Workflows
What is a Workflow?Filters
Portable genotype-free demultiplexing benchmarkign pipeline.
A portable pipeline for benchmarking genotype-free single-cell demultiplexing methods on simulated data.
The pipeline is designed to be generelisable to different datasets with arbitrary numbers of simulated mulitplexed samples. All software as part of pipeline is run through Apptainer containers to ensure reproducibility and ease of use. The pipeline default configuration is to be run on a cluster with a SLURM scheduler, but can be ...
Type: Nextflow
Creators: Michael P Lynch, Leverages scripts developed by Weber et al (2021) DOI: https://doi.org/10.1093/gigascience/giab062
Submitter: Michael Lynch
demux_doublet_sim
Repository for Nextflow pipeline used in demuxSNP demultipelxing paper
Overall workflow
- Simulate doublets
- Add per-sample suffix to barcodes in BAM
- Merge per-sample BAMs
- Generate lookup of barcodes to rename to reach a set % doublets
- Rename barcodes in BAM as per lookup
- 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 ...
Type: Nextflow
Creators: Michael Lynch, Leverages scripts developed by Weber et al (2021) DOI: https://doi.org/10.1093/gigascience/giab062
Submitter: Michael Lynch
