Description

We need to update the documentation for the repo and make sure we implement a system that enforces regular maintenance and document updates.

Acceptance criteria

• .github/CONTRIBUTING.md is updated with:

  • Instructions and best practices for coding
    • installation and dependencies for development - link to nf-core documentation
    • Make sure your code lints (nf-core pipelines lint)
    • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
    • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
    • Add steps for template update in documentation
  • Instructions and best practices for PRs and reviews
    • Conventional PR titles according to semantic-pull-request
    • Review
      • Check information in titles, issue and PR description as well as Changelog. Make sure all items of the checklist have been addressed.
      • leave code suggestions - If possible

• README.md is updated with:

  • tools and citations
  • authors/contributors

• CITATIONS.md is updated.

• Usage Documentation in docs/usage.md is updated.

  • Link to parameters documentation.

• Output Documentation in docs/output.md is updated.

• CHANGELOG.md is reviewed and updated.

• There is a file with parameters documentation - feat: Pre-commit hook for automatic parameters documentation generation #25

  • Parameters settings are reviewed: groups, descriptions, required, etc. + Fix ungrouped parameters #27

• Template description in nf-core.yml is updated.

• Make sure there is a system for continuous update of the relevant documents for every PR Add GitHub templates #23 Adjust GitHub settings and CI checks #17

  • README.md - reminder included in PR checklist
  • docs/usage.md - reminder included in PR checklist
  • docs/output.md - reminder included in PR checklist
  • CHANGELOG.md - required check from CI