nf-core/cellranger/vdj @ 0.0.0-0c7146d
Summary
Module to use Cell Ranger's pipelines analyze sequencing data produced from Chromium Single Cell Immune Profiling.
Get started
Add the following snippet to your workflow script to include this module.
include { CELLRANGER_VDJ } from 'nf-core/cellranger/vdj'
License
MIT License
Process
Name
|
CELLRANGER_VDJ |
|---|
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
reads
file
|
List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. ${Sample_Name}_S1_L00${Lane_Number}_${I1,I2,R1,R2}_001.fastq.gz
|
reference
directory
|
Folder containing all the reference indices needed by Cell Ranger |
|---|
Output
2 channels
#1
outs
tuple
meta
map
|
Groovy Map containing sample information |
|---|---|
**/outs/**
file
|
Files containing the outputs of Cell Ranger, see official 10X Genomics documentation for a complete list ${meta.id}/outs/*
|
#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 18:29:53 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fcellranger%2Fvdj/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/cellranger/vdj/blobs/sha256:3b2e0f405af17822da05852df279b9fcc3e3a4a5903b7d2fc53ad1f9777ccce2 |
| Size | 3.2 KB |
| Checksum | sha256:3b2e0f405af17822da05852df279b9fcc3e3a4a5903b7d2fc53ad1f9777ccce2 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:29:53 (UTC) | 1 | 3.2 KB | - |