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…subwf, fix tests
Implement UMI consensus flow
Join demux FASTQs by RGLB when a sample has multiple libraries, and publish those outputs under LIBRARY/SAMPLENAME. Generated by Cursor Grok 4.6 Co-authored-by: Cursor <cursoragent@cursor.com>
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- Bump template to nf-core v4.1.0 - Bump modules - overhaul tests - various bugfixes supercedes #187 and #188 ## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested, add tests! - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-cmgg/preprocessing/tree/main/.github/CONTRIBUTING.md) - [ ] Make sure your code lints (`nf-core pipelines lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`). - [ ] Usage Documentation in `docs/usage.md` is updated. - [ ] Output Documentation in `docs/output.md` is updated. - [ ] `CHANGELOG.md` is updated. - [ ] `README.md` is updated (including new tool citations and authors/contributors). --------- Co-authored-by: Cursor <cursoragent@cursor.com>
Apply and rework the changes from #183 to fix merge conflicts. Supersedes and closes #183 - maximize in-process streaming for `fgumi` processes - fix sorting mode between steps to resolve conflicts This PR finishes the consensus flow implementation and marks it ready for validation and config tweaking <!-- # nf-cmgg/preprocessing pull request Many thanks for contributing to nf-cmgg/preprocessing! Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs). Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release. Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-cmgg/preprocessing/tree/main/.github/CONTRIBUTING.md) --> ## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested, add tests! - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-cmgg/preprocessing/tree/main/.github/CONTRIBUTING.md) - [ ] Make sure your code lints (`nf-core pipelines lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`). - [ ] Usage Documentation in `docs/usage.md` is updated. - [ ] Output Documentation in `docs/output.md` is updated. - [ ] `CHANGELOG.md` is updated. - [ ] `README.md` is updated (including new tool citations and authors/contributors).
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Preprocessing v3.1.0 release - ready for testing and validation before release.
Release checklist