Fix tophat config

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{Reference, BiopetCommandLineFunction}
+import nl.lumc.sasc.biopet.core.{ Reference, BiopetCommandLineFunction }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
 

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/GenerateIndexes.scala

@@ -193,7 +193,9 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
         bowtie2Index.baseName = "reference"
         add(bowtie2Index)
         outputConfig += "bowtie2" -> Map("reference_fasta" -> bowtie2Index.reference.getAbsolutePath)
-        outputConfig += "tophat" -> Map("bowtie_index" -> bowtie2Index.reference.getAbsolutePath)
+        outputConfig += "tophat" -> Map(
+          "bowtie_index" -> bowtie2Index.reference.getAbsolutePath.stripSuffix(".fa").stripSuffix(".fasta")
+        )
 
         outputConfig
       }