Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

reads{:bash}

: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{:bash}

:directory

Directory containing all the reference indices needed by Cell Ranger ATAC

Output

name:type
description
pattern

outs{:bash}

meta{:bash}

:map

Groovy Map containing sample information

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

:file

Files containing the outputs of Cell Ranger ATAC

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

versions_cellrangeratac{:bash}

${task.process}{:bash}

:string

The name of the process

cellrangeratac{:bash}

:string

The name of the tool

cellranger-atac --version | sed 's/.*cellranger-atac-//'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

cellrangeratac{:bash}

:string

The name of the tool

cellranger-atac --version | sed 's/.*cellranger-atac-//'{:bash}

:eval

The expression to obtain the version of the tool

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 edmundmiller
Github user heylf
get in touch
Ask a question on Slack Open an issue on GitHub