Severus min support param and skip_fibernormal#143
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Pull request overview
This PR renames the normal_fiber parameter to skip_normalfiber (inverting its semantics to match other skip flags), adds a configurable severus_minsupport parameter, reorganizes the nextflow_schema.json into clearer option groups, and rewrites inline channel-shape comments throughout the workflow and subworkflows.
Changes:
- Replaced
normal_fiber(defaulttrue) withskip_normalfiber(defaultfalse) to follow theskip_*naming convention, with corresponding logic inversion in the fiber-seq processing block. - Added
severus_minsupportparameter (default 3) and wired it into the SEVERUS process args. - Reorganized
nextflow_schema.jsonby adding dedicated sections for Fibertools, VEP, Severus, and Wakhan options, and modernized channel-shape comments across workflows.
Reviewed changes
Copilot reviewed 7 out of 7 changed files in this pull request and generated 2 comments.
Show a summary per file
| File | Description |
|---|---|
| nextflow.config | Replaced normal_fiber with skip_normalfiber; added severus_minsupport; has a params.autocorrelation bug |
| nextflow_schema.json | Reorganized parameter groups; moved VEP params; added fibertools/severus/wakhan/skip sections |
| conf/modules.config | Parameterized SEVERUS --min-support (but uses single quotes preventing interpolation) |
| workflows/lrsomatic.nf | Updated fiber logic for skip_normalfiber; refreshed inline channel-shape comments |
| subworkflows/local/tumor_only_happhase.nf | Replaced verbose channel comments with concise tuple-shape annotations |
| subworkflows/local/tumor_normal_happhase.nf | Same comment modernization |
| subworkflows/local/prepare_reference_files.nf | Added inline channel-shape comments to emit block |
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Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).