Window size#52
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Pull request overview
This PR replaces the previous output-naming-only window_size_info parameter with a real window_size integer parameter, wiring it into the FASTAWINDOWS execution and using it to derive consistent output filename labels. It also tightens validation for the selected_fw_output parameter via the Nextflow schema.
Changes:
- Remove
window_size_infofrom theFASTA_WINDOWSsubworkflow interface and associatedmeta.idconstruction. - Add
params.window_size(default1000) and validate it innextflow_schema.json; use it to setFASTAWINDOWSargs and to derive published output prefixes. - Improve
selected_fw_outputschema validation (file-path + exists) and document parameter changes in the changelog.
Reviewed changes
Copilot reviewed 6 out of 6 changed files in this pull request and generated 2 comments.
Show a summary per file
| File | Description |
|---|---|
| workflows/sequencecomposition.nf | Updates the FASTA_WINDOWS call to match the new interface (drops window_size_info). |
| subworkflows/local/fasta_windows.nf | Stops appending window_size_info to meta.id when constructing downstream IDs. |
| nextflow.config | Removes window_size_info, introduces window_size with a default value. |
| nextflow_schema.json | Replaces window_size_info with typed window_size; adds stronger validation for selected_fw_output. |
| conf/modules.config | Passes window size to FASTAWINDOWS and derives output prefixes (e.g., 1k, 500bp) for BGZIPTABIX. |
| CHANGELOG.md | Documents the new parameter and deprecation of window_size_info. |
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…me line Co-authored-by: Copilot Autofix powered by AI <[email protected]>
Co-authored-by: Copilot Autofix powered by AI <[email protected]>
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Now that we have a 26.04-compatible way of making the output name, cf sanger-tol/readmapping#244, here is its application to this pipeline.
No need to provide
.1kas a string, it can be automatically inferred from an actual integerPR 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).