--- /dev/null
+cwlVersion: v1.1
+class: CommandLineTool
+label: Gathering vcf using Picard
+$namespaces:
+ arv: "http://arvados.org/cwl#"
+ cwltool: "http://commonwl.org/cwltool#"
+
+requirements:
+ DockerRequirement:
+ dockerPull: broadinstitute/gatk:4.1.7.0
+ ShellCommandRequirement: {}
+ InitialWorkDirRequirement:
+ listing:
+ - $(inputs.gvcf1)
+ - $(inputs.gvcf2)
+
+hints:
+ ResourceRequirement:
+ ramMin: 20000
+ coresMin: 4
+ arv:RuntimeConstraints:
+ outputDirType: keep_output_dir
+
+inputs:
+ gvcf1:
+ type: File
+ gvcf2:
+ type: File
+ sample: string
+ reference:
+ type: File
+ secondaryFiles:
+ - .amb
+ - .ann
+ - .bwt
+ - .pac
+ - .sa
+ - .fai
+ - ^.dict
+outputs:
+ gatheredgvcf:
+ type: File
+ outputBinding:
+ glob: "*g.vcf.gz"
+
+baseCommand: /gatk/gatk
+
+arguments:
+ - "--java-options"
+ - "-Xmx8G"
+ - MergeVcfs
+ - prefix: "-I"
+ valueFrom: $(inputs.gvcf1.basename)
+ - prefix: "-I"
+ valueFrom: $(inputs.gvcf2.basename)
+ - prefix: "-O"
+ valueFrom: $(inputs.sample)g.vcf.gz
--- /dev/null
+cwlVersion: v1.1
+class: CommandLineTool
+label: Gathering vcf using Picard
+$namespaces:
+ arv: "http://arvados.org/cwl#"
+ cwltool: "http://commonwl.org/cwltool#"
+
+requirements:
+ DockerRequirement:
+ dockerPull: broadinstitute/gatk:4.1.7.0
+ ShellCommandRequirement: {}
+ InitialWorkDirRequirement:
+ listing:
+ - $(inputs.gvcflist)
+ - $(inputs.gvcf1)
+ - $(inputs.gvcf2)
+
+hints:
+ ResourceRequirement:
+ ramMin: 20000
+ coresMin: 4
+ arv:RuntimeConstraints:
+ outputDirType: keep_output_dir
+
+inputs:
+ gvcf1:
+ type: File
+ gvcf2:
+ type: File
+ gvcflist:
+ type: File
+ sample: string
+ reference:
+ type: File
+ secondaryFiles:
+ - .amb
+ - .ann
+ - .bwt
+ - .pac
+ - .sa
+ - .fai
+ - ^.dict
+outputs:
+ gatheredgvcf:
+ type: File
+ outputBinding:
+ glob: "*g.vcf.gz"
+
+baseCommand: /gatk/gatk
+
+arguments:
+ - "--java-options"
+ - "-Xmx8G"
+ - GatherVcfs
+ - prefix: "-I"
+ valueFrom: $(inputs.gvcflist.basename)
+ - prefix: "-O"
+ valueFrom: $(inputs.sample)g.vcf.gz