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Bioinformatics CWL Pipeline Collection

A comprehensive collection of Common Workflow Language (CWL) pipelines and tools for bioinformatics analysis, supporting various types of genomic analyses.

Project Structure

.
├── docs/                        # General documentation
│   ├── README.md               # Documentation overview
│   └── platforms/              # Platform-specific guides
├── pipelines/                  # Analysis pipelines by category
│   └── somatic_variant_calling/
│       └── mutect2_and_strelka2/
│           ├── mutect2_and_strelka2.cwl
│           ├── README.md
│           └── TESTING.md
└── apps/                       # Individual tools
    ├── gatk/                   # GATK-based tools
    │   └── tool_name/         # Each tool in its own directory
    │       ├── tool_name.cwl  # Tool definition
    │       ├── Dockerfile     # Container definition
    │       └── README.md      # Tool documentation & container info
    ├── utilities/
    ├── python_scripts/
    └── variant_callers/

Tools Organization

Each tool is self-contained in its own directory with:

  • CWL tool definition
  • Dockerfile for reproducible environment
  • Documentation including Docker image information

Available Pipelines

Pipelines are organized by analysis type. Each pipeline includes its own documentation and testing protocols.

Requirements

  • CWL runner (e.g., cwltool, toil, cromwell)
  • Docker support
  • Python 3.8+

Quick Start

  1. Clone the repository:
git clone [repository-url]
cd cwl-pipelines
  1. Choose a pipeline and run with your preferred CWL runner:
cwl-runner pipelines/<category>/<pipeline>/<pipeline>.cwl inputs.yml

Docker Configuration

Each tool includes its own Dockerfile and documents:

  • Registry location
  • Image tag
  • Build instructions
  • Version information

Contributing

  1. Fork the repository
  2. Create a feature branch
  3. Commit your changes
  4. Submit a pull request

When adding new tools:

  1. Create a new directory under appropriate category
  2. Include CWL definition, Dockerfile, and README
  3. Document Docker image information
  4. Add tests if applicable

Testing

Each pipeline includes:

  • Pipeline-specific testing documentation
  • Test datasets references
  • Validation criteria
  • Platform-specific testing notes

Platform Support

These pipelines are tested and supported on:

  • Seven Bridges Platform
  • Local execution with cwltool
  • [Other supported platforms]

See docs/platforms/ for implementation guides.

Support and Contact

  • GitHub Issues for bug reports and feature requests
  • [Contact Information]

License

[License Information]

Citation

[Citation Information]