From d1f31cb75537c6ba8e1b5f02648eb1ec659d3d1f Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Wed, 25 Apr 2018 15:32:27 +0200
Subject: [PATCH] add limitBAMsortRAM

---
 gatk.wdl | 2 +-
 star.wdl | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/gatk.wdl b/gatk.wdl
index 160849a..d4613d9 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -271,7 +271,7 @@ task SplitNCigarReads {
         SplitNCigarReads \
         -I ${input_bam} \
         -R ${ref_fasta} \
-        -O ${output_bam} # might have to be -o depending on GATK version \
+        -O ${output_bam} \
         -L ${sep=' -L ' intervals}
     }
 
diff --git a/star.wdl b/star.wdl
index d7d3b7b..32dd056 100644
--- a/star.wdl
+++ b/star.wdl
@@ -12,6 +12,7 @@ task Star {
     String? outStd
     String? twopassMode
     Array[String]? outSAMattrRGline
+    Int? limitBAMsortRAM
 
     Int? memory
 
@@ -34,6 +35,7 @@ task Star {
         ${"--runThreadN " + runThreadN} \
         ${"--outStd " + outStd} \
         ${"--twopassMode " + twopassMode} \
+        ${"--limitBAMsortRAM " + limitBAMsortRAM} \
         ${true="--outSAMattrRGline " false="" defined(outSAMattrRGline)} ${sep=" , " outSAMattrRGline}
     }
 
-- 
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