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
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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