Common Workflow Language integration with Arvados » History » Revision 6
Revision 5 (Peter Amstutz, 08/08/2016 02:59 PM) → Revision 6/7 (Peter Amstutz, 08/08/2016 03:58 PM)
h1. 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 user submits a workflow by running @arvados-cwl-runner@ or through workbench, this workbench # This creates an "workflow job" # The workflow job is dispatched to a compute node (Compute1) # The workflow job runs run @arvados-cwl-runner@ in a the @arvados/jobs@ Docker container image with the associated CWL workflow and workflow inputs as job inputs # The runner job is responsible for actually executing the workflow: ## Create a job for each workflow step (Job A) ## Submit the job to API server (Job A) ## Wait for the job to complete ## Get the output collection for the job (Output A) ## Compute the resulting CWL output object for the workflow step (Result A) step. ## Iterate over the workflow until all steps have been executed and final workflow output is available # Return the final result of the workflow result !cwl-arvados-flow-submit.png!