Common Workflow Language integration with Arvados » History » Version 5
Peter Amstutz, 08/08/2016 02:59 PM
1 | 1 | Peter Amstutz | h1. Common Workflow Language integration with Arvados |
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3 | 3 | Peter Amstutz | 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. |
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5 | 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@. |
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7 | 5 | Peter Amstutz | When running a workflow: |
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9 | # The user submits a workflow by running @arvados-cwl-runner@ or through workbench |
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10 | # 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 |
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11 | # The runner job is responsible for actually executing the workflow: |
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12 | ## Create a job for each workflow step (Job A) |
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13 | ## Submit the job to API server |
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14 | ## Wait for the job to complete |
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15 | ## Get the output collection for the job |
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16 | ## Compute the resulting CWL output object for the workflow step. |
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17 | ## Iterate over the workflow until all steps have been executed and final workflow output is available |
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18 | # Return the final result of the workflow |
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20 | 1 | Peter Amstutz | !cwl-arvados-flow-submit.png! |