genetic_demux/souporcell
Description
souporcell is a method for clustering mixed-genotype scRNAseq experiments by individual.
Input
Name | Type & Properties | Description |
|---|---|---|
--fasta | file | reference fasta file |
--bam | file | cellranger bam |
--bam_index | file | cellranger bam index |
--barcodes | file | barcodes.tsv from cellranger |
--clusters | integer | number cluster, tbd add easy way to run on a range of k |
--ploidy | integer | ploidy, must be 1 or 2 |
--min_alt | integer | min alt to use locus |
--min_ref | integer | min ref to use locus |
--max_loci | integer | max loci per cell, affects speed |
--restarts | integer | number of restarts in clustering, when there are > 12 clusters we recommend increasing this to avoid local minima |
--common_variants | file | common variant loci or known variant loci vcf, must be vs same reference fasta |
--known_genotypes | file | known variants per clone in population vcf mode, must be .vcf right now we dont accept gzip or bcf sorry |
--known_genotypes_sample_names | string | which samples in population vcf from known genotypes option represent the donors in your sample |
--skip_remap | boolean_true | dont remap with minimap2 (not recommended unless in conjunction with --common_variants |
--ignore | boolean_true | set to True to ignore data error assertions |
Output
Name | Type & Properties | Description |
|---|---|---|
--output -o | file output | name of directory to place souporcell files |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
ploidy: [ 2 ]
min_alt: [ 10 ]
min_ref: [ 10 ]
max_loci: [ 2048 ]
output: "$id.$key.output.souporcell_out"
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \
-revision v3.0.1 \
-main-script target/nextflow/genetic_demux/souporcell/main.nf \
-params-file params.yaml Relationships
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Current component
genetic_demux/souporcellopenpipeline v3.0.1
Uses
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