Updating annotation and gatk code

[arvados-tutorial.git] / cwl / gatk-haplotypecaller.cwl

diff --git a/cwl/gatk-haplotypecaller.cwl b/cwl/gatk-haplotypecaller.cwl
index 5480eace46b21e2adca91053aeccd5bf8280c41b..f10178301ae677c272e949e81bae0ff1dfd41689 100644 (file)
--- a/cwl/gatk-haplotypecaller.cwl
+++ b/cwl/gatk-haplotypecaller.cwl
@@ -11,7 +11,7 @@ requirements:
 
 hints:
   ResourceRequirement:
-    ramMin: 10000
+    ramMin: 20000
     coresMin: 4    
 
 inputs:
@@ -32,21 +32,28 @@ inputs:
   sample: string
 
 outputs:
-  vcf:
+  gvcf:
     type: File
     outputBinding:
-      glob: "*vcf"
+      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
-  - -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"