- doc: |
    Test that passing directory indexes works
  job:
    reference:
      class: File
      path: 1.fasta
      filetype: fasta
  outputs:
    output:
      class: File
      file: 1.fasta
- doc: |
    Test that uploading index works
  job:
    reference:
      type: Directory
      file_type: bwa_mem2_index
      value: bwa_mem2_index
  outputs:
    output:
      class: File
      file: 1.fasta