+cwlVersion: v1.1
+class: CommandLineTool
+label: Germline variant calling using GATK with output gvcf
+
+$namespaces:
+ arv: "http://arvados.org/cwl#"
+ cwltool: "http://commonwl.org/cwltool#"
+
+requirements:
+ DockerRequirement:
+ dockerPull: broadinstitute/gatk:4.1.7.0
+
+hints:
+ arv:RuntimeConstraints:
+ outputDirType: keep_output_dir
+ keep_cache: 1024
+ ResourceRequirement:
+ ramMin: 3500
+ coresMin: 2
+
+inputs:
+ bam:
+ type: File
+ secondaryFiles:
+ - .bai
+ reference:
+ type: File
+ secondaryFiles:
+ - .amb
+ - .ann
+ - .bwt
+ - .pac
+ - .sa
+ - .fai
+ - ^.dict
+ intervallist:
+ type: File
+ sample: string
+
+outputs:
+ gvcf:
+ type: File
+ secondaryFiles:
+ - .tbi
+ outputBinding:
+ glob: "*vcf.gz"
+
+baseCommand: /gatk/gatk
+
+arguments:
+ - "--java-options"
+ - "-Xmx4G"
+ - HaplotypeCaller
+ - prefix: "-R"
+ valueFrom: $(inputs.reference)
+ - prefix: "-I"
+ valueFrom: $(inputs.bam)
+ - prefix: "-L"
+ valueFrom: $(inputs.intervallist)
+ - prefix: "-O"
+ valueFrom: $(runtime.outdir)/$(inputs.sample)-$(inputs.intervallist.nameroot).gatk.g.vcf.gz
+ - prefix: "-ERC"
+ valueFrom: "GVCF"
+ - prefix: "-GQB"
+ valueFrom: "5"
+ - prefix: "-GQB"
+ valueFrom: "20"
+ - prefix: "-GQB"
+ valueFrom: "60"