Keywords
Common Workflow Language, CWL, Command Line Software, ToolJig
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. CWL documents can include instructions for executing tools inside software containers. Accordingly, CWL tools are portable—they can be executed on diverse computers—including personal workstations, high-performance clusters, or the cloud. CWL also 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 conform 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. ToolJig and our examples are available at https://github.com/srp33/ToolJi
Original Publication Citation
Miller DB, Robison, R and Piccolo SR. Toward a methodology for evaluating DNA. Variants in nuclear families. PLoS One, 2021, 16(10): e0258375
BYU ScholarsArchive Citation
Piccolo, Stephen; Ence, Zachary E.; Anderson, Elizabeth C.; Chang, Jeffrey T.; and Bild, Andrea H., "Simplifying the Development of Portable, Scalable, and Reproducible Workflows" (2021). Faculty Publications. 7348.
https://scholarsarchive.byu.edu/facpub/7348
Document Type
Peer-Reviewed Article
Publication Date
2021-10-13
Publisher
PLoS One
Language
English
College
Life Sciences
Department
Biology
Copyright Use Information
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