Code formatting

The nf-core community uses automated code formatting tools to maintain a consistent style across repositories. Use Prettier to check that your documentation is correctly formatted.

Learn how to install and run Prettier to correctly format your documentation.

Install Prettier

Install Prettier using conda:

conda install prettier

Editor plugin

You can install Prettier as an extension for your code editor. It will fix formatting issues automatically every time you save a file.

For VS Code, install the Prettier extension.

Run Prettier

If you have Prettier installed, you can run it manually to check for formatting issues or apply fixes:

1. Check for changes:

   prettier -c .

2. Write changes:

   prettier -w .

Run Prettier With pre-commit

Configure pre-commit to run Prettier automatically every time you commit code. Most nf-core repositories already include a .pre-commit-config.yaml file:

- repo: https://github.com/pre-commit/mirrors-prettier
  rev: <SHA_OR_TAG> # Use the sha or tag you want to point at
  hooks:
    - id: prettier

To run Prettier with pre-commit:

1. Install pre-commit:

   pip install pre-commit

2. Install the pre-commit hook in your repository:

   pre-commit install

When you run git commit, Prettier runs automatically

Run Prettier on a pull request

If you’ve already created a pull request, add a comment with @nf-core-bot fix linting. The nf-core bot will run Prettier and apply the required fixes.