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 through Cromwell on the Azure cloud, and uses the GA4GH TES backend for orchestrating the tasks that create a workflow. The installation sets up a VM host to run the Cromwell server and uses Azure Batch to spin up virtual machines that run each task in a workflow. Cromwell workflows can be written using either the WDL or the CWL scripting languages. To see examples of WDL scripts - see this 'Learn WDL' repository on GitHub. To see examples of CWL scripts - see this 'CWL search result' on Dockstore.
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