+++ /dev/null
-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
- reference:
- type: File
- secondaryFiles:
- - .amb
- - .ann
- - .bwt
- - .pac
- - .sa
- - .fai
- - ^.dict
- sample: string
- recaltable:
- type: File
-
-outputs:
- recalbam:
- type: File
- 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: "-O"
- valueFrom: $(inputs.sample)nodups_BQSR.bam