cwlVersion: v1.1
class: CommandLineTool
+label: Germline variant calling using GATK with output gvcf
requirements:
DockerRequirement:
hints:
ResourceRequirement:
- ramMin: 10000
+ ramMin: 20000
coresMin: 4
-arguments:
- - java
- - -jar
- - /gatk/gatk.jar
- - HaplotypeCaller
- - -R
- - $(inputs.reference)
- - -I
- - $(inputs.bam)
- - -O
- - $(runtime.outdir)/$(inputs.sample).gatk.vcf
-
inputs:
bam:
type: File
sample: string
outputs:
- vcf:
+ gvcf:
type: File
outputBinding:
- glob: "*vcf"
+ glob: "*vcf.gz"
+
+baseCommand: /gatk/gatk
+
+arguments:
+ - "--java-options"
+ - "-Xmx8G"
+ - HaplotypeCaller
+ - 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"