Module PR Review Checklist needs some clarifications
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Description
I've been trying to follow the Module PR Review Checklist recently, it's great to have such a list but some points are a bit unclear to me and could be clarified and/or made more specific:
General reviews of submissions to modules:
If running docker containers, check that Nextflow changes the
--entrypointto/bin/bashand that environment variables used by certain programs (e.g., Busco, Merqury) are sourced again to use them in container settings.
- How does one make sure of that? It would be good to have a link to a module that does that correctly.
Check that it adheres to nf-core coding standards (e.g. use of meta map).
- Which coding standards are we talking about here? And what do they entail other than meta map? A link to a page where these standards are described would be welcome here.
In modules/nf-core/modulename/main.nf:
Check that the software version extraction command is optimized, if required.
- What does it mean for the version extraction command to be optimized? Would be good to have examples of a non-optimized vs optimized commands. Can also be links to an old PR where this was an issue.
In ../tests/modules/nf-core/modulename/main.nf and ../tests/modules/nf-core/modulename/meta.yml:
- This should be updated with the new nf-test standard
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 with the Module PR Review Checklist at the linked nf-core documentation page and review the cited sections for container entrypoints, coding standards, version extraction, and nf-test files. Clarify each point with links or examples, and update the references to the new nf-test standard; completion means the checklist gives contributors actionable guidance.
Written by the indexing model from the issue text.
Assessment
- Domain
- documentation
- Issue type
- Documentation
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 38/100