.util.logging.Slf4j
-import nextflow.Const
+import nextflow.BuildInfo
 import nextflow.exception.AbortOperationException
 import nextflow.k8s.client.ClientConfig
 import nextflow.k8s.client.K8sClient
@@ -32,7 +32,6 @@ import nextflow.k8s.model.PodSecurityContext
 import nextflow.k8s.model.PodVolumeClaim
 import nextflow.k8s.model.ResourceType
 import nextflow.util.Duration
-
 /**
  * Model Kubernetes specific settings defined in the nextflow
  * configuration file
@@ -166,7 +165,7 @@ class K8sConfig implements Map<String,Object> {
     String getServiceAccount() { target.serviceAccount }
 
     String getNextflowImageName() {
-        final defImage = "nextflow/nextflow:${Const.APP_VER}"
+        final defImage = "nextflow/nextflow:${BuildInfo.version}"
         return target.navigate('nextflow.image', defImage)
     }
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/util/SimpleHttpClient.groovy b/modules/nextflow/src/main/groovy/nextflow/util/SimpleHttpClient.groovy
index 91e34f5926..f3c953e397 100644
--- a/modules/nextflow/src/main/groovy/nextflow/util/SimpleHttpClient.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/util/SimpleHttpClient.groovy
@@ -20,8 +20,7 @@ package nextflow.util
 import groovy.json.JsonSlurper
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
-import nextflow.Const
-
+import nextflow.BuildInfo
 /**
  * Small and simple http client that sends POST requests
  * to a given URL. Currently used by the MessageObserver class
@@ -41,7 +40,7 @@ class SimpleHttpClient {
     /**
      * Default user agent
      */
-    private static String DEF_USER_AGENT = "Nextflow/$Const.APP_VER"
+    private static String DEF_USER_AGENT = "Nextflow/$BuildInfo.version"
 
     /**
      * Contains the response code of a request
diff --git a/modules/nextflow/src/test/groovy/nextflow/k8s/K8sConfigTest.groovy b/modules/nextflow/src/test/groovy/nextflow/k8s/K8sConfigTest.groovy
index 41f572f4e2..4d63b2e82b 100644
--- a/modules/nextflow/src/test/groovy/nextflow/k8s/K8sConfigTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/k8s/K8sConfigTest.groovy
@@ -16,7 +16,7 @@
 
 package nextflow.k8s
 
-import nextflow.Const
+import nextflow.BuildInfo
 import nextflow.k8s.client.ClientConfig
 import nextflow.k8s.model.PodEnv
 import nextflow.k8s.model.PodSecurityContext
@@ -24,7 +24,6 @@ import nextflow.k8s.model.PodVolumeClaim
 import nextflow.util.Duration
 import spock.lang.Specification
 import spock.lang.Unroll
-
 /**
  *
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
@@ -209,7 +208,7 @@ class K8sConfigTest extends Specification {
         when:
         def cfg = new K8sConfig()
         then:
-        cfg.getNextflowImageName() ==  "nextflow/nextflow:${Const.APP_VER}"
+        cfg.getNextflowImageName() ==  "nextflow/nextflow:${BuildInfo.version}"
 
         when:
         cfg = new K8sConfig(nextflow: [image: 'foo/bar:1.0'])
diff --git a/modules/nf-commons/src/main/nextflow/Const.groovy b/modules/nf-commons/src/main/nextflow/Const.groovy
index b7965713e9..42c5cecfa9 100644
--- a/modules/nf-commons/src/main/nextflow/Const.groovy
+++ b/modules/nf-commons/src/main/nextflow/Const.groovy
@@ -46,17 +46,6 @@ class Const {
      */
     static public final Path APP_HOME_DIR = getHomeDir(APP_NAME)
 
-    /**
-     * The application version
-     */
-    static public final String APP_VER = "23.11.0-edge"
-
-    /**
-     * The app build time as linux/unix timestamp
-     */
-    static public final long APP_TIMESTAMP = 1700857448507
-
-
     private static Path getHomeDir(String appname) {
         def home = System.getenv('NXF_HOME')
         def result = home ? Paths.get(home) : Paths.get(System.getProperty("user.home")).resolve(".$appname")
diff --git a/modules/nf-commons/src/main/nextflow/plugin/BasePlugin.groovy b/modules/nf-commons/src/main/nextflow/plugin/BasePlugin.groovy
index d46f054be5..90cbd483b8 100644
--- a/modules/nf-commons/src/main/nextflow/plugin/BasePlugin.groovy
+++ b/modules/nf-commons/src/main/nextflow/plugin/BasePlugin.groovy
@@ -19,7 +19,7 @@ package nextflow.plugin
 
 import groovy.transform.CompileStatic
 import groovy.transform.PackageScope
-import nextflow.Const
+import nextflow.BuildInfo
 import nextflow.exception.AbortOperationException
 import org.pf4j.Plugin
 import org.pf4j.PluginWrapper
@@ -39,7 +39,7 @@ abstract class BasePlugin extends Plugin {
         super(wrapper)
     }
 
-    @PackageScope boolean verMatches(String requires, String current=Const.APP_VER) {
+    @PackageScope boolean verMatches(String requires, String current=BuildInfo.version) {
         return getWrapper()
                 .getPluginManager()
                 .getVersionManager()
@@ -51,7 +51,7 @@ abstract class BasePlugin extends Plugin {
         final desc = getWrapper().getDescriptor()
         final name = "${desc.pluginId}@${desc.version}"
         if( desc.requires && !verMatches(desc.requires)) {
-            throw new AbortOperationException("Failed requirement - Plugin $name requires Nextflow version $desc.requires (current $Const.APP_VER)")
+            throw new AbortOperationException("Failed requirement - Plugin $name requires Nextflow version $desc.requires (current $BuildInfo.version)")
         }
         log.debug "Plugin started $name"
     }
diff --git a/modules/nf-commons/src/main/nextflow/plugin/CustomPluginManager.groovy b/modules/nf-commons/src/main/nextflow/plugin/CustomPluginManager.groovy
index db6b79e783..d861156081 100644
--- a/modules/nf-commons/src/main/nextflow/plugin/CustomPluginManager.groovy
+++ b/modules/nf-commons/src/main/nextflow/plugin/CustomPluginManager.groovy
@@ -20,13 +20,12 @@ package nextflow.plugin
 import java.nio.file.Path
 
 import groovy.transform.CompileStatic
-import nextflow.Const
+import nextflow.BuildInfo
 import org.pf4j.DefaultPluginManager
 import org.pf4j.ExtensionFactory
 import org.pf4j.PluginWrapper
 import org.pf4j.SingletonExtensionFactory
 import org.pf4j.VersionManager
-
 /**
  * Custom plugin manager to that allow accessing to {@code loadPluginFromPath} and
  * {@code resolvePlugins} method
@@ -59,7 +58,7 @@ class CustomPluginManager extends DefaultPluginManager {
 
     @Override
     String getSystemVersion() {
-        return Const.APP_VER
+        return BuildInfo.version
     }
 
     @Override
diff --git a/modules/nf-commons/src/main/nextflow/plugin/PluginUpdater.groovy b/modules/nf-commons/src/main/nextflow/plugin/PluginUpdater.groovy
index 0fab0ba1c5..0aa2de1294 100644
--- a/modules/nf-commons/src/main/nextflow/plugin/PluginUpdater.groovy
+++ b/modules/nf-commons/src/main/nextflow/plugin/PluginUpdater.groovy
@@ -31,6 +31,7 @@ import dev.failsafe.event.ExecutionAttemptedEvent
 import dev.failsafe.function.CheckedSupplier
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
+import nextflow.BuildInfo
 import nextflow.Const
 import nextflow.SysEnv
 import nextflow.extension.FilesEx
@@ -450,7 +451,7 @@ class PluginUpdater extends UpdateManager {
             if( !versionManager.checkVersionConstraint(rel.version, verConstraint) || !rel.url )
                 continue
 
-            if( versionManager.checkVersionConstraint(Const.APP_VER, rel.requires) )
+            if( versionManager.checkVersionConstraint(BuildInfo.version, rel.requires) )
                 return rel
         }
 
diff --git a/modules/nf-commons/src/test/nextflow/plugin/CustomPluginManagerTest.groovy b/modules/nf-commons/src/test/nextflow/plugin/CustomPluginManagerTest.groovy
index 69181d1590..206f182a34 100644
--- a/modules/nf-commons/src/test/nextflow/plugin/CustomPluginManagerTest.groovy
+++ b/modules/nf-commons/src/test/nextflow/plugin/CustomPluginManagerTest.groovy
@@ -1,8 +1,7 @@
 package nextflow.plugin
 
-import nextflow.Const
+import nextflow.BuildInfo
 import spock.lang.Specification
-
 /**
  *
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
@@ -13,7 +12,7 @@ class CustomPluginManagerTest extends Specification {
         given:
         def manager = Spy(CustomPluginManager)
         expect:
-        manager.getSystemVersion() == Const.APP_VER
+        manager.getSystemVersion() == BuildInfo.version
     }
 
     def 'should create ver manager' () {
diff --git a/modules/nf-commons/src/test/nextflow/plugin/PluginUpdaterTest.groovy b/modules/nf-commons/src/test/nextflow/plugin/PluginUpdaterTest.groovy
index 8e8420d422..30079cf3d9 100644
--- a/modules/nf-commons/src/test/nextflow/plugin/PluginUpdaterTest.groovy
+++ b/modules/nf-commons/src/test/nextflow/plugin/PluginUpdaterTest.groovy
@@ -8,7 +8,7 @@ import java.nio.file.attribute.BasicFileAttributes
 import java.util.zip.ZipEntry
 import java.util.zip.ZipOutputStream
 
