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Added module samtools/samples #9311

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@Schmytzi Schmytzi commented Oct 31, 2025 •
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PR checklist

Closes #9306

  • 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

Joon-Klaps
Joon-Klaps reviewed Oct 31, 2025
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Nice addiiton, some minor comments

modules/nf-core/samtools/samples/main.nf
Comment on lines +46 to +55
def headers = ''
if (args.contains('-h\\n')) {
headers = "#SM\tPATH"
if (args.contains('-i')) {
headers += "\tINDEX"
}
if (fasta) {
headers += "\tREFERENCE"
}
}
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Why have this logic in here and not just add them all by default?
Also if it gets parsed by nextflow, no samples will be there as well so no other processes will be started afterwards.

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I guess if we remove all this logic, it might be better to just write an empty file. Otherwise the header messes with downstream tools which do not expect one.

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Fine for me!

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Generally we just make empty files. I guess it might be important here for workflow logic downstream though, as @Schmytzi says, so I'm happy to include this here.

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new module: samtools/samples

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@Schmytzi @SPPearce @Joon-Klaps