CONTRIBUTING.md

Contributing to nf-modules

Thank you for your interest in contributing to the BigBio nf-modules repository!

Module Standards

All modules in this repository must follow nf-core module standards:

Module Structure

Each module should have:

• main.nf - The main module implementation
• meta.yml - Module metadata and documentation
• environment.yml - Conda environment specification

Module Requirements

1. DSL2 Syntax: All modules must use Nextflow DSL2
2. Container Support: Modules should support both Docker and Singularity
3. Conda Environment: Provide a conda environment.yml file
4. Metadata: Include a meta map for sample tracking
5. Version Reporting: Emit a versions.yml file
6. Stub Section: Include a stub for testing

Example Module Structure

modules/nf-core/toolname/
├── main.nf
├── meta.yml
└── environment.yml

Testing

All modules must include tests:

tests/modules/nf-core/toolname/
├── main.nf
└── nextflow.config

Code Style

• Follow the .editorconfig settings
• Use 4 spaces for indentation in .nf files
• Use 2 spaces for indentation in .yml files
• Run prettier before committing: prettier --write .

Pull Request Process

1. Fork the repository
2. Create a feature branch
3. Add your module following the structure above
4. Add tests for your module
5. Ensure all CI checks pass
6. Submit a pull request

Questions?

If you have questions, please open an issue in the repository.