Presentation Open Access

Running workflows on the cloud with WDL and Cromwell

Geraldine A Van der Auwera

This slide-based presentation provides a brief introduction to the topic of bioinformatics workflows with a particular emphasis on execution in the cloud. It additionally introduces the Workflow Definition Language (WDL) and Cromwell execution engine, outlining the basic syntax and key features of this highly portable open-source workflow system, which can be deployed as a standalone or used as a service as part of the data sharing and analysis platform. Finally, the presentation references three published scientific use cases that exemplify how WDL, Cromwell and Terra can be used to power scalable and reproducible research in the biomedical community.

This presentation was put together for a webinar hosted by Bioinformática UFMG as part of a bioinformatics seminar series for Brazilian PhD programs. A recording of the webinar is available at

A correction was made to slide 15: Cromwell's call caching feature is not specific to its 'server' mode, though its use is most often associated with server mode.
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