Common Workflow Language integration with Arvados » History » Version 3

Peter Amstutz, 08/08/2016 02:35 PM

Common Workflow Language integration with Arvados

The main integration is arvados-cwl-runner. This tool is used both as a client to submit a job to run the workflow (arvados-cwl-runner --submit) and for running the workflow directly (arvados-cwl-runner --local). 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:
  1. creates a job for each workflow steps
  2. submits it
  3. waits for it to complete
  4. gets the output collection for the job
  5. computes the CWL output object for the workflow step.