Bioconductor toolchain for reproducible bioinformatics pipelines using Rcwl and RcwlPipelines

SUMMARY: 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 hav...

Descripción completa

Detalles Bibliográficos
Autores principales: Hu, Qiang, Hutson, Alan, Liu, Song, Morgan, Martin, Liu, Qian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8504628/
https://www.ncbi.nlm.nih.gov/pubmed/33772584
http://dx.doi.org/10.1093/bioinformatics/btab208
Descripción
Sumario:SUMMARY: 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. AVAILABILITY AND IMPLEMENTATION: Project website: https://rcwl.org (Rcwl: https://bioconductor.org/packages/Rcwl; RcwlPipelines: https://bioconductor.org/packages/RcwlPipelines). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Ejemplares similares