systemPipeR

systemPipeR: A Multipurpose Workflow Management System for Reproducible Data Analysis

Bioconductor version: 3.24 · Package version: 2.19.0

systemPipeR is a workflow management environment for reproducible data analysis that integrates R with command-line software. It enables researchers to design, execute, and report complex workflows on local machines and HPC systems. The framework combines R-based analysis with external tools through a Common Workflow Language (CWL) interface, manages workflow dependencies and restart capabilities, and automatically generates reproducible scientific analysis reports. The companion package systemPipeRdata provides ready-to-use workflow templates that simplify workflow setup and customization. Alternatively, workflow templates can be loaded from dedicated GitHub repositories.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("systemPipeR")