From a7104e27237403c38c0b0334407dcaafd524a1cf Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Wed, 21 Mar 2018 16:10:31 +0100
Subject: [PATCH] add intervals option to SplitNCigarReads
---
gatk.wdl | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/gatk.wdl b/gatk.wdl
index ab1c215..6a3d160 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -204,6 +204,8 @@ task SplitNCigarReads {
File ref_dict
String output_bam
String gatk_jar
+ Array[File]+ intervals
+
command {
set -e -o pipefail
@@ -211,7 +213,8 @@ task SplitNCigarReads {
java -Xms4G -jar ${gatk_jar} \
-I ${input_bam} \
-R ${ref_fasta} \
- -O ${output_bam} # might have to be -o depending on GATK version
+ -O ${output_bam} # might have to be -o depending on GATK version \
+ -L ${sep=' -L ' intervals}
}
output {
--
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