label: WGS processing workflow for single sample
requirements:
- - class: SubworkflowFeatureRequirement
+ SubworkflowFeatureRequirement: {}
inputs:
fastq1:
label: Function used to create HTML report
headhtml:
type: File
- format: edam:format_1964 # HTML
+ format: edam:format_2331 # HTML
label: Header for HTML report
tailhtml:
type: File
- format: edam:format_1964 # HTML
+ format: edam:format_2331 # HTML
label: Footer for HTML report
outputs:
qc-html:
type: File[]
label: FASTQ QC reports
- format: edam:format_1964 # HTML
+ format: edam:format_2331 # HTML
outputSource: fastqc/out-html
qc-zip:
type: File[]
report:
type: File
outputSource: generate-report/report
- format: edam:format_1964 # HTML
+ format: edam:format_2331 # HTML
label: ClinVar variant report
steps:
run: report-wf.cwl
in:
gvcf: haplotypecaller/gatheredgvcf
- samplename: sample
+ sample: sample
clinvarvcf: clinvarvcf
reportfunc: reportfunc
headhtml: headhtml
s: https://schema.org/
edam: http://edamontology.org/
-$schemas:
- - https://schema.org/version/latest/schema.rdf
- - http://edamontology.org/EDAM_1.18.owl
+#$schemas:
+# - https://schema.org/version/latest/schema.rdf
+# - http://edamontology.org/EDAM_1.18.owl