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The Rcwl package can be a simple and user-friendly way to manage command line tools and build data analysis pipelines in R using Common Workflow Language (CWL).
The package can be installed from Bioconductor (>= 3.9):
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Rcwl")
# Or from github
BiocManager::install("hubentu/Rcwl")
vignette(package = "Rcwl")
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