Dear Community,

After careful consideration, we have decided to shift our focus to new and innovative initiatives that will better serve our community and align with our long-term goals.

Effective Date: May 12th, 2025

Impact on Users:

The project repository will be archived and set to read-only mode, ensuring that it remains accessible for reference.
While no further updates, bug fixes, or support will be provided, we encourage you to explore the wealth of knowledge and resources available in the repository.
Existing issues and pull requests will be closed, but we invite you to engage with other projects and contribute your expertise.

Licensing: The project will remain under its current open-source license, allowing others to fork and continue development if they choose.

We understand that this change may come as a surprise, but we are incredibly grateful for your support and contributions over the years. Your dedication has been instrumental in the success of this project, and we look forward to your continued involvement in our future endeavors.

Thank you for your understanding and support.

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

This project may contain trademarks or logos for projects, products, or services. Authorized use of Microsoft trademarks or logos is subject to and must follow Microsoft's Trademark & Brand Guidelines. Use of Microsoft trademarks or logos in modified versions of this project must not cause confusion or imply Microsoft sponsorship. Any use of third-party trademarks or logos are subject to those third-party's policies.

License

microsoft/cromwell-output-reorganization

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