Description

Module to use Cell Ranger’s ATAC pipelines analyze sequencing data produced from Chromium Single Cell ATAC.

Input

name:type
description
pattern

meta:map

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

]

reads:file

List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively, plus an additional FastQ for the barcodes

reference:directory

Directory containing all the reference indices needed by Cell Ranger ATAC

Output

name:type
description
pattern

outs:file

Files containing the outputs of Cell Ranger ATAC

sample-${meta.gem}/outs/*

versions:file

File containing software version

versions.yml

Tools

cellranger-atac
10x Genomics EULA

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

support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac
maintainers
Github user ggabernet
Github user Emiller88
Github user heylf
get in touch
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