https://github.com/ga4gh/workflow-execution-service-schemas
The WES API is a standard way to run and manage portable workflows.
https://github.com/ga4gh/workflow-execution-service-schemas
cwl ga4gh wdl workflow
Last synced: 5 months ago
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The WES API is a standard way to run and manage portable workflows.
- Host: GitHub
- URL: https://github.com/ga4gh/workflow-execution-service-schemas
- Owner: ga4gh
- License: apache-2.0
- Created: 2016-03-29T16:57:46.000Z (about 10 years ago)
- Default Branch: develop
- Last Pushed: 2025-10-21T09:24:28.000Z (8 months ago)
- Last Synced: 2025-10-21T09:28:52.211Z (8 months ago)
- Topics: cwl, ga4gh, wdl, workflow
- Homepage:
- Size: 4.4 MB
- Stars: 85
- Watchers: 38
- Forks: 37
- Open Issues: 64
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
Awesome Lists containing this project
README
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](https://ga4gh.github.io/workflow-execution-service-schemas/docs/)
You can also explore the specification in
the [Swagger Editor](https://editor.swagger.io/?url=https://ga4gh.github.io/workflow-execution-service-schemas/openapi.yaml)**
*Manually load the JSON if working from a non-develop branch version.* Preview documentation from
the [gh-openapi-docs](https://github.com/ga4gh/gh-openapi-docs) for the development
branch [here](https://ga4gh.github.io/workflow-execution-service-schemas/preview/develop/docs/index.html)
> All documentation and pages hosted at 'ga4gh.github.io/workflow-execution-service' reflect the latest API release from
> the `master` branch. To monitor the latest development work, add 'preview/\' to the URLs above (e.g., '
> ga4gh.github.io/ga4gh.github.io/workflow-execution-service/preview/\/docs'). To view the latest *stable*
> development API specification, refer to the `develop` branch.
The [Global Alliance for Genomics and Health](http://genomicsandhealth.org/) is an international coalition, formed to
enable the sharing of genomic and clinical data.
Cloud Work Stream
-----------------
The [Cloud Work Stream](https://ga4gh.cloud) 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](http://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](https://starterkit.ga4gh.org/docs/starter-kit-apis/wes/wes_overview/). 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)
Known Implementations
=====================
Implementations listed here are community-provided. No guarantees are made on (level of) compliance, functionality,
maturity, project status, etc. Nor should inclusion in this list be considered an endorsement by GA4GH.
* https://github.com/common-workflow-language/workflow-service/
* https://github.com/elixir-cloud-aai/cwl-WES
* https://github.com/elixir-cloud-aai/proWES
* https://github.com/sapporo-wes/sapporo
* https://gitlab.com/one-touch-pipeline/weskit
How to Contribute Changes
=========================
See [CONTRIBUTING.md](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](LICENSE).
More Information
================
* [Global Alliance for Genomics and Health](http://genomicsandhealth.org)
* [GA4GH Cloud Work Stream](https://ga4gh.cloud)