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Adding sequali module to nf-core modules #6896

Merged
merged 10 commits into from
Oct 31, 2024
Merged

Adding sequali module to nf-core modules #6896

merged 10 commits into from
Oct 31, 2024

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DarkoCucin
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@DarkoCucin DarkoCucin commented Oct 29, 2024 •
edited by irliampa
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PR checklist

It adds sequali tool to nf-core modules.

  • 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:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@DarkoCucin DarkoCucin mentioned this pull request Oct 29, 2024
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@irliampa irliampa added the new module Adding a new module label Oct 30, 2024
@irliampa irliampa requested review from a team and rpetit3 and removed request for a team October 30, 2024 09:08
LouisLeNezet
LouisLeNezet reviewed Oct 30, 2024
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@LouisLeNezet LouisLeNezet left a comment

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This looks fine for me, just a few question as I do not know the tool.
Feel free to ask me again for a review and I will approve 😉

modules/nf-core/sequali/environment.yml Outdated Show resolved Hide resolved
modules/nf-core/sequali/main.nf Show resolved Hide resolved
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@irliampa @LouisLeNezet
Update modules/nf-core/sequali/environment.yml
0957664 
typo fixed

Co-authored-by: Louis LE NEZET <[email protected]>
@DarkoCucin DarkoCucin removed the request for review from rpetit3 October 30, 2024 09:56
LouisLeNezet
LouisLeNezet approved these changes Oct 31, 2024
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This looks fine for me, great job !

modules/nf-core/sequali/tests/main.nf.test Outdated Show resolved Hide resolved
@irliampa
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irliampa commented Oct 31, 2024 •
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Thank you @LouisLeNezet ! So I guess now we update the branch and merge 😃
The PR is to the master branch, is this okay for the nf-core/modules repo?

@LouisLeNezet
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Yeah you can merge !

irliampa
irliampa approved these changes Oct 31, 2024
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Great job @DarkoCucin and @LouisLeNezet, thank you both 🙏

@irliampa irliampa added this pull request to the merge queue Oct 31, 2024
Merged via the queue into nf-core:master with commit 8a94826 Oct 31, 2024
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@LouisLeNezet LouisLeNezet LouisLeNezet approved these changes

@irliampa irliampa irliampa approved these changes

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@DarkoCucin @irliampa @LouisLeNezet