name: cellranger_vdj
description: Module to use Cell Ranger's pipelines analyze sequencing data produced
  from Chromium Single Cell Immune Profiling.
keywords:
  - align
  - vdj
  - reference
  - 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/tutorial/tutorial-vdj
      tool_dev_url: https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/tutorial/tutorial-vdj
      licence: [10X Genomics EULA]
      identifier: ""
input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - reads:
        type: file
        description: |
          List of input FastQ files of size 1 and 2 for single-end and paired-end data,
          respectively.
        pattern: "${Sample_Name}_S1_L00${Lane_Number}_${I1,I2,R1,R2}_001.fastq.gz"
  - - reference:
        type: directory
        description: Folder containing all the reference indices needed by Cell Ranger
output:
  - outs:
      - meta:
          type: file
          description: Files containing the outputs of Cell Ranger, see official 10X Genomics
            documentation for a complete list
          pattern: "${meta.id}/outs/*"
      - "**/outs/**":
          type: file
          description: Files containing the outputs of Cell Ranger, see official 10X Genomics
            documentation for a complete list
          pattern: "${meta.id}/outs/*"
  - versions:
      - versions.yml:
          type: file
          description: File containing software version
          pattern: "versions.yml"
authors:
  - "@ggabernet"
  - "@edmundmiller"
  - "@klkeys"
maintainers:
  - "@ggabernet"
  - "@edmundmiller"
  - "@klkeys"
