last bits

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

@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.extensions.gatk
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{ Argument, Output }
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
 
 /**
  * Created by Sander Bollen on 23-11-16.
@@ -44,6 +44,7 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
   @Output
   var cumulativeCoverageProportionsFile = _cumulativeCoverageProportionsFile
 
+  @Input(required = false)
   var calculateCoverageOverGenes: Option[File] = config("calculate_coverage_over_genes", namespace = "depth_of_coverage", default = None)
 
   var countType: Option[String] = config("count_type", namespace = "depth_of_coverage", default = None)
@@ -126,3 +127,13 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
       conditional(printBinEndpointsAndExit, "--printBinEndPointsAndExit")
   }
 }
+
+object DepthOfCoverage {
+  def apply(root: Configurable, bamFile: List[File], outFile: File, targets: List[File]): DepthOfCoverage = {
+    val dp = new DepthOfCoverage(root)
+    dp.input_file = bamFile
+    dp.intervals = targets
+    dp.out = outFile
+    dp
+  }
+}

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmPca.scala

@@ -13,7 +13,7 @@ class XhmmPca(val root: Configurable) extends Xhmm {
   @Input
   var inputMatrix: File = _
 
-  @Output
+  @Output(required = true)
   var pcaFile: File = _
 
   def cmdLine = {

kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/XhmmMethod.scala

@@ -35,7 +35,9 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference {
   }
 
   def biopetScript() = {
-    val depths = inputBams.map(keyValuePair => depthOfCoverage(keyValuePair._2)).toList
+    val depths = inputBams.map { keyValuePair =>
+      DepthOfCoverage(this, List(keyValuePair._2), swapExt(xhmmDir, ".bam", ".dcov"), List(targets))
+    }.toList
     addAll(depths)
 
     // merging of gatk depths files