Merge branch 'master' into 2527-task-grouping

build.gradle

@@ -100,8 +100,8 @@ allprojects {
 
         // Documentation required libraries
         groovyDoc 'org.fusesource.jansi:jansi:1.11'
-        groovyDoc "org.codehaus.groovy:groovy-groovydoc:3.0.17"
-        groovyDoc "org.codehaus.groovy:groovy-ant:3.0.17"
+        groovyDoc "org.codehaus.groovy:groovy-groovydoc:3.0.18"
+        groovyDoc "org.codehaus.groovy:groovy-ant:3.0.18"
     }
 
     test {

docker/Makefile

@@ -15,9 +15,13 @@
 
 version ?= none
 
-build: dist/docker
+build: dist/docker/amd64
 	cp ../nextflow .
-	docker buildx build --platform linux/amd64 --output=type=docker --progress=plain --tag nextflow/nextflow:${version} .
+	docker buildx build --platform linux/amd64 --output=type=docker --progress=plain --tag nextflow/nextflow:${version} --build-arg TARGETPLATFORM=linux/amd64 .
+
+build-arm: dist/docker/arm64
+	cp ../nextflow .
+	docker buildx build --platform linux/arm64 --output=type=docker --progress=plain --tag nextflow/nextflow:${version} --build-arg TARGETPLATFORM=linux/arm64 .
 
 release: build
 	docker tag nextflow/nextflow:${version} nextflow/nextflow:latest
@@ -35,9 +39,11 @@ release: build
 #  MacOS:   https://download.docker.com/mac/static
 #  Windows: https://download.docker.com/win/static
 
-dist/docker:
+dist/docker/amd64:
 	mkdir -p dist/linux/amd64
 	curl -fsSL https://download.docker.com/linux/static/stable/x86_64/docker-17.09.0-ce.tgz | tar --strip-components=1 -xvz -C dist/linux/amd64
-#	mkdir -p dist/linux/arm64
-#	curl -fsSL https://download.docker.com/linux/static/stable/aarch64/docker-17.09.0-ce.tgz | tar --strip-components=1 -xvz -C dist/linux/arm64
+
+dist/docker/arm64:
+	mkdir -p dist/linux/arm64
+	curl -fsSL https://download.docker.com/linux/static/stable/aarch64/docker-17.09.0-ce.tgz | tar --strip-components=1 -xvz -C dist/linux/arm64
 

docs/azure.md

@@ -335,13 +335,15 @@ The private registry is an addition, not a replacement, to the existing configur
 :::{note}
 When using containers hosted in a private registry, the registry name must also be provided in the container name specified via the {ref}`container <process-container>` directive using the format: `[server]/[your-organization]/[your-image]:[tag]`. Read more about fully qualified image names in the [Docker documentation](https://docs.docker.com/engine/reference/commandline/pull/#pull-from-a-different-registry).
 :::
+
 ### Virtual Network
 
 :::{versionadded} 23.03.0-edge
 :::
 
-Sometimes it might be useful to create a pool in an existing [Virtual Network](https://learn.microsoft.com/en-us/azure/virtual-network/). To do  so, the 
+Sometimes it might be useful to create a pool in an existing [Virtual Network](https://learn.microsoft.com/en-us/azure/virtual-network/). To do so, the 
 `virtualNetwork` option can be added to the pool settings as follows:
+
 ```groovy
 azure {
     batch {
@@ -356,12 +358,16 @@ azure {
     }
 }
 ```
+
 The value of the setting must be the identifier of a subnet available in the virtual network to join. A valid subnet ID has the following form:
 
-`/subscriptions/<YOUR SUBSCRIPTION ID>/resourceGroups/<YOUR RESOURCE GROUP NAME>/providers/Microsoft.Network/virtualNetworks/<YOUR VIRTUAL NETWORK NAME>/subnets/<YOUR SUBNET NAME>`
+```
+/subscriptions/<YOUR SUBSCRIPTION ID>/resourceGroups/<YOUR RESOURCE GROUP NAME>/providers/Microsoft.Network/virtualNetworks/<YOUR VIRTUAL NETWORK NAME>/subnets/<YOUR SUBNET NAME>
+```
 
 :::{warning}
 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
 

docs/container.md

@@ -66,6 +66,10 @@ 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
+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`.
+:::
+
 ### 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::
@@ -575,6 +579,10 @@ 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
+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`.
+:::
+
 ### 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:

docs/fusion.md

@@ -164,7 +164,7 @@ nextflow run <YOUR PIPELINE> -work-dir s3://<YOUR BUCKET>/scratch
 
 ## NVMe storage
 
-The Fusion file system implements a lazy download and upload algorithm that runs in the background to transfer files in parallel to and from object storage into a container-local temporary folder. This means that the performance of the temporary folder inside the container (`/tmp` in a default setup) is key to acheiving maximum performance.
+The Fusion file system implements a lazy download and upload algorithm that runs in the background to transfer files in parallel to and from object storage into a container-local temporary folder. This means that the performance of the temporary folder inside the container (`/tmp` in a default setup) is key to achieving maximum performance.
 
