Common Workflow Language integration with Arvados » History » Revision 5

Revision 4 (Peter Amstutz, 08/08/2016 02:35 PM) → Revision 5/7 (Peter Amstutz, 08/08/2016 02:59 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, the workflow by running @arvados-cwl-runner@ or through workbench runner: 
 # This creates an "workflow job" to run @arvados-cwl-runner@ in the @arvados/jobs@ 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) steps 
 ## Submit the job to API server # submits it 
 ## Wait # waits for the job it to complete 
 ## Get # gets the output collection for the job  
 ## Compute # computes the resulting CWL output object for the workflow step. 
 ## Iterate over the workflow until all steps have been executed and final workflow output is available 
 # Return the final result of the workflow