modules/souporcell

souporcell is a method for clustering mixed-genotype scRNAseq experiments by individual.

clusteringmixed-genotypegenomics

https://github.com/nf-core/modules/[...]/modules/nf-core/souporcell

Description

souporcell is a method for clustering mixed-genotype scRNAseq experiments by individual.

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`bam`
`:file`

A BAM file from cellranger containing single-cell RNA-seq alignments.

*.bam

`barcodes`
`:file`

A barcode or whitelist TSV file from cellranger identifying individual cell barcodes.

*.tsv

`clusters`
`:integer`

Number of clusters.

`meta2`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`fasta`
`:file`

A reference fasta file.

*.fasta

Output

name:type

description

pattern

`clusters`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`*/clusters.tsv`
`:file`

TSV file listing cell barcodes with singlet/doublet status, assigned cluster, and per-cluster log-loss metrics

clusters.tsv

`vcf`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`*/cluster_genotypes.vcf`
`:file`

A vcf with genotypes for each cluster for each variant in the input vcf from freebayes.

cluster_genotypes.vcf

`ambient_rna`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`*/ambient_rna.txt`
`:file`

Contains the ambient RNA percentage detected

ambient_rna.txt

`versions`

`versions.yml`
`:file`

File containing software versions

versions.yml

Tools

souporcell
MIT

Clustering scRNAseq by genotypes.

github.com/wheaton5/souporcell demultiplexing-doublet-detecting-docs.readthedocs.io/en/latest/Souporcell https://github.com/wheaton5/souporcell 10.1101/699637v1

modules/souporcell

Description

Input

`meta`
`:map`

`bam`
`:file`

`barcodes`
`:file`

`clusters`
`:integer`

`meta2`
`:map`

`fasta`
`:file`

Output

`clusters`

`meta`
`:map`

`*/clusters.tsv`
`:file`

`vcf`

`meta`
`:map`

`*/cluster_genotypes.vcf`
`:file`

`ambient_rna`

`meta`
`:map`

`*/ambient_rna.txt`
`:file`

`versions`

`versions.yml`
`:file`

Tools

souporcell
MIT

maintainers

get in touch

modules/souporcell

Description

Input

meta:map

bam:file

barcodes:file

clusters:integer

meta2:map

fasta:file

Output

clusters

meta:map

*/clusters.tsv:file

vcf

meta:map

*/cluster_genotypes.vcf:file

ambient_rna

meta:map

*/ambient_rna.txt:file

versions

versions.yml:file

Tools

souporcell MIT

maintainers

get in touch

`meta`
`:map`

`bam`
`:file`

`barcodes`
`:file`

`clusters`
`:integer`

`meta2`
`:map`

`fasta`
`:file`

`clusters`

`meta`
`:map`

`*/clusters.tsv`
`:file`

`vcf`

`meta`
`:map`

`*/cluster_genotypes.vcf`
`:file`

`ambient_rna`

`meta`
`:map`

`*/ambient_rna.txt`
`:file`

`versions`

`versions.yml`
`:file`

souporcell
MIT