Description

Module to use Cell Ranger’s ARC pipelines analyze sequencing data produced from Chromium Single Cell ARC. Uses the cellranger-arc count command.

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

sample_type:string

The type of sample

sub_sample:string

The name of sub sample

reads:file

FASTQ files produced using Cell Ranger ARC

*.fastq.gz

reference:directory

Directory containing all the reference indices needed by Cell Ranger ARC

Output

name:type
description
pattern

outs

meta:file

Files containing the outputs of Cell Ranger ARC

${meta.id}/outs/*

${meta.id}/outs/**:file

Files containing the outputs of Cell Ranger ARC

${meta.id}/outs/*

lib

${meta.id}_lib.csv:file

Library

*_lib.csv

versions

versions.yml:file

File containing software version

versions.yml

Tools

cellrangerarc
10x Genomics EULA

Cell Ranger ARC is a set of analysis pipelines that process Chromium Single Cell ARC data.

support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc
included in
scrnaseq
maintainers
Github user ggabernet
Github user edmundmiller
Github user heylf
get in touch
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