name: cellranger_mkref
description: Module to build the reference needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkref command.
keywords:
  - reference
  - mkref
  - index
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:
  - fasta:
      type: file
      description: fasta genome file
      pattern: "*.{fasta,fa}"
  - gtf:
      type: file
      description: gtf transcriptome file
      pattern: "*.gtf"
  - reference_name:
      type: val
      description: name to give the reference folder
      pattern: str
output:
  - reference:
      type: folder
      description: Folder containing all the reference indices needed by Cell Ranger
  - versions:
      type: file
      description: File containing software version
      pattern: "versions.yml"
authors:
  - "@ggabernet"