Package: systemPipeR
Type: Package
Title: systemPipeR: A Multipurpose Workflow Management System for
        Reproducible Data Analysis
Version: 2.19.8
Date: 2026-10-17
Authors@R: c(
    person("Thomas", "Girke", email = "thomas.girke@ucr.edu",
           role = c("aut", "cre")),
    person("Le", "Zhang", role = "aut"),
    person("Daniela", "Cassol", role = "aut"),
    person("Brendan", "Gongol", role = "aut"),
    person(c("Tyler", "W.", "H."), "Backman", role = "aut"))
biocViews: Genetics, Infrastructure, DataImport, Sequencing, RNASeq,
        RiboSeq, ChIPSeq, MethylSeq, SNP, GeneExpression, Coverage,
        GeneSetEnrichment, Alignment, QualityControl, ImmunoOncology,
        ReportWriting, WorkflowStep, WorkflowManagement
Description: 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.
Depends: R (>= 4.5.0), Rsamtools (>= 1.31.2), Biostrings, ShortRead (>=
        1.37.1), methods
Imports: GenomicRanges, SummarizedExperiment, ggplot2, yaml, stringr,
        magrittr, S4Vectors, crayon, BiocGenerics, htmlwidgets
Suggests: BiocStyle, knitr, rmarkdown, systemPipeRdata,
        GenomicAlignments, grid, dplyr, testthat, rjson, annotate,
        AnnotationDbi, kableExtra, GO.db, GenomeInfoDb, DT,
        rtracklayer, limma, edgeR, DESeq2, IRanges, batchtools,
        GenomicFeatures, txdbmaker, GenomeInfoDbData, VariantAnnotation
        (>= 1.25.11)
VignetteBuilder: knitr
SystemRequirements: systemPipeR can be used to run external
        command-line software (e.g. short read aligners), but the
        corresponding tool needs to be installed on a system.
License: Artistic-2.0
URL: https://github.com/tgirke/systemPipeR
BugReports: https://github.com/tgirke/systemPipeR/issues
Config/pak/sysreqs: cmake make libbz2-dev libicu-dev libjpeg-dev
        liblzma-dev libpng-dev libuv1-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-10-18 19:04:55 UTC
RemoteUrl: https://github.com/bioc/systemPipeR
RemoteRef: HEAD
RemoteSha: 4fff49838496a9ed3dccef87ff3ded6e78323de2
NeedsCompilation: no
Packaged: 2026-11-01 13:14:17 UTC; root
Author: Thomas Girke [aut, cre],
  Le Zhang [aut],
  Daniela Cassol [aut],
  Brendan Gongol [aut],
  Tyler W. H. Backman [aut]
Maintainer: Thomas Girke <thomas.girke@ucr.edu>