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This repository contains R scripts, CWL tools and examples of CWL workflows for single-cell RNA-Seq and Multiome data analyses.

Each R script can be run directly from the command line following the --help message instructions. However, to guarantee results reproducibility we containerized them and wrapped in CWL format.

CWL tools can be combined into the workflows depending on the type of input datasets and required complexity of the analysis. For example, for single-cell RNA-Seq use 1(a) – 2(a) – 3(a) and optionally 4(a) – 5(a,b); for Multiome ATAC-Seq and RNA-Seq use 1(b) – 2(b) – 2(a) – 3(a) - 3(b) - 3(c) and optionally 4(a) – 5(a,b).