From 3282101e013a8c52d678beeecc7528ac0e22fd95 Mon Sep 17 00:00:00 2001
From: ffinfo <pjrvanthof@gmail.com>
Date: Thu, 13 Sep 2018 06:09:21 +0200
Subject: [PATCH] switch back
---
gatk.wdl | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
diff --git a/gatk.wdl b/gatk.wdl
index 970f6a5..a432405 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -102,7 +102,8 @@ task BaseRecalibrator {
task CombineGVCFs {
input {
String? preCommand
- Array[IndexedVcfFile]+ gvcfFiles
+ Array[File]+ gvcfFiles
+ Array[File]+ gvcfFilesIndex
Array[File]+ intervals
String outputPath
@@ -131,8 +132,8 @@ task CombineGVCFs {
-V ~{sep=' -V ' gvcfFiles} \
-L ~{sep=' -L ' intervals}
else # TODO this should be handeled in wdl
- ln -sf ~{gvcfFiles[0].file} ~{outputPath}
- ln -sf ~{gvcfFiles[0].index} ~{outputPath}.tbi
+ ln -sf ~{gvcfFiles[0]} ~{outputPath}
+ ln -sf ~{gvcfFiles[0]} ~{outputPath}.tbi
fi
}
--
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