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Enabling Biomedical Science with Common Workflow Language

Authors: Zaranek, Sarah Wait;

Enabling Biomedical Science with Common Workflow Language

Abstract

Common Workflow Language (CWL) is an essential technology for describing biomedical analysis workflows used by many organizations. Embracing CWL as a workflow standard enables reproducible research. This ensures that scientific work can be understood, independently verified, and built upon in future work. Improvements to CWL benefit multiple organizations and workflow systems that use the CWL standard. For these organizations, there is an ongoing need to train new users and develop new workflows with CWL. CWL faces barriers to wider use and adoption due to a perceived learning curve and usability challenges. Our proposal outlines a plan to help reduce those barriers through community engagement and improved usability. It covers documentation updates, community feedback aggregation and response, specification development, and tool creation. We propose funding Peter Amstutz to lead this effort alongside the PI Sarah Zaranek and a "community engineer." Peter is a leader in the development of CWL, "cwltool", "cwl-ex" and Arvados. He has demonstrated the ability to serve the needs of the community at large. He is familiar with "wearing many hats", including developer, technical writer, community relations, and project evangelist. Our overarching goals is to make it easier for users to create CWL workflows and run them at scale using any conformant CWL platform (drawing heavily on examples from the open-source Arvados platform developed by Curii.) Throughout the effort we we will use real world public domain (CC0) data and workflows from the global Personal Genome Projects where we have contributed since 2005.

Keywords

EOSS, Reproducible, CWL, CZI, Arvados, Workflow

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selected citations
These citations are derived from selected sources.
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).
BIP!Citations provided by BIP!
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.
BIP!Popularity provided by BIP!
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.
BIP!Impulse provided by BIP!
views
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