class: CommandLineTool
label: Germline variant calling using GATK with output gvcf
+$namespaces:
+ arv: "http://arvados.org/cwl#"
+ cwltool: "http://commonwl.org/cwltool#"
+
requirements:
DockerRequirement:
- dockerPull: broadinstitute/gatk
+ dockerPull: broadinstitute/gatk:4.1.7.0
InitialWorkDirRequirement:
listing:
- $(inputs.bam)
hints:
+ arv:RuntimeConstraints:
+ outputDirType: keep_output_dir
+ keep_cache: 1024
ResourceRequirement:
- ramMin: 10000
- coresMin: 4
+ ramMin: 5000
+ coresMin: 2
inputs:
bam:
sample: string
outputs:
- vcf:
+ gvcf:
type: File
outputBinding:
- glob: "*vcf"
+ glob: "*vcf.gz"
+
+baseCommand: /gatk/gatk
arguments:
- - java
- - -jar
- - /gatk/gatk.jar
+ - "--java-options"
+ - "-Xmx4G"
- HaplotypeCaller
- - -R
- - $(inputs.reference)
- - -I
- - $(inputs.bam)
- - -O
- - $(runtime.outdir)/$(inputs.sample).gatk.g.vcf
- - -ERC
- - "GVCF"
+ - prefix: "-R"
+ valueFrom: $(inputs.reference)
+ - prefix: "-I"
+ valueFrom: $(inputs.bam)
+ - prefix: "-O"
+ valueFrom: $(runtime.outdir)/$(inputs.sample).gatk.g.vcf.gz
+ - prefix: "-ERC"
+ valueFrom: "GVCF"
+ - prefix: "-GQB"
+ valueFrom: "5"
+ - prefix: "-GQB"
+ valueFrom: "20"
+ - prefix: "-GQB"
+ valueFrom: "60"