GA4GH Workflow Execution Service reference implementation
Project description
# Workflow as a Service
This provides client and server implementations of the [GA4GH Workflow Execution Service](https://github.com/ga4gh/workflow-execution-schemas) API for the Common Workflow Language.
It provides an (Arvados)[https://github.com/curoverse/arvados] backend. It also works with any cwl-runner that supports the CWL standard command line interface: http://www.commonwl.org/v1.0/CommandLineTool.html#Executing_CWL_documents_as_scripts
Installation:
` pip install wes-service `
Run a standalone server with default cwl-runner backend:
` $ wes-server `
Submit a workflow to run:
` $ wes-client --host=localhost:8080 myworkflow.cwl myjob.json `
List workflows:
` $ wes-client --list `
Get workflow status:
` $ wes-client --get <workflow-id> `
Get stderr log from workflow:
` $ wes-client --log <workflow-id> `
# Server Options
## Run a standalone server with Arvados backend:
` $ wes-server --backend=wes_service.arvados_wes `
## Use a different executable with cwl_runner backend
` $ wes-server --backend=wes_service.cwl_runner --opt runner=cwltoil `
## Pass parameters to cwl-runner
` $ wes-server --backend=wes_service.cwl_runner --opt extra=--workDir=/ `
# Client environment options
Set service endpoint:
` $ export WES_API_HOST=localhost:8080 `
Set the value to pass in the Authorization header:
` $ export WES_API_AUTH=my_api_token `
Set the protocol (one of http, https)
` $ export WES_API_PROTO=http `
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