Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #
type: File
clinvarvcf:
type: File
-
outputs:
reporttxt: stdout
hints:
ResourceRequirement:
- ramMin: 10000
+ ramMin: 20000
coresMin: 4
inputs:
outputBinding:
glob: "*vcf.gz"
+baseCommand: /gatk/gatk
+
arguments:
- - java
- - -jar
- - /gatk/gatk.jar
+ - "--java-options"
+ - "-Xmx8G"
- HaplotypeCaller
- - -R
- - $(inputs.reference)
- - -I
- - $(inputs.bam)
- - -O
- - $(runtime.outdir)/$(inputs.sample).gatk.g.vcf.gz
- - -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"
- prefix: "--min-ac"
valueFrom: "1"
- $(inputs.gvcf.path)
+ - prefix: "-i"
+ valueFrom: "AVG(GQ)>20"
- valueFrom: "-Ov"
- prefix: "-o"
valueFrom: $(inputs.samplename).vcf