PR Review Checklist for nf-core/tools

While the infrastructure team is responsible for overseeing the PR review process for nf-core/tools, these guidelines can assist community members in reviewing PRs and ensure that the review process is consistent and effective. The following is a collection of points to have into account during the review process.

General

• Check that the added code is covered by tests (either by old or newly added tests).
• Check that documentation exists or is added.
  • Check if a documentation PR to the nf-core/website exists if needed.
• Check that nf-core is not hardcoded, use organisation instead.
• Check that modules/subworkflows is not hardcoded, use component_type instead.

Python styling

• Check that pathlib is used instead of os when possible.
• Check that the code uses typing.
• Check that code comments are sufficient enough and clear.
• Check that docstrings are updated. This is specially important for linting, as the API documentation is automatically generated from these strings.
• If a new command was added, check that it is part of the API documentation skeleton, by running the docs/api/generate-api-docs.sh script

Template modifications

If the PR is modifying the files under nf-core/pipeline-template:

• Check that unnecessary changes are NOT ADDED, to avoid template updates to all pipelines.
• Check if the code/file has to be skipped with any of the template customisations (branding, modules…)?

Command modifications

If the PR modifies how an nf-core command works.

• Check if all references to this command are updated.
• Check that mentions of this command on the nf-core/tools or nf-core/website documentation are updated.
• Make sure that the command in rich-codex.yml from the nf-core/website is updated.