Merge branch 'feature-delly-merge' into shiva-refactor

Conflicts:
	public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala

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

+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+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 BiopetJavaCommandLineFunction with Reference {
+
+  javaMainClass = classOf[org.broadinstitute.gatk.tools.CatVariants].getClass.getName
+
+  @Input(required = true)
+  var inputFiles: List[File] = Nil
+
+  @Output(required = true)
+  var outputFile: File = null
+
+  @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 {
+  def apply(root: Configurable, input: List[File], output: File): CatVariants = {
+    val cv = new CatVariants(root)
+    cv.inputFiles = input
+    cv.outputFile = output
+    cv
+  }
+}
\ No newline at end of file

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

@@ -13,17 +13,20 @@
  * license; For commercial users or users who do not want to follow the AGPL
  * license, please contact us to obtain a separate license.
  */
-package nl.lumc.sasc.biopet.extensions.delly
+package nl.lumc.sasc.biopet.pipelines.shiva
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{ Reference, BiopetQScript, PipelineCommand }
-import nl.lumc.sasc.biopet.utils.config.Configurable
+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
-import org.broadinstitute.gatk.queue.extensions.gatk.CatVariants
 
-class Delly(val root: Configurable) extends QScript with BiopetQScript with Reference {
+class Delly(val root: Configurable) extends QScript with Reference with SummaryQScript {
   def this() = this(null)
 
   @Input(doc = "Input file (bam)")
@@ -49,9 +52,27 @@ class Delly(val root: Configurable) extends QScript with BiopetQScript with Refe
     if (outputVcf == null) outputVcf = new File(workDir, outputName + ".delly.vcf")
   }
 
+  override def summaryFile: File = new File(workDir, "Delly.summary.json")
+
+  override def summaryFiles: Map[String, File] = Map.empty ++
+    Map("input" -> input) ++
+    Map("outputVCF" -> outputVcf)
+
+  override def summarySettings = {
+    Map(
+      "workDir" -> workDir,
+      "outputName" -> outputName,
+      "del" -> del,
+      "dup" -> dup,
+      "inv" -> inv,
+      "tra" -> tra
+    )
+  }
+
   def biopetScript() {
     // write the pipeline here
     logger.info("Configuring Delly pipeline")
+
     var outputFiles: Map[String, File] = Map()
     var vcfFiles: Map[String, File] = Map()
 
@@ -91,15 +112,13 @@ class Delly(val root: Configurable) extends QScript with BiopetQScript with Refe
     // we need to merge the vcf's
     val finalVCF = if (vcfFiles.size > 1) {
       // do merging
-      // CatVariants is a $org.broadinstitute.gatk.utils.commandline.CommandLineProgram$;
-      //TODO: convert to biopet extension
-      val variants = new CatVariants()
-      variants.variant = vcfFiles.values.toList
+      val variants = new CatVariants(this)
+      variants.inputFiles = vcfFiles.values.toList
       variants.outputFile = this.outputVcf
-      variants.reference = referenceFasta()
+      //      variants.reference = referenceFasta()
       // add the job
-      //add(variants)
-      Some(outputVcf)
+      add(variants)
+      Some(variants.outputFile)
     } else if (vcfFiles.size == 1) {
       // TODO: pretify this
       val ln = Ln(this, vcfFiles.head._2, this.outputVcf, relative = true)
@@ -112,8 +131,6 @@ class Delly(val root: Configurable) extends QScript with BiopetQScript with Refe
 }
 
 object Delly extends PipelineCommand {
-  override val pipeline = "/nl/lumc/sasc/biopet/extensions/svcallers/Delly/Delly.class"
-
   def apply(root: Configurable, input: File, workDir: File): Delly = {
     val dellyPipeline = new Delly(root)
     dellyPipeline.input = input

public/yamsvp/src_old/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala

@@ -21,15 +21,15 @@ package nl.lumc.sasc.biopet.pipelines.yamsvp
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.{ MultiSampleQScript, PipelineCommand }
+import nl.lumc.sasc.biopet.core.{MultiSampleQScript, PipelineCommand}
 import nl.lumc.sasc.biopet.extensions.Ln
 import nl.lumc.sasc.biopet.extensions.breakdancer.Breakdancer
 import nl.lumc.sasc.biopet.extensions.clever.CleverCaller
 import nl.lumc.sasc.biopet.extensions.igvtools.IGVToolsCount
-import nl.lumc.sasc.biopet.extensions.sambamba.{ SambambaMarkdup, SambambaMerge }
+import nl.lumc.sasc.biopet.extensions.sambamba.{SambambaMarkdup, SambambaMerge}
+import nl.lumc.sasc.biopet.pipelines.shiva.Delly
+import nl.lumc.sasc.biopet.utils.config.Configurable
 //import nl.lumc.sasc.biopet.extensions.pindel.Pindel
-import nl.lumc.sasc.biopet.extensions.delly.Delly
 import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
 import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
 import org.broadinstitute.gatk.queue.QScript