genetic_demux/vireo

Description

Vireo is primarily designed for demultiplexing cells into donors by modelling of expressed alleles.

Type

bash_script

Contributors

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
n_donor: [ 2 ]  
geno_tag: [ "PL" ]  
no_doublet: [ false ]  
n_init: [ 50 ]  
extra_donor: [ 0 ]  
force_learn_gt: [ false ]  
ase_mode: [ false ]  
no_plot: [ false ]  
call_ambient_rnas: [ false ]  
output: "$id.$key.output.vireo"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision 1.0.2 \  
  -main-script target/nextflow/genetic_demux/vireo/main.nf \  
  -params-file params.yaml

Input

Name	Type & Properties	Description
--cell_data	file	The cell genotype file in VCF format or cellSNP folder with sparse matrices.
--n_donor	integer	Number of donors to demultiplex; can be larger than provided in donor_file.
--vartrix_data	file	The cell genotype files in vartrix outputs.
--donor_file	file	The donor genotype file in VCF format. Please filter the sample and region with bcftools first!
--geno_tag	string	The tag for donor genotype.
--no_doublet	boolean	If use, not checking doublets.
--n_init	integer	Number of random initializations, when GT needs to learn.
--extra_donor	integer	Number of extra donor in pre-cluster, when GT needs to learn.
--extra_donorMode	string	Method for searching from extra donors. size: n_cell per donor; distance: GT distance between donors
--force_learn_gt	boolean	If use, treat donor GT as prior only.
--ase_mode	boolean	If use, turn on SNP specific allelic ratio.
--no_plot	boolean	If use, turn off plotting GT distance.
--rand_seed	integer	Seed for random initialization
--cell_range	string	Range of cells to process.
--call_ambient_rnas	boolean	If use, detect ambient RNAs in each cell.

Name

Type & Properties

--cell_data

file

--n_donor

integer

--vartrix_data

file

--donor_file

file

--geno_tag

string

--no_doublet

boolean

--n_init

integer

--extra_donor

integer

--extra_donorMode

string

--force_learn_gt

boolean

--ase_mode

boolean

--no_plot

boolean

--rand_seed

integer

--cell_range

string

--call_ambient_rnas

boolean

Output

Name	Type & Properties	Description
--output -o	file output	Output directory

Name

Type & Properties

--output

-o

file

output