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Document Qualimap read counting limitation #1625

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Document Qualimap read counting limitation #1625

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@pinin4fjords pinin4fjords commented Nov 14, 2025

Description

Adds documentation warning about a known Qualimap bug where it reports more reads assigned to genomic features than exist in the BAM file.

Details

Addresses

Closes #1273 (via documentation)

References

PR checklist

  • This comment contains a description of changes (with reason).
  • CHANGELOG.md is updated (will update after review if needed)
  • If you've fixed a bug or added code that should be tested, add tests!
  • Documentation in docs is updated.
  • If necessary, also make a PR on the nf-core/rnaseq branch on the nf-core/test-datasets repository.

@pinin4fjords
Add warning about Qualimap read counting bug
33168d3 
Document known limitation where Qualimap reports more reads than exist
in the BAM file when assigning reads to genomic features. Provide
workarounds including using RSeQC as alternative and --skip_qualimap flag.

Addresses #1273
@pinin4fjords pinin4fjords mentioned this pull request Nov 14, 2025
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pinin4fjords commented Nov 14, 2025

Note: This PR cannot be merged until #1618 is merged first, as that PR contains CI fixes needed for tests to pass.

@pinin4fjords pinin4fjords added this to the 3.22.0 milestone Nov 14, 2025
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github-actions bot commented Nov 14, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f2ddd31

+| ✅ 286 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   9 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/rnaseq/rnaseq/subworkflows/local/prepare_genome/main.nf: _ versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
    _

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.4.1
  • Run at 2025-11-14 18:10:58

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