Goals: to collect and collaboratively maintain CWL CommandLineTool descriptions of any biology/life-sciences related applications.

Non-goals: software packaging or containerization, go to https://biocontainers.pro for that

All CWL tool descriptions are licensed under the Apache 2.0 license. The underlying tools are under one or more Free and Open Source Software licenses.

We welcome pull requests to this repository to add new CWL tool descriptions!

For tools we already have, please compare your definition to the existing descriptions, maybe you can help improve them.

If you are using a tool (or its subcommand) for a different purpose than the existing description in this repository, then please submit it as a separate CWL file next to the existing description(s).

Check out CONTRIBUTING.md for a Styleguide and other contribution tips. Thank you for your contribution!

Here are four different ways that you can use tools from this repository in your own workflows:

1. Make add a git submodule of this repository to the Git repository of your workflow, typically under the path tools.

   Example of using git submodule with this repo.

   Then you can control the exact version of this repository used in your workflow.

2. Copy the entire contents of this repo to your repository. You may have a harder time managing updates, but if git submodule is uncomfortable then this might be a good choice.

   Example of copying the this repo

3. Use the in-development CWL Dependency Manager.

4. Refer to the tools in this repository by URL, as in this example which uses a namespace to refer to the bio-cwl-tools repository and then specifies in the individual tool by path within that namespace prefix. If this route is used, cwltool --pack can created a runnable version of the workflow with all remote references resolved.

Thanks goes to these wonderful people (emoji key):

KerstenBreuer 💻	Peter Amstutz 🤔 💻	Michael Kotliar 🤔 💻	pvanheus 💻	medcelerate 🤔	stain 💻	Miguel Boland 💻
fjrmoreews 💻	cjuigne 💻	Martín Beracochea 💻	Denis Yuen 📖	Sehrish Kanwal 💻

This project follows the all-contributors specification. Contributions of any kind welcome!