From fdf3af307457abd5cbe656823bd2a8bfc5bb9b6b Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Wed, 9 May 2018 15:11:38 +0200
Subject: [PATCH] fix SamToFastq
---
picard.wdl | 1 +
1 file changed, 1 insertion(+)
diff --git a/picard.wdl b/picard.wdl
index 8177b26..65b26fe 100644
--- a/picard.wdl
+++ b/picard.wdl
@@ -169,6 +169,7 @@ task SamToFastq {
java \
-Xmx${mem}G \
-jar ${picard_jar} \
+ SamToFastq \
I=${inputBam} \
${"FASTQ=" + outputRead1} \
${"SECOND_END_FASTQ=" + outputRead2} \
--
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