genetic_demux/souporcell

Description

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

Type

bash_script

Contributors

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
ploidy: [ 2 ]  
min_alt: [ 10 ]  
min_ref: [ 10 ]  
max_loci: [ 2048 ]  
output: "$id.$key.output.souporcell_out"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision 1.0.1 \  
  -main-script target/nextflow/genetic_demux/souporcell/main.nf \  
  -params-file params.yaml

Input

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

Name

Type & Properties

--fasta

file

--bam

file

--bam_index

file

--barcodes

file

--clusters

integer

--ploidy

integer

--min_alt

integer

--min_ref

integer

--max_loci

integer

--restarts

integer

--common_variants

file

--known_genotypes

file

--known_genotypes_sample_names

string

--skip_remap

boolean_true

--ignore

boolean_true

Output

Name	Type & Properties	Description
--output -o	file output	name of directory to place souporcell files

Name

Type & Properties

--output

-o

file

output