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fix(mqc): use active aligner display name for fail_mapped header#1850

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fix/multiqc-fail-mapped-header
May 8, 2026
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fix(mqc): use active aligner display name for fail_mapped header#1850
pinin4fjords merged 3 commits into
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fix/multiqc-fail-mapped-header

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@pinin4fjords pinin4fjords commented May 8, 2026

Summary

  • Plumb an aligner_display_name take input through MULTIQC_RNASEQ and replace the hardcoded "STAR uniquely mapped reads (%)" header in the fail_mapped per-sample TSV with the active aligner's display name. Bowtie2 reports now correctly read Bowtie2 overall alignment rate (%).
  • Drop the hardcoded STAR reference from the pipeline-completion min_mapped_reads warning so it reads "samples skipped since they failed the X% mapped threshold" regardless of aligner.

The display name map lives at the top of RNASEQ so the subworkflow stays aligner-agnostic. Map covers star_salmon, star_rsem, hisat2, and bowtie2_salmon, with a generic 'Aligned reads' fallback for forward compatibility.

Note: HISAT2 doesn't currently surface percent_mapped to ch_percent_mapped, so its fail_mapped path is a dead branch today; the HISAT2 entry in the map is forward-looking.

Closes #1846

Test plan

  • nf-test test tests/default.nf.test --profile=+test,docker passes (STAR snapshots unchanged — display name identical)
  • Manual run on Bowtie2 path with -profile test_prokaryotic,docker --min_mapped_reads 99 produces multiqc_fail_mapped_samples_table.txt with header Sample\tBowtie2 overall alignment rate (%)
  • CI pipeline tests on the PR

🤖 Generated with Claude Code

pinin4fjords and others added 2 commits May 8, 2026 12:02
@pinin4fjords @claude
fix(mqc): use active aligner display name for fail_mapped header
303116b 
Plumb an aligner_display_name string from RNASEQ into MULTIQC_RNASEQ so
the fail_mapped per-sample TSV header reflects the metric the active
aligner actually emits, instead of always saying "STAR uniquely mapped
reads (%)". Also drop the hardcoded "STAR" reference from the
pipeline-completion warning that flags samples below min_mapped_reads.

Closes #1846

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
@pinin4fjords @claude
docs(changelog): backfill PR number for #1846 fix [skip ci]
867f51e 
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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github-actions Bot commented May 8, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5bc15d5

+| ✅ 207 tests passed       |+
#| ❔  21 tests were ignored |#
!| ❗   7 tests had warnings |!
Details

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❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.2
  • Run at 2026-05-08 13:32:07

vagkaratzas
vagkaratzas approved these changes May 8, 2026
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LGTM!

@pinin4fjords
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pinin4fjords commented May 8, 2026

Thanks @vagkaratzas !

@pinin4fjords pinin4fjords merged commit add90d8 into dev May 8, 2026
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@pinin4fjords pinin4fjords deleted the fix/multiqc-fail-mapped-header branch May 8, 2026 14:39
@pinin4fjords pinin4fjords linked an issue May 11, 2026 that may be closed by this pull request
MultiQC fail-mapped header is hardcoded to "STAR uniquely mapped reads (%)" #1846
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MultiQC fail-mapped header is hardcoded to "STAR uniquely mapped reads (%)"

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