-import nextflow.Const
+import nextflow.BuildInfo
 import org.pf4j.Plugin
 import org.pf4j.PluginDescriptor
 import org.pf4j.PluginWrapper
@@ -248,9 +248,9 @@ class PluginUpdaterTest extends Specification {
     def 'should find matching plugin' () {
         given:
         def r1 = new PluginInfo.PluginRelease(version: '1.4.0', url: 'http://xyz')
-        def r2 = new PluginInfo.PluginRelease(version: '1.5.0', url: 'http://xyz', requires: ">=${Const.APP_VER}")
-        def r3 = new PluginInfo.PluginRelease(version: '1.5.1', url: 'http://xyz', requires: ">=${Const.APP_VER}")
-        def r4 = new PluginInfo.PluginRelease(version: '2.0.1', url: 'http://xyz', requires: ">=${Const.APP_VER}")
+        def r2 = new PluginInfo.PluginRelease(version: '1.5.0', url: 'http://xyz', requires: ">=${BuildInfo.version}")
+        def r3 = new PluginInfo.PluginRelease(version: '1.5.1', url: 'http://xyz', requires: ">=${BuildInfo.version}")
+        def r4 = new PluginInfo.PluginRelease(version: '2.0.1', url: 'http://xyz', requires: ">=${BuildInfo.version}")
         def r5 = new PluginInfo.PluginRelease(version: '3.0.0', url: 'http://xyz', requires: '99.01.0')
         def PLUGINS = [
                 'nf-foo': new PluginInfo(id:'nf-foo', releases: [r1, r2, r3, r4, r5]),
diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsBatchTaskHandler.groovy b/plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsBatchTaskHandler.groovy
index 08c175dd9d..61e99e6f1b 100644
--- a/plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsBatchTaskHandler.groovy
+++ b/plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsBatchTaskHandler.groovy
@@ -58,6 +58,7 @@ import groovy.transform.Canonical
 import groovy.transform.CompileStatic
 import groovy.transform.Memoized
 import groovy.util.logging.Slf4j
+import nextflow.BuildInfo
 import nextflow.Const
 import nextflow.cloud.types.CloudMachineInfo
 import nextflow.container.ContainerNameValidator
@@ -623,7 +624,7 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
     protected String createJobDef(RegisterJobDefinitionRequest req) {
         // add nextflow tags
         req.addTagsEntry('nextflow.io/createdAt', Instant.now().toString())
-        req.addTagsEntry('nextflow.io/version', Const.APP_VER)
+        req.addTagsEntry('nextflow.io/version', BuildInfo.version)
         // create the job def
         final res = createJobDef0(bypassProxy(client), req) // bypass the client proxy! see #1024
         return "${res.jobDefinitionName}:$res.revision"
diff --git a/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchTaskHandlerTest.groovy b/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchTaskHandlerTest.groovy
index c9568016d4..cbc388db79 100644
--- a/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchTaskHandlerTest.groovy
+++ b/plugins/nf-amazon/src/test/nextflow/cloud/aws/batch/AwsBatchTaskHandlerTest.groovy
@@ -35,7 +35,7 @@ import com.amazonaws.services.batch.model.RetryStrategy
 import com.amazonaws.services.batch.model.SubmitJobRequest
 import com.amazonaws.services.batch.model.SubmitJobResult
 import com.amazonaws.services.batch.model.TerminateJobRequest
-import nextflow.Const
+import nextflow.BuildInfo
 import nextflow.Session
 import nextflow.cloud.aws.config.AwsConfig
 import nextflow.cloud.aws.util.S3PathFactory
@@ -503,7 +503,7 @@ class AwsBatchTaskHandlerTest extends Specification {
         and:
         result == "$JOB_NAME:10"
         and:
-        req.getTags().get('nextflow.io/version') == Const.APP_VER
+        req.getTags().get('nextflow.io/version') == BuildInfo.version
         Instant.parse(req.getTags().get('nextflow.io/createdAt'))
 
     }

From 410c745744365cd38491615edb271f3e5d017630 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Wed, 20 Dec 2023 10:42:43 +0100
Subject: [PATCH 325/350] Update changelog

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 changelog.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/changelog.txt b/changelog.txt
index 68a871571f..4a9717bf9f 100644
--- a/changelog.txt
+++ b/changelog.txt
@@ -17,6 +17,7 @@ NEXTFLOW CHANGE-LOG
 - Improve GLS tests [58590b1c]
 - Load nf-amazon when AWS SES is enabled [887f06f4]
 - Move build num & timestamp to BuildInfo class [ec8083d4]
+- Move app version to BuildInfo class [c7d749e8]
 - Remove deprecated Wave observer [0e009ef7]
 - Remove undocumented userEmulation mode (#4596) [f6c79788]
 - Remove unused DSL2 check [e9ee3b2c]

From b70d646360c121f0fcd6596b04b0ef43f812b966 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Wed, 20 Dec 2023 10:53:10 +0100
Subject: [PATCH 326/350] Fix local time in BuildInfo class

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 modules/nf-commons/src/main/nextflow/BuildInfo.groovy | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-commons/src/main/nextflow/BuildInfo.groovy b/modules/nf-commons/src/main/nextflow/BuildInfo.groovy
index ad236f4ab1..c7acc9ab62 100644
--- a/modules/nf-commons/src/main/nextflow/BuildInfo.groovy
+++ b/modules/nf-commons/src/main/nextflow/BuildInfo.groovy
@@ -74,8 +74,8 @@ class BuildInfo {
             return ''
         }
 
-        final utc = getTimestampUTC().split(' ')
-        final loc = getTimestampLocal().split(' ')
+        final utc = getTimestampUTC().tokenize(' ')
+        final loc = getTimestampLocal().tokenize(' ')
 
         final result = utc[0] == loc[0] ? loc[1,-1].join(' ') : loc.join(' ')
         return "($result)"

From dfd7d09efe8c7d159596433a846ed5c7f8e17423 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Wed, 20 Dec 2023 10:55:30 +0100
Subject: [PATCH 327/350] [release 23.12.0-edge] Update timestamp and build
 number

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 VERSION                                                   | 2 +-
 docs/conf.py                                              | 4 ++--
 .../src/main/resources/META-INF/build-info.properties     | 8 ++++----
 .../nextflow/src/main/resources/META-INF/plugins-info.txt | 6 +++---
 nextflow                                                  | 2 +-
 nextflow.md5                                              | 2 +-
 nextflow.sha1                                             | 2 +-
 nextflow.sha256                                           | 2 +-
 8 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/VERSION b/VERSION
index c412fc2d77..b83786f853 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-23.11.0-edge
+23.12.0-edge
diff --git a/docs/conf.py b/docs/conf.py
index 80b1ac70b2..08a0aff2a1 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -64,9 +64,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '23.11'
+version = '23.12'
 # The full version, including alpha/beta/rc tags.
-release = '23.11.0-edge'
+release = '23.12.0-edge'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
diff --git a/modules/nextflow/src/main/resources/META-INF/build-info.properties b/modules/nextflow/src/main/resources/META-INF/build-info.properties
index 95836440d9..eb9b460c45 100644
--- a/modules/nextflow/src/main/resources/META-INF/build-info.properties
+++ b/modules/nextflow/src/main/resources/META-INF/build-info.properties
@@ -1,4 +1,4 @@
-build=5900
-version=23.11.0-edge
-timestamp=1702494578227
-commitId=887f06f4d
+build=5901
+version=23.12.0-edge
+timestamp=1703065940268
+commitId=410c74574
diff --git a/modules/nextflow/src/main/resources/META-INF/plugins-info.txt b/modules/nextflow/src/main/resources/META-INF/plugins-info.txt
index 74e02769f1..8e6d182f31 100644
--- a/modules/nextflow/src/main/resources/META-INF/plugins-info.txt
+++ b/modules/nextflow/src/main/resources/META-INF/plugins-info.txt
@@ -1,9 +1,9 @@
-nf-amazon@2.2.0
+nf-amazon@2.3.0
 nf-azure@1.4.0
 nf-cloudcache@0.3.1
 nf-codecommit@0.1.6
 nf-console@1.0.7
 nf-ga4gh@1.1.1
-nf-google@1.9.0
+nf-google@1.10.0
 nf-tower@1.7.0
-nf-wave@1.1.0
\ No newline at end of file
+nf-wave@1.2.0
\ No newline at end of file
diff --git a/nextflow b/nextflow
index 7906c2aa67..afae6a255c 100755
--- a/nextflow
+++ b/nextflow
@@ -15,7 +15,7 @@
 #  limitations under the License.
 
 [[ "$NXF_DEBUG" == 'x' ]] && set -x
-NXF_VER=${NXF_VER:-'23.11.0-edge'}
+NXF_VER=${NXF_VER:-'23.12.0-edge'}
 NXF_ORG=${NXF_ORG:-'nextflow-io'}
 NXF_HOME=${NXF_HOME:-$HOME/.nextflow}
 NXF_PROT=${NXF_PROT:-'https'}
diff --git a/nextflow.md5 b/nextflow.md5
index 574adce9f0..e36331a486 100644
--- a/nextflow.md5
+++ b/nextflow.md5
@@ -1 +1 @@
-8a4583bb84d6e8304cc0b1ff5446f21f
+c7be306ce627f428fcd977ef80520d1c
diff --git a/nextflow.sha1 b/nextflow.sha1
index 5214121c92..dbbdd64dac 100644
--- a/nextflow.sha1
+++ b/nextflow.sha1
@@ -1 +1 @@
-965e377c383f399cb01e2c109ed2edd8335671e6
+bf23b6cdf50eea71af9bf85f4058864a8f2ca8fc
diff --git a/nextflow.sha256 b/nextflow.sha256
index 5fd857dc00..d50c671673 100644
--- a/nextflow.sha256
+++ b/nextflow.sha256
@@ -1 +1 @@
-ddb037f134a8289215fa41b45f85e678e4bd45b8da2a3379caf326a99dfbbeeb
+8370b1bba8447e995c89c6038d4d769de78265c6853411e8b56111a5ffe605a2

From 8812138f4446f030e1f239d75158b28803822886 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Wed, 20 Dec 2023 14:44:11 +0100
Subject: [PATCH 328/350] Improve detection of sys home variable

