cwlVersion: v1.1
class: Workflow
label: Report generation workflow

inputs:
  gvcf: 
    type: File
    format: edam:format_3016 # GVCF
    label: Gathered GVCF
  sample:
    type: string
    label: Sample Name
  clinvarvcf:
    type: File
    format: edam:format_3016 # VCF
    label: Reference VCF for ClinVar
  reportfunc:
    type: File
    label: Function used to create HTML report
  headhtml:
    type: File
    format: edam:format_2331# HTML
    label: Header for HTML report
  tailhtml:   
    type: File
    format: edam:format_2331 # HTML
    label: Footer for HTML report

outputs:
  report:
    type: File
    format: edam:format_1964 # HTML
    label: ClinVar variant report
    outputSource: generate-report/report

steps:
  gvcf-to-vcf:
    run: gvcf-to-vcf.cwl
    in:
      gvcf: gvcf
      sample: sample
    out: [vcf]
  annotate:
    run: annotate-vcf.cwl
    in:
      vcf: gvcf-to-vcf/vcf
      clinvarvcf: clinvarvcf
    out: [reporttxt]
  generate-report:
    run: generate-report.cwl
    in:
      reportfunc: reportfunc
      sampletxt: annotate/reporttxt
      headhtml: headhtml
      tailhtml: tailhtml
    out: [report]

s:codeRepository: https://github.com/arvados/arvados-tutorial
s:license: https://www.gnu.org/licenses/agpl-3.0.en.html

$namespaces:
 s: https://schema.org/
 edam: http://edamontology.org/

$schemas:
 - https://schema.org/version/latest/schema.rdf
 - http://edamontology.org/EDAM_1.18.owl