Vireo

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

Info

ID: vireo
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 2.1.1 -latest \
  -main-script target/nextflow/genetic_demux/vireo/main.nf \
  --help

Run command

Example of params.yaml

# Input
# cell_data: "path/to/file"
n_donor: 2
# vartrix_data: "path/to/file"
# donor_file: "path/to/file"
geno_tag: "PL"
no_doublet: false
n_init: 50
extra_donor: 0
# extra_donorMode: "foo"
force_learn_gt: false
ase_mode: false
no_plot: false
# rand_seed: 123
# cell_range: "foo"
call_ambient_rnas: false

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

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

# Arguments

nextflow run openpipelines-bio/openpipeline \
  -r 2.1.1 -latest \
  -profile docker \
  -main-script target/nextflow/genetic_demux/vireo/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
--cell_data	The cell genotype file in VCF format or cellSNP folder with sparse matrices.	file
--n_donor	Number of donors to demultiplex; can be larger than provided in donor_file.	integer, default: 2
--vartrix_data	The cell genotype files in vartrix outputs.	file
--donor_file	The donor genotype file in VCF format. Please filter the sample and region with bcftools first!	file
--geno_tag	The tag for donor genotype.	string, default: "PL"
--no_doublet	If use, not checking doublets.	boolean, default: FALSE
--n_init	Number of random initializations, when GT needs to learn.	integer, default: 50
--extra_donor	Number of extra donor in pre-cluster, when GT needs to learn.	integer, default: 0
--extra_donorMode	Method for searching from extra donors. size: n_cell per donor; distance: GT distance between donors	string
--force_learn_gt	If use, treat donor GT as prior only.	boolean, default: FALSE
--ase_mode	If use, turn on SNP specific allelic ratio.	boolean, default: FALSE
--no_plot	If use, turn off plotting GT distance.	boolean, default: FALSE
--rand_seed	Seed for random initialization	integer
--cell_range	Range of cells to process.	string
--call_ambient_rnas	If use, detect ambient RNAs in each cell.	boolean, default: FALSE

Output

Name	Description	Attributes
--output	Output directory	file, example: "vireo"

Authors

• Xichen Wu (author)