samtools-docker-cwl

This repository provides a Common Workflow Language (CWL) tool for running the samtools program. Samtools is packaged in a Docker container, allowing it to run on any system with Docker or Singularity installed.

Prerequisites

To use this tool, you must have the following software installed on your system:

• CWL tool
• Docker OR Singularity

Installation

To install and run the tool, follow these steps:

1. Clone this repository to your local machine.

2. Install Docker, if you haven't already done so.

3. (optional) Build the Docker image by running the following command from the root of the repository:

   docker build -t samtools-docker-cwl .
   

   OR pull from the built container.

   docker pull ghcr.io/bwbioinfo/samtools-docker-cwl:latest
   

   Note: this is only needed if you wish to access the container commands directly via docker.

4. Run the CWL tool by running the following command from the root of the repository:

   cwl-runner samtools-docker-cwl.cwl samtools-docker-cwl-inputs.yml
   

   OR

   cwl-runner --singularity samtools-docker-cwl.cwl samtools-docker-cwl-inputs.yml
   

   This will run the samtools-docker-cwl software on the input sequence specified in the samtools-docker-cwl-inputs.yml file.

Usage

To use the tool, you will need to create a YAML file specifying the input sequence and any other parameters you wish to specify. An example YAML file is provided in the example directory of this repository.

The samtools-docker-cwl.cwl file is the main workflow file that describes the steps of the samtools analysis. The samtools-docker-cwl-inputs.yaml file is an example input file that specifies the input and any other options you wish to specify. The samtools-docker-cwl.cwl file includes the docker specification. You can also use Singularity via the cwl-runner option --singularity

The output of the analysis will be written to a directory named output in the current working directory.

Contributing

If you wish to contribute to this project, please follow the standard GitHub workflow:

1. Fork the repository
2. Create a new branch for your changes
3. Make your changes and commit them
4. Push your changes to your fork
5. Submit a pull request to this repository

License

This project is licensed under the MIT License.

Contact

If you have any questions or feedback, please contact the author via GitHub.