Remove vendored nf-core utils subworkflows, use plugin imports - #241
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maxulysse wants to merge 16 commits into
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Remove vendored nf-core utils subworkflows, use plugin imports#241maxulysse wants to merge 16 commits into
maxulysse wants to merge 16 commits into
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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
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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.
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 displayChanges:
subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf— imports now come from plugins, all function calls inlinedworkflows/seqinspector.nf—paramsSummaryMultiqcimport changed to pluginmodules.json— removed references to deleted subworkflowsAll functionality preserved. No loss of features.