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Pull request overview
This pull request applies strict Nextflow/Groovy syntax rules and consistent formatting across the entire codebase, aligning with modern nf-core linting standards.
Changes:
- Standardized use of lowercase
channelinstead ofChannelfor channel factory methods - Removed unnecessary spaces before function call parentheses
- Removed quotes from simple process names in
withNameselectors (keeping them only for wildcards) - Added proper spacing around operators and consistent indentation
- Added trailing commas to multi-line lists and maps
- Added
exists: truevalidation to the fasta parameter in the schema - Added
indexemit output to the FASTA_WINDOWS workflow - Renamed
monochrome_logsparameter to_monochrome_logsin PIPELINE_INITIALISATION (underscore prefix indicates unused parameter)
Reviewed changes
Copilot reviewed 11 out of 13 changed files in this pull request and generated 1 comment.
Show a summary per file
| File | Description |
|---|---|
| workflows/sequencecomposition.nf | Applied strict syntax: lowercase channel, removed spaces before parentheses, proper spacing in operators |
| main.nf | Removed unnecessary blank lines, standardized function call spacing, added fasta parameter to workflow call |
| subworkflows/local/utils_nfcore_sequencecomposition_pipeline/main.nf | Major formatting overhaul: aligned parameters, updated Channel to channel, renamed unused parameter with underscore prefix, improved conditional formatting |
| subworkflows/local/params_check.nf | Applied strict syntax, replaced ++ with += 1, added def keyword, used underscore prefix for unused variables |
| subworkflows/local/fasta_windows.nf | Consistent formatting, improved branch closure readability, added index emit for downstream use |
| modules/local/extract_column.nf | Removed quotes from tag interpolation, improved container conditional formatting, removed parentheses from val |
| nextflow.config | Extensive alignment of parameter assignments and profile configurations, improved readability |
| nextflow_schema.json | Added exists: true validation for fasta parameter |
| conf/base.config | Aligned assignments, removed quotes from simple process names |
| conf/modules.config | Removed quotes from simple withName selectors |
| conf/test.config | Added trailing comma, aligned parameter assignment |
| conf/test_full.config | Aligned parameter assignment |
| tests/nextflow.config | Aligned parameter assignment |
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prototaxites
approved these changes
Feb 2, 2026
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PR checklist
nf-core lint).nextflow run . -profile 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).