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fix(tximport): handle tx2gene files with extra columns #1654

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pinin4fjords merged 7 commits into from
Dec 11, 2025
Merged

fix(tximport): handle tx2gene files with extra columns #1654

pinin4fjords merged 7 commits into from
Dec 11, 2025
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@pinin4fjords pinin4fjords commented Dec 9, 2025 •
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Summary

Fixes an issue from a comment in #1626

Syncs tximport module from nf-core/modules#9520 and fixes a related issue in deseq2_qc.r that caused sample name mangling.

Changes

tximeta/tximport module (from nf-core/modules#9520):

  • Read tx2gene file with proper header handling instead of hardcoded column names
  • Select columns by name (transcript_id, gene_id, gene_name) with positional fallback for compatibility
  • Add configurable column names via ext.args (--tx_col, --gene_id_col, --gene_name_col)

deseq2_qc.r:

  • Add check.names=FALSE to read.delim() to prevent R from mangling sample names that start with numbers (e.g., "66130_Ascites" becoming "X66130_Ascites")

Problem

When users specify multiple comma-separated values for --gtf_extra_attributes (e.g., gene_name,gene_biotype), the custom/tx2gene module produces a file with more than 3 columns. The previous read.csv() call used hardcoded col.names, which caused data corruption. Additionally, deseq2_qc.r was mangling sample names starting with digits, causing a mismatch between count matrix column names and coldata rownames.

Test plan

  • Run with --gtf_extra_attributes 'gene_name,gene_biotype' to verify 4-column tx2gene handling
  • Verify DESEQ2_QC completes successfully with sample names starting with numbers
nextflow run . -profile test,docker --gtf_extra_attributes 'gene_name,gene_biotype' --outdir results_extra_attrs

🤖 Generated with Claude Code

@pinin4fjords pinin4fjords mentioned this pull request Dec 9, 2025
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github-actions bot commented Dec 9, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4ef1313

+| ✅ 285 tests passed       |+
#| ❔   8 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 3.5.1
  • Run at 2025-12-11 11:48:20

pinin4fjords and others added 3 commits December 10, 2025 09:45
@pinin4fjords @claude
Fix single-sample DESeq2 QC rownames bug
e6168a6 
R's data.frame(..., row.names=1) fails to use column 1 as rownames
when there is only one row. Explicitly pass row.names=samples.vec
to ensure correct behavior regardless of sample count.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <[email protected]>
@pinin4fjords
Merge branch 'dev' into tximport_fix
1052802
@pinin4fjords @claude
Add changelog entry for PR #1654
0d29a7b 
🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <[email protected]>
LouisLeNezet
LouisLeNezet approved these changes Dec 11, 2025
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Everything seems fine for me !

@pinin4fjords @claude
Increase MultiQC export_plots_timeout to 60s
4ef1313 
Plot export can be slower on ARM architecture, causing timeouts.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <[email protected]>
@pinin4fjords
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pinin4fjords commented Dec 11, 2025

Thanks @LouisLeNezet !

@pinin4fjords pinin4fjords merged commit 8ce68db into dev Dec 11, 2025
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@pinin4fjords pinin4fjords mentioned this pull request Dec 11, 2025
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