From 8bb2e6d9760fadd691e26878aab54c803e94ed33 Mon Sep 17 00:00:00 2001
From: Sander Bollen <a.h.b.bollen@lumc.nl>
Date: Mon, 9 May 2016 11:24:46 +0200
Subject: [PATCH] fix stuff that went wrong during merge
---
.../pipelines/shiva/variantcallers/HaplotypeCallerGvcf.scala | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerGvcf.scala b/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerGvcf.scala
index 585c33d64..a08703e95 100644
--- a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerGvcf.scala
+++ b/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerGvcf.scala
@@ -27,7 +27,7 @@ class HaplotypeCallerGvcf(val root: Configurable) extends Variantcaller {
sample -> hc.out
}
- val genotypeGVCFs = gatk.GenotypeGVCFs(this, gvcfFiles.toList, outputFile)
+ val genotypeGVCFs = gatk.GenotypeGVCFs(this, gvcfFiles.values.toList, outputFile)
add(genotypeGVCFs)
}
}
--
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