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Simplifying the development of portable, scalable, and reproducible workflows

View ORCID ProfileStephen R. Piccolo, Zachary E. Ence, Elizabeth C. Anderson, Jeffrey T. Chang, Andrea H. Bild
doi: https://doi.org/10.1101/2021.04.30.442204
Stephen R. Piccolo
1Department of Biology, Brigham Young University, Provo, UT, 84602, USA
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  • For correspondence: stephen_piccolo@byu.edu
Zachary E. Ence
1Department of Biology, Brigham Young University, Provo, UT, 84602, USA
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Elizabeth C. Anderson
1Department of Biology, Brigham Young University, Provo, UT, 84602, USA
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Jeffrey T. Chang
2Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
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Andrea H. Bild
3Department of Medical Oncology and Therapeutics, City of Hope Comprehensive Cancer Institute, Monrovia, CA, 91016, USA
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Abstract

Command-line software plays a critical role in biology research. However, processes for installing and executing software differ widely. The Common Workflow Language (CWL) is a community standard that addresses this problem. Using CWL, tool developers can formally describe a tool’s inputs, outputs, and other execution details in a manner that fosters use of shared computational methods and reproducibility of complex analyses. CWL documents can include instructions for executing tools inside software containers—isolated, operating-system environments. Accordingly, CWL tools are portable—they can be executed on diverse computers—including personal workstations, high-performance clusters, or the cloud. This portability enables easier adoption of bioinformatics pipelines. CWL supports workflows, which describe dependencies among tools and using outputs from one tool as inputs to others. To date, CWL has been used primarily for batch processing of large datasets, especially in genomics. But it can also be used for analytical steps of a study. This article explains key concepts about CWL and software containers and provides examples for using CWL in biology research. CWL documents are text-based, so they can be created manually, without computer programming. However, ensuring that these documents confirm to the CWL specification may prevent some users from adopting it. To address this gap, we created ToolJig, a Web application that enables researchers to create CWL documents interactively. ToolJig validates information provided by the user to ensure it is complete and valid. After creating a CWL tool or workflow, the user can create “input-object” files, which store values for a particular invocation of a tool or workflow. In addition, ToolJig provides examples of how to execute the tool or workflow via a workflow engine.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/srp33/ToolJig

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted May 01, 2021.
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Simplifying the development of portable, scalable, and reproducible workflows
Stephen R. Piccolo, Zachary E. Ence, Elizabeth C. Anderson, Jeffrey T. Chang, Andrea H. Bild
bioRxiv 2021.04.30.442204; doi: https://doi.org/10.1101/2021.04.30.442204
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Simplifying the development of portable, scalable, and reproducible workflows
Stephen R. Piccolo, Zachary E. Ence, Elizabeth C. Anderson, Jeffrey T. Chang, Andrea H. Bild
bioRxiv 2021.04.30.442204; doi: https://doi.org/10.1101/2021.04.30.442204

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