DESCRIPTION

Package: Bioc2020RCWL
Type: Package
Title: Bioconductor toolchain for usage and development of reproducible bioinformatics pipelines in CWL
Version: 0.1.5
Authors@R: c(person("Qian", "Liu", role = c("aut", "cre"), email =
   "qian.liu@roswellpark.org", comment = c(ORCID = "0000-0003-1456-5099")),
   person("Qiang", "Hu", role = c("aut"), email = "qiang.hu@roswellpark.org"))
Maintainer: Qian Liu <qian.liu@roswellpark.org>
Description: This workshop introduces the Bioconductor toolchain for
    usage and development of reproducible bioinformatics pipelines
    using packages of Rcwl and RcwlPipelines. The Common Workflow
    Language (CWL) is an open standard for development of data
    analysis workflows that is portable and scalable across different
    tools and working environments. Rcwl provides a simple way to wrap
    command line tools and build CWL data analysis pipelines
    programmatically within R. It increases the ease of development,
    usage, and maintenance of CWL pipelines, and furthermore offers
    higher performance by intuitively supporting parallel work on high
    performance computing (HPC). hundreds of pre-built bioinformatics
    pipelines in CWL are included in RcwlPipelines. The tools and
    pipelines are highly modularized for easy customization of complex
    bioinformatics analysis. An scRNA-seq pipeline using STARsolo for
    alignment and quantification, DropletUtils for filtering raw
    gene-barcode matrix will demonstrate the typical use case of these
    two packages. More details for usage and examples are available on
    Rcwl website(https://hubentu.github.io/Rcwl/). 
Depends: R (>= 4.0.0), Rcwl, RcwlPipelines
Imports: BiocParallel, shiny, DropletUtils
Encoding: UTF-8
LazyData: true
License: CC BY 4.0  + file LICENSE
RoxygenNote: 7.1.1
VignetteBuilder:
    knitr,
    rmarkdown
SystemRequirements: python (>= 3.6), cwltool (>= 1.0.2018)
Suggests: knitr, rmarkdown, pkgdown, SingleCellExperiment
URL: https://Liubuntu.github.io/Bioc2020RCWL
DockerImage: liubuntu/bioc2020rcwl:latest