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Fix MultiQC sample name collisions with shared FASTQ filenames #1659

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pinin4fjords merged 12 commits into from
Dec 11, 2025
Merged

Fix MultiQC sample name collisions with shared FASTQ filenames #1659

pinin4fjords merged 12 commits into from
Dec 11, 2025
+31 −12

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@pinin4fjords pinin4fjords commented Dec 10, 2025 •
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Summary

  • Fixes MultiQC sample name corruption when multiple samples share the same FASTQ filename (in different directories)
  • Fixes QualiMap sample names showing .namesorted suffix in MultiQC
  • Moves _raw/_trimmed suffix handling to multiqc_config.yml using extra_fn_clean_exts with type: remove

Problem

When two samples have FASTQ files with the same filename (e.g., P30162_607.R1.fastq.gz in different directories), the name_replacement.txt file contained duplicate search patterns with different replacement values:

P30162_607	P30162_607_1
P30162_607	P30162_607_0.8X_1

This caused MultiQC to apply replacements incorrectly, corrupting sample names in the report.

Additionally, QualiMap results were showing .namesorted suffixes in sample names.

Solution

  1. Only add FASTQ-to-sample mappings when the FASTQ simpleName differs from the sample ID. When they match, no renaming is needed.
Sample FASTQ simpleName Action
P30162_607 P30162_607 Skip FASTQ mapping (names match)
P30162_607_0.8X P30162_607 Add mapping (names differ)

  1. Added .namesorted to extra_fn_clean_exts in multiqc_config.yml.

  2. Moved _raw/_trimmed suffix handling from main.nf to multiqc_config.yml using extra_fn_clean_exts with type: remove. This removes only the matched substring (not everything after it), preserving read numbers like _1/_2.

Test plan

  • Run pipeline with samples that share FASTQ filenames to verify correct MultiQC naming
  • Verify QualiMap sample names no longer show .namesorted suffix

Fixes #1657

🤖 Generated with Claude Code

@pinin4fjords @claude
Fix MultiQC sample name collisions with shared FASTQ filenames
f4a31aa 
When multiple samples share the same FASTQ filename (in different
directories), the MultiQC name replacement file would contain duplicate
search patterns with different replacement values, causing sample names
to be corrupted in the report.

This fix only adds FASTQ filename-based mappings when the FASTQ
simpleName differs from the sample ID, preventing duplicate entries
while still supporting renaming when FASTQ names differ from sample IDs.

Fixes #1657

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

Co-Authored-By: Claude Opus 4.5 <[email protected]>
@pinin4fjords pinin4fjords mentioned this pull request Dec 10, 2025
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@pinin4fjords pinin4fjords linked an issue Dec 10, 2025 that may be closed by this pull request
Sample renaming in MultiQC report #1657
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github-actions bot commented Dec 10, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5a82e32

+| ✅ 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 15:43:14

pinin4fjords and others added 8 commits December 11, 2025 10:30
@pinin4fjords
Merge branch 'dev' into fix/multiqc-sample-rename-collision
8530e72
@pinin4fjords @claude
Increase MultiQC export_plots_timeout to 60s
df134b6 
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
Add namsorted to multiqc remove patterns
c0201e7
@pinin4fjords @claude
refactor: simplify MultiQC name replacement logic
c59c4cd 
Use tuple-based mappings and loop over suffixes to reduce code duplication.

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

Co-Authored-By: Claude <[email protected]>
@pinin4fjords @claude
refactor: move _raw/_trimmed handling to multiqc_config.yml
c720427 
Use extra_fn_clean_exts with type: remove to strip _raw/_trimmed
suffixes in MultiQC config instead of generating explicit mappings.
This simplifies the name replacement logic in main.nf.

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

Co-Authored-By: Claude <[email protected]>
@pinin4fjords @claude
docs: add credits section to changelog
b566a1e 
🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>
@pinin4fjords
Merge branch 'dev' into fix/multiqc-sample-rename-collision
4172e5b
@pinin4fjords
Add contributors to CHANGELOG
5a82e32
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pinin4fjords commented Dec 11, 2025

Thanks @maxulysse !

@pinin4fjords pinin4fjords merged commit a6d817c into dev Dec 11, 2025
250 of 280 checks passed
@pinin4fjords pinin4fjords deleted the fix/multiqc-sample-rename-collision branch December 11, 2025 16:42
@pinin4fjords pinin4fjords mentioned this pull request Dec 11, 2025
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Sample renaming in MultiQC report

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