nf-core/cellranger/mkvdjref @ 0.0.0-0c7146d
Summary
Module to build the VDJ reference needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkvdjref command.
Get started
Add the following snippet to your workflow script to include this module.
include { CELLRANGER_MKVDJREF } from 'nf-core/cellranger/mkvdjref'
License
MIT License
Process
Name
|
CELLRANGER_MKVDJREF |
|---|
Input
4 channels
fasta
file
|
Reference genome FASTA file (optional) *.{fasta,fa}
|
|---|
gtf
file
|
Reference genome GTF file (optional) *.gtf
|
|---|
seqs
file
|
Reference genome FASTA file from the 10X Genomics fetch-imgt workflow (optional) *.{fasta,fa}
|
|---|
reference_name
string
|
The name to give the new reference folder, e.g. 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 processes data from 10X Genomics Chromium kits. `cellranger vdj` takes FASTQ files from `cellranger mkfastq` or `bcl2fastq` for V(D)J libraries and performs sequence assembly and paired clonotype calling. It uses the Chromium cellular barcodes and UMIs to assemble V(D)J transcripts per cell. Clonotypes and CDR3 sequences are output as a `.vloupe` file which can be loaded into Loupe V(D)J Browser. | https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/what-is-cell-ranger |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 4e8e48c04e24c2159a5589a36bae0f038809cd48 |
| Release Date | 08 Apr 2026 18:29:49 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fcellranger%2Fmkvdjref/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/cellranger/mkvdjref/blobs/sha256:3ce04912c9cb08c09da7a67d01bfa571ed2a34198bfae26fb77a486f9372dce6 |
| Size | 2.9 KB |
| Checksum | sha256:3ce04912c9cb08c09da7a67d01bfa571ed2a34198bfae26fb77a486f9372dce6 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:29:49 (UTC) | 1 | 2.9 KB | - |