Add developer guidelines and CLAUDE.md#2144
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Comprehensive reference covering code style (Harshil alignment, strict syntax, channel naming), channel operations and gotchas, meta map handling, module/subworkflow patterns, configuration, testing with nf-test, documentation requirements, and PR checklist. Intended for both human developers and AI agents working on sarek. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Move DEVELOPER_GUIDELINES.md to docs/DEVELOPER_GUIDELINES.md - Add topic channels section (migrating versions collection etc.) - Remove deprecated if(params.tools) guards from config examples Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Add contributing principles, git workflow, and changelog conventions to DEVELOPER_GUIDELINES.md so it serves both humans and agents - Slim CLAUDE.md to a pointer to the guidelines plus agent-only rules Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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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: 3.5.1. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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Document the 6 locations that must be updated when adding a new variant caller (schema, dispatcher subworkflows, post_variantcalling lists, individual subworkflow metadata). Missing any of these causes silent bugs — especially the small_variantcallers list in post_variantcalling which silently excludes callers from normalization/filtering/consensus. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Replace vague topic channel guidance with actionable instruction: check if installed/updated modules use topics for versions/multiqc, and remove explicit .mix() wiring if so - Add one-PR-one-feature to contributing principles Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Add pre-commit requirement to PR checklist in developer guidelines - Add nf-core conda env and don't-ask-for-confirmation rules to CLAUDE.md Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
heuermh
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Feb 20, 2026
| │ ├── local/ # Pipeline-specific modules | ||
| │ └── nf-core/ # Imported nf-core modules (120+) | ||
| ├── subworkflows/ | ||
| │ ├── local/ # Pipeline-specific subworkflows (66) |
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Probably not worth using actual numbers here, will easily get out of sync
| // CORRECT | ||
| channel.map({ meta, file -> [meta, file] }) | ||
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| // ALSO CORRECT (trailing closure) |
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Suggest dropping this example, even if also correct, since it breaks rule 2 above.
Alternatively, since most .map {, .branch {, .filter {, .set { etc. calls in examples below do not use parentheses, consider dropping this rule
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Summary
docs/DEVELOPER_GUIDELINES.md— comprehensive reference for contributing to sarek, covering code style (Harshil alignment, strict syntax, topic channels), channel operations, meta map handling, module/subworkflow patterns, configuration, testing, documentation requirements, and PR checklistCLAUDE.mdat repo root pointing to the guidelines, plus agent-specific rulesDetails
The guidelines document covers:
origin/dev, naming conventions, PR targetsXXXplaceholderif (params.tools...)guards in config filesTest plan
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