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.
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
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
rmthe 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.