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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

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

Reference data must be uploaded to Azure Blob Storage

10.5281/zenodo.17086906

Reference data is hosted on Zenodo at 10.5281/zenodo.17086906. Download the reference data bundle and extract it to a location on your HPC, then update the input template file with the path to the reference data.

## download the reference data bundle
wget https://zenodo.org/record/17086906/files/hifi-wdl-resources-v3.1.0.tar

## extract the reference data bundle and rename as dataset
tar -xvf hifi-wdl-resources-v3.1.0.tar

Upload the hifi-wdl-resources-v3.1.0 directory to Azure Blob Storage. The reference data can be uploaded to any blob storage container for which your Cromwell on Azure instance has access. Update the Azure input file template with the path to the reference data in blob storage.