This release comes with a lot of neat little improvements and bug fixes.

Highlights

  • More responsive nf-core-bot: If you add a @nf-core-bot fix linting comment in a PR to fix linting errors, there will be reactions added to the comment to indicate the status of the fix:

    • 👀 fixing action has started
    • 👍🏻 Everything looks good, nothing to fix
    • 🎉 Fixed errors and commited the changes
    • 😕 Something went wrong, please check the logs (also a comment with a link to the logs is added) Screenshot of the nf-core-bot fix linting comment
  • The nf-core tui subcommand launches a TUI (terminal user interface) to intuitively explore the command line flags, built using Trogon (more TUIs to come!)

    Demo gif of the TUI.
  • If you need an svg version or a bigger png version of an nf-core pipeline logo, you can now use the new nf-core logo-create subcommand to output one.

  • Speaking of logos, the pipeline READMEs now use the new(-ish) github image syntax.

  • Every pipeline now has a GitHub Action Workflow that tests a successful download with nf-core download.

  • Goodbye -profile docker, test errors: We check now if the -profile parameter is well formatted to avoid this common pitfall.

  • Fun changes on the tooling side:

    • The longer CI tests for the tools repo are now run on self-hosted runners on AWS (thanks for the sponsorship AWS!).

    • We’ve got a new bot which helps us to keep the changelog up to date. Big thanks to @vladsavelyev for the code!

    • We now use ruff for linting and formatting, goodbye to Black, isort and pyupgrae and thank you for your service!🫡.

      Tip
      • We included ruff to the pre-commit config. Use pre-commit install to install the git hook scripts.

      • To lint on save with VSCode, add the following settings:

      .vscode/settings.json
      "[python]": {
          "editor.formatOnSave": true,
          "editor.codeActionsOnSave": {
              "source.fixAll": true,
              "source.organizeImports": true
          },
          "editor.defaultFormatter": "charliermarsh.ruff"
      }
      • To run ruff manually you can use ruff check . and ruff format ..

You can find the whole changelog on GitHub.

Published on
28 January 2024