Nextflow Lint Pre-commit Hook

A pre-commit hook for running nextflow lint on Nextflow pipeline files.

What is Nextflow Lint?

nextflow lint is a command provided by Nextflow that checks your pipeline scripts for common issues and best practices. It helps ensure your Nextflow workflows follow proper conventions and can catch potential problems early in development.

Installation

Prerequisites

• Nextflow must be installed and available in your PATH
• pre-commit must be installed

Setup

1. Add this hook to your .pre-commit-config.yaml file:

yaml repos: - repo: https://github.com/adamrtalbot/nf-lint-pre-commit rev: v0.1.0 # Use the ref you want to point at hooks: - id: nextflow-lint

1. Install the pre-commit hook:

bash pre-commit install

Usage

Once installed, the hook will automatically run nextflow lint whenever you commit changes to .nf or .config files in your repository.

Manual Execution

You can also run the hook manually:

```bash

Run on all files

pre-commit run nextflow-lint --all-files

Run on specific files

pre-commit run nextflow-lint --files main.nf ```

Passing Arguments to Nextflow Lint

You can pass any nextflow lint arguments through the hook by adding them to your .pre-commit-config.yaml:

```yaml repos: - repo: https://github.com/adamrtalbot/nf-lint-pre-commit rev: v0.1.0 hooks: - id: nextflow-lint # Basic linting with no arguments (default)

  # Or with formatting
  - id: nextflow-lint
    args: [-format]

  # Or with concise output
  - id: nextflow-lint
    args: [-output, concise]

  # Or with multiple options
  - id: nextflow-lint
    args: [-format, -sort-declarations]

  # Or with JSON output for CI systems
  - id: nextflow-lint
    args: [-output, json]

```

For detailed information about what nextflow lint checks, refer to the Nextflow documentation.

Troubleshooting

Nextflow Not Found

If you get an error that nextflow is not found:

1. Make sure Nextflow is installed: curl -s https://get.nextflow.io | bash
2. Make sure it's in your PATH: export PATH="$PATH:/path/to/nextflow"
3. Verify installation: nextflow -version

Hook Fails

If the lint check fails:

1. Review the output to understand what issues were found
2. Fix the issues in your Nextflow files
3. Commit again

Skip Hook Temporarily

If you need to skip the hook for a specific commit:

bash git commit -m "Your commit message" --no-verify

Contributing

Contributions are welcome! Please:

1. Fork the repository
2. Create a feature branch
3. Add tests for new functionality in the GitHub Actions workflows
4. Ensure all CI tests pass
5. Submit a pull request

Development Workflow

Please feel free to contribute to this project by opening an issue or a pull request.

Running Tests Locally

You can test the hook directly during development:

```bash

Install Nextflow (if not already installed)

curl -s https://get.nextflow.io | bash

Test the hook directly

chmod +x nextflow-lint-hook ./nextflow-lint-hook

Test with arguments

./nextflow-lint-hook -format ./nextflow-lint-hook -output concise

Test with pre-commit

pip install pre-commit pre-commit run --all-files ```

License

This project is licensed under the MIT License.