Trying out Queue for the first time.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4705 348d0f76-0448-11de-a6fe-93d51630548a

scala/qscript/hanna/DoC.scala

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+import org.broadinstitute.sting.gatk.DownsampleType
+import org.broadinstitute.sting.queue.QScript
+import org.broadinstitute.sting.queue.extensions.gatk._
+
+/**
+ * A pipeline for Queue that runs a custom walker outside of the GATK jar.
+ * NOTE: This code is an unsupported example for soliciting feedback on how to improve Queue.
+ * Future syntax will simplify running the GATK so please expect the syntax below to change significantly.
+ */
+class DoC extends QScript {
+  // The full packaged jar should be used.
+  // You can build this jar via 'ant package' and then find it under
+  // 'Sting/dist/packages/GenomeAnalysisTK-*/GenomeAnalysisTK.jar'
+  @Input(doc="The path to the packaged GenomeAnalysisTK.jar file.", shortName="gatk")
+  var gatkJar: File = null
+
+  @Input(doc="The reference file for the bam files.", shortName="R")
+  var referenceFile: File = null
+
+  // NOTE: Do not initialize List, Set, or Option to null
+  // as you won't be able to update the collection.
+  // By default set:
+  //   List[T] = Nil
+  //   Set[T] = Set.empty[T]
+  //   Option[T] = None
+  @Input(doc="One or more bam files.", shortName="I")
+  var bamFiles: List[File] = Nil
+
+  @Input(doc="An optional file with a list of intervals to proccess.", shortName="L", required=false)
+  var intervalsString: List[String] = List("2:87000001-90000000")
+
+  // This trait allows us set the variables below in one place,
+  // and then reuse this trait on each CommandLineGATK function below.
+  trait DepthOfCoverageArguments extends CommandLineGATK {
+    this.jarFile = DoC.this.gatkJar
+    this.reference_sequence = DoC.this.referenceFile
+    this.intervalsString = DoC.this.intervalsString
+    this.memoryLimit = Some(8)
+  }
+
+
+  def script = {
+    // Create the four function that we can run.
+    val doc = new DepthOfCoverage with DepthOfCoverageArguments
+    doc.downsampling_type = Some(DownsampleType.NONE)
+    doc.omitLocusTable = true
+    doc.omitIntervals = true
+    doc.omitSampleSummary = true        
+
+    // If you are running this on a compute farm, make sure that the Sting/shell
+    // folder is in your path to use mergeText.sh and splitIntervals.sh.
+    //doc.scatterCount = 3
+    doc.input_file = DoC.this.bamFiles
+    doc.out = new File("doc-all.out")
+
+    add(doc)
+  }
+
+}