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

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

Module to build the reference needed by the 10x Genomics Cell Ranger Arc tool. Uses the cellranger-arc mkref command.

reference mkref index

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @ggabernet @heylf

Module to build the reference needed by the 10x Genomics Cell Ranger Arc tool. Uses the cellranger-arc mkref command.

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

include { CELLRANGERARC_MKREF } from 'nf-core/cellrangerarc/mkref'

MIT License

Process

`Name`	`CELLRANGERARC_MKREF`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing genome information e.g. `[ id:'genome' ]`
`fasta` file	Reference genome FASTA file `*.{fasta,fa}`
`gtf` file	Reference transcriptome GTF file `*.gtf`
`motifs` file	Sequence motif file (e.g., from transcription factors) `*.txt`
`reference_config` file	JSON-like file holding organism, genome, reference fasta path, reference annotation gtf path, contigs that should be excluded and sequence format motif file path `config`

Output 3 channels

#1 config tuple

`meta` map	Groovy Map containing genome information e.g. `[ id:'genome' ]`
`config` file	Configuration file

#2 reference tuple

`meta` map	Groovy Map containing genome information e.g. `[ id:'genome' ]`
`${prefix}` directory	Folder called like the reference_name containing all the reference indices needed by Cell Ranger Arc

#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 18:30:01 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fcellrangerarc%2Fmkref/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/cellrangerarc/mkref/blobs/sha256:20071098952467724a71d35645e6471f8c96ca361aa2e4dbd5757f041e029a20
Size	4.0 KB
Checksum	sha256:20071098952467724a71d35645e6471f8c96ca361aa2e4dbd5757f041e029a20
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:30:01 (UTC)		1	4.0 KB	-