From 74e704f067c198fd93d8255b7f19933b531656c1 Mon Sep 17 00:00:00 2001 From: Luis Kress Date: Sat, 14 Mar 2026 19:37:03 +0100 Subject: [PATCH] docs: Add documentation --- docs/further.md | 11 +++++++++++ docs/intro.md | 2 ++ 2 files changed, 13 insertions(+) create mode 100644 docs/further.md create mode 100644 docs/intro.md diff --git a/docs/further.md b/docs/further.md new file mode 100644 index 0000000..68fd2e4 --- /dev/null +++ b/docs/further.md @@ -0,0 +1,11 @@ +### Example setup + +The cluster generic plugin enables access to workflow variables (such as `rule`, `resources`, or `threads`) within the strings used to define cluster generic plugin arguments. +This makes it possible to create custom configurations for running workflows on various cluster systems that support a submission command accepting the path to a job script. The following example Snakemake profile (see [Profiles](https://snakemake.readthedocs.io/en/stable/executing/cli.html#profiles)) shows this for a custom SLURM execution configuration setup. Submitting jobs with this setup would result in having the rule name of the current job contained in the SLURM job name. + +```yaml +executor: cluster-generic +cluster-generic-submit-cmd: sbatch --cpus-per-task {threads} --mem={resources.mem_mb} --job-name=smk-{rule} --parsable +cluster-generic-cancel-cmd: scancel +``` + diff --git a/docs/intro.md b/docs/intro.md new file mode 100644 index 0000000..9de593f --- /dev/null +++ b/docs/intro.md @@ -0,0 +1,2 @@ +The cluster generic plugin allows submitting jobs to cluster systems that provide a submission command that accepts the path to a job script. +