WGS-processing/cwl/helper/report-wf.cwl

   1 cwlVersion: v1.1
   2 class: Workflow
   3
   4 inputs:
   5   gvcf:
   6     type: File
   7   samplename:
   8     type: string
   9   clinvarvcf:
  10     type: File
  11   reportfunc:
  12     type: File
  13   headhtml:
  14     type: File
  15   tailhtml:
  16     type: File
  17
  18 outputs:
  19   report:
  20     type: File
  21     outputSource: generate-report/report
  22
  23 steps:
  24   gvcf-to-vcf:
  25     run: gvcf-to-vcf.cwl
  26     in:
  27       gvcf: gvcf
  28       samplename: samplename
  29     out: [vcf]
  30
  31   annotate:
  32     run: annotate-vcf.cwl
  33     in:
  34       vcf: gvcf-to-vcf/vcf
  35       clinvarvcf: clinvarvcf
  36     out: [reporttxt]
  37
  38   generate-report:
  39     run: generate-report.cwl
  40     in:
  41       reportfunc: reportfunc
  42       sampletxt: annotate/reporttxt
  43       headhtml: headhtml
  44       tailhtml: tailhtml
  45     out: [report]