From f16e6e59b1b76019fa08892a347cde18409ccdce Mon Sep 17 00:00:00 2001
From: Sarah Wait Zaranek <swz@curii.com>
Date: Wed, 1 Apr 2020 03:39:07 +0000
Subject: [PATCH 1/1] Updating annotation and gatk code
 Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com> no issue #

---
 cwl/annotate-vcf.cwl         |  1 -
 cwl/gatk-haplotypecaller.cwl | 31 +++++++++++++++++++------------
 cwl/gvcf-to-vcf.cwl          |  2 ++
 3 files changed, 21 insertions(+), 13 deletions(-)

diff --git a/cwl/annotate-vcf.cwl b/cwl/annotate-vcf.cwl
index fc20bfc..019fa1a 100644
--- a/cwl/annotate-vcf.cwl
+++ b/cwl/annotate-vcf.cwl
@@ -18,7 +18,6 @@ inputs:
     type: File
   clinvarvcf:
     type: File
-
 outputs:
   reporttxt: stdout
 
diff --git a/cwl/gatk-haplotypecaller.cwl b/cwl/gatk-haplotypecaller.cwl
index ae34a00..f101783 100644
--- a/cwl/gatk-haplotypecaller.cwl
+++ b/cwl/gatk-haplotypecaller.cwl
@@ -11,7 +11,7 @@ requirements:
 
 hints:
   ResourceRequirement:
-    ramMin: 10000
+    ramMin: 20000
     coresMin: 4    
 
 inputs:
@@ -37,16 +37,23 @@ outputs:
     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"
diff --git a/cwl/gvcf-to-vcf.cwl b/cwl/gvcf-to-vcf.cwl
index ecba357..dfa3e24 100644
--- a/cwl/gvcf-to-vcf.cwl
+++ b/cwl/gvcf-to-vcf.cwl
@@ -31,6 +31,8 @@ arguments:
   - prefix: "--min-ac"
     valueFrom: "1"
   - $(inputs.gvcf.path)
+  - prefix: "-i"
+    valueFrom: "AVG(GQ)>20"
   - valueFrom: "-Ov"
   - prefix: "-o"
     valueFrom: $(inputs.samplename).vcf
-- 
2.30.2