Open AccessBioconductor toolchain for reproducible bioinformatics pipelines using Rcwl and RcwlPipelines
Author(s) -
Qiang Hu,
Alan D. Hutson,
Song Liu,
Martin Morgan,
Qian Liu
Publication year - 2021
Publication title -
bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.599
H-Index - 390
eISSN - 1367-4811
pISSN - 1367-4803
DOI - 10.1093/bioinformatics/btab208
Subject(s) - bioconductor , toolchain , workflow , computer science , pipeline (software) , preprocessor , software , software engineering , workbench , pipeline transport , interface (matter) , programming language , data mining , database , operating system , visualization , engineering , biology , biochemistry , bubble , maximum bubble pressure method , environmental engineering , gene
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 more than 100 pre-built tools and pipelines in RcwlPipelines, ready to be queried and used by researchers in their own analysis. A single-cell RNA sequencing preprocessing pipeline demonstrates use of the software.