Add ShiveGatk

protected/biopet-gatk-pipelines/pom.xml

@@ -39,5 +39,10 @@
             <artifactId>Mapping</artifactId>
             <version>${project.version}</version>
         </dependency>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>Shiva</artifactId>
+            <version>${project.version}</version>
+        </dependency>
     </dependencies>
 </project>

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaGatk.scala

+package nl.lumc.sasc.biopet.pipelines.gatk
+
+import nl.lumc.sasc.biopet.core.PipelineCommand
+import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.pipelines.shiva.{ShivaTrait, Shiva}
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+ * Created by pjvan_thof on 2/26/15.
+ */
+class ShivaGatk(val root: Configurable) extends QScript with ShivaTrait {
+  def this() = this(null)
+
+  override def makeSample(id: String) = new this.Sample(id)
+  class Sample(sampleId: String) extends super.Sample(sampleId) {
+    override def makeLibrary(id: String) = new this.Library(id)
+    class Library(libId: String) extends super.Library(libId) {
+      override def preProcess(input:File): Option[File] = {
+        //TODO: add preproces
+        None
+      }
+    }
+
+    override def doublePreProcess(input: List[File], isIntermediate: Boolean = false): Option[File] = {
+      if (input.size <= 1) super.doublePreProcess(input)
+      else {
+        super.doublePreProcess(input)
+        //TODO: Add indel realignment
+      }
+    }
+  }
+
+}
+
+object ShivaGatk extends PipelineCommand
\ No newline at end of file

protected/biopet-protected-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutableProtected.scala

@@ -12,6 +12,7 @@ object BiopetExecutableProtected extends BiopetExecutable {
     nl.lumc.sasc.biopet.pipelines.gatk.GatkVariantcalling,
     nl.lumc.sasc.biopet.pipelines.gatk.GatkPipeline,
     nl.lumc.sasc.biopet.pipelines.gatk.GatkVariantRecalibration,
+    nl.lumc.sasc.biopet.pipelines.gatk.ShivaGatk,
     nl.lumc.sasc.biopet.pipelines.basty.Basty)
 
   def tools = BiopetExecutablePublic.tools