Dev -> master for nf-core/rnaseq 3.22.0 #1639
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Bump after release 3.21.0
Merged dev branch into nf-core-template-merge-3.4.1, resolving conflicts by keeping pipeline-specific features while adopting template improvements. ## Conflict resolutions: ### Infrastructure improvements (adopted from template): - Update nf-test to v0.9.3 - Update minimum Nextflow version to 25.04.0 - Add new help system parameters (--help, --help_full, --show_hidden) - Update utility subworkflow git_sha values - Adopt `removeNextflowVersion` function for test snapshots - Use vars.AWS_S3_BUCKET instead of secrets for non-sensitive config ### Pipeline-specific features (retained): - Keep aligner matrix testing (star_salmon, star_rsem) in AWS full tests - Retain Sentieon authentication environment variables - Keep commit-pinned test data URL for reproducibility - Preserve pipeline metadata and real Zenodo DOI - Maintain existing CHANGELOG format ### Merged additions: - Combined test ignore patterns (both pipeline-specific and template) - Added both fastqc pattern variants for compatibility All changes follow the principle of preserving pipeline functionality while adopting template infrastructure improvements for better maintainability. Follows merge patterns from nf-core/sarek#2031 and guidance from https://nf-co.re/docs/tutorials/sync/merging_automated_prs 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
Co-authored-by: James A. Fellows Yates <[email protected]>
Important! Template update for nf-core/tools v3.4.1
- Add entry for PR #1613: Fix broken link and add latest kit version for Takara UMI prep - Add entry for PR #1614: Template update for nf-core/tools v3.4.1 🤖 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]>
This updates the bbmap/bbsplit module to address staging issues reported in the original PR. 🤖 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]>
The nf-test workflow used paths-ignore at the workflow level, which prevented the entire workflow (including the confirm-pass job) from running when only docs/markdown files were changed. This caused PRs with only documentation changes to fail merge requirements if confirm-pass was configured as a required status check. Changes: - Remove paths-ignore from workflow trigger to ensure workflow always runs - Add dorny/paths-filter action to detect docs/markdown-only changes - Make nf-test job conditional on skip_tests output - Update confirm-pass job to always run and pass when tests are skipped - Add skip_tests output to nf-test-changes job This ensures the confirm-pass required check is always present while still skipping expensive test execution for documentation-only changes. 🤖 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 <[email protected]>
The default 'some' quantifier returns true if ANY file matches ANY pattern, which incorrectly skips tests when a PR has mixed changes (e.g., both README.md and src/main.nf). Using 'every' ensures ALL files must match at least one pattern for tests to be skipped. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
Co-authored-by: pinin4fjords <[email protected]>
Co-authored-by: pinin4fjords <[email protected]>
Add validation error for incompatible transcript_fasta and additional_fasta params
Co-authored-by: pinin4fjords <[email protected]>
Add validation error for incompatible transcript_fasta and additional_fasta params
- Update custom/tx2gene module to parse comma-separated extra attributes - Fix deprecated parameter name in docs (`--gtf_group_features_type` → `--featurecounts_group_type`) Fixes #1626 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
The test profile's transcript_fasta already contains spike-in sequences (GFP) from when it was generated. Setting only additional_fasta = null prevents GFP from being added to the GTF, but Kallisto still builds its index from the existing transcript_fasta (which has GFP). This causes a mismatch where Kallisto outputs GFP counts but the GTF-based metadata doesn't include GFP, causing SE_GENE_UNIFIED to fail. The fix is to also set transcript_fasta = null so the pipeline regenerates the transcriptome from the GTF (consistently without spike-ins). 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
…le-values Fix `--gtf_extra_attributes` to support multiple comma-separated values
