Fixing compile issues

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/MuTect2.scala

@@ -3,9 +3,7 @@ package nl.lumc.sasc.biopet.extensions.gatk
 import java.io.File
 
 import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
-import nl.lumc.sasc.biopet.extensions.gatk.CommandLineGATK.isFileWithTag
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
 import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Input, Output}
 
 class MuTect2(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
@@ -181,8 +179,7 @@ class MuTect2(val parent: Configurable) extends CommandLineGATK with ScatterGath
   @Argument(fullName = "useNewAFCalculator", shortName = "newQual", required = false)
   var useNewAFCalculator: Boolean = config("use_new_af_calculator", default = false)
 
-
-  override def cmdLine = super.cmdLine +
+  override def cmdLine: String = super.cmdLine +
     optional("--cosmic", cosmic) +
     optional("--dbsnp", dbsnp) +
     optional("--normal_panel", ponFile) +
@@ -213,13 +210,3 @@ class MuTect2(val parent: Configurable) extends CommandLineGATK with ScatterGath
     conditional(useNewAFCalculator, "--useNewAFCalculator") +
     (if (outputAsStdout) "" else required("--out", outputVcf))
 }
-
-object MuTect2 {
-  def apply(parent: Configurable, tumorSampleBam: File, normalSampleBam: File, output: File): MuTect2 = {
-    val mutect2 = new MuTect2(parent)
-    mutect2.tumorSampleBam = tumorSampleBam
-    mutect2.normalSampleBam = normalSampleBam
-    mutect2.outputVcf = output
-    mutect2
-  }
-}

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala

@@ -416,8 +416,8 @@ object ConfigUtils extends Logging {
         Logging.addError(
           "Value does not exist but is required, key: " + value.requestIndex.key +
             "  namespace: " + value.requestIndex.module,
-          if (value.requestIndex.path != Nil) "  path: " + value.requestIndex.path.mkString("->")
-          else null
+          if (value.requestIndex.path != Nil) Some("  path: " + value.requestIndex.path.mkString("->"))
+          else None
         )
       exist
     }