AWS HealthOmics variant stores and annotation stores will no longer be open to new customers starting November 7th, 2025. If you would like to use variant stores or annotation stores, sign up prior to that date. Existing customers can continue to use the service as normal. For more information, see AWS HealthOmics variant store and annotation store availability change.
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 --idworkflow 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-idworkflow 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 \ --idrun id
