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Replace three subworkflows/nf-core/utils_* subworkflows with direct imports from plugin/nf-core-utils and plugin/nf-schema, matching the pattern used by rnavar and createpanelrefs pipelines. - utils_nextflow_pipeline: version display, params dump, conda check - utils_nfcore_pipeline: config validation, email, versions YAML - utils_nfschema_plugin: parameter validation, help display All functionality preserved in the local utils subworkflow using plugin functions directly.
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Move author/year/title/journal fields into a nested publication object
in meta.yml tool entries to align with the new meta-schema.json structure.
New meta.yml structure:
tools:
- samtools:
doi: "10.1093/bioinformatics/btp352"
publication:
author: "Li Heng, et al."
year: 2009
title: "The Sequence Alignment/Map format and SAMtools"
source: "Bioinformatics"
Changes:
- Moved author, year, title, journal into publication object
- Renamed journal to source (covers journals, conferences, workshops)
- Renamed authors (plural) to author (singular) for consistency
- Updated 16 meta.yml files across nf-core modules
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…bworkflows Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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The dev merge restored the hardcoded toolReferencesMap(). Build the methods description citations from module meta.yml with citationsOnTheFly() and methodsDescriptionText() from nf-core-utils, keeping the Seqtk subsampling sentence. Cite MultiQC always and MultiQC_SAV when selected, since both run after the versions topic is collected. Add a multiqcsav tool entry to its meta.yml. Patch the modules whose meta.yml carries publication blocks not yet upstream, add a publication to fastqscreen, fix the seqkit author string, and document the setup in CONTRIBUTING.md. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Format pipeline Nextflow code and configs with nextflow lint -format -harshil-alignment. Add trailing commas to resourceLimits, the bam_qc test ext.args list and the citation function calls so the formatter keeps them on multiple lines. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
❌ nf-test failed with latest Nextflow versionNote Tests with Nextflow's latest version failed but it will not cause a CI workflow failure.
See the full run for details. |
These dependencies have no meta.yml tool entry. Keep the warning for any other tool so new modules without citation metadata show up in snapshots. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Replace the vendored
subworkflows/nf-core/utils_*subworkflows with direct imports fromplugin/nf-core-utils(0.7.0) andplugin/nf-schema, matching the pattern used by rnavar and createpanelrefs. Build the MultiQC methods tool citations on the fly from modulemeta.ymlfiles instead of a hardcoded map.Removed
subworkflows/nf-core/utils_nextflow_pipeline/: version display, params dump, conda checksubworkflows/nf-core/utils_nfcore_pipeline/: config validation, email, versions YAMLsubworkflows/nf-core/utils_nfschema_plugin/: parameter validation, help displaytoolReferencesMap(),toolReferencesText()and the localmethodsDescriptionText()insubworkflows/local/utils_nfcore_seqinspector_pipeline/main.nfChanges
subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf: imports come from the plugins, function calls inlined.subsampledMethodsText()keeps the Seqtk subsampling sentence in the methods description.workflows/seqinspector.nf:paramsSummaryMultiqc,citationsOnTheFlyandmethodsDescriptionTextcome fromplugin/nf-core-utils. Citations cover the tools found in theversionstopic, plus MultiQC (always) and MultiQC_SAV (when selected), because both run after the topic is collected.nextflow.config: pinnf-core-utils@0.7.0.modules.json: remove references to the deleted subworkflows, add patch entries.docs/CONTRIBUTING.md: document the citation setup and the module patch workflow.Module
meta.ymlpatchescitationsOnTheFly()reads the nestedpublicationblock of each tool inmeta.yml. This block is not yet upstream for every module, so the following modules carry a patch (new, or regenerated to includemeta.yml):checkqcfastqefastqscreen/fastqscreen(cites Wingett & Andrews 2018 instead of the Zenodo DOI)multiqcmultiqcsav(restores the MultiQC entry and adds amultiqcsavtool entry)samtools/faidxsamtools/indexseqkit/statssequaliThese
meta.ymlchanges need to be upstreamed to nf-core/modules.Modules without a publication (
bbmap/clumpify,chelae/trim,fastqc,fq/lint,picard/*,riker/multi,seqtk/sample,toulligqc,untar) fall back to their DOI or homepage.Testing
nf-core pipelines lint: 0 failuresnf-test test tests/NovaSeq6000.nf.test tests/sample_size.nf.test tests/tools_multiqcsav.nf.testtestprofile with--sample_sizeand--tools multiqcsav🤖 Generated with Claude Code