From 4bb43f8e3d82277c271cbe7a53080e5316b283af Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 26 Nov 2019 08:35:55 +0100
Subject: [PATCH] make intervals optional
---
gatk.wdl | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/gatk.wdl b/gatk.wdl
index 60b81cd..ce8d4c4 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -95,7 +95,7 @@ task CombineGVCFs {
input {
Array[File]+ gvcfFiles
Array[File]+ gvcfFilesIndex
- Array[File]+ intervals
+ Array[File] intervals = []
String outputPath
File referenceFasta
File referenceFastaDict
@@ -114,7 +114,7 @@ task CombineGVCFs {
-R ~{referenceFasta} \
-O ~{outputPath} \
-V ~{sep=' -V ' gvcfFiles} \
- -L ~{sep=' -L ' intervals}
+ ~{true='-L' false='' length(intervals) > 0} ~{sep=' -L ' intervals}
}
output {
--
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