Dev -> master for nf-core/rnaseq 3.22.2 #1662
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Skip processes that are already covered by default.nf.test to reduce redundant test execution while maintaining meaningful integration testing. Changes by test file: - sentieon_default: skip QC, StringTie, bigwig (Sentieon STAR ≈ STAR BAMs) - remove_ribo_rna: skip QC, StringTie, bigwig (rRNA removal doesn't change BAM structure) - min_mapped_reads: skip QC, StringTie, bigwig (sample filtering doesn't change BAMs) - featurecounts_group_type: skip QC, StringTie, bigwig (only counting differs) - hisat2: skip bigwig only (keep QC/StringTie for different BAM characteristics) - umi: skip StringTie, bigwig (keep QC for deduplicated BAM testing) 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
When mark duplicates is enabled (skip_markduplicates=false) and UMI deduplication is disabled (with_umi=false), both the aligner's flagstat files (showing 0 duplicates) and the markduplicates flagstat files (showing actual duplicate counts) were being passed to MultiQC. This caused MultiQC to randomly select one of the flagstat files per sample, sometimes showing incorrect zero duplicate counts. The fix ensures that when markduplicates will run, only its stats are passed to MultiQC. The aligner stats are only added when both with_umi is false AND skip_markduplicates is true. Co-authored-by: GitHub Copilot <[email protected]>
🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]>
Bump after release 3.22.1
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]>
🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]>
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]>
Bump nf-core/multiqc module
The ARM config was using MultiQC 1.31 while the main module uses 1.33, causing CI test failures due to missing plot outputs. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]>
🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]>
Update MultiQC ARM container to 1.33
🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]>
Fix duplicate flagstat files in MultiQC report
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]>
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]>
fix(tximport): handle tx2gene files with extra columns
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]>
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]>
🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]>
Reduce duplicate coverage in pipeline tests
…sion Fix MultiQC sample name collisions with shared FASTQ filenames
🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
Bump version to 3.22.2 ahead of release
|
maxulysse
approved these changes
Dec 11, 2025
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|
Multiqc 1.33 allows the plotting and summary of BBSplit stats.txt files to have an overview over the number of reads removed. Might be worth adding here or latest in the next release |
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Author
Thanks, yep, mostly trying to hit bugs here- that can go in the next minor (needs a modules PR first to update a subworkflow) |
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d4straub
approved these changes
Dec 12, 2025
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d4straub
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d4straub
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LGTM, didnt find anything to complain about.
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nf-core/rnaseq 3.22.2 Release
This is a patch release with bug fixes and improvements.
Bug Fixes
tximport Extra Columns Fix (#1654)
--gtf_extra_attributesDuplicate Flagstat Files (#1655)
MultiQC Sample Name Collisions (#1659)
Improvements
MultiQC Update (#1658, #1660)
CI Optimizations (#1648)
Contributors
Special thanks to: @ahwanpandey, @ggrimes, @pontushojer
Full Changelog
See CHANGELOG.md for complete details.