+cwlVersion: v1.1
+class: CommandLineTool
+label: Applying base quality score recalibration
+
+$namespaces:
+ arv: "http://arvados.org/cwl#"
+ cwltool: "http://commonwl.org/cwltool#"
+
+requirements:
+ DockerRequirement:
+ dockerPull: broadinstitute/gatk:4.1.7.0
+ InitialWorkDirRequirement:
+ listing:
+ - $(inputs.bam)
+
+hints:
+ arv:RuntimeConstraints:
+ outputDirType: keep_output_dir
+ keep_cache: 1024
+ ResourceRequirement:
+ ramMin: 5000
+ coresMin: 2
+
+inputs:
+ bam:
+ type: File
+ secondaryFiles:
+ - .bai
+ reference:
+ type: File
+ secondaryFiles:
+ - .amb
+ - .ann
+ - .bwt
+ - .pac
+ - .sa
+ - .fai
+ - ^.dict
+ sample: string
+ recaltable:
+ type: File
+ intervallist:
+ type: File
+
+outputs:
+ recalbam:
+ type: File
+ secondaryFiles:
+ - .bai
+ outputBinding:
+ glob: "*nodups_BQSR.bam"
+
+baseCommand: /gatk/gatk
+
+arguments:
+ - "--java-options"
+ - "-Xmx4G"
+ - ApplyBQSR
+ - prefix: "-R"
+ valueFrom: $(inputs.reference)
+ - prefix: "-I"
+ valueFrom: $(inputs.bam.basename)
+ - prefix: "--bqsr-recal-file"
+ valueFrom: $(inputs.recaltable)
+ - prefix: "-L"
+ valueFrom: $(inputs.intervallist)
+ - prefix: "-O"
+ valueFrom: $(inputs.sample)nodups_BQSR.bam