Move Gentrap-specific scripts and their wrappers to the Gentrap package

public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala

@@ -132,20 +132,20 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
     /** Adds output merge jobs for the given expression mode */
     // TODO: can we combine the enum with the file extension (to reduce duplication and potential errors)
     def makeMergeTableJob(inFunc: (Sample => Option[File]), ext: String, idCols: List[Int], valCol: Int,
-                                  outBaseName: String = "all_samples"): Option[MergeTables] = {
+                          outBaseName: String = "all_samples"): Option[MergeTables] = {
       val tables = samples.values.map { inFunc }.toList.flatten
       tables.nonEmpty
         .option {
-        val job = new MergeTables(qscript)
-        job.inputTables = tables
-        job.output = new File(outputDir, outBaseName + ext)
-        job.idColumnIndices = idCols.map(_.toString)
-        job.valueColumnIndex = valCol
-        job.fileExtension = Option(ext)
-        // TODO: separate the addition into another function?
-        add(job)
-        job
-      }
+          val job = new MergeTables(qscript)
+          job.inputTables = tables
+          job.output = new File(outputDir, outBaseName + ext)
+          job.idColumnIndices = idCols.map(_.toString)
+          job.valueColumnIndex = valCol
+          job.fileExtension = Option(ext)
+          // TODO: separate the addition into another function?
+          add(job)
+          job
+        }
     }
 
     // merge htseq outputs

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/scripts/AggrBaseCount.scala → public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/AggrBaseCount.scala

@@ -7,9 +7,10 @@
 package nl.lumc.sasc.biopet.pipelines.gentrap.scripts
 
 import java.io.File
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.extensions.RScriptCommandLineFunction
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**
  * Wrapper for the aggr_base_count.R script, used internally in Gentrap

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/scripts/Hist2Count.scala → public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/Hist2Count.scala

@@ -7,9 +7,10 @@
 package nl.lumc.sasc.biopet.pipelines.gentrap.scripts
 
 import java.io.File
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**
  * Wrapper for the hist2count.py script, used internally in Gentrap