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johanneskoester avatar johanneskoester commented on May 20, 2024

Thanks for reporting. Here, deleting the directory is mandatory, because the directory flag shall guarantee that it is completely created by the shell command of that rule. But as you say you create files, maybe you can have those files as output files, instead of just the directory. This way, the log can be in there as well.

It is best practice to have a separate log directory though, see here.

from snakemake.

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