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)

• 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!)

  

• 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:

    "[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

Written by

@mashehu

@mirpedrol