# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "systemPipeR" in publications use:'
type: software
license: Artistic-2.0
title: 'systemPipeR: systemPipeR: A Multipurpose Workflow Management System for Reproducible
  Data Analysis'
version: 2.18.0
doi: 10.1186/s12859-016-1241-0
identifiers:
- type: doi
  value: 10.32614/CRAN.package.systemPipeR
abstract: 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.
authors:
- family-names: Girke
  given-names: Thomas
  email: thomas.girke@ucr.edu
preferred-citation:
  type: article
  title: 'systemPipeR: NGS workflow and report generation environment'
  authors:
  - family-names: Backman
    given-names: Tyler W. H.
  - family-names: Girke
    given-names: Thomas
    email: thomas.girke@ucr.edu
  year: '2016'
  month: '9'
  publisher:
    name: Springer Science and Business Media LLC
  journal: BMC Bioinformatics
  doi: 10.1186/s12859-016-1241-0
  url: https://doi.org/10.1186/s12859-016-1241-0
  volume: '17'
  issue: '1'
repository: https://bioc-release.r-universe.dev
repository-code: https://github.com/tgirke/systemPipeR
commit: be8e3e0951e7ddff3796c38443d670ae1afe11fe
url: https://github.com/tgirke/systemPipeR
date-released: '2026-03-05'
contact:
- family-names: Girke
  given-names: Thomas
  email: thomas.girke@ucr.edu