cwlVersion: v1.1
class: Workflow
+label: Report generation workflow
inputs:
gvcf:
type: File
- samplename:
+ 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:
run: gvcf-to-vcf.cwl
in:
gvcf: gvcf
- samplename: samplename
+ 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
+ sample: sample
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