Init for mini pipeline for combining reads

public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/CombineReads.scala

+package nl.lumc.sasc.biopet.pipelines.gears
+
+import nl.lumc.sasc.biopet.core.SampleLibraryTag
+import nl.lumc.sasc.biopet.core.summary.SummaryQScript
+import nl.lumc.sasc.biopet.extensions.Flash
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+  * Created by pjvanthof on 29/12/15.
+  */
+class CombineReads(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag {
+  @Input(doc = "R1 reads in FastQ format", shortName = "R1", required = false)
+  var fastqR1: File = _
+
+  @Input(doc = "R2 reads in FastQ format", shortName = "R2", required = false)
+  var fastqR2: File = _
+
+  /** Init for pipeline */
+  def init(): Unit = {
+  }
+
+  /** Pipeline itself */
+  def biopetScript(): Unit = {
+    val flash = new Flash(this)
+    flash.outputDirectory = new File(outputDir, "flash")
+    flash.fastqR1 = fastqR1
+    flash.fastqR2 = fastqR2
+    add(flash)
+  }
+
+  /** 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(outputDir, "combine_reads.summary.json")
+}