Strict-syntax compliance: Nextflow 25.10.4, nf-schema 2.6.1#1680
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Update nf-schema plugin from 2.5.1 to 2.6.1 to fix unrecognized config warnings (`validation.defaultIgnoreParams`, `validation.monochromeLogs`) when running with the Nextflow v2 strict syntax parser. This is part of the effort to achieve strict syntax compliance for the `--help` check in nf-core/strict-syntax-health. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
This PR is against the
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
# Conflicts: # CHANGELOG.md
Bumps `nextflowVersion` from `!>=25.04.3` to `!>=25.10.4` so the Seqera Plugin Registry resolves `nf-schema` 2.6.1 (deliberately not published to the legacy nextflow-io/plugins index, per nextflow-io/plugins#197). CI matrix, README badge, and ro-crate metadata follow. Silences the strict-syntax v2-parser warnings flagged in the nf-core/strict-syntax-health report: - local subworkflows: replace implicit `it` closure params with named ones; prefix unused `meta` parameters with `_` - nf-core subworkflows: carry the upstream-merged fixes for bam_dedup_umi, bam_markduplicates_picard, bam_qc_rnaseq, and fastq_qc_trim_filter_setstrandedness so CI exercises them now; proper modules.json resync to follow once the nf-core/modules changes for gtffilter and gtf2bed land. Two `args` warnings on the gtffilter/gtf2bed templated modules remain deferred to the upstream nf-core/modules PR. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
pinin4fjords
changed the title
Bump modules.json SHAs and refresh on-disk files for the components
whose strict-syntax fixes were previously carried inline:
- modules: custom/gtffilter, ea-utils/gtf2bed
- subworkflows: bam_dedup_umi, bam_markduplicates_picard,
bam_qc_rnaseq, fastq_qc_trim_filter_setstrandedness
Subworkflow main.nf files were already byte-equivalent with master
after the prior inline edits, so only the SHA pins change for those.
The two module main.nf files also pick up apptainer container-engine
support and fully-qualified quay.io biocontainer URIs from upstream
along with the strict-syntax `args` workaround.
modules.json is touched as six single-line SHA updates rather than the
full reformat nf-core/tools 4.0.2's `install --force` would produce.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
…s_transcripts_fasta_gencode Silences the repeated `WARNING Could not find meta.yml for ...` emissions seen during every `nf-core modules`/`subworkflows` invocation, and documents inputs/outputs/tool versions in the schema-validated nf-core meta-schema format. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
mashehu
approved these changes
May 11, 2026
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
pinin4fjords
commented
May 11, 2026
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Summary
Brings nf-core/rnaseq to a 0-warning state under the Nextflow v2 strict-syntax parser, and closes the local-module documentation gap that was causing repeated
meta.ymlwarnings from nf-core tooling.nextflowVersionfloor to!>=25.10.4(matches the current nf-core template) and align the CI matrix (nf-test.yml,nf-test-arm.yml,nf-test-gpu.yml), README badge, and ro-crate metadata.nf-schemafrom 2.5.1 to 2.6.1. The 2.6.x line is only published to the new Seqera Plugin Registry, which Nextflow 25.10+ consults; the Nextflow bump is the prerequisite for resolving it. Adds support forvalidation.defaultIgnoreParamsandvalidation.monochromeLogsunder the v2 parser.multiqc_rnaseq,prepare_genome_indices,prepare_genome_references): replace implicititclosure params with named ones; prefix unusedmetaparameters with_.modules.json(no transitive cascade):modules/nf-core/custom/gtffilter(also picks up apptainer support and the fully-qualifiedquay.io/biocontainers/...container URI)modules/nf-core/ea-utils/gtf2bed(same)subworkflows/nf-core/bam_dedup_umisubworkflows/nf-core/bam_markduplicates_picardsubworkflows/nf-core/bam_qc_rnaseqsubworkflows/nf-core/fastq_qc_trim_filter_setstrandednessmeta.ymlfor the localDESEQ2_QCandPREPROCESS_TRANSCRIPTS_FASTA_GENCODEmodules so the repeatedWARNING Could not find meta.yml for ...lines no longer appear duringnf-core modules/subworkflowsinvocations.Test plan
25.10.4andlatest-everything.NXF_SYNTAX_PARSER=v2 nextflow run nf-core/rnaseq --helppasses (already shown green on the strict-syntax-health report against Nextflow 26.04.0).nf-core modules lintno longer emits theCould not find meta.ymlwarnings forDESEQ2_QC/PREPROCESS_TRANSCRIPTS_FASTA_GENCODE.