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https://github.com/broadinstitute/cromwell

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
https://github.com/broadinstitute/cromwell

application bioinformatics cloud containers docker executor ga4gh hpc scala wdl workflow workflow-description-language workflow-execution

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Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

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README 

        
[![codecov](https://codecov.io/gh/broadinstitute/cromwell/branch/develop/graph/badge.svg)](https://codecov.io/gh/broadinstitute/cromwell)



## Welcome to Cromwell



Cromwell is an open-source Workflow Management System for bioinformatics. Licensing is [BSD 3-Clause](LICENSE.txt).



The [Cromwell documentation has a dedicated site](https://cromwell.readthedocs.io/en/stable).



First time to Cromwell? Get started with [Tutorials](https://cromwell.readthedocs.io/en/stable/tutorials/FiveMinuteIntro/).



### Community



Thinking about contributing to Cromwell? Get started by reading our [Contributor Guide](CONTRIBUTING.md).



Cromwell has a growing ecosystem of community-backed projects to make your experience even better! Check out our [Ecosystem](https://cromwell.readthedocs.io/en/stable/Ecosystem/) page to learn more.



Talk to us:

- [Join the Cromwell Slack workspace](https://join.slack.com/t/cromwellhq/shared_invite/zt-dxmmrtye-JHxwKE53rfKE_ZWdOHIB4g) to discuss the Cromwell workflow engine.

- [Join the OpenWDL Slack workspace](https://join.slack.com/t/openwdl/shared_invite/zt-ctmj4mhf-cFBNxIiZYs6SY9HgM9UAVw) to discuss the evolution of the WDL language itself.

    - More information about WDL is available in [that project's repository](https://github.com/openwdl/wdl).  



### Capabilities and roadmap



Many users today run their WDL workflows in [Terra](https://app.terra.bio/), a managed cloud bioinformatics platform with built-in WDL support provided by Cromwell. See [here](https://support.terra.bio/hc/en-us/articles/360036379771-Get-started-running-workflows) for a quick-start guide.



Users with specialized needs who wish to install and maintain their own Cromwell instances can [download](https://github.com/broadinstitute/cromwell/releases) a JAR or Docker image. The development team accepts reproducible bug reports from self-managed instances, but cannot feasibly provide direct support.



[Cromwell's backends](https://cromwell.readthedocs.io/en/stable/backends/Backends/) receive development resources proportional to user demand. The team is actively developing for Google Cloud and Microsoft Azure (see [Cromwell on Azure](https://github.com/microsoft/CromwellOnAzure)). Maintenance of other backends is primarily community-based.



Cromwell [supports](https://cromwell.readthedocs.io/en/stable/LanguageSupport/) the WDL workflow language. Cromwell version 80 and above no longer support CWL.



CWL will be re-introduced at a later date in the [Terra platform](https://terra.bio/), using a solution other than Cromwell. See the blog post ["Terra’s roadmap to supporting more workflow languages"](https://terra.bio/terras-roadmap-to-supporting-more-workflow-languages/) for details.



### Security reports



If you believe you have found a security issue please contact `[email protected]`.



### Issue tracking



Need to file an issue? Head over to [Github Issues](https://github.com/broadinstitute/cromwell/issues).



If you previously filed an issue in JIRA, the link is [here](https://broadworkbench.atlassian.net/jira/software/c/projects/CROM/issues). New signups are no longer accepted.



![Jamie, the Cromwell pig](docs/jamie_the_cromwell_pig.png)