cwlVersion: v1.1
class: Workflow
-label: Variant calling workflow for given interval
+label: Variant calling workflow for given interval
requirements:
- class: SubworkflowFeatureRequirement
- .sa
- .fai
- ^.dict
- sample:
+ sample:
type: string
label: Sample Name
knownsites:
- .tbi
intervallist:
type: File
- label: Scatter intervals file
+ label: Scatter intervals file
outputs:
gvcf:
out: [recaltable]
applyBQSR:
run: gatk-applyBSQR-with-interval.cwl
- in:
+ in:
reference: reference
bam: bam
sample: sample
out: [gvcf]
selectvariants:
run: gatk-selectvariants.cwl
- in:
+ in:
gvcf: haplotypecaller/gvcf
reference: reference
sample: sample
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