# 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).