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
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}_${I1,I2,R1,R2}_001.fastq.gz"
  - reference:
      type: directory
      description: Folder containing all the reference indices needed by Cell Ranger
output:
  - outs:
      type: file
      description: Files containing the outputs of Cell Ranger, see official 10X Genomics documentation for a complete list
      pattern: "${meta.id}/outs/*"
  - versions:
      type: file
      description: File containing software version
      pattern: "versions.yml"
authors:
  - "@ggabernet"
  - "@Emiller88"
  - "@klkeys"
maintainers:
  - "@ggabernet"
  - "@Emiller88"
  - "@klkeys"
