Vireo
Vireo is primarily designed for demultiplexing cells into donors by modelling of expressed alleles.
Info
ID: vireo
Namespace: genetic_demux
Links
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/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.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/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" |