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 modules/nf-commons/src/main/nextflow/Const.groovy | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/modules/nf-commons/src/main/nextflow/Const.groovy b/modules/nf-commons/src/main/nextflow/Const.groovy
index 42c5cecfa9..46f8f213d0 100644
--- a/modules/nf-commons/src/main/nextflow/Const.groovy
+++ b/modules/nf-commons/src/main/nextflow/Const.groovy
@@ -46,9 +46,18 @@ class Const {
      */
     static public final Path APP_HOME_DIR = getHomeDir(APP_NAME)
 
+    static Path sysHome() {
+        def home = System.getProperty("user.home")
+        if( !home || home=='?' )
+            home = System.getenv('HOME')
+        if( !home )
+            throw new IllegalStateException("Unable to detect system home path - Make sure the variable HOME or NXF_HOME is defined in your environment")
+        return Path.of(home)
+    }
+
     private static Path getHomeDir(String appname) {
-        def home = System.getenv('NXF_HOME')
-        def result = home ? Paths.get(home) : Paths.get(System.getProperty("user.home")).resolve(".$appname")
+        final home = System.getenv('NXF_HOME')
+        final result = home ? Paths.get(home) : sysHome().resolve(".$appname")
 
         if( !result.exists() && !result.mkdir() ) {
             throw new IllegalStateException("Cannot create path '${result}' -- check file system access permission")

From 63e83702beb92358f851ac26f357a0c93ec5164d Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Tue, 26 Dec 2023 11:34:55 +0100
Subject: [PATCH 329/350] Bump nextflow 23.12.0-edge as min version

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF | 2 +-
 plugins/nf-google/src/resources/META-INF/MANIFEST.MF | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF b/plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF
index e77069ebe8..59814f862e 100644
--- a/plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-amazon/src/resources/META-INF/MANIFEST.MF
@@ -3,4 +3,4 @@ Plugin-Class: nextflow.cloud.aws.AmazonPlugin
 Plugin-Id: nf-amazon
 Plugin-Version: 2.3.0
 Plugin-Provider: Seqera Labs
-Plugin-Requires: >=23.11.0-edge
+Plugin-Requires: >=23.12.0-edge
diff --git a/plugins/nf-google/src/resources/META-INF/MANIFEST.MF b/plugins/nf-google/src/resources/META-INF/MANIFEST.MF
index 638f05f9d4..b5c31d7bce 100644
--- a/plugins/nf-google/src/resources/META-INF/MANIFEST.MF
+++ b/plugins/nf-google/src/resources/META-INF/MANIFEST.MF
@@ -3,4 +3,4 @@ Plugin-Class: nextflow.cloud.google.GoogleCloudPlugin
 Plugin-Id: nf-google
 Plugin-Version: 1.10.0
 Plugin-Provider: Seqera Labs
-Plugin-Requires: >=23.11.0-edge
+Plugin-Requires: >=23.12.0-edge

From da382ddfe9822c321c96aa186fc7642866d38c9b Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Tue, 26 Dec 2023 19:17:32 +0100
Subject: [PATCH 330/350] Fix Wave container replicable checksum

The checksum of a Wave container can change across runs
when it includes module files whose timestamps have been
changed across runs.

This commonly happens when launching a pipeline execution
in a cloud environment since all pipeline assets are downloaded
in the container file system assuming the download time as the
file timestamp, and therefore resulting into a new layer checksum.

This commit prevent this behavior discarding the file module creation
time setting the file time to zero.

To keep the original file timestamp the following setting can be
specified in the nextflow.config file

```
wave.preserveFileTimestamp = true|false
```

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../io/seqera/wave/plugin/WaveClient.groovy   |  2 +-
 .../wave/plugin/config/WaveConfig.groovy      |  4 ++
 .../seqera/wave/plugin/packer/Packer.groovy   | 22 +++++-
 .../seqera/wave/plugin/WaveClientTest.groovy  | 28 +++++++-
 .../wave/plugin/config/WaveConfigTest.groovy  | 14 +++-
 .../wave/plugin/packer/PackerTest.groovy      | 68 ++++++++++++++++++-
 .../plugin/packer/WaveCmdEntryTest.groovy     |  8 +--
 7 files changed, 131 insertions(+), 15 deletions(-)

diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
index 367ac8d4be..237d0e8e94 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
@@ -129,7 +129,7 @@ class WaveClient {
         this.endpoint = config.endpoint()
         this.condaChannels = session.getCondaConfig()?.getChannels() ?: DEFAULT_CONDA_CHANNELS
         log.debug "Wave config: $config"
-        this.packer = new Packer()
+        this.packer = new Packer().withPreserveTimestamp(config.preserveFileTimestamp())
         this.waveRegistry = new URI(endpoint).getAuthority()
         // create cache
         cache = CacheBuilder<String, SubmitContainerTokenResponse>
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/WaveConfig.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/WaveConfig.groovy
index 5a47010a78..ae30212f66 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/WaveConfig.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/config/WaveConfig.groovy
@@ -49,11 +49,13 @@ class WaveConfig {
     final private RetryOpts retryOpts
     final private HttpOpts httpClientOpts
     final private Boolean freezeMode
+    final private Boolean preserveFileTimestamp
 
     WaveConfig(Map opts, Map<String,String> env=System.getenv()) {
         this.enabled = opts.enabled
         this.endpoint = (opts.endpoint?.toString() ?: env.get('WAVE_API_ENDPOINT') ?: DEF_ENDPOINT)?.stripEnd('/')
         this.freezeMode = opts.freeze as Boolean
+        this.preserveFileTimestamp = opts.preserveFileTimestamp as Boolean
         this.containerConfigUrl = parseConfig(opts, env)
         this.tokensCacheMaxDuration = opts.navigate('tokens.cache.maxDuration', '30m') as Duration
         this.condaOpts = opts.navigate('build.conda', Collections.emptyMap()) as CondaOpts
@@ -85,6 +87,8 @@ class WaveConfig {
 
     boolean freezeMode() { return this.freezeMode }
 
+    boolean preserveFileTimestamp() { return this.preserveFileTimestamp }
+
     boolean bundleProjectResources() { bundleProjectResources }
 
     String buildRepository() { buildRepository }
diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/packer/Packer.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/packer/Packer.groovy
index 5cd35507b8..8d17e2e2c5 100644
--- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/packer/Packer.groovy
+++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/packer/Packer.groovy
@@ -20,6 +20,7 @@ package io.seqera.wave.plugin.packer
 import java.nio.file.Files
 import java.nio.file.Path
 import java.nio.file.attribute.BasicFileAttributes
+import java.nio.file.attribute.FileTime
 
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
@@ -49,6 +50,21 @@ class Packer {
      */
     private static final int FILE_MODE = 0100000;
 
+    /**
+     * Timestamp when {@link #preserveFileTimestamp} is false
+     */
+    private static final FileTime ZERO = FileTime.fromMillis(0)
+
+    /**
+     * Whenever the timestamp of compressed files should be preserved.
+     * By default it is used the timestamp ZERO to guarantee reproducible builds
+     */
+    private boolean preserveFileTimestamp
+
+    Packer withPreserveTimestamp(boolean value) {
+        this.preserveFileTimestamp = value
+        return this
+    }
 
     def <T extends OutputStream> T makeTar(Path root, List<Path> files, T target) {
         final entries = new HashMap<String,Path>()
@@ -64,12 +80,14 @@ class Packer {
             final sorted = new TreeSet<>(entries.keySet())
             for (String name : sorted ) {
                 final targetPath = entries.get(name)
-                final attrs = Files.readAttributes(targetPath, BasicFileAttributes)
+                final ftime = preserveFileTimestamp
+                    ? Files.readAttributes(targetPath, BasicFileAttributes.class).lastModifiedTime()
+                    : ZERO
                 final entry = new TarArchiveEntry(targetPath, name)
                 entry.setIds(0,0)
                 entry.setGroupName("root")
                 entry.setUserName("root")
-                entry.setModTime(attrs.lastModifiedTime())
+                entry.setModTime(ftime)
                 entry.setMode(getMode(targetPath))
                 // file permissions
                 archive.putArchiveEntry(entry)
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
index 07e0635442..7e70745c27 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
@@ -22,6 +22,7 @@ import static java.nio.file.StandardOpenOption.*
 import java.net.http.HttpRequest
 import java.nio.file.Files
 import java.nio.file.Path
+import java.nio.file.attribute.BasicFileAttributes
 import java.nio.file.attribute.FileTime
 
 import com.sun.net.httpserver.HttpExchange
@@ -95,7 +96,7 @@ class WaveClientTest extends Specification {
     def 'should tar file' () {
         given:
         def LAST_MODIFIED = FileTime.fromMillis(1_000_000_000_000)
-        def sess = Mock(Session) { getConfig() >> [wave:[:]]}
+        def sess = Mock(Session) { getConfig() >> [wave:[preserveFileTimestamp:true]]}
         def folder = Files.createTempDirectory('test')
         and:
         def bundlePath = folder.resolve('bundle'); bundlePath.mkdir()
@@ -130,7 +131,8 @@ class WaveClientTest extends Specification {
         result.resolve('this/hola.txt').text == bundlePath.resolve('this/hola.txt').text
         result.resolve('this/hello.txt').text == bundlePath.resolve('this/hello.txt').text
         result.resolve('this/that/ciao.txt').text == bundlePath.resolve('this/that/ciao.txt').text
-
+        and:
+        Files.readAttributes(result.resolve('main.nf'), BasicFileAttributes).lastModifiedTime() == LAST_MODIFIED
         /*
          * create a bundle using different base directory
          */
@@ -148,6 +150,28 @@ class WaveClientTest extends Specification {
         result2.resolve('usr/local/this/hello.txt').text == bundlePath.resolve('this/hello.txt').text
         result2.resolve('usr/local/this/that/ciao.txt').text == bundlePath.resolve('this/that/ciao.txt').text
 
