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Welcome to Cromwell on Azure


Cromwell is a workflow management system for scientific workflows, orchestrating the computing tasks needed for genomics analysis. Originally developed by the Broad Institute, Cromwell is also used in the GATK Best Practices genome analysis pipeline. Cromwell supports running scripts at various scales, including your local machine, a local computing cluster, and on the cloud.

Cromwell on Azure configures all Azure resources needed to run workflows with Cromwell on the Microsoft Azure cloud, and uses the GA4GH TES backend for orchestrating the tasks that create a workflow. The installation sets up an Azure Kubernetes cluster to run the Cromwell, TES, and Trigger Service containers, and uses the Azure Batch PaaS service to execute each task in a workflow on its own VM, enabling scale-out to thousands of machines. Cromwell workflows can be written using the WDL scripting language. To see examples of WDL scripts - see this 'Learn WDL' repository on GitHub.

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All documentation has been moved to our wiki!

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Related Projects

Genomics Data Analysis with Jupyter Notebooks on Azure


Microsoft Genomics implementation of the Broad Institute's Cromwell workflow engine on Azure



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