From 1bc3f6ccde7dd3c28321fa09c2f22f770f0ce7f4 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Thu, 9 Aug 2018 14:27:24 +0200
Subject: [PATCH] add memory to vardict

---
 vardict.wdl | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/vardict.wdl b/vardict.wdl
index 4d80738..3fcdb22 100644
--- a/vardict.wdl
+++ b/vardict.wdl
@@ -22,12 +22,14 @@ task VarDict {
         Int geneColumn = 4
 
         String? preCommand
+        Int memory = 4
+        Float memoryMultiplier = 2.0
     }
 
     String toolCommand = if defined(installDir)
         then installDir + "/VarDict"
         else if useJavaVersion
-            then "vardict-java" #probably needs memory stuff
+            then "vardict-java -Xmx${memory}"
             else "vardict"
 
     command {
@@ -54,4 +56,8 @@ task VarDict {
     output {
         File vcfFile = outputVcf
     }
+
+    runtime {
+        memory: ceil(memory * memoryMultiplier)
+    }
 }
-- 
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