Meiss, T. | Search bioRxiv

bioRxiv2017

Building containerized workflows for RNA-seq data using the BioDepot-workflow-Builder (BwB)

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 Bwbs native format or exported as shell scripts.

bioinformatics↗

bioRxiv2017

Software solutions for reproducible RNA-seq workflows

Computational workflows typically consist of many tools that are usually distributed as compiled binaries or source code. Each of these software tools typically depends on other installed software, and performance could potentially vary due to versions, updates, and operating systems. We show here that the analysis of mRNA-seq data can depend on the computing environment, and we demonstrate that software containers represent practical solutions that ensure the reproducibility of RNAseq data analyses.

bioinformatics↗