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Samtools mpileup input update #9810

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Samtools mpileup input update #9810

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@Krannich479 Krannich479 commented Jan 30, 2026

PR checklist

Closes #9802

  • 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.
  • Broadcast software version numbers to topic: versions - See version_topics
  • 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

@Krannich479 Krannich479 self-assigned this Jan 30, 2026
@Krannich479 Krannich479 added the enhancement New feature or request label Jan 30, 2026
SPPearce
SPPearce reviewed Jan 31, 2026
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modules/nf-core/samtools/mpileup/main.nf
tuple val(meta), path(input), path(intervals)
tuple val(meta2), path(fasta)
tuple val(meta), path(input) // sam/bam/cram
tuple val(meta), path(index) // csi/bai/crai - optional, only required when using '-r'
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@SPPearce SPPearce Jan 31, 2026

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I think you want:
tuple val(meta), path(input), path(index), path(intervals)
as the input tuple.

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Samtools mpileup requires another input parameter to parallelize across chromosomes/regions

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