Rcwl/RcwlPipelines: Use R To Build, Read, Write, And execute CWL Workflows***

Rcwl/RcwlPipelines: Use R To Build, Read, Write, And execute CWL Workflows***


Author(s): Qian Liu, Qiang Hu

Affiliation(s): Roswell Park Comprehensive Cancer Center



The Common Workflow Language (CWL) is used to provide portable and reproducible data analysis workflows across different tools and computing environments. We have developed Rcwl, an R interface to CWL, to provide easier development, use and maintenance of CWL pipelines from within R. We have also collected nearly 200 pre-built tools and pipelines in RcwlPipelines, ready to be queried and used by researchers in their own analysis. A single-cell RNA-seq pre-processing pipeline demonstrates use of the software.