From ce4cef8b75349d2fc37acbf35bd4c5379e7c5238 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Mon, 24 Sep 2018 11:59:58 +0200
Subject: [PATCH] remove link creation from CombineGVCFs
---
gatk.wdl | 18 ++++++------------
1 file changed, 6 insertions(+), 12 deletions(-)
diff --git a/gatk.wdl b/gatk.wdl
index 99a5b2c..25c273a 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -123,18 +123,12 @@ task CombineGVCFs {
command {
set -e -o pipefail
~{preCommand}
-
- if [ ~{length(gvcfFiles)} -gt 1 ]; then
- ~{toolCommand} \
- CombineGVCFs \
- -R ~{reference.fasta} \
- -O ~{outputPath} \
- -V ~{sep=' -V ' gvcfFiles} \
- -L ~{sep=' -L ' intervals}
- else # TODO this should be handeled in wdl
- ln -sf ~{gvcfFiles[0]} ~{outputPath}
- ln -sf ~{gvcfFiles[0]} ~{outputPath}.tbi
- fi
+ ~{toolCommand} \
+ CombineGVCFs \
+ -R ~{reference.fasta} \
+ -O ~{outputPath} \
+ -V ~{sep=' -V ' gvcfFiles} \
+ -L ~{sep=' -L ' intervals}
}
output {
--
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