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Use --delete-all-output instead of creating a clean rule #10

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andrewsanchez opened this issue Apr 5, 2019 · 1 comment
Open

Use --delete-all-output instead of creating a clean rule #10

andrewsanchez opened this issue Apr 5, 2019 · 1 comment

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@andrewsanchez
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To remove all files created by snakemake as output files to start from scratch, you can use

$ snakemake some_target --delete-all-output

https://snakemake.readthedocs.io/en/stable/project_info/faq.html#how-do-i-remove-all-files-created-by-snakemake-i-e-like-make-clean
andrewsanchez referenced this issue Apr 5, 2019
@andrewsanchez
Use rm instead of rm -f
8b0c2e1 
The force flag is unnecessary and perhaps encouraging of bad habits.
@tkphd
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tkphd commented Apr 5, 2019

Cool! It would definitely be useful to introduce this as the Snakemake alternative to rm -f, which is an intrinsically unsafe command to show beginners.

andrewsanchez added a commit to andrewsanchez/hpc-python that referenced this issue May 10, 2019
@andrewsanchez
Revert "Use rm instead of rm -f"
cb95e04 
This reverts commit 8b0c2e1.

Leave it this way for now; otherwise, Snakemake will complain if the files
aren't present. See hpc-carpentry#10 for a better long-term solution.
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@tkphd @andrewsanchez