+        /*
+         * should create a bundle without preserving the file timestamps
+         */
+
+        when:
+        def wave3 = new WaveClient(Mock(Session) { getConfig()>>[wave:[:]] })
+        def bundle3 = ResourcesBundle.scan(bundlePath)
+        def layer3 = wave3.makeLayer(bundle3)
+        then:
+        layer3.tarDigest == 'sha256:f556b94e9b6f5f72b86e44833614b465df9f65cb4210e3f4416292dca1618360'
+        layer3.gzipDigest == 'sha256:e58685a82452a11faa926843e7861c94bdb93e2c8f098b5c5354ec9b6fee2b68'
+        layer3.gzipSize == 251
+        and:
+        def gzip3 = layer3.location.replace('data:','').decodeBase64()
+        def tar3 = uncompress(gzip3)
+        def result3 = folder.resolve('result3')
+        untar( new ByteArrayInputStream(tar3), result3)
+        and:
+        result3.resolve('main.nf').text == bundlePath.resolve('main.nf').text
+        and:
+        Files.readAttributes(result3.resolve('main.nf'), BasicFileAttributes).lastModifiedTime() == FileTime.fromMillis(0)
+
         cleanup:
         folder?.deleteDir()
     }
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy
index 16e8dd6aa8..901d724cad 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy
@@ -199,7 +199,7 @@ class WaveConfigTest extends Specification {
         given:
         def config = new WaveConfig([enabled: true])
         expect:
-        config.toString() == 'WaveConfig(enabled:true, endpoint:https://wave.seqera.io, containerConfigUrl:[], tokensCacheMaxDuration:30m, condaOpts:CondaOpts(mambaImage=mambaorg/micromamba:1.5.5; basePackages=conda-forge::procps-ng, commands=null), spackOpts:SpackOpts(basePackages=null, commands=null), strategy:[container, dockerfile, conda, spack], bundleProjectResources:null, buildRepository:null, cacheRepository:null, retryOpts:RetryOpts(delay:450ms, maxDelay:1m 30s, maxAttempts:10, jitter:0.25), httpClientOpts:HttpOpts(), freezeMode:null)'
+        config.toString() == 'WaveConfig(enabled:true, endpoint:https://wave.seqera.io, containerConfigUrl:[], tokensCacheMaxDuration:30m, condaOpts:CondaOpts(mambaImage=mambaorg/micromamba:1.5.5; basePackages=conda-forge::procps-ng, commands=null), spackOpts:SpackOpts(basePackages=null, commands=null), strategy:[container, dockerfile, conda, spack], bundleProjectResources:null, buildRepository:null, cacheRepository:null, retryOpts:RetryOpts(delay:450ms, maxDelay:1m 30s, maxAttempts:10, jitter:0.25), httpClientOpts:HttpOpts(), freezeMode:null, preserveFileTimestamp:null)'
     }
 
     def 'should not allow invalid settinga' () {
@@ -228,4 +228,16 @@ class WaveConfigTest extends Specification {
         e.message == "Config setting 'wave.build.cacheRepository' should not include any protocol prefix - offending value: 'http://foo.com'"
     }
 
+    def 'should set preserve timestamp' () {
+        when:
+        def config = new WaveConfig([:])
+        then:
+        !config.preserveFileTimestamp()
+
+        when:
+        config = new WaveConfig(preserveFileTimestamp: true)
+        then:
+        config.preserveFileTimestamp()
+    }
+
 }
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/packer/PackerTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/packer/PackerTest.groovy
index 34ee8c32b2..3229822a96 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/packer/PackerTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/packer/PackerTest.groovy
@@ -21,7 +21,6 @@ import java.nio.file.Files
 import java.nio.file.Path
 import java.nio.file.attribute.FileTime
 
-import io.seqera.wave.plugin.packer.Packer
 import nextflow.extension.FilesEx
 import nextflow.file.FileHelper
 import spock.lang.Specification
@@ -31,8 +30,71 @@ import spock.lang.Specification
  */
 class PackerTest extends Specification implements TarHelper {
 
-
     def 'should tar bundle' () {
+        given:
+        def folder = Files.createTempDirectory('test')
+        and:
+        def result = folder.resolve('result')
+        def result2 = folder.resolve('result2')
+        and:
+        def rootPath = folder.resolve('bundle'); rootPath.mkdir()
+        rootPath.resolve('main.nf').text = "I'm the main file"
+        rootPath.resolve('this/that').mkdirs()
+        Files.write(rootPath.resolve('this/hola.txt'), "Hola".bytes)
+        Files.write(rootPath.resolve('this/hello.txt'), "Hello".bytes)
+        Files.write(rootPath.resolve('this/that/ciao.txt'), "Ciao".bytes)
+        and:
+        def files = new ArrayList<Path>()
+        FileHelper.visitFiles([type:'any'], rootPath, '**', {
+            final mode = it.isDirectory() ? 0700 : 0600
+            FilesEx.setPermissionsMode(it, mode)
+            //
+            files.add(it)
+        })
+        and:
+        def packer = new Packer()
+
+        when:
+        def buffer = new ByteArrayOutputStream()
+        packer.makeTar(rootPath, files, buffer)
+        and:
+        untar( new ByteArrayInputStream(buffer.toByteArray()), result )
+        then:
+        result.resolve('main.nf').text == rootPath.resolve('main.nf').text
+        result.resolve('this/hola.txt').text == rootPath.resolve('this/hola.txt').text
+        result.resolve('this/hello.txt').text == rootPath.resolve('this/hello.txt').text
+        result.resolve('this/that/ciao.txt').text == rootPath.resolve('this/that/ciao.txt').text
+        and:
+        result.resolve('main.nf').getPermissionsMode() == 0600
+        result.resolve('this/hola.txt').getPermissionsMode() == 0600
+        result.resolve('this/that').getPermissionsMode() == 0700
+        and:
+        Files.getLastModifiedTime(result.resolve('main.nf')) == FileTime.fromMillis(0)
+
+        when:
+        def layer = packer.layer(rootPath, files)
+        then:
+        layer.tarDigest == 'sha256:f556b94e9b6f5f72b86e44833614b465df9f65cb4210e3f4416292dca1618360'
+        layer.gzipDigest == 'sha256:e58685a82452a11faa926843e7861c94bdb93e2c8f098b5c5354ec9b6fee2b68'
+        layer.gzipSize == 251
+        and:
+        def gzip = layer.location.replace('data:','').decodeBase64()
+        def tar = uncompress(gzip)
+        untar( new ByteArrayInputStream(tar), result2)
+        and:
+        result2.resolve('main.nf').text == rootPath.resolve('main.nf').text
+        result2.resolve('this/hola.txt').text == rootPath.resolve('this/hola.txt').text
+        result2.resolve('this/hello.txt').text == rootPath.resolve('this/hello.txt').text
+        result2.resolve('this/that/ciao.txt').text == rootPath.resolve('this/that/ciao.txt').text
+        and:
+        Files.getLastModifiedTime(result2.resolve('main.nf')) == FileTime.fromMillis(0)
+
+        cleanup:
+        folder?.deleteDir()
+    }
+
+
+    def 'should tar bundle and preserve timestamps' () {
         given:
         def LAST_MODIFIED = FileTime.fromMillis(1_000_000_000_000)
         def folder = Files.createTempDirectory('test')
@@ -56,7 +118,7 @@ class PackerTest extends Specification implements TarHelper {
             files.add(it)
         })
         and:
-        def packer = new Packer()
+        def packer = new Packer(preserveFileTimestamp: true)
 
         when:
         def buffer = new ByteArrayOutputStream()
diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/packer/WaveCmdEntryTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/packer/WaveCmdEntryTest.groovy
index 225f649007..7cc3465bdd 100644
--- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/packer/WaveCmdEntryTest.groovy
+++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/packer/WaveCmdEntryTest.groovy
@@ -19,7 +19,6 @@ package io.seqera.wave.plugin.packer
 
 import java.nio.file.Files
 import java.nio.file.Path
-import java.nio.file.attribute.FileTime
 
 import groovy.json.JsonSlurper
 import io.seqera.wave.plugin.cli.WaveCmdEntry
@@ -46,8 +45,6 @@ class WaveCmdEntryTest extends Specification implements TarHelper {
 
     def 'should create create pack' () {
         given:
-        def LAST_MODIFIED = FileTime.fromMillis(1_000_000_000_000)
-        and:
         def rootPath = folder.resolve('bundle'); rootPath.mkdir()
         def untarPath = folder.resolve('untar'); untarPath.mkdir()
         rootPath.resolve('main.nf').text = "I'm the main file"
@@ -57,7 +54,6 @@ class WaveCmdEntryTest extends Specification implements TarHelper {
         Files.write(rootPath.resolve('this/that/ciao.txt'), "Ciao".bytes)
         and:
         FileHelper.visitFiles([type:'any'], rootPath, '**', {
-            Files.setLastModifiedTime(it, LAST_MODIFIED)
             final mode = it.isDirectory() ? 0700 : 0600
             FilesEx.setPermissionsMode(it, mode)
         })
@@ -74,8 +70,8 @@ class WaveCmdEntryTest extends Specification implements TarHelper {
         and:
         json.layers[0].gzipSize == Files.size(gzipFile)
         json.layers[0].location == gzipFile.toUri().toString()
-        json.layers[0].tarDigest == 'sha256:81200f6ad32793567d8070375dc51312a1711fedf6a1c6f5e4a97fa3014f3491'
-        json.layers[0].gzipDigest == 'sha256:09a2deca4293245909223db505cf69affa1a8ff8acb745fe3cad38bc0b719110'
+        json.layers[0].tarDigest == 'sha256:f556b94e9b6f5f72b86e44833614b465df9f65cb4210e3f4416292dca1618360'
+        json.layers[0].gzipDigest == 'sha256:e58685a82452a11faa926843e7861c94bdb93e2c8f098b5c5354ec9b6fee2b68'
         
         when:
         def tar = uncompress(Files.readAllBytes(gzipFile))

From 331ff425522ca586cca94f77dc63c896e76bf1bd Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 30 Dec 2023 06:09:06 -0600
Subject: [PATCH 331/350] Bump logback@1.4.12 + guava@33.0.0-jre

