From 57ac6f2c2272ca30812333bf58e7b7fcdf249161 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 25 Feb 2020 15:42:28 +0100
Subject: [PATCH] change default mem requirements

---
 rtg.wdl | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/rtg.wdl b/rtg.wdl
index bc2caef..c528c3a 100644
--- a/rtg.wdl
+++ b/rtg.wdl
@@ -26,13 +26,14 @@ task Format {
         String outputPath = "seq_data.sdf"
         Array[File]+ inputFiles
         String dockerImage = "quay.io/biocontainers/rtg-tools:3.10.1--0"
-        String memory = "4G"
+        String rtgMem = "8G"
+        String memory = "16G"
     }
 
     command {
         set -e
         mkdir -p $(dirname ~{outputPath})
-        rtg format -f ~{format} \
+        rtg RTG_MEM=~{rtgMem} format -f ~{format} \
         -o ~{outputPath} \
         ~{sep=' ' inputFiles}
     }
@@ -74,14 +75,15 @@ task VcfEval {
         Boolean squashPloidy = false
         String outputMode = "split"
         Int threads = 1  # tool default is number of cores in the system 😱
-        String memory = "4G"
+        String rtgMem = "4G"
+        String memory = "8G"
         String dockerImage = "quay.io/biocontainers/rtg-tools:3.10.1--0"
     }
 
     command <<<
         set -e
         mkdir -p "$(dirname ~{outputDir})"
-        rtg vcfeval \
+        rtg RTG_MEM=~{rtgMem} vcfeval \
         --baseline ~{baseline} \
         --calls ~{calls} \
         ~{"--evaluation-regions " + evaluationRegions} \
-- 
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