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I am running snakemake with a lot of files and rules. As a consequence the .snakemake folder contains ~500,000 files. This is kind of problematic for me as we have a quota on the number of files on the working folders.

Is there a way or plans to reduce the number of files in the .snakemake folder?

Thanks,
Jan

Jan Schreiber
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  • There was quite some reduction in one of the last releases. Do you use the latest release, and are you sure that the files haven't been created by an older version of Snakemake? I will probably add some kind of cleanup functionality. – Johannes Köster Dec 13 '17 at 09:20
  • related: https://stackoverflow.com/q/45607951/1878788 – bli Dec 13 '17 at 13:43
  • Thanks for the hint. I am still using Snakemake 3.13.3 but will try to upgrade as soon as possible. Until then I'll be using onsuccess: shutil.rmtree(".snakemake") – Jan Schreiber Dec 13 '17 at 16:06

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