The Global Alliance for Genomics and Health is an international coalition, formed to enable the sharing of genomic and clinical data.
The Cloud Work Stream concentrates on data representation, storage, and analysis, including working with platform development partners and industry leaders to develop standards that will facilitate interoperability. The Cloud Work Stream is an informal, multi-vendor working group focused on standards for exchanging Docker-based tools and CWL/WDL workflows, execution of Docker-based tools and workflows on clouds, and abstract access to cloud object stores.
The Workflow Execution Schema is a minimal common API describing how a user can submit workflow requests to workflow execution systems in standardized ways. Workflow execution engines (SevenBridges, FireCloud, etc) can support this API so users can make workflow requests programmatically, adding the ability to scale up. In addition, these workflow services could have (and probably do have) UIs that would (possibly) use this API under the hood to facilitate workflow execution requests.
Having this standard API supported by multiple execution engines will give people options of processing the same workflow (CWL or WDL) across different workflow execution platforms running across various clouds/environments. As an example use case, one can find a workflow in CWL on Dockstore.org, use Dockstore to generate a JSON parameterization file, and submit this to a GA4GH-compliant workflow execution service.
Key features of the current API proposal:
- ability to request a workflow run using CWL or WDL (and maybe future formats)
- ability to parameterize that workflow using a JSON schema (ideally a future version would be in common between CWL and WDL)
- ability to get information about running workflows, status, errors, output file locations, etc.
Outstanding questions:
- a common JSON parameterization format
- standardizing terms, job, workflow, steps, tools, etc
- reference implementation at https://github.com/common-workflow-language/cwltool-service/tree/ga4gh-wes
- validation service for testing WES implementations' conformance to the spec
- Including all task_logs in the workflow log request may present a scaling problem when there are 100s-1000s of tasks
- Providing a state notification callback URL (eg a webhook)
- Passing through authentication (user role)
The file openapi/workflow_execution_service.swagger.yaml contains the API description.
Please visit http://ga4gh.github.io/workflow-execution-service-schemas to view this document in Swagger UI.
The OpenAPI description is in the openapi directory.
Take cues for now from the ga4gh/schemas document.
We like HubFlow and using pull requests to suggest changes.
If a security issue with any of the above specifications is realised please send an email to [email protected] detailing your concerns.
See the [LICENSE]