Add tinycap to aggregate for scoverage

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

@@ -47,9 +47,6 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction with Vers
   var nogroup: Boolean = config("nogroup", default = false)
   var extract: Boolean = config("extract", default = true)
 
-  // The following variable is specific for biopet
-  var sensitiveAdapterSearch: Boolean = config("sensitiveAdapterSearch", default = false)
-
   def versionRegex = """FastQC (.*)""".r
   def versionCommand = executable + " --version"
   override def defaultThreads = 4

public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala

@@ -33,6 +33,9 @@ import htsjdk.samtools.util.SequenceUtil.reverseComplement
  */
 class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(root) with Summarizable {
 
+  /** Allow reporting of all found (potentially adapter) sequences in the FastQC */
+  var sensitiveAdapterSearch: Boolean = config("sensitiveAdapterSearch", default = false)
+
   /** Class for storing a single FastQC module result */
   protected case class FastQCModule(name: String, status: String, lines: Seq[String])
 

public/tinycap/src/main/scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCap.scala

@@ -69,11 +69,11 @@ class TinyCap(val root: Configurable) extends QScript
     )
   )
 
-  lazy val fragmentsPerGene = Some(new FragmentsPerGene(this))
-  lazy val fragmentsPerSmallRna = Some(new FragmentsPerSmallRna(this))
-  lazy val baseCounts = Some(new BaseCounts(this))
+  lazy val fragmentsPerGene = new FragmentsPerGene(this)
+  lazy val fragmentsPerSmallRna = new FragmentsPerSmallRna(this)
+  lazy val baseCounts = new BaseCounts(this)
 
-  def executedMeasures = (fragmentsPerGene :: fragmentsPerSmallRna :: baseCounts :: Nil).flatten
+  def executedMeasures = (fragmentsPerGene :: fragmentsPerSmallRna :: baseCounts :: Nil)
 
   override def init = {
     super.init()