nf-core/cellranger/mkref @ 0.0.0-3fc6d40
Summary
Module to build the reference needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkref command.
Get started
Add the following snippet to your workflow script to include this module.
include { CELLRANGER_MKREF } from 'nf-core/cellranger/mkref'
License
MIT License
Process
Name
|
CELLRANGER_MKREF |
|---|
Input
3 channels
fasta
file
|
Reference genome FASTA file *.{fasta,fa}
|
|---|
gtf
file
|
Reference transcriptome GTF file *.gtf
|
|---|
reference_name
string
|
The name to give the new reference folder str
|
|---|
Output
2 channels
#1
reference
${reference_name}
directory
|
Folder containing all the reference indices needed by Cell Ranger |
|---|
#2
versions_cellranger
tuple
${task.process}
string
|
The name of the process |
|---|---|
cellranger
string
|
The name of the tool |
cellranger --version | sed "s/.*-//"
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| cellranger | Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more. | https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger |
| Version | 0.0.0-3fc6d40 |
|---|---|
| Commit ID | 3fc6d40d163d89ae44d40a00b9017d5a9df5170e |
| Release Date | 22 Apr 2026 15:05:25 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fcellranger%2Fmkref/0.0.0-3fc6d40/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/cellranger/mkref/blobs/sha256:be4af6d8feddbfa0de20538478d2a49d23cc9a15e1ffb40f15029910025a563a |
| Size | 2.9 KB |
| Checksum | sha256:be4af6d8feddbfa0de20538478d2a49d23cc9a15e1ffb40f15029910025a563a |
| Downloads | 4 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-3fc6d40 | 22 Apr 2026 15:05:25 (UTC) | 4 | 2.9 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 18:50:53 (UTC) | 3 | 2.8 KB |