fix several issues

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

@@ -16,40 +16,44 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
   This tool creates several files with `out` as the root
    */
   @Output(fullName = "out", shortName = "o", doc = "File name base to which coverage metric should be written")
-  var out: String = _
-
-  lazy val outFile: File = {
-    new File(out)
-  }
+  var out: File = _
 
+  @Output
   lazy val summaryFile: File = {
     new File(out + "_summary")
   }
 
+  @Output
   lazy val statisticsFile: File = {
     new File(out + "_statistics")
   }
 
+  @Output
   lazy val intervalSummaryFile: File = {
     new File(out + "_interval_summary")
   }
 
+  @Output
   lazy val intervalStatisticsFile: File = {
     new File(out + "_interval_statistics")
   }
 
+  @Output
   lazy val geneSummaryFile: File = {
     new File(out + "_gene_summary")
   }
 
+  @Output
   lazy val geneStatisticsFile: File = {
     new File(out + "_gene_statistics")
   }
 
+  @Output
   lazy val cumulativeCoverageCountsFile: File = {
     new File(out + "_cumulative_coverage_counts")
   }
 
+  @Output
   lazy val cumulativeCoverageProportionsFile: File = {
     new File(out + "_cumulative_coverage_proportions")
   }

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

@@ -11,6 +11,6 @@ abstract class Xhmm extends BiopetCommandLineFunction with Version {
 
   executable = config("exe", namespace = "xhmm", default = "xhmm")
 
-  def versionCommand = executable + "--version"
+  def versionCommand = executable + required("--version")
   def versionRegex = """xhmm (.*)""".r
 }

kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/Kopisu.scala

@@ -78,6 +78,7 @@ class Kopisu(val root: Configurable) extends QScript with SummaryQScript with Re
     xhmmMethod.foreach { method =>
       method.inputBams = inputBams
       method.outputDir = new File(outputDir, "xhmm_method")
+      add(method)
     }
 
     addSummaryJobs()

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

@@ -95,6 +95,7 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference {
     genotype.inputXcnv = discover.outputXcnv
     genotype.inputMatrix = secondMatrix.outputMatrix
     genotype.outputVcf = new File(xhmmDir, "xhmm.vcf")
+    add(genotype)
 
     addSummaryJobs()