Cromwell Output Reorganization

This repository is an example of WDL workflow for organizing outputs from Cromwell, specifically Cromwell On Azure.

Learn more about using Azure for your Cromwell WDL workflows on our GitHub repo! - Cromwell on Azure.

This example takes advantage of Croo, a python package to reorganize outputs.

Here, you can find the WDL files and an example inputs JSON files.

The croro.trigger.json trigger files is a template trigger. You can start the workflow on your instance of Cromwell on Azure, using these instructions.

croro:

This WDL is the Cromwell Output Reorganization (croro) workflow. This example shows the minimum options that must be specified to perform an reorganization and move of data other Storage accounts and Containers.

Requirements/expectations

Metdata Json, Path for a metadata.json for a workflow
Output definition JSON file for a WDL file corresponding to the specified metadata.json file [Optional]
Input Directory, URL for Azure Blob Storage with shared access signature token
Output Directory, URL for Azure Blob Storage with shared access signature token
Docker image to run with AzCopy and Croo

Outputs

None

Contributing

This project welcomes contributions and suggestions. Most contributions require you to agree to a Contributor License Agreement (CLA) declaring that you have the right to, and actually do, grant us the rights to use your contribution. For details, visit https://cla.opensource.microsoft.com.

When you submit a pull request, a CLA bot will automatically determine whether you need to provide a CLA and decorate the PR appropriately (e.g., status check, comment). Simply follow the instructions provided by the bot. You will only need to do this once across all repos using our CLA.

This project has adopted the Microsoft Open Source Code of Conduct. For more information see the Code of Conduct FAQ or contact opencode@microsoft.com with any additional questions or comments.

Trademarks