Added annotation traits

public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/annotations/Annotations.scala

+package nl.lumc.sasc.biopet.core.annotations
+
+import nl.lumc.sasc.biopet.core.BiopetQScript
+import nl.lumc.sasc.biopet.core.BiopetQScript.InputFile
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+  * Created by pjvan_thof on 1/12/16.
+  */
+trait AnnotationGtf extends BiopetQScript { qscript: QScript =>
+  /** GTF reference file */
+  lazy val annotationGtf: File = {
+    val file: File = config("annotation_gtf")
+    inputFiles :+ InputFile(file, config("annotation_gtf_md5"))
+    file
+  }
+}
+
+trait AnnotationBed extends BiopetQScript { qscript: QScript =>
+  /** GTF reference file */
+  lazy val annotationBed: File = {
+    val file: File = config("annotation_bed")
+    inputFiles :+ InputFile(file, config("annotation_bed_md5"))
+    file
+  }
+}
+
+trait AnnotationRefFlat extends BiopetQScript { qscript: QScript =>
+  /** GTF reference file */
+  lazy val annotationRefFlat: File = {
+    val file: File = config("annotation_refflat")
+    inputFiles :+ InputFile(file, config("annotation_refflat_md5"))
+    file
+  }
+}
+
+trait RibosomalRefFlat extends BiopetQScript { qscript: QScript =>
+  /** GTF reference file */
+  lazy val ribosomalRefFlat: File = {
+    val file: File = config("ribosome_refflat")
+    inputFiles :+ InputFile(file, config("ribosome_refflat_md5"))
+    file
+  }
+}