Workflow Locking for Clinical Genomics and Trials

Aleksandra Zalcman

Locked-Down WorkflowsWhen working in a clinical environment, DNAnexus users need the ability to restrict how workflows on the platform can be run so that stricter guarantees can be placed on how analyses are performed and reproduced in this setting. As we continue to improve workflow management on DNAnexus, we are excited to introduce a new feature called ‘workflow locking’.

When a user attempts to run a typical DNAnexus workflow, our platform allows the user to set and override parameters to any stage within the workflow.  However, in clinical settings, this flexibility may not be desired and the developer needs to restrict the user from making certain changes that could conflict with organizational policies. For example, the developer may want to enforce that the user supplies only certain inputs while others are unchangeable or ‘locked’.

To address this need, the DNAnexus platform now supports the ability to add explicit workflow input and output specifications to the workflow configuration.   This enables the developer to package and share workflows so that specific inputs to stages within the workflow cannot be modified by the user at run-time.

For example, the developer can now set specific fixed parameters for an alignment stage of a workflow, or the developer can enforce that the reference genome is fixed to a specific file on the DNAnexus platform. Since the workflow itself has an explicit input and output specification, this feature also will enable the developer to refer to a workflow as a stage of another workflow much like they would refer to a DNAnexus application within a workflow.  The ability to embed workflows within other workflows promotes reusability since developers can directly use components of more complex pipelines without having to duplicate code or workflow definitions. Finally, these features make execution of CWL or WDL workflows on our platform more seamless since they too explicitly specify inputs and outputs to workflows.

Workflow locking was built by the Developer Experience team at DNAnexus. Thanks to Geet Duggal and Nihar Sheth for contributions to the design and review of this feature. Please see our documentation for more information on how to build and use locked-down workflows and contact if you have any feedback or questions.