Added CatVariants

protected/biopet-gatk-extensions/pom.xml

@@ -25,7 +25,7 @@
     <dependencies>
         <dependency>
             <groupId>nl.lumc.sasc</groupId>
-            <artifactId>BiopetCore</artifactId>
+            <artifactId>BiopetExtensions</artifactId>
             <version>${project.version}</version>
         </dependency>
         <dependency>

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CatVariants.scala

@@ -17,24 +17,32 @@ package nl.lumc.sasc.biopet.extensions.gatk
 
 import java.io.File
 
+import nl.lumc.sasc.biopet.core.{ Reference, BiopetJavaCommandLineFunction }
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
-class CatVariants(val root: Configurable) extends Gatk {
-  val analysisType = "CatVariants"
+class CatVariants(val root: Configurable) extends BiopetJavaCommandLineFunction with Reference {
 
-  @Input(doc = "", required = true)
+  javaMainClass = classOf[org.broadinstitute.gatk.tools.CatVariants].getClass.getName
+
+  @Input(required = true)
   var inputFiles: List[File] = Nil
 
-  @Output(doc = "", required = true)
+  @Output(required = true)
   var outputFile: File = null
 
-  override def cmdLine = super.cmdLine +
-    (for (file <- inputFiles) yield {
-      required("-V", file)
-    }).mkString +
-    required("-o", outputFile)
+  @Input
+  var reference: File = null
 
+  override def beforeGraph(): Unit = {
+    super.beforeGraph()
+    if (reference == null) reference = referenceFasta()
+  }
+
+  override def cmdLine = super.cmdLine +
+    repeat("-V", inputFiles) +
+    required("-out", outputFile) +
+    required("-R", reference)
 }
 
 object CatVariants {

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala → public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala

@@ -10,8 +10,6 @@ import org.broadinstitute.gatk.engine.phonehome.GATKRunReport
 import org.broadinstitute.gatk.queue.extensions.gatk.CommandLineGATK
 
 trait GatkGeneral extends CommandLineGATK with CommandLineResources with Reference with Version {
-  memoryLimit = Option(3)
-
   var executable: String = config("java", default = "java", submodule = "java", freeVar = false)
 
   override def subPath = "gatk" :: super.subPath

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Delly.scala

@@ -21,6 +21,7 @@ import nl.lumc.sasc.biopet.core.summary.SummaryQScript
 import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference }
 import nl.lumc.sasc.biopet.extensions.Ln
 import nl.lumc.sasc.biopet.extensions.delly.DellyCaller
+
 import nl.lumc.sasc.biopet.extensions.gatk.CatVariants
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript