scAN10: A reproducible and standardized pipeline for processing 10X single cell RNAseq data

The recent explosion of single cell transcriptomics has led to the challenge of developing data analysis pipelines that are both fully reproducible and modular while allowing interoperability across multiple systems and institutions. We present scAN10, a processing pipeline of 10X single cell RNAseq data, that inherits the ability to be executed on most computational infrastructures, thanks to Nextflow DSL2. The modular nature of Nextflow pipelines allows to easily integrate and assess different blocks for a given analysis step.We illustrate the benefit of using scAN10 by showing its ability to assess the impact of the mapping step on the resulting output using a clinical 10X scRNAseq analysis of a human pituitary gonadotroph tumour.