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add readgroup to fq2bam #8624

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add readgroup to fq2bam #8624

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famosab
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@famosab famosab commented Jun 11, 2025

PR checklist

Closes #XXX

  • 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

maxulysse
maxulysse reviewed Jun 11, 2025
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modules/nf-core/parabricks/fq2bam/tests/main.nf.test
])
input[1] = Channel.of([
[ id:'test' ], // meta map
file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true)
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why are these files in the methylseq repo?

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these are tests that were already there @sateeshperi might be responsible

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Let's move them all in the modules branch

famosab
famosab commented Jun 12, 2025
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@famosab famosab added Ready for Review gpu module uses GPU labels Jun 16, 2025
@famosab famosab mentioned this pull request Jun 16, 2025
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famosab commented Jun 16, 2025

@famosab famosab marked this pull request as draft June 18, 2025 10:24
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