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 modules/nextflow/build.gradle   | 4 ++--
 modules/nf-commons/build.gradle | 4 ++--
 modules/nf-httpfs/build.gradle  | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/modules/nextflow/build.gradle b/modules/nextflow/build.gradle
index c24f235cdc..c531e09a6b 100644
--- a/modules/nextflow/build.gradle
+++ b/modules/nextflow/build.gradle
@@ -26,8 +26,8 @@ dependencies {
     api "org.slf4j:jcl-over-slf4j:2.0.7"
     api "org.slf4j:jul-to-slf4j:2.0.7"
     api "org.slf4j:log4j-over-slf4j:2.0.7"
-    api "ch.qos.logback:logback-classic:1.4.6"
-    api "ch.qos.logback:logback-core:1.4.6"
+    api "ch.qos.logback:logback-classic:1.4.12"
+    api "ch.qos.logback:logback-core:1.4.12"
     api "org.codehaus.gpars:gpars:1.2.1"
     api("ch.artecat.grengine:grengine:3.0.0") { exclude group: 'org.codehaus.groovy' }
     api "commons-lang:commons-lang:2.6"
diff --git a/modules/nf-commons/build.gradle b/modules/nf-commons/build.gradle
index 1d09cf4f76..1255938632 100644
--- a/modules/nf-commons/build.gradle
+++ b/modules/nf-commons/build.gradle
@@ -25,11 +25,11 @@ sourceSets {
 }
 
 dependencies {
-    api "ch.qos.logback:logback-classic:1.4.6"
+    api "ch.qos.logback:logback-classic:1.4.12"
     api "org.codehaus.groovy:groovy:3.0.19"
     api "org.codehaus.groovy:groovy-nio:3.0.19"
     api "commons-lang:commons-lang:2.6"
-    api 'com.google.guava:guava:31.1-jre'
+    api 'com.google.guava:guava:33.0.0-jre'
     api 'org.pf4j:pf4j:3.10.0'
     api 'org.pf4j:pf4j-update:2.3.0'
     api 'dev.failsafe:failsafe:3.1.0'
diff --git a/modules/nf-httpfs/build.gradle b/modules/nf-httpfs/build.gradle
index 9db2f0da7b..a2ad74ca01 100644
--- a/modules/nf-httpfs/build.gradle
+++ b/modules/nf-httpfs/build.gradle
@@ -29,7 +29,7 @@ sourceSets {
 
 dependencies {
     api project(':nf-commons')
-    api "ch.qos.logback:logback-classic:1.4.6"
+    api "ch.qos.logback:logback-classic:1.4.12"
     api "org.codehaus.groovy:groovy:3.0.19"
     api "org.codehaus.groovy:groovy-nio:3.0.19"
     api("com.esotericsoftware.kryo:kryo:2.24.0") { exclude group: 'com.esotericsoftware.minlog', module: 'minlog' }

From e7a20aff740750b296d77daf9dcbdd1e18a833b7 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 30 Dec 2023 07:06:26 -0600
Subject: [PATCH 332/350] Use canonical init method for plugins initialization

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../nextflow/src/main/groovy/nextflow/cli/CmdClean.groovy    | 2 +-
 .../nextflow/src/main/groovy/nextflow/cli/CmdConsole.groovy  | 2 +-
 modules/nextflow/src/main/groovy/nextflow/cli/CmdFs.groovy   | 2 +-
 modules/nextflow/src/main/groovy/nextflow/cli/CmdNode.groovy | 2 +-
 .../nextflow/src/main/groovy/nextflow/cli/CmdPlugin.groovy   | 2 +-
 modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy  | 1 -
 .../nextflow/src/main/groovy/nextflow/cli/CmdSecret.groovy   | 2 +-
 modules/nf-commons/src/main/nextflow/plugin/Plugins.groovy   | 4 ----
 .../nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy | 5 -----
 .../src/test/nextflow/plugin/PluginsFacadeTest.groovy        | 3 ++-
 10 files changed, 8 insertions(+), 17 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdClean.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdClean.groovy
index 7ae9f224a6..48be429229 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdClean.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdClean.groovy
@@ -96,7 +96,7 @@ class CmdClean extends CmdBase implements CacheBase {
         init()
         validateOptions()
         createSession()
-        Plugins.setup()
+        Plugins.init()
         listIds().each { entry -> cleanup(entry) }
     }
 
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdConsole.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdConsole.groovy
index 64bed3d695..afd58640aa 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdConsole.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdConsole.groovy
@@ -37,7 +37,7 @@ class CmdConsole extends CmdBase {
     String getName() { 'console' }
 
     void run() {
-        Plugins.setup()
+        Plugins.init()
         Plugins.start('nf-console')
         final console = Plugins.getExtension(ConsoleExtension)
         if( !console )
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdFs.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdFs.groovy
index 78daaa5ea6..65320890b1 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdFs.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdFs.groovy
@@ -215,7 +215,7 @@ class CmdFs extends CmdBase implements UsageAware {
             return
         }
 
-        Plugins.setup()
+        Plugins.init()
         final session = createSession()
         try {
             run0()
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdNode.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdNode.groovy
index b937a437d8..43339652ec 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdNode.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdNode.groovy
@@ -140,7 +140,7 @@ class CmdNode extends CmdBase {
      * @throws IllegalStateException when no class implementing {@code DaemonLauncher} is available
      */
     static DaemonLauncher loadDaemonFirst() {
-        Plugins.setup()
+        Plugins.init()
         final loader = Plugins.getExtension(DaemonLauncher)
         if( !loader )
             throw new IllegalStateException("No cluster services are available -- Cannot launch Nextflow in cluster mode")
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdPlugin.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdPlugin.groovy
index 5eb6568fa1..38414fc052 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdPlugin.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdPlugin.groovy
@@ -46,7 +46,7 @@ class CmdPlugin extends CmdBase {
         if( !args )
             throw new AbortOperationException("Missing plugin command - usage: nextflow plugin install <pluginId,..>")
         // setup plugins system
-        Plugins.setup()
+        Plugins.init()
         // check for the plugins install
         if( args[0] == 'install' ) {
             if( args.size()!=2 )
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
index b4ca9bccce..98b90f5d01 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
@@ -30,7 +30,6 @@ import groovy.transform.Memoized
 import groovy.util.logging.Slf4j
 import groovyx.gpars.GParsConfig
 import nextflow.BuildInfo
-import nextflow.Const
 import nextflow.NF
 import nextflow.NextflowMeta
 import nextflow.SysEnv
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdSecret.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdSecret.groovy
index d7e86278d3..1d7c54bcb2 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdSecret.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdSecret.groovy
@@ -107,7 +107,7 @@ class CmdSecret extends CmdBase implements UsageAware {
         }
 
         // setup the plugins system and load the secrets provider
-        Plugins.setup()
+        Plugins.init()
         provider = SecretsLoader.instance.load()
 
         // run the command
diff --git a/modules/nf-commons/src/main/nextflow/plugin/Plugins.groovy b/modules/nf-commons/src/main/nextflow/plugin/Plugins.groovy
index 0ed48a86a4..5842d4fe25 100644
--- a/modules/nf-commons/src/main/nextflow/plugin/Plugins.groovy
+++ b/modules/nf-commons/src/main/nextflow/plugin/Plugins.groovy
@@ -45,10 +45,6 @@ class Plugins {
         INSTANCE.init(root, mode, pluginManager)
     }
 
-    static synchronized void setup(Map config = Collections.emptyMap()) {
-        INSTANCE.setup(config)
-    }
-
     /**
      * @param config
      */
diff --git a/modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy b/modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy
index 331181d647..2b0d013f31 100644
--- a/modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy
+++ b/modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy
@@ -221,11 +221,6 @@ class PluginsFacade implements PluginStateListener {
         }
     }
 
-    synchronized void setup(Map config = Collections.emptyMap()) {
-        init()
-        load(config)
-    }
-
     void load(Map config) {
         if( !manager )
             throw new IllegalArgumentException("Plugin system has not been initialized")
diff --git a/modules/nf-commons/src/test/nextflow/plugin/PluginsFacadeTest.groovy b/modules/nf-commons/src/test/nextflow/plugin/PluginsFacadeTest.groovy
index 5bb8aa4bf7..f9bd54d5d4 100644
--- a/modules/nf-commons/src/test/nextflow/plugin/PluginsFacadeTest.groovy
+++ b/modules/nf-commons/src/test/nextflow/plugin/PluginsFacadeTest.groovy
@@ -25,7 +25,8 @@ class PluginsFacadeTest extends Specification {
         plugins.indexUrl = 'http://localhost:9900/plugins.json'
 
         when:
-        plugins.setup([plugins: [ 'nf-console@1.0.0' ]])
+        plugins.init()
+        plugins.load([plugins: [ 'nf-console@1.0.0' ]])
         then:
         folder.resolve('nf-console-1.0.0').exists()
 

From d5a6a963a2b7fd9433da61d3cbd13399a619674e Mon Sep 17 00:00:00 2001
From: Nathan Spix <56930974+njspix@users.noreply.github.com>
Date: Fri, 5 Jan 2024 16:27:16 -0500
Subject: [PATCH 333/350] Fix typo in Hyperqueue section (#4635)

Signed-off-by: Nathan Spix <56930974+njspix@users.noreply.github.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/executor.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/executor.md b/docs/executor.md
index 08aba7bc2d..f623d56892 100644
--- a/docs/executor.md
+++ b/docs/executor.md
@@ -270,7 +270,7 @@ Nextflow manages each process as a separate job that is submitted to the cluster
 
 The pipeline must be launched from a node where the `hq` command is available, which is typically the cluster login node.
 
-To enable the HTCondor executor, set `process.executor = 'hyperqueue'` in the `nextflow.config` file.
+To enable the HyperQueue executor, set `process.executor = 'hq'` in the `nextflow.config` file.
 
