Bioconductor toolchain for reproducible bioinformatics pipelines using Rcwl and RcwlPipelines

Area of Science:

• Bioinformatics
• Computational Biology
• Genomics

Background:

• The Common Workflow Language (CWL) facilitates portable and reproducible data analysis across diverse computational environments.
• Developing and managing CWL pipelines can be complex for researchers without specialized programming expertise.

Purpose of the Study:

• To introduce Rcwl, an R interface designed to simplify the development, utilization, and maintenance of CWL pipelines within the R environment.
• To provide a readily accessible collection of pre-built bioinformatics tools and pipelines for researchers.

Main Methods:

• Development of Rcwl as an R package interfacing with CWL.
• Curating and organizing over 100 pre-built CWL tools and pipelines into the RcwlPipelines R package.
• Demonstration of Rcwl and RcwlPipelines using a single-cell RNA sequencing preprocessing pipeline.

Main Results:

• Rcwl enables seamless integration of CWL workflows into R-based analyses.
• RcwlPipelines offers a substantial library of reusable bioinformatics workflows.
• The single-cell RNA sequencing pipeline showcases the practical application and ease of use of the developed software.

Conclusions:

• Rcwl simplifies CWL pipeline management and execution for R users.
• The availability of Rcwl and RcwlPipelines enhances reproducibility and efficiency in biological data analysis.
• This software empowers researchers to leverage complex computational workflows with greater ease.