This repository provides a Common Workflow Language (CWL) tool for running the dorado program. dorado
is packaged in a Docker container, allowing it to run on any system with Docker or Singularity installed.
To use this tool, you must have the following software installed on your system:
To install and run the tool, follow these steps:
-
Clone this repository to your local machine.
-
Install Docker, if you haven't already done so.
-
(optional) Build the Docker image by running the following command from the root of the repository:
docker build -f docker/Dockerfile -t dorado-docker-cwl .
OR pull from the built container.
docker pull ghcr.io/~user~/~tool-docker-cwl~:latest
Note: this is only needed if you wish to access the container commands directly via docker.
-
Run the CWL tool by running the following command from the root of the repository:
cwl-runner <tool>.cwl <tool>.yml
OR
cwl-runner --singularity <tool>.cwl <tool>.yml
This will run the software on the input sequence specified in the
<tool>.yml
file.
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 <tool>.cwl
file is the main workflow file that describes the steps of the analysis. The <tool>.yaml
file is an example input file that specifies the input and any other options you wish to specify. The <tool>.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.
If you wish to contribute to this project, please follow the standard GitHub workflow:
- Fork the repository
- Create a new branch for your changes
- Make your changes and commit them
- Push your changes to your fork
- Submit a pull request to this repository
This project is licensed under the MIT License.
If you have any questions or feedback, please contact the author via GitHub.