backend-azure.md

Configuring Cromwell on Azure

Workflows can be run in Azure by setting up Cromwell on Azure (CoA). Documentation on deploying and configuring an instance of CoA can be found here.

Requirements

• Cromwell on Azure version 3.2+; version 4.0+ is recommended

Configuring and running the workflow

Filling out workflow inputs

Fill out any information missing in the inputs file.

See the inputs section of the main README for more information on the structure of the inputs.json file.

Running via Cromwell on Azure

Instructions for running a workflow from Cromwell on Azure are described in the Cromwell on Azure documentation.

Reference data hosted in Azure

To use Azure reference data, add the following line to your containers-to-mount file in your Cromwell on Azure installation (more info here):

https://datasetpbrarediseases.blob.core.windows.net/dataset?si=public&spr=https&sv=2021-06-08&sr=c&sig=o6OkcqWWlGcGOOr8I8gCA%2BJwlpA%2FYsRz0DMB8CCtCJk%3D

The Azure input file template has paths to the reference files in this blob storage prefilled.