name: cellranger_mkvdjref
description: Module to build the VDJ reference needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkvdjref command.
keywords:
  - reference
  - mkvdjref
  - index
  - immunoprofiling
  - single-cell
  - cellranger
tools:
  - cellranger:
      description: 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.
      homepage: https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/what-is-cell-ranger
      documentation: https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/advanced/references
      tool_dev_url: https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/advanced/references
      licence: 10x Genomics EULA
input:
  - fasta:
      type: file
      description: Reference genome FASTA file
      pattern: "*.{fasta,fa}"
  - genes:
      type: file
      description: Reference transcriptome GTF file
      pattern: "*.gtf"
  - genome:
      type: string
      description: The name to give the new reference folder, e.g. `my_vdj_ref`
      pattern: str
output:
  - reference:
      type: directory
      description: Folder containing all the reference indices needed by Cell Ranger
  - versions:
      type: file
      description: File containing software version
      pattern: "versions.yml"
authors:
  - "@ggabernet"
  - "@klkeys"
maintainers:
  - "@ggabernet"
  - "@klkeys"
