FYI @junyk I believe this is because a `SystemExit` error is raised (by calling `sys.exit`) if the workflow / tool fails to run: https://github.com/PMCC-BioinformaticsCore/janis-assistant/blob/fbcefc665a9a23073830acb8f87cc41ea58bcf8f/janis_assistant/management/workflowmanager.py#L595-L598. These need to [be caught separately](https://www.tutorialspoint.com/How-to-catch-SystemExit-Exception-in-Python).