--- /dev/null
+cwlVersion: v1.1
+class: CommandLineTool
+label: Marking Duplicates using Picard
+$namespaces:
+ arv: "http://arvados.org/cwl#"
+ cwltool: "http://commonwl.org/cwltool#"
+
+requirements:
+ DockerRequirement:
+ dockerPull: broadinstitute/gatk
+
+hints:
+ ResourceRequirement:
+ ramMin: 20000
+ coresMin: 4
+ arv:RuntimeConstraints:
+ outputDirType: keep_output_dir
+
+inputs:
+ bam:
+ type: File
+
+outputs:
+ dupbam:
+ type: File
+ outputBinding:
+ glob: "*.bam"
+ dupmetrics:
+ type: File
+ outputBinding:
+ glob: "*.txt"
+
+baseCommand: /gatk/gatk
+
+arguments:
+ - "--java-options"
+ - "-Xmx8G"
+ - MarkDuplicates
+ - prefix: "-I"
+ valueFrom: $(inputs.bam.path)
+ - prefix: "-O"
+ valueFrom: marked_dups$(inputs.bam.basename)
+ - prefix: "-M"
+ valueFrom: "metrics.txt"