Add compact inline channel structure comments to key workflow files#140
Merged
robert-a-forsyth merged 9 commits intodevfrom Mar 13, 2026
Merged
Add compact inline channel structure comments to key workflow files#140robert-a-forsyth merged 9 commits intodevfrom
robert-a-forsyth merged 9 commits intodevfrom
Conversation
Document tuple structures for all major channels in lrsomatic.nf, tumor_normal_happhase.nf, tumor_only_happhase.nf, and prepare_reference_files.nf using [meta, elem1, elem2] style comments. Replaces verbose multi-line comments with consistent single-line format and fixes one mislabelled comment (tumor_bams_phasedvcf was labelled as tumor_bams_germlinevcf). Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Contributor
|
Contributor
There was a problem hiding this comment.
Pull request overview
This PR updates the pipeline’s user-facing documentation and improves in-code workflow/channel tuple documentation to make channel shapes and provenance clearer throughout LRSomatic.
Changes:
- Add/refresh inline comments describing Nextflow channel tuple shapes across the main workflow and subworkflows.
- Update CHM13 usage documentation (including manual VEP cache guidance).
- Update pipeline citation information to reference the bioRxiv preprint.
Reviewed changes
Copilot reviewed 7 out of 7 changed files in this pull request and generated 4 comments.
Show a summary per file
| File | Description |
|---|---|
| workflows/lrsomatic.nf | Adds/updates channel-shape comments through the main LRSOMATIC workflow. |
| subworkflows/local/tumor_only_happhase.nf | Adds/updates tuple-shape comments for tumor-only phasing + calling path. |
| subworkflows/local/tumor_normal_happhase.nf | Adds/updates tuple-shape comments for tumor-normal path (incl. Clair3 model combination). |
| subworkflows/local/prepare_reference_files.nf | Adds comments clarifying emitted tuple formats for prepared references and downloaded Clair3 models. |
| docs/usage.md | Adds a CHM13 support section with VEP cache setup instructions. |
| README.md | Replaces Zenodo DOI citation with a formatted bioRxiv citation block. |
| CITATIONS.md | Adds an LRSomatic citation entry pointing to the bioRxiv DOI. |
💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
robert-a-forsyth
approved these changes
Mar 13, 2026
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Document tuple structures for all major channels in lrsomatic.nf, tumor_normal_happhase.nf, tumor_only_happhase.nf, and prepare_reference_files.nf using [meta, elem1, elem2] style comments. Replaces verbose multi-line comments with consistent single-line format and fixes one mislabelled comment (tumor_bams_phasedvcf was labelled as tumor_bams_germlinevcf).
PR 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).