Bioconductor toolchain for reproducible bioinformatics pipelines using Rcwl and RcwlPipelines

Qiang Hu; Alan Hutson; Song Liu; Martin Morgan; Qian Liu

doi:10.1093/bioinformatics/btab208

Bioconductor toolchain for reproducible bioinformatics pipelines using Rcwl and RcwlPipelines

Qiang Hu
, Alan Hutson
, Song Liu
, Martin Morgan
, Qian Liu

Department of Biostatistics

University at Buffalo

Roswell Park Cancer Institute

Research output: Contribution to journal › Article › peer-review

6 Scopus citations

Abstract

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.

Original language	English
Pages (from-to)	3351-3352
Number of pages	2
Journal	Bioinformatics
Volume	37
Issue number	19
DOIs	https://doi.org/10.1093/bioinformatics/btab208
State	Published - Oct 1 2021

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10.1093/bioinformatics/btab208

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abstract = "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.",

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AU - Morgan, Martin

AU - Liu, Qian

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AB - 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.

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Bioconductor toolchain for reproducible bioinformatics pipelines using Rcwl and RcwlPipelines

Abstract

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