Keep the citations file in sync with installed modules (nf-core/tools lint)
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- Dominant language
- Python
- Stars
- 322
- Forks
- 255
- Avg merge
- 2d 3h
- Merged PRs (30d)
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Description
Follow-up from nf-core/nf-core-utils#43 (review by @maxulysse). Tracking issue — the implementation likely belongs in nf-core/tools.
Goal: a lint/test that verifies a pipeline's citations file is up to date based on all installed modules' meta.yml, and ideally regenerates it (so the file is populated by tooling when a module is added/removed). Combined with nf-core/nf-core-utils#43's plugin functions, the data lives once in meta.yml and the citations file is recomputed rather than hand-edited.
- Requires good
meta.ymltools:coverage (author/year/doi) in local and nf-core modules. - Pairs with the structured-output work for a non-MD citations file.
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Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by locating the nf-core/tools lint and test entry points that inspect installed modules and their meta.yml files. Compare the current citations file behavior with the stated goal, and consider the work complete when tooling verifies or regenerates citations from module metadata, including modules added or removed.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, tooling
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100