Arvados

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 creates an "workflow orchestrator"

# The workflow orchestrator is dispatched to a compute node (Compute1)

# The workflow orchestrator runs @arvados-cwl-runner@ in a @arvados/jobs@ Docker container with the associated CWL workflow and workflow inputs as job inputs

# The orchestrator job is responsible for actually executing the workflow:

## Create a container request (job) for each workflow step 

## Submit the job to API server (Container 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)

## Iterate over the workflow until all steps have been executed and final workflow output is available

# Return the final workflow result

!cwl-arvados-flow-submit.png!