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"
