Documentation #3
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qclayssen
commented
Apr 29, 2025
qclayssen
commented
- detailed description of pipeline
- Usage
- Output example
- test example
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Pull Request Overview
This PR updates the project documentation, adding a new architectural decision record (ADR) and enhancing the usage, output, and README pages.
- Updated usage instructions with a CSV sample sheet example and removed outdated multiple-run examples.
- Revised output documentation to include detailed directory structure and comprehensive workflow explanations.
- Added an ADR outlining the VCF chunking and parallelization approach for PCGR processing.
- Updated documentation index and project overview in the main README.
Reviewed Changes
Copilot reviewed 9 out of 10 changed files in this pull request and generated 3 comments.
Show a summary per file
| File | Description |
|---|---|
| docs/usage.md | Updates to usage documentation by replacing outdated examples with a CSV sample sheet format. |
| docs/output.md | Extensive revisions to output documentation including directory structure and detailed workflow summaries. |
| docs/adr.md | New ADR detailing the implementation of VCF chunking and parallel processing for improved PCGR scalability. |
| docs/README.md | Updated index linking to new details and ADR documentation. |
| README.md | Enhanced project overview and quick start guide with updated pipeline descriptions and installation instructions. |
Files not reviewed (1)
- assets/samplesheet.csv: Language not supported
docs/usage.md
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| ```csv | ||
| id,subject_name,sample_name,filetype,filepath | ||
| subject_a.example,subject_a,sample_germline,dragen_germline_dir,/path/to/dragen_germline/ | ||
| subject_a.example,subject_a,sample_germline,dragen_germline_dir,/path/to/dragen_germline/ |
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Duplicate CSV row for sample_germline detected; please remove the duplicate entry if it is not intended to avoid potential confusion.
| subject_a.example,subject_a,sample_germline,dragen_germline_dir,/path/to/dragen_germline/ |
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docs/output.md
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| └── prioritise/ | ||
| ``` | ||
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| i |
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Extraneous character 'i' found in the documentation; please remove it to improve clarity.
| i |
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docs/output.md
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| ├── purple/ | ||
| ├── smlv_germline/ | ||
| │ └── prepare/ | ||
| | └── report/ |
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Formatting error in the directory structure tree: the pipe character should be replaced with the correct vertical line symbol to ensure consistent formatting.
| | └── report/ | |
| │ └── report/ |
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