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possibility to quickly rerun given target, without all upstream rules #188

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alexg9010 opened this issue Oct 6, 2022 · 0 comments
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alexg9010 commented Oct 6, 2022

It would be great to quickly rerun a given target, if .e.g. a setting has changed in the settings file, without having to rerun the whole upstream workflow.

Snakemake exposes a potentially helpful argument

 --forcerun [TARGET ...], -R [TARGET ...]
                        Force the re-execution or creation of the given rules
                        or files. Use this option if you changed a rule and
                        want to have all its output in your workflow updated.
                        (default: None)

but this requires the target/output files to be specified already at the subshell where we call snakemake.

The quick and dirty way is to manually remove the target files by hand.
I already implemented a rule "clean" to rm the list of requested output files with ad975dd66286b9adda2cc0ab5ac439183db8580a but this is quite rough and will through an error at the end.

I need to either find a better way or at least improve the error handling.

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