genetic_demux/vireo
Description
Vireo is primarily designed for demultiplexing cells into donors by modelling of expressed alleles.
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. |
Output
Name | Type & Properties | Description |
|---|---|---|
--output -o | file output | Output directory |
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 v4.0.1 \
-main-script target/nextflow/genetic_demux/vireo/main.nf \
-params-file params.yaml Relationships
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Current component
genetic_demux/vireoopenpipeline v4.0.1
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