From 4ce21f9fff26347c807f84f8ae51bcc0291ecfa1 Mon Sep 17 00:00:00 2001 From: Johannes Koester Date: Fri, 29 Nov 2024 12:57:52 +0100 Subject: [PATCH] docs: explain how to mask envvars --- docs/further.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/docs/further.md b/docs/further.md index 9ae5d12..438dfe2 100644 --- a/docs/further.md +++ b/docs/further.md @@ -23,7 +23,7 @@ If the shared scratch is e.g. specific for each job (e.g. controlled by a ``$JOB ```yaml default-storage-provider: fs local-storage-prefix: /local/work/$USER -remote-job-local-storage-prefix: /local/work/$USER/$JOBID +remote-job-local-storage-prefix: /local/work/$USER/\$JOBID shared-fs-usage: - persistence - software-deployment @@ -31,5 +31,7 @@ shared-fs-usage: - source-cache ``` +Here, in case a used variable can only expanded within the remote job, make sure to mask the expansion upon starting Snakemake by preceeding the variable declaration with a backslash (``\$JOBID``). + Note that the non-remote job local storage prefix is still always needed, because Snakemake can also decide to run certain jobs without submission to the cluster or cloud. This can happen either on dev request because a certain rule is very lightweight, or by Snakemake's own decision, e.g. in case of rules that just format a template (see `docs `_). \ No newline at end of file