From d341e328f48afa797c704a5c59dcea33b016f64f Mon Sep 17 00:00:00 2001
From: Szilveszter Juhos <Szilveszter.Juhos@scilifelab.se>
Date: Wed, 1 Aug 2018 17:21:04 +0200
Subject: [PATCH] MarkDuplicates MAX_RECORDS_IN_RAM decreased to 50000

---
 main.nf | 1 +
 1 file changed, 1 insertion(+)

diff --git a/main.nf b/main.nf
index ac7b102b2..44f8384cc 100644
--- a/main.nf
+++ b/main.nf
@@ -263,6 +263,7 @@ process MarkDuplicates {
   """
   gatk --java-options -Xmx${task.memory.toGiga()}g \
   MarkDuplicates \
+  --MAX_RECORDS_IN_RAM 50000 \
   --INPUT ${bam} \
   --METRICS_FILE ${bam}.metrics \
   --TMP_DIR . \