Updated both real and stub test snapshots to reflect changes from disabling additional_fasta and transcript_fasta: Real test: - Task count: 48 → 47 - Removed CUSTOM_CATADDITIONALFASTA and GUNZIP_ADDITIONAL_FASTA - Added MAKE_TRANSCRIPTS_FASTA (pipeline now generates transcriptome) - Removed custom/out/genome_gfp.* from output files - Updated tx2gene.tsv hash (different without spike-ins) Stub test: - Task count: 22 → 21 - Same process changes as real test - Removed custom/out/genome_transcriptome.* from output files - Empty stable_path array 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
- Simplify boolean logic in SAMTOOLS_SORT/INDEX publishDir conditions - Merge duplicate DESeq2 QC blocks for star_salmon and star_rsem - Fix bitwise & to logical && operators in conditional checks - Consolidate enabled:false publishDir blocks into single regex pattern - Merge TX2GENE/TXIMPORT, SE_GENE_UNIFIED, SE_TRANSCRIPT_UNIFIED configs - Merge SAMTOOLS_SORT/INDEX publishDir for general and UMI alignments - Consolidate BAM_STATS_SAMTOOLS publishDir for GENOME/TRANSCRIPTOME - Remove dead HISAT2 patterns from star_salmon-only block Reduces config from ~490 to ~423 lines while maintaining identical behavior. 🤖 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]>
The TRANSCRIPTOME BAM_STATS_SAMTOOLS publishDir was incorrectly merged into the general UMI block (which applies to both star_salmon and hisat2). This restores the original behavior where: - GENOME BAM_STATS publishDir is in the general UMI block (for both aligners) - TRANSCRIPTOME BAM_STATS publishDir is only in the star_salmon+UMI block 🤖 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]>
Simplify workflow nextflow.config by consolidating redundant patterns
…-fasta-validation Add validation error for incompatible transcript_fasta and additional_fasta params
🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
Bump version to 3.22.0 ahead of release
pinin4fjords
changed the title
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FriederikeHanssen
approved these changes
Nov 26, 2025
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looks good. thanks
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Pending failing tests and this one passing: https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/54JcBOUFII7GYf/v2/tasks |
maxulysse
reviewed
Nov 26, 2025
| @@ -1,4 +1,5 @@ | |||
| lint: | |||
| actions_nf_test: false | |||
maxulysse
reviewed
Nov 26, 2025
| .DS_Store | ||
| bbsplit/*.stats.txt | ||
| fastqc/*/*.{html,zip} | ||
| fastqc/*_fastqc.{html,zip} |
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why this new file to ignore, is this coming from TEMPLATE?
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It was there before, just further down
maxulysse
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Nov 26, 2025
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| multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt | ||
| multiqc/multiqc_data/multiqc.parquet | ||
| multiqc/multiqc_data/multiqc.log | ||
| multiqc/multiqc_data/multiqc_data.json | ||
| multiqc/multiqc_data/multiqc_sources.txt | ||
| multiqc/multiqc_data/multiqc_software_versions.txt | ||
| multiqc/multiqc_data/llms-full.txt | ||
| multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png} | ||
| multiqc/multiqc_report.html |
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I don't think this reflect the actual multiQC outpur we currently have, as it's a duplicate of what is already around line 55-60
maxulysse
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Nov 26, 2025
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All good to me, just minor comments
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nf-core/rnaseq 3.22.0 Release
This release focuses on bug fixes, performance improvements, enhanced ARM64 support, and better parameter validation.
Bug Fixes
Bigwig Strand Labeling (#1620)
BBSplit Index Staging (#1617, #1631)
Sample Name Mangling (#1622)
check.namesfrom mangling sample names (e.g., converting dashes to dots)GTF Extra Attributes (#1635)
--gtf_extra_attributesto properly support multiple comma-separated valuesParameter Validation (#1632)
--transcript_fastaand--additional_fastawithout a pre-built pseudo-aligner indextranscript_fastaandadditional_fastaare provided. #1450Performance Improvements
Qualimap Optimization (#1621)
-nflagARM64 Support
ARM Container Fixes (#1630)
Documentation
inner_distancelimitation for genomes with large chromosomes (>500 Mb) such as plant genomes (Document RSeQC inner_distance limitation for large chromosomes #1624)Template Updates
Contributors
Special thanks to: @ahwanpandey, @ctuni, @EladH1, @emilymiyoshi, @pinin4fjords, @pontushojer, @siddharthab
Full Changelog
See CHANGELOG.md for complete details.