On Microsoft Azure

On Microsoft Azure

Backend services

Cromwell is an open-source workflow execution engine developed by the Broad Institute of MIT and Harvard. It is designed to run workflows written in the Workflow Description Language (WDL, pronounced ‘widdle’) on either local or cloud infrastructure.

Cromwell on Azure is a workflow execution management package provided by Microsoft Research that simplifies the deployment of Azure resources for running genomics workflows. It bundles the Cromwell execution engine and uses the GA4GH Task Execution Service (TES) API to orchestrate the execution of individual tasks by the Azure Batch service.

Main operations

These are the main operations that occur when using Cromwell on Azure as the workflow execution backend for Workbench:

  1. Workbench submits the workflow to Cromwell;

  2. Cromwell generates individual task definitions;

  3. Cromwell dispatches task definitions to Azure Batch via the GA4GH Task Execution Service (TES);

  4. Tasks are executed on Azure instances using the tool containers and computing resources specified in the workflow;

  5. Outputs are written to Azure Cloud Storage;

  6. Cromwell returns the result of running the workflow to Workbench.

Various status monitoring operations also take place and are reported by Workbench as described in the User Guide.

Deployment and configuration

For your convenience, we provide an installer script that uses Microsoft's Cromwell on Azure installer and Terraform to create a suitable installation of Cromwell on Azure.

For complete step-by-step instructions, see the installer README.

In this deployment, An Azure Container App is used as the ingress for all requests to Cromwell, and calling this service requires an Azure Active Directory token from a pre-configured Azure Application Registration.

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