cwlVersion: v1.1
class: CommandLineTool
-label: Gathering vcf using Picard
-$namespaces:
- arv: "http://arvados.org/cwl#"
- cwltool: "http://commonwl.org/cwltool#"
+label: Gather GVCFs
requirements:
DockerRequirement:
inputs:
gvcfarray:
type: File[]
- sample: string
+ format: edam:format_3016 # GVCF
+ label: GVCFs for given intervals
+ sample:
+ type: string
+ label: Sample Name
reference:
type: File
+ format: edam:format_1929 # FASTA
+ label: Reference genome
secondaryFiles:
- .amb
- .ann
outputs:
gatheredgvcf:
type: File
+ format: edam:format_3016 # GVCF
+ label: Gathered GVC
secondaryFiles:
- .tbi
outputBinding:
}
- prefix: "-O"
valueFrom: $(inputs.sample).g.vcf.gz
+
+s:codeRepository: https://github.com/arvados/arvados-tutorial
+s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
+
+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/
+ arv: "http://arvados.org/cwl#"
+ cwltool: "http://commonwl.org/cwltool#"
+
+#$schemas:
+# - https://schema.org/version/latest/schema.rdf
+# - http://edamontology.org/EDAM_1.18.owl