From 360d0bb76ce5db5df77806563c859eddc7fa007d Mon Sep 17 00:00:00 2001
From: beboche <davi.baux@inserm.fr>
Date: Fri, 17 Aug 2018 18:05:35 +0200
Subject: [PATCH] removed unproper use or Pair

---
 modules/gatkHaplotypeCaller.wdl | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules/gatkHaplotypeCaller.wdl b/modules/gatkHaplotypeCaller.wdl
index a2d211c..5ac21b7 100644
--- a/modules/gatkHaplotypeCaller.wdl
+++ b/modules/gatkHaplotypeCaller.wdl
@@ -16,7 +16,8 @@ task gatkHaplotypeCaller {
 	File BamFile
 	File BamIndex
 	#when callcaching on, seem to keep Bam and index in the same directory for HC execution
-	Pair[File, File] Bam = (BamFile, BamIndex)
+	#does not work in fine...
+	#Pair[File, File] Bam = (BamFile, BamIndex)
 	String SwMode
 	command {
 		${SrunLow} ${GatkExe} HaplotypeCaller \