Introduction

nf-core/scdownstream is a bioinformatics pipeline that can be used to process already quantified single-cell RNA-seq data. It takes a samplesheet and H5AD-, SingleCellExperiment/Seurat- or CSV files as input and performs quality control, integration, dimensionality reduction and clustering. The pipeline produces an integrated H5AD file and an extensive QC report. With --tords, it also converts the final H5AD file to a SingleCellExperiment RDS file.

The pipeline is based on the learnings and implementations from the following pipelines (alphabetical):

• panpipes
• scFlow
• scRAFIKI
• YASCP

The pipeline uses the following tools:

1. Per-sample preprocessing
   1. Convert all RDS files to H5AD format
   2. Create filtered matrix (if not provided)
      • CellBender
      • EmptyDrops
   3. Present QC for raw counts (MultiQC)
   4. Remove ambient RNA…