Souporcell

souporcell is a method for clustering mixed-genotype scRNAseq experiments by individual.

Info

ID: souporcell
Namespace: genetic_demux

Links

Source

Example commands

You can run the pipeline using nextflow run.

View help

You can use --help as a parameter to get an overview of the possible parameters.

nextflow run openpipelines-bio/openpipeline \
  -r 1.0.2 -latest \
  -main-script target/nextflow/genetic_demux/souporcell/main.nf \
  --help

Run command

Example of params.yaml

# Input
# fasta: "path/to/file"
# bam: "path/to/file"
# bam_index: "path/to/file"
# barcodes: "path/to/file"
# clusters: 123
ploidy: 2
min_alt: 10
min_ref: 10
max_loci: 2048
# restarts: 123
# common_variants: "path/to/file"
# known_genotypes: "path/to/file"
# known_genotypes_sample_names: "foo"
skip_remap: false
ignore: false

# Output
# output: "$id.$key.output.output"

# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"

nextflow run openpipelines-bio/openpipeline \
  -r 1.0.2 -latest \
  -profile docker \
  -main-script target/nextflow/genetic_demux/souporcell/main.nf \
  -params-file params.yaml

Note

Replace -profile docker with -profile podman or -profile singularity depending on the desired backend.

Argument groups

Input

Name	Description	Attributes
--fasta	reference fasta file	file
--bam	cellranger bam	file
--bam_index	cellranger bam index	file
--barcodes	barcodes.tsv from cellranger	file
--clusters	number cluster, tbd add easy way to run on a range of k	integer
--ploidy	ploidy, must be 1 or 2	integer, default: 2
--min_alt	min alt to use locus	integer, default: 10
--min_ref	min ref to use locus	integer, default: 10
--max_loci	max loci per cell, affects speed	integer, default: 2048
--restarts	number of restarts in clustering, when there are > 12 clusters we recommend increasing this to avoid local minima	integer
--common_variants	common variant loci or known variant loci vcf, must be vs same reference fasta	file
--known_genotypes	known variants per clone in population vcf mode, must be .vcf right now we dont accept gzip or bcf sorry	file
--known_genotypes_sample_names	which samples in population vcf from known genotypes option represent the donors in your sample	string
--skip_remap	dont remap with minimap2 (not recommended unless in conjunction with –common_variants	boolean_true
--ignore	set to True to ignore data error assertions	boolean_true

Output

Name	Description	Attributes
--output	name of directory to place souporcell files	file, example: "souporcell_out"

Authors

• Xichen Wu (author)