src/preprocessing/cwl/createSingleBam-wf.cwl

   1 cwlVersion: v1.1
   2 class: Workflow
   3 $namespaces:
   4   arv: "http://arvados.org/cwl#"
   5   cwltool: "http://commonwl.org/cwltool#"
   6
   7 requirements:
   8   ScatterFeatureRequirement: {}
   9
  10 inputs:
  11   bamdir:
  12     type: Directory
  13     label: Directory of zipped bam files
  14
  15 outputs:
  16   fastqs:
  17     type:
  18       type: array
  19       items:
  20         type: array
  21         items: File
  22     outputSource: convert-bams/fastqs
  23
  24 steps:
  25   get-bams:
  26     run: getfiles.cwl
  27     in:
  28       bamdir: bamdir
  29     out: [tarzipbams,samplenames]
  30
  31   convert-bams:
  32     run: createSingleBam.cwl
  33     scatter: [tarzipbam,samplename]
  34     scatterMethod: dotproduct
  35     in:
  36       tarzipbam: get-bams/tarzipbams
  37       samplename: get-bams/samplenames
  38     out: [fastqs]