@davelunt just stumbled over the #Snakemake hashtag. Snakemake has the directory() function just for that purpose: https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#directories-as-outputs
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@rupdecat agree, directory() is a life saver, really helps. But in this case it’s solving a problem that needn’t exist, and now my beautiful workflow has a dark place, with badly named files
Oh, I am dealing with plenty of quirky programs myself. And I hate it. 😉
In the off-chance that this might be new: there is the #Snakemake wrapper project, with plenty of wrappers to make a programmer's life easier. See https://snakemake-wrappers.readthedocs.io/en/stable/
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