Name change

protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala

@@ -56,7 +56,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
     gatkPipeline.biopetScript
     addAll(gatkPipeline.functions)
 
-    addPerSampleJobs()
+    addSamplesJobs()
   }
 
   def addMultiSampleJobs(): Unit = {

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala

@@ -151,7 +151,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
   }
 
   def biopetScript(): Unit = {
-    addPerSampleJobs
+    addSamplesJobs()
   }
 
   def addMultiSampleJobs(): Unit = {

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala

@@ -128,7 +128,7 @@ trait MultiSampleQScript extends BiopetQScript {
   protected def sampleIds: Set[String] = ConfigUtils.any2map(Config.global.map("samples")).keySet
 
   /** Runs addAndTrackJobs method for each sample */
-  final def addPerSampleJobs() {
+  final def addSamplesJobs() {
     if (onlySamples.isEmpty) {
       samples.foreach { case (sampleId, sample) => sample.addAndTrackJobs() }
       addMultiSampleJobs()

public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala

@@ -102,7 +102,7 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript {
     // Third step is calling peaks on the bam files produced with the mapping pipeline, this will be done with MACS2
     logger.info("Starting CArP pipeline")
 
-    addPerSampleJobs
+    addSamplesJobs()
   }
 
   def addMultiSampleJobs(): Unit = {

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

@@ -30,7 +30,7 @@ class Kopisu(val root: Configurable) extends QScript with MultiSampleQScript {
   }
 
   def biopetScript() {
-    this.addPerSampleJobs()
+    addSamplesJobs()
   }
 
   def makeSample(id: String) = new Sample(id)

public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala

@@ -151,7 +151,7 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
       tagsLibrary = cdl.output
     }
 
-    addPerSampleJobs
+    addSamplesJobs()
   }
 
   def addMultiSampleJobs(): Unit = {