Nextflow Registry | nf-core/cellrangerarc/count@0.0.0-0c7146d

nf-core/cellrangerarc/count @ 0.0.0-0c7146d

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

align count reference

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @ggabernet @edmundmiller @heylf

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

Add the following snippet to your workflow script to include this module.

include { CELLRANGERARC_COUNT } from 'nf-core/cellrangerarc/count'

MIT License

Process

`Name`	`CELLRANGERARC_COUNT`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`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`

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`reference` directory	Directory containing all the reference indices needed by Cell Ranger ARC

Output 3 channels

#1 lib tuple

`meta` map	Groovy Map containing sample information
`${prefix}_lib.csv` file	Library `${prefix}_lib.csv`

#2 outs tuple

`meta` map	Groovy Map containing sample information
`${prefix}/outs/**` file	Files containing the outputs of Cell Ranger ARC `${prefix}/outs/*`

#3 versions_cellrangerarc tuple

`${task.process}` string	The name of the process
`cellrangerarc` string	The name of the tool
`cellranger-arc --version 2>&1 \| sed 's/cellranger-arc cellranger-arc-//'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
cellrangerarc	Cell Ranger ARC is a set of analysis pipelines that process Chromium Single Cell ARC data.	https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc

Version	0.0.0-0c7146d
Commit ID	4e8e48c04e24c2159a5589a36bae0f038809cd48
Release Date	08 Apr 2026 18:29:55 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fcellrangerarc%2Fcount/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/cellrangerarc/count/blobs/sha256:749d0d6020d947759beb993b064b3d338ec9780887df601e1501b73ca8a4d678
Size	5.5 KB
Checksum	sha256:749d0d6020d947759beb993b064b3d338ec9780887df601e1501b73ca8a4d678
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:29:55 (UTC)		1	5.5 KB	-