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 1/3] Fix typo in Hyperqueue section (#4635) Signed-off-by: Nathan Spix <56930974+njspix@users.noreply.github.com> Co-authored-by: Paolo Di Tommaso --- 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 Date: Sat, 6 Jan 2024 05:49:06 +0800 Subject: [PATCH 2/3] Fix typo in OCI mode warning message (#4633) [ci fast] Signed-off-by: Dr Marco Claudio De La Pierre --- .../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 Date: Sun, 7 Jan 2024 21:07:30 -0300 Subject: [PATCH 3/3] Fix typo in the docs (#4636) [ci-skip] Signed-off-by: Marcel Ribeiro-Dantas --- 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`).