Template update to version 3.5.1#118
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Pull request overview
This PR updates the nf-core template to version 3.5.1, introducing major changes to versioning output using topic-based versioning for modules and updating meta.yml descriptions for tools/inputs/outputs.
Key Changes:
- Migrates channel factory methods from
Channeltochannel(lowercase) throughout the codebase - Implements topic-based versioning system that collects versions via topics instead of mixing channel outputs
- Updates module versions (samtools 1.21→1.22.1, longphase 1.7.3→2.0, mosdepth 0.3.10→0.3.11, modkit 0.4.4→0.6.0, multiqc 1.32→1.33, etc.)
- Removes many
ch_versions.mix()statements in favor of topic-based collection - Updates test snapshots with new md5 hashes and version numbers
Reviewed changes
Copilot reviewed 113 out of 118 changed files in this pull request and generated no comments.
Show a summary per file
| File | Description |
|---|---|
workflows/lrsomatic.nf |
Main workflow updated with lowercase channel factory, topic-based versioning implementation, removed version mixing, fixed severus input to remove tbi parameter |
tests/default.nf.test.snap |
Updated test snapshots with new tool versions and file hashes, removed SV_VEP output references |
subworkflows/nf-core/utils_nfschema_plugin/main.nf |
Removed trailing whitespace |
subworkflows/nf-core/bam_stats_samtools/main.nf |
Removed one version mixing statement |
subworkflows/local/tumor_only_happhase.nf |
Channel factory updates, removed version mixing, fixed variable naming (snps→vcf), updated longphase output references |
subworkflows/local/tumor_normal_happhase.nf |
Channel factory updates, removed version mixing, fixed variable naming, updated longphase output references, formatting fixes |
subworkflows/local/prepare_reference_files.nf |
Channel factory method updates |
subworkflows/local/prepare_annotation.nf |
Channel factory method updates |
modules/nf-core/severus/ |
Major refactoring with prefix-based output paths, removed tbi input/output, updated meta.yml with detailed descriptions |
modules/nf-core/samtools/*/ |
Updated to version 1.22.1 with topic-based versioning |
modules/nf-core/longphase/*/ |
Updated to version 2.0 with separate SNV/SV/mod VCF outputs and indices |
modules/nf-core/modkit/pileup/ |
Updated to 0.6.0, outputs bgzf-compressed bed files, removed bedgraph output |
modules/nf-core/multiqc/ |
Updated to 1.33 with topic-based versioning |
modules/nf-core/mosdepth/ |
Updated to 0.3.11 |
nextflow.config |
Added duplicate parameter definitions, renamed arm→arm64/emulate_amd64, removed gitpod profile, updated nf-schema plugin version, removed validation help config |
nextflow_schema.json |
Added help, help_full, and show_hidden parameter definitions |
ro-crate-metadata.json |
Updated dates and test suite IDs |
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robert-a-forsyth
approved these changes
Dec 29, 2025
robert-a-forsyth
approved these changes
Jan 8, 2026
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Template update to version 3.5.1
Including major updates to versioning output of all modules (where possible) to topics.
PR also includes updates to
meta.ymlfiles to complete the descriptions of tools/input/outputs where it was still missing.PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).