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     format: edam:format_3016 # GVCF
   9     label: Gathered GVCF
  10   samplename:
  11     type: string
  12     label: Sample Name
  13   clinvarvcf:
  14     type: File
  15     format: edam:format_3016 # VCF
  16     label: Reference VCF for ClinVar
  17   reportfunc:
  18     type: File
  19     label: Function used to create HTML report
  20   headhtml:
  21     type: File
  22     format: edam:format_2331# HTML
  23     label: Header for HTML report
  24   tailhtml:
  25     type: File
  26     format: edam:format_2331 # HTML
  27     label: Footer for HTML report
  28
  29 outputs:
  30   report:
  31     type: File
  32     format: edam:format_1964 # HTML
  33     label: ClinVar variant report
  34     outputSource: generate-report/report
  35
  36 steps:
  37   gvcf-to-vcf:
  38     run: gvcf-to-vcf.cwl
  39     in:
  40       gvcf: gvcf
  41       samplename: samplename
  42     out: [vcf]
  43
  44   annotate:
  45     run: annotate-vcf.cwl
  46     in:
  47       vcf: gvcf-to-vcf/vcf
  48       clinvarvcf: clinvarvcf
  49     out: [reporttxt]
  50
  51   generate-report:
  52     run: generate-report.cwl
  53     in:
  54       reportfunc: reportfunc
  55       sampletxt: annotate/reporttxt
  56       headhtml: headhtml
  57       tailhtml: tailhtml
  58     out: [report]
  59
  60 s:codeRepository: https://github.com/arvados/arvados-tutorial
  61 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
  62
  63 $namespaces:
  64  s: https://schema.org/
  65  edam: http://edamontology.org/
  66
  67 $schemas:
  68  - https://schema.org/version/latest/schema.rdf
  69  - http://edamontology.org/EDAM_1.18.owl