This short manual introduces an R package, scFlow, and its accompanying workflow pipeline nf-core/scflow. The goal of scFlow is to provide a toolkit for analysing single-cell/nuclei RNA sequencing data with high levels of abstraction. It is written in R and runs on top of state-of-art analysis packages including Seurat and Monocle. The nf-core-scflow pipeline streamlines and fully automates end-to-end analyses with scFlow reproducibly and at scale in the cloud or HPC.