 Resource requests and other job characteristics can be controlled via the following process directives:
 

From e216a876453fb4b05f1ab479c3de19f1be7d05ef Mon Sep 17 00:00:00 2001
From: Dr Marco Claudio De La Pierre <marco.delapierre@gmail.com>
Date: Sat, 6 Jan 2024 05:49:06 +0800
Subject: [PATCH 334/350] Fix typo in OCI mode warning message (#4633) [ci
 fast]

Signed-off-by: Dr Marco Claudio De La Pierre <marco.delapierre@seqera.io>
---
 .../src/main/groovy/nextflow/container/ContainerConfig.groovy   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/container/ContainerConfig.groovy b/modules/nextflow/src/main/groovy/nextflow/container/ContainerConfig.groovy
index 5a372ed6e8..44cc070156 100644
--- a/modules/nextflow/src/main/groovy/nextflow/container/ContainerConfig.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/container/ContainerConfig.groovy
@@ -84,7 +84,7 @@ class ContainerConfig extends LinkedHashMap {
             return false
         }
         if( get('oci')?.toString()=='true' ) {
-            log.warn "The setting `singularity.oci` is deprecated - use `singularity.ociNative` instead"
+            log.warn "The setting `singularity.oci` is deprecated - use `singularity.ociMode` instead"
             return true
         }
         if( get('ociMode')?.toString()=='true' )

From 4727f174b781e3cd6cd8b26be3f2cdfc6cba899f Mon Sep 17 00:00:00 2001
From: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
Date: Sun, 7 Jan 2024 21:07:30 -0300
Subject: [PATCH 335/350] Fix typo in the docs (#4636) [ci-skip]

Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
---
 docs/config.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/config.md b/docs/config.md
index f85e8c7977..a0f6e51a84 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -1446,12 +1446,12 @@ The following settings are available:
 `singularity.ociAutoPull`
 : :::{versionadded} 23.12.0-edge
   :::
-: When enabled, OCI (and Docker) container images are pull and converted to a SIF image file format implicitly by the Singularity run command, instead of Nextflow. Requires Singulairty 3.11 or later (default: `false`).
+: When enabled, OCI (and Docker) container images are pull and converted to a SIF image file format implicitly by the Singularity run command, instead of Nextflow. Requires Singularity 3.11 or later (default: `false`).
 
 `singularity.ociMode`
 : :::{versionadded} 23.12.0-edge
   :::
-: Enable OCI-mode, that allows running native OCI compliant container image with Singularity using `crun` or `runc` as low-level runtime. Note: it requires Singulairty 4 or later. See `--oci` flag in the [Singularity documentation](https://docs.sylabs.io/guides/4.0/user-guide/oci_runtime.html#oci-mode) for more details and requirements (default: `false`).
+: Enable OCI-mode, that allows running native OCI compliant container image with Singularity using `crun` or `runc` as low-level runtime. Note: it requires Singularity 4 or later. See `--oci` flag in the [Singularity documentation](https://docs.sylabs.io/guides/4.0/user-guide/oci_runtime.html#oci-mode) for more details and requirements (default: `false`).
 
 `singularity.pullTimeout`
 : The amount of time the Singularity pull can last, exceeding which the process is terminated (default: `20 min`).

From dc0402266b89170ff2facbea9a1527deee38684b Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sun, 31 Dec 2023 14:30:27 -0600
Subject: [PATCH 336/350] Remove preview from cmd secret

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 modules/nextflow/src/main/groovy/nextflow/cli/CmdSecret.groovy | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdSecret.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdSecret.groovy
index 1d7c54bcb2..51b6e879c7 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdSecret.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdSecret.groovy
@@ -32,7 +32,7 @@ import nextflow.secret.SecretsProvider
  */
 @Slf4j
 @CompileStatic
-@Parameters(commandDescription = "Manage pipeline secrets (preview)")
+@Parameters(commandDescription = "Manage pipeline secrets")
 class CmdSecret extends CmdBase implements UsageAware {
 
     interface SubCmd {

From 1b72d9984c4be6f8b13fa1cb47828484a06b256d Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sun, 31 Dec 2023 14:33:12 -0600
Subject: [PATCH 337/350] Undocument removed preview wave report feature [ci
 fast]

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/wave.md | 10 ----------
 1 file changed, 10 deletions(-)

diff --git a/docs/wave.md b/docs/wave.md
index 426267ffe1..ac2a0fd041 100644
--- a/docs/wave.md
+++ b/docs/wave.md
@@ -230,16 +230,6 @@ container freeze mode, the container repository authentication needs to be manag
 `wave.strategy`
 : The strategy to be used when resolving ambiguous Wave container requirements (default: `'container,dockerfile,conda,spack'`).
 
-`wave.report.enabled` (preview)
-: :::{versionadded} 23.06.0-edge
-  :::
-: Enable the reporting of the Wave containers used during the pipeline execution (default: `false`).
-
-`wave.report.file` (preview)
-: :::{versionadded} 23.06.0-edge
-  :::
-: The name of the containers report file (default: `'containers-<timestamp>.config'`).
-
 `wave.retryPolicy.delay`
 : :::{versionadded} 22.06.0-edge
   :::

From 43df1d88921ddf3c2c384f32a287a44e9e812e4d Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Tue, 9 Jan 2024 17:28:19 +0100
Subject: [PATCH 338/350] [Docs] Mention conda.channels on wave docs page
 (#4640) [ci skip]

Signed-off-by: Phil Ewels <phil.ewels@seqera.io>
---
 docs/wave.md | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/docs/wave.md b/docs/wave.md
index ac2a0fd041..f632850a3b 100644
--- a/docs/wave.md
+++ b/docs/wave.md
@@ -94,6 +94,16 @@ wave.strategy = ['conda']
 
 The above setting instructs Wave to use the `conda` directive to provision the pipeline containers and ignore the `container` directive and any Dockerfile(s).
 
+:::{tip}
+Some configuration options in the `conda` scope are used when Wave is used to build Conda-based containers.
+For example, the Conda channels and their priority can be set with `conda.channels`:
+
+```groovy
+wave.strategy = ['conda']
+conda.channels = 'seqera,conda-forge,bioconda,defaults'
+```
+:::
+
 ### Build Spack based containers
 
 :::{warning}
@@ -195,7 +205,7 @@ The following configuration options are available:
 : When enabling the container freeze mode, Wave will provision an non-ephemeral container image
 that will be pushed to a container repository your choice. It requires the use of the `wave.build.repository` setting.
 It is also suggested to specify a custom cache repository via the setting `wave.build.cacheRepository`. Note: when using
-container freeze mode, the container repository authentication needs to be managed by the underlying infrastructure.    
+container freeze mode, the container repository authentication needs to be managed by the underlying infrastructure.
 
 `wave.build.repository`
 : The container repository where images built by Wave are uploaded (note: the corresponding credentials must be provided in your Nextflow Tower account).
@@ -233,7 +243,7 @@ container freeze mode, the container repository authentication needs to be manag
 `wave.retryPolicy.delay`
 : :::{versionadded} 22.06.0-edge
   :::
-: The initial delay when a failing HTTP request is retried (default: `150ms`). 
+: The initial delay when a failing HTTP request is retried (default: `150ms`).
 
 `wave.retryPolicy.maxDelay`
 : :::{versionadded} 22.06.0-edge

From 2e02afbfa54a16703662f0a52d51b19c3db6a8cc Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Tue, 9 Jan 2024 10:48:56 -0600
Subject: [PATCH 339/350] Use AZURE_STORAGE_SAS_TOKEN environment variable
 (#4627)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 .../src/main/nextflow/cloud/azure/config/AzStorageOpts.groovy   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/plugins/nf-azure/src/main/nextflow/cloud/azure/config/AzStorageOpts.groovy b/plugins/nf-azure/src/main/nextflow/cloud/azure/config/AzStorageOpts.groovy
index eeff4bbe3c..1bfecfb780 100644
--- a/plugins/nf-azure/src/main/nextflow/cloud/azure/config/AzStorageOpts.groovy
+++ b/plugins/nf-azure/src/main/nextflow/cloud/azure/config/AzStorageOpts.groovy
@@ -41,7 +41,7 @@ class AzStorageOpts {
         this.sysEnv = env==null ? new HashMap<String,String>(System.getenv()) : env
         this.accountKey = config.accountKey ?: sysEnv.get('AZURE_STORAGE_ACCOUNT_KEY')
         this.accountName = config.accountName ?: sysEnv.get('AZURE_STORAGE_ACCOUNT_NAME')
-        this.sasToken = config.sasToken
+        this.sasToken = config.sasToken ?: sysEnv.get('AZURE_STORAGE_SAS_TOKEN')
         this.tokenDuration = (config.tokenDuration as Duration) ?: Duration.of('48h')
         this.fileShares = parseFileShares(config.fileShares instanceof Map ? config.fileShares as Map<String, Map>
                 : Collections.<String,Map> emptyMap())

From 85bab699e4a8270247607f2db73ecae541844c3d Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Tue, 9 Jan 2024 11:51:02 -0500
Subject: [PATCH 340/350] Fix azure retry policy (#4638)

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../cloud/azure/batch/AzBatchService.groovy     | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

diff --git a/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchService.groovy b/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchService.groovy
index 170a0f6e11..74df0fc1a3 100644
--- a/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchService.groovy
+++ b/plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchService.groovy
@@ -20,6 +20,7 @@ import java.math.RoundingMode
 import java.nio.file.Path
 import java.time.Instant
 import java.time.temporal.ChronoUnit
+import java.util.concurrent.TimeoutException
 import java.util.function.Predicate
 
 import com.microsoft.azure.batch.BatchClient
@@ -912,8 +913,22 @@ class AzBatchService implements Closeable {
      * @return The result of the supplied action
      */
     protected <T> T apply(CheckedSupplier<T> action) {
-        final cond = (e -> e instanceof BatchErrorException && e.body().code() in RETRY_CODES)  as Predicate<? extends Throwable>
+        // define the retry condition
+        final cond = new Predicate<? extends Throwable>() {
+            @Override
+            boolean test(Throwable t) {
+                if( t instanceof BatchErrorException && t.body().code() in RETRY_CODES )
+                    return true
+                if( t instanceof IOException || t.cause instanceof IOException )
+                    return true
+                if( t instanceof TimeoutException || t.cause instanceof TimeoutException )
+                    return true
+                return false
+            }
+        }
+        // create the retry policy object
         final policy = retryPolicy(cond)
+        // apply the action with
         return Failsafe.with(policy).get(action)
     }
 }

