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.