Use vireo to perform donor deconvolution for multiplexed scRNA-seq data
Input
name:type
description
pattern
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:'sample1']
cell_data{:bash}
:file
The cell genotype file in VCF format or cellSNP folder with sparse matrices.
*.vcf|*/
n_donor{:bash}
:integer
Number of donors to demultiplex.
donor_file{:bash}
:file
The optional donor genotype file in VCF format.
*.vcf
vartrix_data{:bash}
:file
The optional cell genotype files in vartrix outputs.
Output
name:type
description
pattern
summary{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:'sample1' ]
*_summary.tsv{:bash}
:file
Summary tsv file of deconvolution result.
*_summary.tsv
donor_ids{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:'sample1' ]
*_donor_ids.tsv{:bash}
:file
Donor assignment with detailed statistics.
*_donor_ids.tsv
prob_singlets{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:'sample1' ]
*_prob_singlet.tsv.gz{:bash}
:file
contains probability of classifing singlets
*_prob_singlet.tsv.gz
prob_doublets{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:'sample1' ]
*_prob_doublet.tsv.gz{:bash}
:file
contains probability of classifing doublets
*_prob_doublet.tsv.gz
genotype_vcf{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:'sample1' ]
*_GT_donors.vireo.vcf.gz{:bash}
:file
contains vireo’s inferred donor genotypes at each SNP (only created if --forceLearnGT is set in ext.args, see n)
*_GT_donors.vireo.vcf.gz
filtered_variants{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:'sample1' ]
*_filtered_variants.tsv{:bash}
:file
contains the minimal set of discriminatory variants created by GTbarcode (only created if --forceLearnGT is set in ext.args, see the hadge pipeline as an example, and only shows consistent results if --randSeed is set)
*_filtered_variants.tsv
versions{:bash}
versions.yml{:bash}
:file
File containing software versions
versions.yml
Tools
vireo
Apache-2.0
vireoSNP - donor deconvolution for multiplexed scRNA-seq data
