Description

Module to build the VDJ reference needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkvdjref command.

Input

name:type
description
pattern

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. my_vdj_ref. This flag is required

str

Output

name:type
description
pattern

reference

${reference_name}:directory

Folder containing all the reference indices needed by Cell Ranger

versions

versions.yml:file

File containing software version

versions.yml

Tools

cellranger
10x Genomics EULA

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.

support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/what-is-cell-ranger support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/advanced/references
included in
airrflow scrnaseq
maintainers
Github user ggabernet
Github user klkeys
get in touch
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