From 4c0b93851015fcc7f14addafc2b6b99469cbab98 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 14 May 2018 12:55:42 +0200
Subject: [PATCH] SamToFastq needs high memory
---
picard.wdl | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/picard.wdl b/picard.wdl
index 65b26fe..2c638df 100644
--- a/picard.wdl
+++ b/picard.wdl
@@ -161,7 +161,7 @@ task SamToFastq {
String picard_jar
Float? memory
Float? memoryMultiplier
- Int mem = ceil(select_first([memory, 4.0]))
+ Int mem = ceil(select_first([memory, 16.0])) # High memory default to avoid crashes.
command {
set -e -o pipefail
--
GitLab