 The temporary folder is used only as a temporary cache, so the size of the volume can be much lower than the actual needs of your pipeline processes. Fusion has a built-in garbage collector that constantly monitors remaining disk space on the temporary folder and immediately evicts old cached entries when necessary.
 

docs/operator.md

@@ -1312,7 +1312,7 @@ result = 15
 ```
 
 :::{tip}
-A common use case for this operator is to use the first paramter as an accumulator and the second parameter as the `i-th` item to be processed.
+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:
@@ -1705,7 +1705,7 @@ Available options:
 : 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).
 
 `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 oder 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 folder.
 
 `keepHeader`
 : Parses the first line as header and prepends it to each emitted chunk.

docs/process.md

@@ -1201,9 +1201,10 @@ This directive is only used by certain executors. Refer to the {ref}`executor-pa
 :::{note}
 The accelerator `type` option depends on the target execution platform. Refer to the platform-specific documentation for details on the available accelerators:
 
-- [AWS](https://aws.amazon.com/batch/faqs/?#GPU_Scheduling_)
 - [Google Cloud](https://cloud.google.com/compute/docs/gpus/)
 - [Kubernetes](https://kubernetes.io/docs/tasks/manage-gpus/scheduling-gpus/#clusters-containing-different-types-of-gpus)
+
+The accelerator `type` option is not supported for AWS Batch. You can control the accelerator type indirectly through the allowed instance types in your Compute Environment. See the [AWS Batch FAQs](https://aws.amazon.com/batch/faqs/?#GPU_Scheduling_) for more information.
 :::
 
 (process-afterscript)=
@@ -1333,7 +1334,7 @@ process foo {
 
 Multiple packages can be specified separating them with a blank space e.g. `bwa=0.7.15 fastqc=0.11.5`. The name of the channel from where a specific package needs to be downloaded can be specified using the usual Conda notation i.e. prefixing the package with the channel name as shown here `bioconda::bwa=0.7.15`.
 
-The `conda` directory also allows the specification of a Conda environment file path or the path of an existing environment directory. See the {ref}`conda-page` page for further details.
+The `conda` directive also allows the specification of a Conda environment file path or the path of an existing environment directory. See the {ref}`conda-page` page for further details.
 
 (process-container)=
 
@@ -2112,7 +2113,7 @@ Available options:
 
 ### queue
 
-The `queue` directory allows you to set the `queue` where jobs are scheduled when using a grid based executor in your pipeline. For example:
+The `queue` directive allows you to set the `queue` where jobs are scheduled when using a grid based executor in your pipeline. For example:
 
 ```groovy
 process grid_job {

docs/script.md

@@ -523,7 +523,7 @@ The following functions are available in Nextflow scripts:
 `file( filePattern, options = [:] )`
 : Get one or more files from a path or glob pattern. Returns a [Path](https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/nio/file/Path.html) or list of Paths if there are multiple files. See [Files and I/O](#files-and-io).
 
-`files( filePatten, options = [:] )`
+`files( filePattern, options = [:] )`
 : Convenience method for `file()` that always returns a list.
 
 `groupKey( key, size )`

modules/nextflow/build.gradle

@@ -17,12 +17,12 @@ compileGroovy {
 dependencies {
     api(project(':nf-commons'))
     api(project(':nf-httpfs'))
-    api "org.codehaus.groovy:groovy:3.0.17"
-    api "org.codehaus.groovy:groovy-nio:3.0.17"
-    api "org.codehaus.groovy:groovy-xml:3.0.17"
-    api "org.codehaus.groovy:groovy-json:3.0.17"
-    api "org.codehaus.groovy:groovy-templates:3.0.17"
-    api "org.codehaus.groovy:groovy-yaml:3.0.17"
+    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.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:3.0.17") { exclude group: 'org.codehaus.groovy' }
+    testFixturesApi ("org.codehaus.groovy:groovy-test:3.0.18") { 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' }

modules/nextflow/src/main/groovy/nextflow/container/SingularityBuilder.groovy

@@ -33,13 +33,20 @@ class SingularityBuilder extends ContainerBuilder<SingularityBuilder> {
 
     private boolean autoMounts
 
+    private boolean homeMount
+
     private boolean newPidNamespace
 
     SingularityBuilder(String name) {
         this.image = name
+        this.homeMount = defaultHomeMount()
         this.newPidNamespace = defaultNewPidNamespace()
     }
 
+    private boolean defaultHomeMount() {
+        SysEnv.get("NXF_${getBinaryName().toUpperCase()}_HOME_MOUNT", 'false').toString() == 'true'
+    }
+
     private boolean defaultNewPidNamespace() {
         SysEnv.get("NXF_${getBinaryName().toUpperCase()}_NEW_PID_NAMESPACE", 'true').toString() == 'true'
     }
@@ -92,6 +99,9 @@ class SingularityBuilder extends ContainerBuilder<SingularityBuilder> {
 
         result << 'exec '
 
+        if( !homeMount )
+            result << '--no-home '
+
         if( newPidNamespace )
             result << '--pid '