diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/BasesPerExon.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/BasesPerExon.scala
new file mode 100644
index 0000000000000000000000000000000000000000..3803b5dce9101c66525393a3c3efd4a3037330d3
--- /dev/null
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/BasesPerExon.scala
@@ -0,0 +1,24 @@
+package nl.lumc.sasc.biopet.pipelines.gentrap.measures
+
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+  * Created by pjvan_thof on 1/12/16.
+  */
+class BasesPerExon(val root: Configurable) extends QScript with Measurement {
+  /** Init for pipeline */
+  def init(): Unit = ???
+
+  /** Pipeline itself */
+  def biopetScript(): Unit = ???
+
+  /** Must return a map with used settings for this pipeline */
+  def summarySettings: Map[String, Any] = Map()
+
+  /** File to put in the summary for thie pipeline */
+  def summaryFiles: Map[String, File] = Map()
+
+  /** Name of summary output file */
+  def summaryFile: File = new File("BasesPerExon.summary.json")
+}
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/BasesPerGene.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/BasesPerGene.scala
new file mode 100644
index 0000000000000000000000000000000000000000..a550a02c126cf8875234f892ca31f1054c176449
--- /dev/null
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/BasesPerGene.scala
@@ -0,0 +1,24 @@
+package nl.lumc.sasc.biopet.pipelines.gentrap.measures
+
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+  * Created by pjvan_thof on 1/12/16.
+  */
+class BasesPerGene(val root: Configurable) extends QScript with Measurement {
+  /** Init for pipeline */
+  def init(): Unit = ???
+
+  /** Pipeline itself */
+  def biopetScript(): Unit = ???
+
+  /** Must return a map with used settings for this pipeline */
+  def summarySettings: Map[String, Any] = Map()
+
+  /** File to put in the summary for thie pipeline */
+  def summaryFiles: Map[String, File] = Map()
+
+  /** Name of summary output file */
+  def summaryFile: File = new File("BasesPerGene.summary.json")
+}
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksBlind.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksBlind.scala
new file mode 100644
index 0000000000000000000000000000000000000000..3615540f2c0a32246cabbf5347f031d635fa716d
--- /dev/null
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksBlind.scala
@@ -0,0 +1,24 @@
+package nl.lumc.sasc.biopet.pipelines.gentrap.measures
+
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+  * Created by pjvan_thof on 1/12/16.
+  */
+class CufflinksBlind(val root: Configurable) extends QScript with Measurement {
+  /** Init for pipeline */
+  def init(): Unit = ???
+
+  /** Pipeline itself */
+  def biopetScript(): Unit = ???
+
+  /** Must return a map with used settings for this pipeline */
+  def summarySettings: Map[String, Any] = Map()
+
+  /** File to put in the summary for thie pipeline */
+  def summaryFiles: Map[String, File] = Map()
+
+  /** Name of summary output file */
+  def summaryFile: File = new File("CufflinksBlind.summary.json")
+}
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksGuided.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksGuided.scala
new file mode 100644
index 0000000000000000000000000000000000000000..900c707f609ffab36a0ca4c08cff28cc27d3a94b
--- /dev/null
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksGuided.scala
@@ -0,0 +1,24 @@
+package nl.lumc.sasc.biopet.pipelines.gentrap.measures
+
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+  * Created by pjvan_thof on 1/12/16.
+  */
+class CufflinksGuided(val root: Configurable) extends QScript with Measurement {
+  /** Init for pipeline */
+  def init(): Unit = ???
+
+  /** Pipeline itself */
+  def biopetScript(): Unit = ???
+
+  /** Must return a map with used settings for this pipeline */
+  def summarySettings: Map[String, Any] = Map()
+
+  /** File to put in the summary for thie pipeline */
+  def summaryFiles: Map[String, File] = Map()
+
+  /** Name of summary output file */
+  def summaryFile: File = new File("CufflinksGuided.summary.json")
+}
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksStrict.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksStrict.scala
new file mode 100644
index 0000000000000000000000000000000000000000..0055d46bcf844675e4eb8fe9298593b3fe951d37
--- /dev/null
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksStrict.scala
@@ -0,0 +1,24 @@
+package nl.lumc.sasc.biopet.pipelines.gentrap.measures
+
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+  * Created by pjvan_thof on 1/12/16.
+  */
+class CufflinksStrict(val root: Configurable) extends QScript with Measurement {
+  /** Init for pipeline */
+  def init(): Unit = ???
+
+  /** Pipeline itself */
+  def biopetScript(): Unit = ???
+
+  /** Must return a map with used settings for this pipeline */
+  def summarySettings: Map[String, Any] = Map()
+
+  /** File to put in the summary for thie pipeline */
+  def summaryFiles: Map[String, File] = Map()
+
+  /** Name of summary output file */
+  def summaryFile: File = new File("CufflinksStrict.summary.json")
+}
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerExon.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerExon.scala
new file mode 100644
index 0000000000000000000000000000000000000000..623dd039bc3052d1952a8dab500b241d72a108d6
--- /dev/null
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerExon.scala
@@ -0,0 +1,24 @@
+package nl.lumc.sasc.biopet.pipelines.gentrap.measures
+
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+  * Created by pjvan_thof on 1/12/16.
+  */
+class FragmentsPerExon(val root: Configurable) extends QScript with Measurement {
+  /** Init for pipeline */
+  def init(): Unit = ???
+
+  /** Pipeline itself */
+  def biopetScript(): Unit = ???
+
+  /** Must return a map with used settings for this pipeline */
+  def summarySettings: Map[String, Any] = Map()
+
+  /** File to put in the summary for thie pipeline */
+  def summaryFiles: Map[String, File] = Map()
+
+  /** Name of summary output file */
+  def summaryFile: File = new File("FragmentsPerExon.summary.json")
+}
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerGene.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerGene.scala
new file mode 100644
index 0000000000000000000000000000000000000000..c3c24e268b08fc12502e0be31382a27e01879187
--- /dev/null
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerGene.scala
@@ -0,0 +1,24 @@
+package nl.lumc.sasc.biopet.pipelines.gentrap.measures
+
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+  * Created by pjvan_thof on 1/12/16.
+  */
+class FragmentsPerGene(val root: Configurable) extends QScript with Measurement {
+  /** Init for pipeline */
+  def init(): Unit = ???
+
+  /** Pipeline itself */
+  def biopetScript(): Unit = ???
+
+  /** Must return a map with used settings for this pipeline */
+  def summarySettings: Map[String, Any] = Map()
+
+  /** File to put in the summary for thie pipeline */
+  def summaryFiles: Map[String, File] = Map()
+
+  /** Name of summary output file */
+  def summaryFile: File = new File("FragmentsPerGene.summary.json")
+}
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/Measurement.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/Measurement.scala
new file mode 100644
index 0000000000000000000000000000000000000000..eb39c09c9302b6da38979bdb2babebef5099e5a4
--- /dev/null
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/Measurement.scala
@@ -0,0 +1,17 @@
+package nl.lumc.sasc.biopet.pipelines.gentrap.measures
+
+import nl.lumc.sasc.biopet.core.Reference
+import nl.lumc.sasc.biopet.core.summary.SummaryQScript
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+  * Created by pjvan_thof on 1/12/16.
+  */
+trait Measurement extends SummaryQScript with Reference { qscript : QScript =>
+  private var bamFiles: Map[String, File] = Map()
+
+  def addBamfile(id: String, file: File): Unit = {
+    require(!bamFiles.contains(id), s"'$id' already exist")
+    bamFiles += id -> file
+  }
+}