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Running workflows on the cloud with WDL and Cromwell

Authors: Van Der Auwera, Geraldine A;

Running workflows on the cloud with WDL and Cromwell

Abstract

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 Terra.bio 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 https://www.youtube.com/watch?v=3AMJ-LlWRtE&t=774s

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.

Keywords

computational biology, reproducible, portable, genomics, scalable, workflows, bioinformatics

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This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
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popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
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influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
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