From f9ba47ef322376b7e83c48be42b84b238c8bcea9 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Thu, 11 Jan 2024 04:53:08 -0600
Subject: [PATCH 341/350] Fix Ignore stored process message when ansi log is
 enabled (#4645)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../src/main/groovy/nextflow/trace/AnsiLogObserver.groovy     | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/trace/AnsiLogObserver.groovy b/modules/nextflow/src/main/groovy/nextflow/trace/AnsiLogObserver.groovy
index fddae54250..aaf96f3a44 100644
--- a/modules/nextflow/src/main/groovy/nextflow/trace/AnsiLogObserver.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/trace/AnsiLogObserver.groovy
@@ -121,7 +121,9 @@ class AnsiLogObserver implements TraceObserver {
         boolean warn
         if( isHashLogPrefix(message) && !(warn=message.indexOf('NOTE:')>0) )
             return
-        
+        if( message.startsWith('[skipping]') )
+            return
+
         if( !started || !statsObserver.hasProgressRecords() ) {
             println message
         }

From d67aef5fecf09132a02276cc6735d431b7c84c42 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 11 Jan 2024 11:53:51 +0100
Subject: [PATCH 342/350] Bump tj-actions/changed-files from 35 to 41 in
 /.github/workflows (#4622) [ci skip]

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 .github/workflows/build.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index d2cb25c27f..994a729c26 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -38,7 +38,7 @@ jobs:
 
       - name: Get changed files
         id: changed-files
-        uses: tj-actions/changed-files@v35
+        uses: tj-actions/changed-files@v41
         with:
           files_ignore: docs
 

From da2f95c97ddb8ec083cdc1d5acaa6c5336b4b5d4 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Fri, 12 Jan 2024 21:53:03 +0100
Subject: [PATCH 343/350] Update changelog

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 changelog.txt | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/changelog.txt b/changelog.txt
index 4a9717bf9f..33ddeb0f67 100644
--- a/changelog.txt
+++ b/changelog.txt
@@ -1,5 +1,8 @@
 NEXTFLOW CHANGE-LOG
 ===================
+23.04.5 - 12 Jan 2023
+- Fix container environment with special chars (#4594) [663b2936]
+
 23.12.0-edge - 20 Dec 2023 
 - Add AWS_SESSION_TOKEN to Fusion environment (#4581) [552f29b0]
 - Add ability to disable Cloudinfo service (#4606) [f7251895]
@@ -166,6 +169,14 @@ NEXTFLOW CHANGE-LOG
 - Bump nf-wave@0.13.0 [0cf2476c]
 - Bump wave-utils@0.7.8 [d0c47d49]
 
+23.04.4 - 25 Sep 2023
+- Fix use of GITHUB_TOKEN variable to access GitHub repo [108c6b55]
+- Fix allow_other vulnerability preventing google-batch submissions (#4332) [4895d547]
+- Fix Prevent false positive resumable task [aae87715]
+- Fix Always emit publish event for cached task outputs (#4227) [c4cd53c2]
+- Fix Too long Http connection pool timeout [ce5e9930]
+- Bump nf-google@1.7.3-patch1 [d881728c]
+
 23.09.1-edge - 11 Sep 2023
 - Revert "Allow setting shell directive when using the trace file (#4210)" [9f9edcdc]
 

From d9b8e7ef243966e26c9018713633fcbfb0fe1edd Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Fri, 12 Jan 2024 23:51:37 +0100
Subject: [PATCH 344/350] Build on stable branch

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .github/workflows/build.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 994a729c26..04d8fef5ae 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -12,6 +12,7 @@ on:
       - 'master'
       - 'test*'
       - 'dev*'
+      - 'STABLE-*'
   pull_request:
     types: [opened, reopened, synchronize]
   workflow_dispatch:

From 66f37f646bc821286721b6adbb2b97450df9c592 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Fri, 12 Jan 2024 23:15:29 +0100
Subject: [PATCH 345/350] Update changelog

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 changelog.txt | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/changelog.txt b/changelog.txt
index 33ddeb0f67..6b2be1e2ef 100644
--- a/changelog.txt
+++ b/changelog.txt
@@ -1,5 +1,20 @@
 NEXTFLOW CHANGE-LOG
 ===================
+23.10.1 - 12 Jan 2023 
+- Fix bug with Fusion symlink resolution (#4593) [f28c9e48]
+- Fix Fusion symlinks when publishing files (#4348) [1fa5878a]
+- Fix Inspect command fails with Singularity [25883df3]
+- Fix Allow the use of error build-in function in onComplete handler (#4458) [ci fast] [4be10cd3]
+- Fix Harden regular expression to used to strip secrets in logs (#4563) [ci fast] [0102d4d6]
+- Fix custom notification template [40980bcb]
+- Fix container environment with special chars (#4594) [f4e00601]
+- Fix AZURE_STORAGE_SAS_TOKEN environment variable (#4627) [2e1cb413]
+- Fix azure retry policy (#4638) [2bc3cf0e]
+- Fix BitBucket get source API with custom branch [5ef75e32]
+- Improve error details for AbortOperationException [9e795a62]
+- Bump nf-wave@1.0.1 [206f2614]
+- Bump nf-azure@1.3.3 [50bcad59]
+
 23.04.5 - 12 Jan 2023
 - Fix container environment with special chars (#4594) [663b2936]
 

From 682a68066b8567973a01abdd5e9b8e1c54082ffb Mon Sep 17 00:00:00 2001
From: Dr Marco Claudio De La Pierre <marco.delapierre@gmail.com>
Date: Tue, 16 Jan 2024 21:49:26 +0800
Subject: [PATCH 346/350] LocalSecretsProvider: invalid permissions tests made
 more robust (#4663) [ci fast]

Signed-off-by: Dr Marco Claudio De La Pierre <marco.delapierre@gmail.com>
---
 changelog.txt                                                   | 2 +-
 .../test/groovy/nextflow/secret/LocalSecretsProviderTest.groovy | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/changelog.txt b/changelog.txt
index 6b2be1e2ef..5eafa10eff 100644
--- a/changelog.txt
+++ b/changelog.txt
@@ -4,7 +4,7 @@ NEXTFLOW CHANGE-LOG
 - Fix bug with Fusion symlink resolution (#4593) [f28c9e48]
 - Fix Fusion symlinks when publishing files (#4348) [1fa5878a]
 - Fix Inspect command fails with Singularity [25883df3]
-- Fix Allow the use of error build-in function in onComplete handler (#4458) [ci fast] [4be10cd3]
+- Fix Allow the use of error built-in function in onComplete handler (#4458) [ci fast] [4be10cd3]
 - Fix Harden regular expression to used to strip secrets in logs (#4563) [ci fast] [0102d4d6]
 - Fix custom notification template [40980bcb]
 - Fix container environment with special chars (#4594) [f4e00601]
diff --git a/modules/nextflow/src/test/groovy/nextflow/secret/LocalSecretsProviderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/secret/LocalSecretsProviderTest.groovy
index c7a91828ec..0c00292b73 100644
--- a/modules/nextflow/src/test/groovy/nextflow/secret/LocalSecretsProviderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/secret/LocalSecretsProviderTest.groovy
@@ -106,6 +106,8 @@ class LocalSecretsProviderTest extends Specification {
         and:
         Files.write(secretFile, json.getBytes('utf-8'), StandardOpenOption.CREATE_NEW)
         and:
+        secretFile.setPermissions('rw-r-----')
+        and:
         def provider = new LocalSecretsProvider(storeFile: secretFile)
 
         when:

From fde56bf6126c5ab4f1f74872ae581d1889f1b09c Mon Sep 17 00:00:00 2001
From: Dr Marco Claudio De La Pierre <marco.delapierre@gmail.com>
Date: Fri, 19 Jan 2024 17:12:56 +0800
Subject: [PATCH 347/350] Add yaml example for pip packages to docs (#4677)

Signed-off-by: Dr Marco Claudio De La Pierre <marco.delapierre@gmail.com>
---
 docs/conda.md | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/docs/conda.md b/docs/conda.md
index b4f05092ef..d3ea9ee56c 100644
--- a/docs/conda.md
+++ b/docs/conda.md
@@ -76,6 +76,20 @@ dependencies:
   - bwa=0.7.15
 ```
 
+This other example shows how to leverage a Conda environment file to install Python packages from the [PyPI repository](https://pypi.org/)), through the `pip` package manager (which must also be explicitly listed as a required package):
+
+```yaml
+name: my-env-2
+channels:
+  - defaults
+dependencies:
+  - pip
+  - pip:
+    - numpy
+    - pandas
+    - matplotlib
+```
+
 Read the Conda documentation for more details about how to create [environment files](https://conda.io/docs/user-guide/tasks/manage-environments.html#creating-an-environment-file-manually).
 
 The path of an environment file can be specified using the `conda` directive:

From 9d17e407939ead57b0e43addda5924422d202360 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Sat, 20 Jan 2024 10:12:48 -0600
Subject: [PATCH 348/350] Set scratch default to false when using Fusion
 (#4675)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 .../src/main/groovy/nextflow/fusion/FusionScriptLauncher.groovy | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/fusion/FusionScriptLauncher.groovy b/modules/nextflow/src/main/groovy/nextflow/fusion/FusionScriptLauncher.groovy
index 274ecc8861..639f976174 100644
--- a/modules/nextflow/src/main/groovy/nextflow/fusion/FusionScriptLauncher.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/fusion/FusionScriptLauncher.groovy
@@ -62,7 +62,7 @@ class FusionScriptLauncher extends BashWrapperBuilder {
         bean.headerScript = headerScript(bean)
         // enable use of local scratch dir
         if( bean.scratch==null )
-            bean.scratch = true
+            bean.scratch = false
 
         return new FusionScriptLauncher(bean, scheme, remoteWorkDir)
     }

From 36090b70e8de4854a409959f76e08c9f69b62c49 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Sat, 20 Jan 2024 10:59:37 -0600
Subject: [PATCH 349/350] Truncate max size exceeded error message (#4644)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 .../main/io/seqera/tower/plugin/TowerJsonGenerator.groovy  | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerJsonGenerator.groovy b/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerJsonGenerator.groovy
index 46d3a99881..11251c2a2c 100644
--- a/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerJsonGenerator.groovy
+++ b/plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerJsonGenerator.groovy
@@ -122,8 +122,11 @@ class TowerJsonGenerator extends DefaultJsonGenerator {
         final key = stack.join('.')
         final max = scheme.get(key)
         if( seq!=null && max && seq.length()>max ) {
-            log.warn "Tower request field `$key` exceeds expected size | offending value: `$seq`, size: ${seq.size()} (max: $max)"
-            return seq.toString().substring(0,max)
+            final result = seq.toString().substring(0,max)
+            // show only the first 100 chars in the log as a preview
+            final preview = result.length()>100 ? result.substring(0,100) + '(truncated)' : result
+            log.warn "Tower request field `$key` exceeds expected size | offending value: `${preview}`, size: ${seq.size()} (max: $max)"
+            return result
         }
         return seq
     }

From a1e3319332952ed7e750a7f97c0121cf15ac7159 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 20 Jan 2024 19:17:01 +0100
Subject: [PATCH 350/350] Add support for custom fuse device plugin (#4612) [ci
 fast]

This commit allows customising the FUSE plugin device required
by Fusion when using the Kubernetes executor. The FUSE plugin
name  can be specified by using the setting `k8s.fuseDevicePlugin`
for example:

