Merge branch 'feature-gatk_et_option' into 'develop'

Add et option to gatk jobs

Added the et option to gatk.

@a.h.b.bollen: could you maybe test this? I don't have a key

See merge request !169

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala

@@ -5,7 +5,8 @@
  */
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
-import nl.lumc.sasc.biopet.core.{ BiopetJavaCommandLineFunction, Reference }
+import nl.lumc.sasc.biopet.core.{ Reference, BiopetJavaCommandLineFunction }
+import org.broadinstitute.gatk.engine.phonehome.GATKRunReport
 import org.broadinstitute.gatk.queue.extensions.gatk.CommandLineGATK
 
 trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction with Reference {
@@ -20,6 +21,15 @@ trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction wit
 
   if (config.contains("intervals")) intervals = config("intervals").asFileList
   if (config.contains("exclude_intervals")) excludeIntervals = config("exclude_intervals").asFileList
+
+  Option(config("et").value) match {
+    case Some("NO_ET")  => et = GATKRunReport.PhoneHomeOption.NO_ET
+    case Some("AWS")    => et = GATKRunReport.PhoneHomeOption.AWS
+    case Some("STDOUT") => et = GATKRunReport.PhoneHomeOption.STDOUT
+    case Some(x)        => throw new IllegalArgumentException(s"Unknown et option for gatk: $x")
+    case _              =>
+  }
+
   if (config.contains("gatk_key")) gatk_key = config("gatk_key")
   if (config.contains("pedigree")) pedigree = config("pedigree")
 

public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala

@@ -49,6 +49,8 @@ abstract class Gatk extends BiopetJavaCommandLineFunction with Reference {
   @Input(required = false)
   var pedigree: List[File] = config("pedigree", default = Nil)
 
+  var et: Option[String] = config("et")
+
   override def versionRegex = """(.*)""".r
   override def versionExitcode = List(0, 1)
   override def versionCommand = executable + " -jar " + jarFile + " -version"
@@ -65,6 +67,7 @@ abstract class Gatk extends BiopetJavaCommandLineFunction with Reference {
     required("-T", analysisType) +
     required("-R", reference) +
     optional("-K", gatkKey) +
+    optional("-et", et) +
     repeat("-I", intervals) +
     repeat("-XL", excludeIntervals) +
     repeat("-ped", pedigree)