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

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