nf-core / nf-core/website

Module PR Review Checklist needs some clarifications

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enhancement
Dominant language
MDX
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98
Forks
298
Avg merge
14h 38m
Merged PRs (30d)
38

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 --entrypoint to /bin/bash and 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

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. 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

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