<p>If you want Snakemake to ignore the previous output of all rules, add the flag <code>--forceall</code>. Otherwise, if you just want to ignore the output of a specific rule to rerun that rule, add <code>--force</code>:</p>
<pre><code>snakemake --forceall -c1
</code></pre>
<p>The command line interface documentation is helpful as a reference: <a href="https://snakemake.readthedocs.io/en/stable/executing/cli.html#all-options" rel="nofollow noreferrer">https://snakemake.readthedocs.io/en/stable/executing/cli.html#all-options</a></p>

CC BY-SA 4.0
2021-07-14T10:14:26.907Z
Why is this answer downvoted? Does it not answer the question? Could the downvoter please speak up?
haci
CC BY-SA 4.0
2021-07-12T14:25:14.823Z
2021-08-05T09:09:20.513Z
2021-08-05T09:09:20.513Z
Cornelius Roemer
<p>I want to rerun a Snakemake workflow, ignoring all previously produced intermediary outputs.</p>
<p>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?</p>

CC BY-SA 4.0
2021-07-13T21:54:52.200Z
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?
Cornelius Roemer
CC BY-SA 4.0
2021-07-14T02:34:12.977Z
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!
Ram RS
<snakemake>
How can I make Snakemake ignore all previously produced/cached output files?
# How can I make Snakemake ignore all previously produced/cached output files?

(Asked by: username_0 on 2021-07-12)

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?

**Tags:** snakemake
> **Comments:**
> **username_0**: 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?  
> **username_1**: 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!  

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## 1 answers

### Answer by username_0 on 2021-07-12. Score: 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

> **Comments:**
> **username_2**: Why is this answer downvoted? Does it not answer the question? Could the downvoter please speak up?  

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