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nextstrain / zika

Nextstrain build for Zika virus
https://nextstrain.org/zika
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chore: Nextstrain/styleguide #27

Closed j23414 closed 1 year ago

j23414 commented 1 year ago

Description of proposed changes

Conform to documented Nextstrain snakemake styleguide. See commits for details.

Related issue(s)

Testing

j23414 commented 1 year ago

Merging without review since these are stylistic changes.

victorlin commented 1 year ago

These changes look good to me! Is it possible to enforce the Nextstrain Snakemake style guide somehow (using snakefmt options, run in pathogen-repo-ci)? Otherwise, there's nothing preventing deviation from it in the future.

corneliusroemer commented 1 year ago

Is it possible to enforce the Nextstrain Snakemake style guide somehow (using snakefmt options, run in pathogen-repo-ci)? Otherwise, there's nothing preventing deviation from it in the future.

I'm all for using snakefmt, there were some bugs in the past but they've been fixed now.

However, snakefmt doesn't get rid of messages, they are legal snakemake, we just have a preference against it. We could write our own little add sed/python formatting script to replace message with a comment though!