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Add cd-hit module #2676

Merged
merged 31 commits into from
Dec 20, 2022
Merged

Add cd-hit module #2676

merged 31 commits into from
Dec 20, 2022

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timslittle
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@timslittle timslittle commented Dec 16, 2022 •
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PR checklist

Closes #2665

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware

@muffato muffato self-requested a review December 18, 2022 23:53
muffato
muffato requested changes Dec 19, 2022
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muffato
muffato reviewed Dec 19, 2022
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Thanks ! A few changes, and I think it'll be all good

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timslittle and others added 3 commits December 19, 2022 16:42
@timslittle @muffato
Remove comment hint
43d5fe8 
Co-authored-by: Matthieu Muffato <[email protected]>
@timslittle @muffato
Update modules/nf-core/cdhit/cdhit/meta.yml
307b154 
Change name of cluster output in yaml

Co-authored-by: Matthieu Muffato <[email protected]>
@timslittle @muffato
Update modules/nf-core/cdhit/cdhit/main.nf
39dc6d3 
Remove superfluous parameter arguments

Co-authored-by: Matthieu Muffato <[email protected]>
muffato
muffato reviewed Dec 19, 2022
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@timslittle
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Thank you @muffato :)

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muffato commented Dec 19, 2022

Slowly getting there 😅 . I just found what the last error is. Will post soon

muffato
muffato reviewed Dec 19, 2022
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🤞🏼 the last batch of changes

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muffato reviewed Dec 20, 2022
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All CI tests now pass except the linting, which flagged this inconsistency

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muffato
muffato approved these changes Dec 20, 2022
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That's it ! 🎉

@timslittle timslittle merged commit 4a29d43 into nf-core:master Dec 20, 2022
@timslittle timslittle deleted the cdhitest branch December 20, 2022 22:28
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new module: cdhit
2 participants
@timslittle @muffato