name: cellranger_count
description: Module to use Cell Ranger's pipelines analyze sequencing data produced from Chromium Single Cell Gene Expression.
keywords:
    - align
    - count
    - reference
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:
    - 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.
    - reference:
        type: folder
        description: Folder containing all the reference indices needed by Cell Ranger
output:
    - outs:
        type: file
        description: Files containing the outputs of Cell Ranger
        pattern: "sample-${meta.gem}/outs/*"
    - versions:
        type: file
        description: File containing software version
        pattern: "versions.yml"
authors:
  - "@ggabernet"
  - "@Emiller88"
