kane9530 / nextflow-cellrangeratac-scatacseq

Description

A Nextflow DSL-2 implementation of the cellranger-atac (v2.1.0) pipeline for single-cell ATAC-seq analysis. This is a prototype that will be deployed on AWS via the Amazon Genomics CLI (AGC), as part of the suite of scalable omics analysis pipelines offered by the Genomics and Data Analytics Core (GeDaC) core facility in the Singapore Cancer Science Institute (CSI).

The simple pipeline first runs fastp on all the R1 and R3 fastq reads as quality control, and then collates all the *fastp.json files into a single report with multiQC. This is followed by an implementation of the cellranger-atac count step to identify the ATAC peaks.