Long workshop: systemPipe: Workflow and Visualization Toolkit

systemPipe: Workflow and Visualization Toolkit

Daniela Cassol,Le Zhang,Thomas Girke Institute for Integrative Genome Biology, University of California, Riverside, California, USA.


This workshop introduces systemPipe (SP), a generic toolkit for designing and running reproducible data analysis workflows. The environment consists of three major modules implemented as R/Bioconductor packages. systemPipeR (SPR) provides core functionalities for defining workflows, interacting with command-line software, and executing both R and/or command-line software, as well as generating publication-quality analysis reports. systemPipeShiny (SPS) integrates a graphical user interface for managing workflows and visualizing results interactively. systemPipeWorkflow (SPW) offers a collection of pre-configured workflow templates. This hand-on event will include the following topics: (1) brief overview of the design principles and functionalities of the SP toolkit; (2) design and usage of SPR’s command-line interface based on an object-oriented R implementation of CWL; (3) configuration and execution of workflows; (4) construction of custom workflows; (5) configuration and execution of a pre-configured workflow example from start to finish, e.g. smallRNA-Seq template; (6) parallel execution of workflows on HPC and cloud systems with and without schedulers; (7) generation of technical and scientific analysis reports including visualization; and (8) demonstration of SPS’ core functionalities, the project’s Shiny App.

Keywords: workflow environment,automation,interactive visualization,reporting infrastructure