Engines
Last updated
Was this helpful?
Last updated
Was this helpful?
An engine is an external service that executes WDL ( ) workflows in . These engines interpret your workflows, generate task definitions, and manage their execution in your chosen computing environment. You can running in your own environment to your Workbench account, which will then use that engine to submit and monitor workflow runs.
The engine is responsible for processing WDL, an open, community-driven workflow language stewarded by the . WDL is designed to be both easy to read and write, while scaling effectively from simple command-line tools to complex parallel workflows.
When you submit a workflow, your engine:
Interprets the WDL script
Generates individual task definitions
Manages task dependencies and scheduling
Dispatches tasks to execution services
Handles resource allocation and management
Workflow engines that support WDL, such as Cromwell and miniWDL, provide these capabilities while managing the resources required for workflow execution.
You can run Workbench engines in various environments:
Access your engines through either:
From the Settings page, use the search bar to find specific engines. Click any engine row to view detailed information about its state, configuration, and parameters.
The first engine you create in Workbench becomes your default engine. This default engine is pre-populated whenever you submit a workflow run, though you can change engines for specific runs. When submitting workflow runs from the CLI, the default engine is used if you omit the --engine flag.
To change your default engine:
Navigate to Settings
Hover over your chosen engine
Click the "Set as Default" star button
When viewing the engine list, hover over any row to access these actions:
Clicking on the Edit Engine pencil icon button will allow you to update the engine configuration, engine name, and engine parameters
Clicking on the Set as Default star icon button will set the engine as the default engine in Workbench
Clicking on the Copy Engine Id duplicate icon button will copy the engine ID to your clipboard. This is useful when you need to reference the engine ID in the CLI or API
Clicking on the Delete Engine trashcan icon will remove the engine from Workbench.
This action is irreversible.
You must set a new default before deleting a default engine
Currently running workflows will be marked as failed but continue running
The underlying infrastructure remains unaffected and must be deleted separately
Previous runs remain visible but you cannot submit new runs or view logs
Workbench continuously monitors connected engines to ensure availability. The system checks:
Connectivity to API endpoints
Credential authentication
Permission verification
Storage access
Log streaming capability
Each engine runs only the checks relevant to its type and configuration. Failed checks put the engine in ERROR state until resolved, while passing checks keep it ONLINE. You can view engine status in the UI - a green dot indicates ONLINE, while a red dot shows ERROR. For troubleshooting help, consult your engine's configuration guide.
The in the Workbench UI
The (CLI)