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docs: explain how to mask envvars #27

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docs: explain how to mask envvars #27

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4 changes: 3 additions & 1 deletion docs/further.md
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Original file line number Diff line number Diff line change
Expand Up @@ -23,13 +23,15 @@ 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
- sources
- 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 <https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#template-rendering-integration>`_).