Renaming values

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

@@ -34,14 +34,14 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
   class Sample(sampleId: String) extends AbstractSample(sampleId) {
     def makeLibrary(id: String) = new Library(id)
     class Library(libraryId: String) extends AbstractLibrary(libraryId) {
-      protected def addLibJobsInternal(): Unit = {}
+      protected def addJobs(): Unit = {}
     }
 
     var output: FastaOutput = _
     var outputSnps: FastaOutput = _
 
-    protected def addSampleJobsInternal(): Unit = {
-      runLibsJobs()
+    protected def addJobs(): Unit = {
+      addLibsJobs()
       output = addGenerateFasta(sampleId, sampleDir)
       outputSnps = addGenerateFasta(sampleId, sampleDir, snpsOnly = true)
     }

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

@@ -54,7 +54,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
       gatkVariantcalling.sampleID = sampleId
       gatkVariantcalling.outputDir = libDir
 
-      protected def addLibJobsInternal(): Unit = {
+      protected def addJobs(): Unit = {
         val bamFile: Option[File] = if (config.contains("R1")) {
           mapping.input_R1 = config("R1")
           mapping.input_R2 = config("R2")
@@ -126,8 +126,8 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
     gatkVariantcalling.sampleID = sampleId
     gatkVariantcalling.outputDir = sampleDir + "/variantcalling/"
 
-    protected def addSampleJobsInternal(): Unit = {
-      runLibsJobs()
+    protected def addJobs(): Unit = {
+      addLibsJobs()
       gatkVariantcalling.inputBams = libraries.map(_._2.mapping.finalBamFile).toList
       gatkVariantcalling.preProcesBams = false
       if (!singleSampleCalling) {

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

@@ -47,10 +47,10 @@ trait MultiSampleQScript extends BiopetQScript {
       val config = new ConfigFunctions(defaultSample = sampleId, defaultLibrary = libraryId)
 
       /** Adds the library jobs */
-      final def addLibJobs(): Unit = {
+      final def addAndTrackJobs(): Unit = {
         currentSample = Some(sampleId)
         currentLib = Some(libraryId)
-        addLibJobsInternal()
+        addJobs()
         currentLib = None
         currentSample = None
       }
@@ -62,7 +62,7 @@ trait MultiSampleQScript extends BiopetQScript {
       def libDir = sampleDir + "lib_" + libraryId + File.separator
 
       /** Function that add library jobs */
-      protected def addLibJobsInternal()
+      protected def addJobs()
     }
 
     /** Library type, need implementation in pipeline */
@@ -84,19 +84,19 @@ trait MultiSampleQScript extends BiopetQScript {
     }
 
     /** Adds sample jobs */
-    final def addSampleJobs(): Unit = {
+    final def addAndTrackJobs(): Unit = {
       currentSample = Some(sampleId)
-      addSampleJobsInternal()
+      addJobs()
       currentSample = None
     }
 
     /** Function to add sample jobs */
-    protected def addSampleJobsInternal()
+    protected def addJobs()
 
     /** function runs all libraries in one call */
-    protected final def runLibsJobs(): Unit = {
+    protected final def addLibsJobs(): Unit = {
       for ((libraryId, library) <- libraries) {
-        library.addLibJobs()
+        library.addAndTrackJobs()
       }
     }
 
@@ -132,7 +132,7 @@ trait MultiSampleQScript extends BiopetQScript {
   /** Runs runSingleSampleJobs method for each sample */
   final def addSamplesJobs() {
     for ((sampleId, sample) <- samples) {
-      sample.addSampleJobs()
+      sample.addAndTrackJobs()
     }
   }
 

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/MultisamplePipelineTemplate.scala

@@ -27,12 +27,12 @@ class MultisamplePipelineTemplate(val root: Configurable) extends QScript with M
 
     def makeLibrary(id: String) = new Library(id)
     class Library(libraryId: String) extends AbstractLibrary(libraryId) {
-      protected def addLibJobsInternal(): Unit = {
+      protected def addJobs(): Unit = {
         // Library jobs
       }
     }
 
-    protected def addSampleJobsInternal(): Unit = {
+    protected def addJobs(): Unit = {
       // Sample jobs
     }
   }

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

@@ -74,7 +74,7 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
       mapping.libraryId = libraryId
       mapping.sampleId = sampleId
 
-      protected def addLibJobsInternal(): Unit = {
+      protected def addJobs(): Unit = {
         flexiprep.outputDir = libDir + "flexiprep/"
         flexiprep.input_R1 = inputFastq
         flexiprep.init
@@ -102,8 +102,8 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
       }
     }
 
-    protected def addSampleJobsInternal(): Unit = {
-      runLibsJobs()
+    protected def addJobs(): Unit = {
+      addLibsJobs()
       val libraryBamfiles = libraries.map(_._2.mapping.finalBamFile).toList
       val libraryFastqFiles = libraries.map(_._2.prefixFastq).toList