extensions arround extensions!

public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesDownload.scala

@@ -9,10 +9,12 @@ import org.broadinstitute.gatk.utils.commandline.Argument
 class ManweDataSourcesDownload(val root: Configurable) extends Manwe {
 
   @Argument(doc = "uri to data source to download")
-  var uri: Option[String] = _
+  var uri: String = _
 
   def subCommand = {
     required("data-sources") + required("download") + required(uri)
   }
 
+  this.deps
+
 }

public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesActivate.scala

@@ -11,7 +11,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Output }
 class ManweSamplesActivate(val root: Configurable) extends Manwe {
 
   @Argument(doc = "uri to sample to activate")
-  var uri: Option[String] = _
+  var uri: String = _
 
   def subCommand = {
     required("samples") + required("activate") +

public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/ManweActivateAfterAnnotImport.scala

+package nl.lumc.sasc.biopet.pipelines.toucan
+
+import nl.lumc.sasc.biopet.extensions.manwe.{ManweAnnotateVcf, ManweSamplesActivate, ManweSamplesImport}
+import nl.lumc.sasc.biopet.utils.config.Configurable
+
+import scala.io.Source
+
+/**
+ * Created by ahbbollen on 9-10-15.
+ * Wrapper for manwe activate after importing and annotating
+ */
+class ManweActivateAfterAnnotImport(root: Configurable,
+                                     annotate: ManweAnnotateVcf,
+                                     imported: ManweSamplesImport) extends ManweSamplesActivate(root) {
+
+  override def beforeGraph: Unit = {
+    super.beforeGraph
+    require(annotate != null, "Annotate should be defined")
+    require(imported != null, "Imported should be defined")
+    this.deps :+= annotate.jobOutputFile
+    this.deps :+= imported.jobOutputFile
+  }
+
+  override def beforeCmd: Unit = {
+    super.beforeCmd
+
+    val reader = Source.fromFile(imported.output)
+    this.uri = reader.getLines().toList.head
+    reader.close()
+  }
+
+}

public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/ManweDownloadAfterAnnotate.scala

+package nl.lumc.sasc.biopet.pipelines.toucan
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.extensions.manwe.{ManweAnnotateVcf, ManweDataSourcesDownload}
+import nl.lumc.sasc.biopet.utils.config.Configurable
+
+import scala.io.Source
+
+/**
+ * Created by ahbbollen on 9-10-15.
+ */
+class ManweDownloadAfterAnnotate(root: Configurable,
+                                 annotate: ManweAnnotateVcf) extends ManweDataSourcesDownload(root) {
+
+
+  override def beforeGraph: Unit = {
+    super.beforeGraph
+    require(annotate != null, "Annotate should be defined")
+    this.deps :+= annotate.jobOutputFile
+  }
+
+  override def beforeCmd: Unit = {
+    super.beforeCmd
+
+
+    val reader = Source.fromFile(annotate.output)
+    this.uri = reader.getLines().toList.head
+    reader.close()
+  }
+
+}