```
k8s.fuseDevicePlugin = ['my-plugin/fuse': 1]
```

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 docs/config.md                                |  5 +++
 docs/kubernetes.md                            | 17 ++++++++
 .../main/groovy/nextflow/k8s/K8sConfig.groovy | 11 +++++
 .../groovy/nextflow/k8s/K8sTaskHandler.groovy |  3 +-
 .../groovy/nextflow/k8s/K8sConfigTest.groovy  | 12 ++++++
 .../nextflow/k8s/K8sTaskHandlerTest.groovy    | 43 ++++++++++++++++++-
 6 files changed, 89 insertions(+), 2 deletions(-)

diff --git a/docs/config.md b/docs/config.md
index a0f6e51a84..26db447620 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -1006,6 +1006,11 @@ The following settings are available:
   :::
 : If you trace the hostname, activate this option (default: `false`).
 
+`k8s.fuseDevicePlugin`
+: :::{versionadded} 24.01.0-edge
+  :::
+: The FUSE device plugin to be used when enabling Fusion in unprivileged mode (default: `['nextflow.io/fuse': 1]`).
+
 `k8s.httpConnectTimeout`
 : :::{versionadded} 22.10.0
   :::
diff --git a/docs/kubernetes.md b/docs/kubernetes.md
index e6f38a9542..357d97f207 100644
--- a/docs/kubernetes.md
+++ b/docs/kubernetes.md
@@ -120,6 +120,23 @@ Then the pipeline execution can be launched using the usual run command and spec
 nextflow run <YOUR PIPELINE> -work-dir s3://<YOUR-BUCKET>/scratch
 ```
 
+:::{note}
+When using Fusion, pods will run as *privileged* by default.
+:::
+
+To use Fusion with without the need for escalating privileges, it is required to install in the Kubernetes cluster the
+Nextflow [FUSE device plugin](https://github.com/nextflow-io/k8s-fuse-plugin) and add in your Nextflow configuration the following
+setting:
+
+```
+fusion {
+  privileged = false
+}
+```
+
+To use a custom FUSE device plugin, specify it via the setting `k8s.fuseDevicePlugin`. See
+the {ref}`Kubernetes configuration section<config-k8s>` for details.
+
 ### Running in a pod
 
 Nextflow can be executed directly from a pod running in a Kubernetes cluster. In these cases you will need to use the plain Nextflow `run` command and specify the `k8s` executor and the required persistent volume claim in the `nextflow.config` file as shown below:
diff --git a/modules/nextflow/src/main/groovy/nextflow/k8s/K8sConfig.groovy b/modules/nextflow/src/main/groovy/nextflow/k8s/K8sConfig.groovy
index 0be59bd423..aed5d977e3 100644
--- a/modules/nextflow/src/main/groovy/nextflow/k8s/K8sConfig.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/k8s/K8sConfig.groovy
@@ -42,6 +42,8 @@ import nextflow.util.Duration
 @CompileStatic
 class K8sConfig implements Map<String,Object> {
 
+    static final private Map<String,?> DEFAULT_FUSE_PLUGIN = Map.of('nextflow.io/fuse', 1)
+
     @Delegate
     private Map<String,Object> target
 
@@ -116,6 +118,15 @@ class K8sConfig implements Map<String,Object> {
         target.storageSubPath
     }
 
+    Map<String,?> fuseDevicePlugin() {
+        final result = target.fuseDevicePlugin
+        if( result instanceof Map && result.size()==1 )
+            return result as Map<String,?>
+        if( result )
+            log.warn1 "Setting 'fuseDevicePlugin' should be a map object providing exactly one entry - offending value: $result"
+        return DEFAULT_FUSE_PLUGIN
+    }
+
     /**
      * Whenever the pod should honour the entrypoint defined by the image (default: false)
      *
diff --git a/modules/nextflow/src/main/groovy/nextflow/k8s/K8sTaskHandler.groovy b/modules/nextflow/src/main/groovy/nextflow/k8s/K8sTaskHandler.groovy
index f782e423d6..91d8dbc160 100644
--- a/modules/nextflow/src/main/groovy/nextflow/k8s/K8sTaskHandler.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/k8s/K8sTaskHandler.groovy
@@ -252,7 +252,8 @@ class K8sTaskHandler extends TaskHandler implements FusionAwareTask {
             if( fusionConfig().privileged() )
                 builder.withPrivileged(true)
             else {
-                builder.withResourcesLimits(["nextflow.io/fuse": 1])
+                final device= k8sConfig.fuseDevicePlugin()
+                builder.withResourcesLimits(device)
             }
 
             final env = fusionLauncher().fusionEnv()
diff --git a/modules/nextflow/src/test/groovy/nextflow/k8s/K8sConfigTest.groovy b/modules/nextflow/src/test/groovy/nextflow/k8s/K8sConfigTest.groovy
index 4d63b2e82b..5e843bd2c9 100644
--- a/modules/nextflow/src/test/groovy/nextflow/k8s/K8sConfigTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/k8s/K8sConfigTest.groovy
@@ -129,6 +129,18 @@ class K8sConfigTest extends Specification {
 
     }
 
+    def 'should set device plugin' () {
+        when:
+        def cfg = new K8sConfig([:])
+        then:
+        cfg.fuseDevicePlugin() == ['nextflow.io/fuse':1]
+
+        when:
+        cfg = new K8sConfig([fuseDevicePlugin:['foo/fuse':10]])
+        then:
+        cfg.fuseDevicePlugin() == ['foo/fuse':10]
+    }
+
     def 'should create client config' () {
 
         given:
diff --git a/modules/nextflow/src/test/groovy/nextflow/k8s/K8sTaskHandlerTest.groovy b/modules/nextflow/src/test/groovy/nextflow/k8s/K8sTaskHandlerTest.groovy
index 8ac5093294..c3c7f8b5a0 100644
--- a/modules/nextflow/src/test/groovy/nextflow/k8s/K8sTaskHandlerTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/k8s/K8sTaskHandlerTest.groovy
@@ -938,7 +938,9 @@ class K8sTaskHandlerTest extends Specification {
         def client = Mock(K8sClient)
         def builder = Mock(K8sWrapperBuilder)
         def launcher = Mock(FusionScriptLauncher)
-        def handler = Spy(new K8sTaskHandler(builder:builder, client: client))
+        def k8sConfig = Spy(K8sConfig)
+        def exec = Mock(K8sExecutor) { getK8sConfig()>>k8sConfig  }
+        def handler = Spy(new K8sTaskHandler(builder:builder, client: client, executor: exec))
         Map result
 
         when:
@@ -973,6 +975,45 @@ class K8sTaskHandlerTest extends Specification {
         result.spec.containers[0].env == [[name:'FUSION_BUCKETS', value:'this,that']]
         result.spec.containers[0].resources == [limits:['nextflow.io/fuse':1]]
         !result.spec.containers[0].securityContext
+
+
+        /*
+         * use custom fuse device
+         */
+        when:
+        result = handler.newSubmitRequest(task)
+        then:
+        launcher.fusionEnv() >> [FUSION_BUCKETS: 'this,that']
+        launcher.toContainerMount(WORK_DIR.resolve('.command.run')) >> Path.of('/fusion/http/work/dir/.command.run')
+        launcher.fusionSubmitCli(task) >> ['/usr/bin/fusion', 'bash', '/fusion/http/work/dir/.command.run']
+        and:
+        k8sConfig.fuseDevicePlugin() >> ['custom/device/fuse': 1]
+        and:
+        handler.getTask() >> task
+        handler.fusionEnabled() >> true
+        handler.fusionLauncher() >> launcher
+        handler.fusionConfig() >> new FusionConfig(privileged: false)
+        and:
+        task.getContainer() >> 'debian:latest'
+        task.getWorkDir() >> WORK_DIR
+        task.getConfig() >> config
+        and:
+        1 * handler.fixOwnership() >> false
+        1 * handler.entrypointOverride() >> false
+        1 * handler.getPodOptions() >> new PodOptions()
+        1 * handler.getSyntheticPodName(task) >> 'nf-123'
+        1 * handler.getLabels(task) >> [:]
+        1 * handler.getAnnotations() >> [:]
+        1 * handler.getContainerMounts() >> []
+        and:
+        1 * config.getCpus() >> 0
+        1 * config.getMemory() >> null
+        1 * client.getConfig() >> new ClientConfig()
+        and:
+        result.spec.containers[0].args == ['/usr/bin/fusion', 'bash', '/fusion/http/work/dir/.command.run']
+        result.spec.containers[0].env == [[name:'FUSION_BUCKETS', value:'this,that']]
+        result.spec.containers[0].resources == [limits:['custom/device/fuse':1]]
+        !result.spec.containers[0].securityContext
     }
 
     def 'get fusion submit command' () {