modules/cellrangeratac_count

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

aligncountreference

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

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:false ]

`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`

`meta:file`

Files containing the outputs of Cell Ranger ATAC

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

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

Files containing the outputs of Cell Ranger ATAC

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

`versions`

`versions.yml: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

modules/cellrangeratac_count

Description

Input

meta:map

reads:file

reference:directory

Output

outs

meta:file

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

versions

versions.yml:file