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elsasserlab / minute

MINUTE-ChIP data analysis workflow
https://minute.readthedocs.io
MIT License
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command line cheat sheet #157

Closed simonelsasser closed 1 year ago

simonelsasser commented 2 years ago

I wonder if you have a list of command line parameters that can be used, I noticed you are using some like --no-temp but I'm not sure what exactly those do. I there one for a dry run, just to check that the files supplied are correct? Some of them may be inherited from snakemake, but would be good to summarize the most useful ones in a 'cheatsheet'

marcelm commented 2 years ago

The minute run command just forwards all supplied arguments to snakemake, so you can use everything that snakemake accepts.

In our Snakefile, some output files are marked as temporary, that is, they are deleted as soon as they are not needed anymore (most of the files under the tmp/ folder). With --notemp, they are not deleted, which is nice for debugging.

cnluzon commented 1 year ago

I will close this since it is more of a snakemake question than minute specific functionality.