demux_doublet_sim

Repository for Nextflow pipeline used in demuxSNP demultipelxing paper

Overall workflow

1. Simulate doublets

2. Benchmark methods

• Experiments 1: Vary doublet rate
• Experiment 2: Vary SNP subsetting

Inputs

Most inputs are specified in nextflow.config: container__souporcell: path to souporcell apptainer image, ideally at top level of project.
bam_path: Path to demultiplexed bam files.
barcodes_path: Path to demultiplexed barcodes.
tenx: Path to barcodes.tsv, features.tsv and matrix.mtx files from multiplexed 10X output.
common_variants: common variants e.g. from 1K genome project.
ref: path to reference genome, ideally in data/input directory.

Doublet simulation parameters are specified in params_ccrcc.csv The workflow caters for subsampling (also specified in params_ccrcc.csv) although this was not explored in the paper.

Outputs

Folder for each simulated scenario (e.g. seed, % doublets, number of genes used to subset) SingleCellExperiment object in each demuxSNP folder.

Known issues

Input files used by souporcell/apptainer need to be stored below the image. Apptainer must be bound to the project directory (variable in nextflow.config).