Nextflow Registry | nf-core/cellrangerarc/mkref@0.0.0-3fc6d40

nf-core/cellrangerarc/mkref @ 0.0.0-3fc6d40

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: 0.0.0-3fc6d40

Total downloads: 16

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	0.0.0-3fc6d40
Commit ID	3fc6d40d163d89ae44d40a00b9017d5a9df5170e
Release Date	22 Apr 2026 15:05:34 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fcellrangerarc%2Fmkref/0.0.0-3fc6d40/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/cellrangerarc/mkref/blobs/sha256:e54bb77238f006e3d1e5318cdb2579546a6ea1e982bbf72551770041b6b51b3e
Size	4.2 KB
Checksum	sha256:e54bb77238f006e3d1e5318cdb2579546a6ea1e982bbf72551770041b6b51b3e
Downloads	3

Version	Date	Downloads	Size
0.0.0-3fc6d40	22 Apr 2026 15:05:34 (UTC)	3	4.2 KB
0.0.0-5d5b444	21 Apr 2026 15:00:45 (UTC)	4	4.2 KB
0.0.0-f484e07	18 Apr 2026 15:00:06 (UTC)	4	4.0 KB
0.0.0-7f68141	16 Apr 2026 15:00:40 (UTC)	2	4.0 KB
0.0.0-0c7146d	08 Apr 2026 18:51:05 (UTC)	3	4.0 KB