Dockstore integrates with the DNAnexus platform, allowing you to launch WDL-based workflows from Dockstore in DNAnexus. Here is some information on what that looks like from a user point of view in a mini tutorial.

Exporting into DNAnexus

When browsing WDL workflows from within Dockstore, you will see a “Launch with DNAnexus” button on the right. The currently selected version of the workflow will be exported.

WDL workflow

WDL workflow

If not logged into DNAnexus, you will be prompted to login. Otherwise, or after login, you will be presented with the following screen.

WDL workflow import

WDL workflow import

You will need to pick a folder to export it into. You can either select a folder from an existing project, or you can create a new project.

Then hit the “Submit” button and continue from within the DNAnexus interface to configure and run your workflow.


  1. While we support launching of WDL workflows, tools as listed in Dockstore are currently not supported.

  2. Only the WDL language is supported.

See Also