Cell Systems
Volume 9, Issue 5, 27 November 2019, Pages 508-514.e3
Journal home page for Cell Systems

Brief Report
Building Containerized Workflows Using the BioDepot-Workflow-Builder

https://doi.org/10.1016/j.cels.2019.08.007Get rights and content
Under a Creative Commons license
open access

Highlights

  • An open-source graphical tool for constructing and executing bioinformatics workflows

  • Uses Docker containers to ensure reproducibility and facilitate workflow installation

  • Interactive graphical modules such as Jupyter and Cytoscape are supported

  • Workflows can be saved in Bwb’s native format or exported as portable shell scripts

Summary

We present the BioDepot-workflow-builder (Bwb), a software tool that allows users to create and execute reproducible bioinformatics workflows using a drag-and-drop interface. Graphical widgets represent Docker containers executing a modular task. Widgets are linked graphically to build bioinformatics workflows that can be reproducibly deployed across different local and cloud platforms. Each widget contains a form-based user interface to facilitate parameter entry and a console to display intermediate results. Bwb provides tools for rapid customization of widgets, containers, and workflows. Saved workflows can be shared using Bwb’s native format or exported as shell scripts.

Keywords

reproducibility of research
bioinformatics workflows
software development
RNA sequencing
Docker

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