Fixed config conversions

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

@@ -54,16 +54,16 @@ class Gentrap(val root: Configurable) extends QScript
   /** Expression measurement modes */
   // see the enumeration below for valid modes
   lazy val expMeasures = config("expression_measures", default = Nil).asStringList.map(value =>
-    ExpMeasures.values.find(x => Gentrap.camelize(x.toString) == value) match {
+    ExpMeasures.values.find(_.toString == Gentrap.camelize(value)) match {
       case Some(v) => v
       case _       => throw new IllegalArgumentException(s"'$value' is not a valid Expression measurement")
     }
   ).toSet
 
   /** Strandedness modes */
-  lazy val strandProtocol: StrandProtocol.Value = {
+  val strandProtocol: StrandProtocol.Value = {
     val value: String = config("strand_protocol")
-    StrandProtocol.values.find(x => Gentrap.camelize(x.toString) == value) match {
+    StrandProtocol.values.find(_.toString == Gentrap.camelize(value)) match {
       case Some(v) => v
       case other =>
         Logging.addError(s"'$other' is no strand_protocol or strand_protocol is not given")
@@ -122,7 +122,7 @@ class Gentrap(val root: Configurable) extends QScript
     Some(new FragmentsPerExon(this)) else None
 
   lazy val baseCounts = if (expMeasures.contains(ExpMeasures.BaseCounts))
-    Some(new FragmentsPerExon(this)) else None
+    Some(new BaseCounts(this)) else None
 
   lazy val cufflinksBlind = if (expMeasures.contains(ExpMeasures.CufflinksBlind))
     Some(new CufflinksBlind(this)) else None

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

@@ -15,14 +15,15 @@ class BaseCounts(val root: Configurable) extends QScript with Measurement with A
 
   /** Pipeline itself */
   def biopetScript(): Unit = {
-    val jobs = bamFiles.map { case (id, file) =>
-      val baseCounter = new BaseCounter(this)
-      baseCounter.bamFile = file
-      baseCounter.outputDir = new File(outputDir, id)
-      baseCounter.prefix = id
-      baseCounter.refFlat = annotationRefFlat
-      add(baseCounter)
-      id -> baseCounter
+    val jobs = bamFiles.map {
+      case (id, file) =>
+        val baseCounter = new BaseCounter(this)
+        baseCounter.bamFile = file
+        baseCounter.outputDir = new File(outputDir, id)
+        baseCounter.prefix = id
+        baseCounter.refFlat = annotationRefFlat
+        add(baseCounter)
+        id -> baseCounter
     }
 
     def addTableAndHeatmap(countFiles: List[File], outputName: String): Unit = {

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

@@ -16,10 +16,11 @@ trait CufflinksMeasurement extends QScript with Measurement {
   }
 
   def biopetScript(): Unit = {
-    val jobs = bamFiles.map { case (id, file) =>
-      val cufflinks = makeCufflinksJob(id, file)
-      add(cufflinks)
-      id -> cufflinks
+    val jobs = bamFiles.map {
+      case (id, file) =>
+        val cufflinks = makeCufflinksJob(id, file)
+        add(cufflinks)
+        id -> cufflinks
     }
 
     addMergeTableJob(jobs.values.map(_.outputGenesFpkm).toList, mergeGenesFpkmTable, "genes_fpkm")

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

@@ -13,19 +13,20 @@ class FragmentsPerGene(val root: Configurable) extends QScript with Measurement
 
   /** Pipeline itself */
   def biopetScript(): Unit = {
-    val jobs = bamFiles.map { case (id, file) =>
-    //TODO: ID sorting job
+    val jobs = bamFiles.map {
+      case (id, file) =>
+        //TODO: ID sorting job
 
-    val job = new HtseqCount(this)
-    job.inputAnnotation = annotationGtf
-    job.inputAlignment = file
-    job.output = new File(outputDir, s"$name.$id.counts")
-    job.format = Option("bam")
-    // We are forcing the sort order to be ID-sorted, since HTSeq-count often chokes when using position-sorting due
-    // to its buffer not being large enough.
-    //TODO: ID sorting job
-    //job.order = Option("name")
-    id -> job
+        val job = new HtseqCount(this)
+        job.inputAnnotation = annotationGtf
+        job.inputAlignment = file
+        job.output = new File(outputDir, s"$name.$id.counts")
+        job.format = Option("bam")
+        // We are forcing the sort order to be ID-sorted, since HTSeq-count often chokes when using position-sorting due
+        // to its buffer not being large enough.
+        //TODO: ID sorting job
+        //job.order = Option("name")
+        id -> job
     }
 
     addMergeTableJob(jobs.values.map(_.output).toList, mergedTable, "fragments_per_gene")