name: cellranger_mkfastq
description: Module to create fastqs needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkfastq command.
keywords:
  - reference
  - mkfastq
  - fastq
  - illumina
  - bcl2fastq
tools:
    - cellranger:
        description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
        homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
        documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
        tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
        doi: ""
        licence: 10x Genomics EULA
input:
    - bcl:
        type: file
        description: Base call files
        pattern: "*.bcl.bgzf"
    - csv:
        type: file
        description: Sample sheet
        pattern: "*.csv"
output:
    - fastq:
          type: file
          description: Unaligned FastQ files
          pattern: "*.fastq.gz"
    - versions:
        type: file
        description: File containing software version
        pattern: "versions.yml"
authors:
  - "@ggabernet"
  - "@Emiller88"
  - "@RHReynolds"
