This workshop introduces the Bioconductor toolchain for usage and development of reproducible bioinformatics pipelines using packages of Rcwl and RcwlPipelines. The Common Workflow Language (CWL) is an open standard for development of data analysis workflows that is portable and scalable across different tools and working environments. Rcwl provides a simple way to wrap command line tools and build CWL data analysis pipelines programmatically within R. It increases the ease of development, usage, and maintenance of CWL pipelines, and furthermore offers higher performance by intuitively supporting parallel work on high performance computing (HPC). hundreds of pre-built bioinformatics pipelines in CWL are included in RcwlPipelines. The tools and pipelines are highly modularized for easy customization of complex bioinformatics analysis. An scRNA-seq pipeline using STARsolo for alignment and quantification, DropletUtils for filtering raw gene-barcode matrix, fastqc and multiqc for reads quality control will demonstrate the typical use case of these two packages. More details for usage and examples are available on Rcwl website: https://hubentu.github.io/Rcwl/.