Building Containerized Workflows Using the BioDepot-Workflow-Builder

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

doi:10.1016/j.cels.2019.08.007

Ling-Hong Hung, Wes Lloyd + Show 7 more

Open Access

PDF Available

https://doi.org/10.1016/j.cels.2019.08.007

Copy DOI

Export

Save

Cite

Abstract
Highlights/Summary
Full-Text PDF
Similar Papers

Abstract

Listen

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.

Highlights

One of the key challenges for biomedical science is the rapidly increasing number and complexity of analytical methods
Reproducing the results of a bioinformatics workflow can be challenging given the number of components, each having its own set of parameters, dependencies, supporting files, and installation requirements
We present the BioDepot-workflow-builder (Bwb), a graphical utility that builds and executes workflows using reproducible Docker containers as modules

Summary

Introduction

One of the key challenges for biomedical science is the rapidly increasing number and complexity of analytical methods. Reproducing the results of a bioinformatics workflow can be challenging given the number of components, each having its own set of parameters, dependencies, supporting files, and installation requirements. We present the BioDepot-workflow-builder (Bwb), a graphical utility that builds and executes workflows using reproducible Docker containers as modules. Bwb draws workflows as graphical nodes (widgets) that represent executable modules. The nodes are connected by links to form a directed acyclic graph indicating the order of execution and flow of data. Users drag and drop widgets onto the screen and connect them to construct a workflow, which can be executed locally, saved, or exported as a shell script

Methods

Results

Conclusion