On Microsoft Azure
Understanding Cromwell on Azure
Cromwell is an open-source workflow execution engine from the Broad Institute of MIT and Harvard, designed to run Workflow Description Language (WDL) workflows on local or cloud infrastructure. Microsoft Research provides Cromwell on Azure, a workflow execution management package that:
Simplifies Azure resource deployment for genomics workflows
Bundles the Cromwell execution engine
Uses GA4GH Task Execution Service (TES) API
Orchestrates tasks through Azure Batch service
How It Works
When using Cromwell on Azure with Workbench, the process flows as follows:
Workbench submits the workflow to Cromwell
Cromwell generates individual task definitions
Cromwell dispatches tasks to Azure Batch via TES
Tasks execute on Azure instances using specified containers and resources
Outputs write to Azure Cloud Storage
Cromwell returns results to Workbench
Workbench monitors and reports status throughout this process, as detailed in the User Guide.
Deployment
For simplified setup, we provide an installer script that combines:
Microsoft's Cromwell on Azure installer
Terraform configuration tools
The deployment uses an Azure Container App as the ingress point for Cromwell requests. This requires an Azure Active Directory token from a pre-configured Azure Application Registration.
For complete deployment instructions, refer to the installer README.
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