Building containerized workflows using the BioDepot-workflow-builder (Bwb)

Ling-Hong Hung; Jiaming Hu; Trevor Meiss; Alyssa Ingersoll; Wes Lloyd; Daniel Kristiyanto; Yuguang Xiong; Eric Sobie; Ka Yee Yeung

doi:10.1101/099010

Abstract

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 then graphically linked 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.

List of abbreviations

AWS: = Amazon Web Services
BWA: = Burroughs-Wheeler Aligner
Bwb: = BioDepot-workflow-Builder
DToxS: = Drug Toxicity Signature Generation Center
RNA-seq: = RNA sequencing
SOP: = standard operating procedure
VNC: = virtual network computing

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