fix more arguments

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

@@ -38,6 +38,7 @@ class XhmmDiscover(val root: Configurable) extends Xhmm with Summarizable {
       required("-R", r) +
       required("-c", outputXcnv) +
       required("-a", outputXcnvAuxFile) +
+      required("-p", discoverParamsFile) +
       required("-s", xhmmAnalysisName)
   }
 

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

@@ -65,7 +65,10 @@ class XhmmMatrix(val root: Configurable) extends Xhmm {
     if (inputExcludeSamples.nonEmpty && inputExcludeTargets.nonEmpty) {
       repeat("--excludeTargets", inputExcludeTargets) + repeat("--excludeSamples", inputExcludeSamples)
     } else if (centerData && zScoreData) {
-      conditional(centerData, "--centerData") + conditional(zScoreData, "--centerData") + required("--maxSdTargetRD", maxsdTargetRD)
+      conditional(centerData, "--centerData") +
+        required("--centerType", centerType) +
+        conditional(zScoreData, "--zScoreData") +
+        required("--maxSdTargetRD", maxsdTargetRD)
     } else {
       required("--minTargetSize", minTargetSize) +
         required("--maxTargetSize", maxTargetSize) +