Added MultisamplePipeline

external-example/src/main/scala/org/example/group/ExecutableExample.scala

@@ -9,6 +9,7 @@ object ExecutableExample extends BiopetExecutable {
 
   /** This list defines the pipeline that are usable from the executable */
   def pipelines: List[MainCommand] = List(
+    org.example.group.pipelines.MultisamplePipeline,
     org.example.group.pipelines.BiopetPipeline,
     org.example.group.pipelines.SimplePipeline
   )

external-example/src/main/scala/org/example/group/pipelines/MultisamplePipeline.scala

+package org.example.group.pipelines
+
+import nl.lumc.sasc.biopet.core.{ PipelineCommand, MultiSampleQScript }
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+ * Created by pjvanthof on 30/08/15.
+ */
+class MultisamplePipeline(val root: Configurable) extends QScript with MultiSampleQScript {
+  qscript =>
+  def this() = this(null)
+
+  def init: Unit = {
+  }
+
+  def biopetScript: Unit = {
+    addSamplesJobs() // This executes jobs for all samples
+  }
+
+  def addMultiSampleJobs: Unit = {
+    // this code will be executed after all code of all samples is executed
+  }
+
+  def summaryFile: File = new File(outputDir, "MultisamplePipeline.summary.json")
+
+  //TODO: Add summary
+  def summaryFiles: Map[String, File] = Map()
+
+  //TODO: Add summary
+  def summarySettings: Map[String, Any] = Map()
+
+  def makeSample(id: String) = new Sample(id)
+  class Sample(sampleId: String) extends AbstractSample(sampleId) {
+
+    def makeLibrary(id: String) = new Library(id)
+    class Library(libId: String) extends AbstractLibrary(libId) {
+      //TODO: Add summary
+      def summaryFiles: Map[String, File] = Map()
+
+      //TODO: Add summary
+      def summaryStats: Map[String, Any] = Map()
+
+      def addJobs: Unit = {
+        //TODO: add library specific jobs
+      }
+    }
+
+    //TODO: Add summary
+    def summaryFiles: Map[String, File] = Map()
+
+    //TODO: Add summary
+    def summaryStats: Map[String, Any] = Map()
+
+    def addJobs: Unit = {
+      addPerLibJobs() // This add jobs for each library
+      //TODO: add sample specific jobs
+    }
+  }
+
+}
+
+object MultisamplePipeline extends PipelineCommand
\ No newline at end of file

external-example/src/main/scala/org/example/group/pipelines/SimplePipeline.scala

@@ -10,6 +10,7 @@ import org.broadinstitute.gatk.queue.QScript
  */
 //TODO: Replace class name, must be the same as the class of the pipeline
 class SimplePipeline(val root: Configurable) extends QScript with BiopetQScript {
+  // A constructor without arguments is needed if this pipeline is a root pipeline
   def this() = this(null)
 
   @Input(required = true)