+++ /dev/null
-cwlVersion: v1.1
-class: CommandLineTool
-
-$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: 5000
- coresMin: 2
-
-inputs:
- gvcf:
- type: File
- secondaryFiles:
- - .tbi
- reference:
- type: File
- secondaryFiles:
- - .amb
- - .ann
- - .bwt
- - .pac
- - .sa
- - .fai
- - ^.dict
- sample: string
-
-outputs:
- filteredgvcf:
- type: File
- outputBinding:
- glob: "*g.vcf.gz"
-
-baseCommand: /gatk/gatk
-
-arguments:
- - "--java-options"
- - "-Xmx4G"
- - SelectVariants
- - prefix: "-R"
- valueFrom: $(inputs.reference)
- - prefix: "--remove-unused-alternates"
- valueFrom: "true"
- - prefix: "-V"
- valueFrom: $(inputs.gvcf.path)
- - prefix: "-O"
- valueFrom: selected$(inputs.gvcf.basename)