Starting HealthOmics Ready2Run workflows using the API

Most of the API operations behave in a similar fashion for Ready2Run workflows and private workflows.

To return a list of available Ready2Run workflows, use list-workflows with the type parameter set to READY2RUN.

aws omics list-workflows --type READY2RUN                            

After you identify the workflow to run from the list-workflows response, you can use get-workflow with the --id parameter to get more details.

aws omics get-workflow --type READY2RUN --id workflow id    

To run a Ready2Run workflow, you can use start-run API operation with the workflow-type parameter set to READY2RUN, as shown in the following example

aws-omics start-run \
  --workflow-type READY2RUN \
  --workflow-id workflow id \
  --output-uri &example-s3-bucket; \
  --role-arn arn:aws:iam::1234567892012:role/service-role/OmicsWorkflow-20221004T164236 \
  --parameters file:///path/to/parameters.json

To specify a workflow version, use the workflow-version parameter, as shown in this example.

aws-omics start-run \
  --workflow-type READY2RUN \ 
  ...
  --version-name '3.0.0'

To monitor your run, you can use the get-run API operation, as shown.

aws-omics get-run \
  --id run id