Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-07-14T10:14:26.907Z
Answers.Text: Why is this answer downvoted? Does it not answer the question? Could the downvoter please speak up?
Answers.UserDisplayName: haci
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-07-12T14:25:14.823Z
Answers.LastActivityDate: 2021-08-05T09:09:20.513Z
Answers.LastEditDate: 2021-08-05T09:09:20.513Z
Answers.UserDisplayName: Cornelius Roemer
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-07-13T21:54:52.200Z
Comments.Text: 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?
Comments.UserDisplayName: Cornelius Roemer
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-07-14T02:34:12.977Z
Comments.Text: 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!
Comments.UserDisplayName: Ram RS
Tags: <snakemake>
Title: How can I make Snakemake ignore all previously produced/cached output files?
ThreadText: # 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!  
  
  ---
  
  ## 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?  
  
  ---
  
  