Common Workflow Language integration with Arvados » History » Version 3

Version 2 (Peter Amstutz, 08/08/2016 02:23 PM) → Version 3/7 (Peter Amstutz, 08/08/2016 02:35 PM)

h1. Common Workflow Language integration with Arvados

The main integration is @arvados-cwl-runner@. This tool is can be used both to either run the workflow directly (@arvados-cwl-runner --local@) or as a client to submit which submits a job to run the workflow (@arvados-cwl-runner --submit@) and for running the workflow directly (@arvados-cwl-runner --local@). --submit@). When the user starts a CWL workflow from workbench, it functions similar to @--submit@ mode.

Because submit mode works by creating a "runner" job whose purpose is to manage execution of the workflow, it requires an @arvados/jobs@ Docker image with an up-to-date @arvados-cwl-runner@.

When running a workflow, the workflow runner:
# creates a job for each workflow steps
# submits it
# waits for it to complete
# gets the output collection for the job
# computes the CWL output object for the workflow step.

!cwl-arvados-flow-local.png!

!cwl-arvados-flow-submit.png!