Migrate template to nf-core-utils plugin #3790
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edmundmiller
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mashehu
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Oct 1, 2025
nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
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| plugins { | ||
| id '[email protected]' // Validation of pipeline parameters and creation of an input channel from a sample sheet | ||
| id '[email protected]' // Validation of pipeline parameters and creation of an input channel from a sample sheet | ||
| id '[email protected]' // Utility functions for nf-core pipelines |
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| 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 |
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Is this because you want nf-core-utils to be at a stable release?
tests/subworkflows/test_lint.py
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| 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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| 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. |
Integrate nf-core-utils plugin v0.3.0 to replace utility subworkflows with centralized plugin functions, following RFC proposal #51. Major changes: - Add [email protected] 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 [email protected] 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
Add Jinja2 conditional to only include completionEmail function from nf-core-utils plugin when email functionality is enabled.
Remove implementation details from docstring.
Add Jinja2 conditional to only include paramsSummaryMultiqc function when MultiQC is enabled in the pipeline.
adamrtalbot
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See nf-core/rnavar#256 as an example PR |
adamrtalbot
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Oct 28, 2025
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| include { paramsSummaryMultiqc } from '../subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'{% endif %} | ||
| include { softwareVersionsToYAML } from '../subworkflows/local/utils_nfcore_{{ short_name }}_pipeline' |
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@edmundmiller can we remove this from the subworkflow as well? It doesn't add much.
- paramsSummaryMultiQc can probably be moved to nf-core-utils
- softwareVersionsToYAML can be moved to nf-core-utils
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| include { paramsSummaryMultiqc } from '../subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'{% endif %} | |
| include { softwareVersionsToYAML } from '../subworkflows/local/utils_nfcore_{{ short_name }}_pipeline' | |
| include { paramsSummaryMultiqc } from 'plugin/nf-core-utils'{% endif %} | |
| include { softwareVersionsToYAML } from 'plugin/nf-core-utils' |
mirpedrol
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Oct 29, 2025
| if (validate_params) { | ||
| validateParameters() | ||
| } | ||
| {%- endif %} |
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I think you need an additional {%- endif %}, this one is for the {%- if nf_schema %} on line 70
| // | ||
| // Get channel of software versions used in pipeline in YAML format | ||
| // | ||
| def softwareVersionsToYAML(ch_versions) { |
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should this function be also added to the plugin?
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CHANGELOG.mdis updateddocsis updated