When running on premises, Workbench uses a combination of the Cromwell execution engine and the Cromwell Server and DNAstack's (https://github.com/DNAstack/cromwell-wes-service). This allows you to run workflows on your own infrastructure, whether it is on a local server or a cloud provider.

The WES service passes through all the parameters that are supported by Cromwell, and you can find the full list of Cromwell parameters in the Cromwell documentation. Additionally, the WES service has normalized the DELETE_INTERMEDIATE_OUTPUT_FILES parameter, allowing you to clean-up intermediate files on any supported infrastructure when running workflows through Workbench.

Available Parameters


Specifies whether to delete intermediate output files. Default is false. If set to true, any File variables referenced in task output sections that are not found in the workflow output section will be considered an intermediate File. Additionally, log files will not be deleted.

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