I want to rerun a Snakemake workflow, ignoring all previously produced intermediary outputs.

Snakemake has about 100 different flags. I just want to make it easier to find an answer to this. What's the syntax/CLI flag I need to add?

  • $\begingroup$ Over at SO it seemed that people felt these questions were not programmy enough, I hoped that bioinformatics SO may be more tolerant. If you down vote a few questions like this I get an asking ban. Don't care if you close it, the answer is there. But down voting? $\endgroup$ Commented Jul 13, 2021 at 21:54
  • $\begingroup$ I was unaware that you get consequences because of downvotes, I apologize for that. Please make some minor edits to your Q and your A, and I'll be able to remove my downvotes. Sorry again! $\endgroup$
    – Ram RS
    Commented Jul 14, 2021 at 2:34

1 Answer 1


If you want Snakemake to ignore the previous output of all rules, add the flag --forceall. Otherwise, if you just want to ignore the output of a specific rule to rerun that rule, add --force:

snakemake --forceall -c1

The command line interface documentation is helpful as a reference: https://snakemake.readthedocs.io/en/stable/executing/cli.html#all-options

  • $\begingroup$ Why is this answer downvoted? Does it not answer the question? Could the downvoter please speak up? $\endgroup$
    – haci
    Commented Jul 14, 2021 at 10:14

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