RcwlPipelines and Rcwl

Rcwl and RcwlPipelines: R Interface for Common Workflow Language (CWL) Bioinformatics Pipelines

Rcwl provides an R interface to Common Workflow Language (CWL) for developing, executing, and managing CWL-based pipelines, while RcwlPipelines supplies a collection of pre-configured bioinformatics tools and workflows for standardized data analysis.

Key Features:

• R Interface to CWL: Enables programmatic creation, execution, and management of CWL workflows directly within the R environment.
• Programmatic Workflow Construction: Wraps command-line bioinformatics tools into CWL pipelines using R functions.
• Pre-built Tools and Pipelines: Provides over 100 pre-configured tools and workflows, including pipelines for single-cell RNA sequencing (scRNA-seq) preprocessing.
• Portability and Reproducibility: Implements CWL standards to ensure consistent execution across computational environments.

Scientific Applications:

• Genomic and Transcriptomic Analysis: Supports genomic data analysis, transcriptomics, and single-cell sequencing studies, including scRNA-seq preprocessing workflows.

Methodology:

Encapsulates command-line bioinformatics tools within CWL workflow specifications and manipulates them programmatically through R, enabling standardized, portable, and reproducible execution across heterogeneous computing environments.