workflow-execution-service-schemas
Workflow Execution Service (WES) API
This repository is the home for the schema for the GA4GH Workflow Execution Service API. The Goal of the API is to provide a standardized way to submit and manage workflows described in a workflow language (eg. WDL, CWL, Nextflow, Galaxy, Snakemake) against an execution backend.
See the human-readable Reference Documentation You can also explore the specification in the Swagger Editor** Manually load the JSON if working from a non-develop branch version. Preview documentation from the gh-openapi-docs for the development branch here
All documentation and pages hosted at ‘ga4gh.github.io/workflow-execution-service’ reflect the latest API release from the
masterbranch. To monitor the latest development work, add ‘preview/<branch>’ to the URLs above (e.g., ‘ ga4gh.github.io/ga4gh.github.io/workflow-execution-service/preview/<branch>/docs’). To view the latest stable development API specification, refer to thedevelopbranch.
The Global Alliance for Genomics and Health is an international coalition, formed to enable the sharing of genomic and clinical data.
Cloud Work Stream
The Cloud Work Stream helps the genomics and health communities take full advantage of modern cloud environments. Our initial focus is on “bringing the algorithms to the data”, by creating standards for defining, sharing, and executing portable workflows.
We work with platform development partners and industry leaders to develop standards that will facilitate interoperability.
What is WES?
The Workflow Execution Service API describes a standard programmatic way to run and manage workflows. Having this standard API supported by multiple execution engines will let people run the same workflow using various execution platforms running on various clouds/environments. Key features include:
- ability to request a workflow run using CWL or WDL
- ability to parameterize that workflow using a JSON schema
- ability to get information about running workflows
Use Cases
Use cases include:
- “Bring your code to the data”: a researcher who has built their own custom analysis can submit it to run on a dataset owned by an external organization, instead of having to make a copy of the data
- Best-practices pipelines: a researcher who maintains their own controlled data environment can find useful workflows in a shared directory (e.g., Dockstore.org), and run them over their data
Starter Kit
If you are a future implementor or would like to start using a WES API locally you can try the GA4GH WES Starter Kit. This project provides a fully functioning WES API written in java and allows you to run workflows using the Nextflow workflow language.
Possible Future Enhancements
- common JSON parameterization format that works with CWL and WDL
- validation service for testing WES implementations’ conformance to the spec
- improved tools for troubleshooting execution failures, especially when there are 100s-1000s of tasks
- a callback mechanism for monitoring status changes in running workflows (e.g., a webhook)
- integration with GA4GH data access APIs (e.g., htsget, DOS)
How to Contribute Changes
See CONTRIBUTING.md.
If a security issue is identified with the specification, please send an email to security-notification@ga4gh.org detailing your concerns.
License
See the LICENSE.