Reviewing nf-core/tools

nf-core/tools reviews ensure that changes to the tooling meet project standards and work reliably across the nf-core ecosystem. When you review an nf-core/tools pull request, you examine the proposed changes and provide constructive feedback before maintainers merge them into the repository.

The infrastructure team oversees the review process for nf-core/tools, but community input helps catch issues and ensures changes work well in real-world scenarios. Your perspective as a user of the tools is valuable, even if you’re not familiar with all the internal code.

General checklist items

Check the fundamentals of the PR:

• Tests cover the added code (either old or newly added tests)
• Documentation exists or the PR adds it, including checking for corresponding PR updates to nf-core/website if needed
• Code does not hardcode “nf-core”; verify it uses organisation variable instead
• Code does not hardcode modules/subworkflows; verify it uses component_type instead

Python styling checklist

Ensure the code follows Python best practices:

• Prefers pathlib over os module when possible for file operations
• Code uses typing
• Comments are sufficient and clear for readability
• Docstrings are updated (they generate API documentation automatically)
• If the PR adds a new command, verify that the API documentation skeleton includes it

Template modifications

Template changes propagate to all pipelines through nf-core pipelines sync, so they require careful consideration:

• Avoid unnecessary changes to prevent unnecessary updates across all pipelines
• Verify if the template should skip code/files based on customisations (branding, modules)

Command modifications

When the PR modifies commands, check that documentation is updated:

• All references to modified commands are updated throughout documentation
• Mentions in nf-core/tools and nf-core/website documentation are current
• The rich-codex.yml file in nf-core/website repository is updated
  Note

  Command changes often require updates in multiple places. Missing documentation updates can confuse users who see different information in different locations.