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 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 on Azure supports workflows written in the Workflow Description Language or WDL format.

Get started in a few quick steps! See our Quickstart guide
Run Broad Insitute of MIT and Harvard's Best Practices Genome Analysis Pipeline on Cromwell on Azure
Need to debug or configure your Cromwell on Azure runs? See Advanced configuration instructions
Questions? Check our FAQs or open a GitHub issue