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Update nf-schema to 3.0.0 - #163
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Migrate paramsHelp, paramsSummaryLog, and paramsSummaryMap to their single-options-map signatures; 3.0.0 requires Nextflow >= 26.04.0, matching our floor. Generated by OpenCode
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 4.1.0. For more documentation on how to update your pipeline, please see the Synchronisation documentation. |
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PR checklist
CHANGELOG.mdis updatednextflow_schema.jsonis updated (if needed)docs/usage.mdis updated (if needed)docs/output.mdis updated (if needed)assets/is updated (if needed)TODOcommentsDescription
Bumps
nf-schemafrom 2.7.2 to 3.0.0 and migrates the four affected call sites.3.0.0 removes the positional arguments from three plugin functions, so each call moves to the single options map that is now the only parameter:
paramsSummaryMap(workflow, parameters_schema: ...)→paramsSummaryMap(parameters_schema: ...)inmain.nfand in the utils subworkflow. Theworkflowobject is fetched from the running session internally.paramsSummaryLog(summary_options, workflow)→paramsSummaryLog(summary_options).paramsHelp(help_options, X)→paramsHelp(help_options + [parameter: X]).No Nextflow floor change is needed: 3.0.0 requires >= 26.04.0, which matches our
!>=26.04.0.Unaffected:
samplesheetToListandvalidateParametersare unchanged in 3.0.0, so datasheet parsing is untouched. Theparameter: ""fallback keeps its 2.x behaviour (getShortMessagetreats an empty string as falsy and prints all parameters). This pipeline never set the removedvalidation.help.enabledor the deprecatedfailUnrecognised*options, so there was nothing to clean up.Template divergence
Three of the four edits are in the template-owned
subworkflows/local/utils_nfcore_references_pipeline/main.nf. The upstream template is still on nf-schema 2.7.3 with the 2.x call shapes, so this branch deliberately diverges from it. These changes need to be upstreamed to the template before the next template sync, otherwise the sync will revert them. Tracking this in the roadmap decisions log; a template PR againstnf-core/toolsis the follow-up.Testing
nextflow lintclean; the 23 warnings are pre-existingwhen-section deprecations in nf-core modules and none touch the edited files.nf-test test tests/ --profile=+docker: 26/26 passing (this branch includes thesplice_sitesfix merged in Merge prepare_genome subworkflows into a single prepare_genome #162).nf-core pipelines lint: 364 passed, 0 failed; 21 warnings, all pre-existing template TODOs. No template-version mismatch flagged.Generated by OpenCode