Migrate template to nf-core-utils plugin #3790
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Integrate nf-core-utils plugin v0.3.0 to replace utility subworkflows with centralized plugin functions, following RFC proposal #51. Major changes: - Add nf-core-utils@0.3.0 plugin to nextflow.config - Replace UTILS_NEXTFLOW_PIPELINE subworkflow with direct plugin calls - Replace UTILS_NFCORE_PIPELINE subworkflow with plugin functions - Replace UTILS_NFSCHEMA_PLUGIN subworkflow with nf-schema plugin calls - Remove entire subworkflows/nf-core/ directory - Update modules.json to remove nf-core subworkflows Functions now provided by nf-core-utils plugin: - getWorkflowVersion, dumpParametersToJSON, checkCondaChannels - completionEmail, completionSummary, imNotification - checkConfigProvided, checkProfileProvided - processVersionsFromFile, workflowVersionToChannel Functions retained in local subworkflow: - paramsSummaryMultiqc, softwareVersionsToYAML (uses plugin functions) - getGenomeAttribute, validateInputSamplesheet - toolCitationText, methodsDescriptionText Closes: #3685 Related: nf-core/proposals#51 feat(template): migrate to nf-core-utils plugin - Add nf-core-utils@0.3.0 plugin to nextflow.config - Replace all nf-core subworkflow imports with plugin imports - utils_nextflow_pipeline functions -> direct plugin calls - utils_nfcore_pipeline functions -> plugin/nf-core-utils - utils_nfschema_plugin functions -> plugin/nf-schema - Use plugin functions for version processing: - processVersionsFromFile() instead of local implementation - workflowVersionToChannel() instead of local implementation - Remove entire subworkflows/nf-core/ directory - Update modules.json: empty nf-core subworkflows section - Update test expectations for removed subworkflows Closes #3685
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mashehu
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Oct 1, 2025
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| // | ||
| // Get workflow summary for MultiQC | ||
| // | ||
| def paramsSummaryMultiqc(summary_params) { |
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wrap this whole function inside a {% if multiqc %
| include { getWorkflowVersion } from 'plugin/nf-core-utils' | ||
| include { dumpParametersToJSON } from 'plugin/nf-core-utils' | ||
| include { checkCondaChannels } from 'plugin/nf-core-utils' | ||
| include { completionEmail } from 'plugin/nf-core-utils' |
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needs a {% if email %} wrapper
| plugins { | ||
| id 'nf-schema@2.5.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet | ||
| id 'nf-schema@2.4.2' // Validation of pipeline parameters and creation of an input channel from a sample sheet | ||
| id 'nf-core-utils@0.3.0' // Utility functions for nf-core pipelines |
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Suggested change
| id 'nf-core-utils@0.3.0' // Utility functions for nf-core pipelines | |
| id 'nf-core-utils@1.0.0' // Utility functions for nf-core pipelines |
| self.subworkflow_remove.remove("utils_nfschema_plugin", force=True) | ||
| """Test linting a pipeline with no nf-core subworkflows installed. | ||
| The template now has no nf-core subworkflows by default (migrated to nf-core-utils plugin). |
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Suggested change
| The template now has no nf-core subworkflows by default (migrated to nf-core-utils plugin). |
|
should we ask the maintainers team for test implementations before we add it to the template. we currently only have two pipelines, both done by maxime. |
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PR checklist
CHANGELOG.mdis updateddocsis updated