cwlVersion: v1.1
class: CommandLineTool
+label: Generate ClinVar Report
requirements:
DockerRequirement:
inputs:
reportfunc:
type: File
+ label: Function used to create HTML report
sampletxt:
type: File
+ label: Annotated text from VCF
+ sample:
+ type: string
+ label: Sample Name
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
outputBinding:
glob: "*html"
arguments:
- $(inputs.reportfunc)
- $(inputs.sampletxt)
- - $(inputs.sampletxt.basename)
+ - $(inputs.sample)
- $(inputs.headhtml)
- $(inputs.tailhtml)
+
+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/
+
+$schemas:
+ - https://schema.org/version/latest/schema.rdf
+ - http://edamontology.org/EDAM_1.18.owl