fix stuff that went wrong during merge

8bb2e6d9 · Sander Bollen · 0f4c6e15 · 8bb2e6d9
Commit 8bb2e6d9 authored May 09, 2016 by Sander Bollen
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shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerGvcf.scala .../pipelines/shiva/variantcallers/HaplotypeCallerGvcf.scala +1 -1

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--- 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)
  }
 }