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) {
-      def addJobs(): Unit = {}
+      protected def addLibJobsInternal(): Unit = {}
     }
 
     var output: FastaOutput = _
     var outputSnps: FastaOutput = _
 
-    def addJobs(): Unit = {
-      runLibraryJobs()
+    protected def addSampleJobsInternal(): Unit = {
+      runLibsJobs()
       output = addGenerateFasta(sampleId, sampleDir)
       outputSnps = addGenerateFasta(sampleId, sampleDir, snpsOnly = true)
     }
@@ -59,7 +59,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
     val refVariants = addGenerateFasta(null, outputDir + "reference/", outputName = "reference")
     val refVariantSnps = addGenerateFasta(null, outputDir + "reference/", outputName = "reference", snpsOnly = true)
 
-    runSamplesJobs()
+    addSamplesJobs()
 
     val catVariants = Cat(this, refVariants.variants :: samples.map(_._2.output.variants).toList, outputDir + "fastas/variant.fasta")
     add(catVariants)

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

@@ -65,7 +65,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
       gatkVariantcalling.sampleID = sampleId
       gatkVariantcalling.outputDir = libDir
 
-      def addJobs(): Unit = {
+      protected def addLibJobsInternal(): Unit = {
         val bamFile: Option[File] = if (config.contains("R1")) {
           mapping.input_R1 = config("R1")
           mapping.input_R2 = config("R2")
@@ -137,8 +137,8 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
     gatkVariantcalling.sampleID = sampleId
     gatkVariantcalling.outputDir = sampleDir + "/variantcalling/"
 
-    def addJobs(): Unit = {
-      runLibraryJobs()
+    protected def addSampleJobsInternal(): Unit = {
+      runLibsJobs()
       gatkVariantcalling.inputBams = libraries.map(_._2.mapping.finalBamFile).toList
       gatkVariantcalling.preProcesBams = false
       if (!singleSampleCalling) {
@@ -162,7 +162,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
   }
 
   def biopetScript() {
-    runSamplesJobs
+    addSamplesJobs
 
     //SampleWide jobs
     val gvcfFiles: List[File] = if (mergeGvcfs && externalGvcfs.size + samples.size > 1) {

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 add(): Unit = {
+      final def addLibJobs(): Unit = {
         currentSample = Some(sampleId)
         currentLib = Some(libraryId)
-        addJobs()
+        addLibJobsInternal()
         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 addJobs()
+      protected def addLibJobsInternal()
     }
 
     /** Library type, need implementation in pipeline */
@@ -84,19 +84,19 @@ trait MultiSampleQScript extends BiopetQScript {
     }
 
     /** Adds sample jobs */
-    final def add(): Unit = {
+    final def addSampleJobs(): Unit = {
       currentSample = Some(sampleId)
-      addJobs()
+      addSampleJobsInternal()
       currentSample = None
     }
 
-    /** Function to add library jobs */
-    protected def addJobs()
+    /** Function to add sample jobs */
+    protected def addSampleJobsInternal()
 
     /** function runs all libraries in one call */
-    protected final def runLibraryJobs(): Unit = {
+    protected final def runLibsJobs(): Unit = {
       for ((libraryId, library) <- libraries) {
-        library.add()
+        library.addLibJobs()
       }
     }
 
@@ -130,9 +130,9 @@ trait MultiSampleQScript extends BiopetQScript {
   }
 
   /** Runs runSingleSampleJobs method for each sample */
-  final def runSamplesJobs() {
+  final def addSamplesJobs() {
     for ((sampleId, sample) <- samples) {
-      sample.add()
+      sample.addSampleJobs()
     }
   }
 

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) {
-      def addJobs(): Unit = {
+      protected def addLibJobsInternal(): Unit = {
         // Library jobs
       }
     }
 
-    def addJobs(): Unit = {
+    protected def addSampleJobsInternal(): Unit = {
       // Sample jobs
     }
   }

public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

@@ -39,10 +39,10 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
   var skipClip: Boolean = config("skip_clip", default = false)
 
   /** Sample name */
-  var sampleName: String = _
+  var sampleId: String = _
 
   /** Library name */
-  var libraryName: String = _
+  var libraryId: String = _
 
   var paired: Boolean = (input_R2 != null)
   var R1_ext: String = _
@@ -60,8 +60,8 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
   def init() {
     if (input_R1 == null) throw new IllegalStateException("Missing R1 on flexiprep module")
     if (outputDir == null) throw new IllegalStateException("Missing Output directory on flexiprep module")
-    if (sampleName == null) throw new IllegalStateException("Missing Sample name on flexiprep module")
-    if (libraryName == null) throw new IllegalStateException("Missing Library name on flexiprep module")
+    if (sampleId == null) throw new IllegalStateException("Missing Sample name on flexiprep module")
+    if (libraryId == null) throw new IllegalStateException("Missing Library name on flexiprep module")
     else if (!outputDir.endsWith("/")) outputDir += "/"
     paired = (input_R2 != null)
 
@@ -79,7 +79,7 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
       R2_name = R2_name.substring(0, R2_name.lastIndexOf(R2_ext))
     }
 
-    summary.out = outputDir + sampleName + "-" + libraryName + ".qc.summary.json"
+    summary.out = outputDir + sampleId + "-" + libraryId + ".qc.summary.json"
   }
 
   def biopetScript() {

public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala

@@ -120,8 +120,8 @@ class FlexiprepSummary(val root: Configurable) extends InProcessFunction with Co
     logger.debug("Start")
     md5Summary()
     val summary = 
-      ("samples" := ( flexiprep.sampleName :=
-        ("libraries" := ( flexiprep.libraryName := (
+      ("samples" := ( flexiprep.sampleId :=
+        ("libraries" := ( flexiprep.libraryId := (
           ("flexiprep" := (
             ("clipping" := !flexiprep.skipClip) ->:
             ("trimming" := !flexiprep.skipTrim) ->:

public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

@@ -126,8 +126,8 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
       flexiprep.outputDir = outputDir + "flexiprep/"
       flexiprep.input_R1 = input_R1
       if (paired) flexiprep.input_R2 = input_R2
-      flexiprep.sampleName = this.sampleId
-      flexiprep.libraryName = this.libraryId
+      flexiprep.sampleId = this.sampleId
+      flexiprep.libraryId = this.libraryId
       flexiprep.init
       flexiprep.runInitialJobs
     }

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

@@ -67,14 +67,14 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
       val prefixFastq: File = createFile(".prefix.fastq")
 
       val flexiprep = new Flexiprep(qscript)
-      flexiprep.sampleName = sampleId
-      flexiprep.libraryName = libraryId
+      flexiprep.sampleId = sampleId
+      flexiprep.libraryId = libraryId
 
       val mapping = new Mapping(qscript)
       mapping.libraryId = libraryId
       mapping.sampleId = sampleId
 
-      def addJobs(): Unit = {
+      protected def addLibJobsInternal(): Unit = {
         flexiprep.outputDir = libDir + "flexiprep/"
         flexiprep.input_R1 = inputFastq
         flexiprep.init
@@ -102,8 +102,8 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
       }
     }
 
-    def addJobs(): Unit = {
-      runLibraryJobs()
+    protected def addSampleJobsInternal(): Unit = {
+      runLibsJobs()
       val libraryBamfiles = libraries.map(_._2.mapping.finalBamFile).toList
       val libraryFastqFiles = libraries.map(_._2.prefixFastq).toList
 
@@ -151,7 +151,7 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
       tagsLibrary = cdl.output
     }
 
-    runSamplesJobs
+    addSamplesJobs
   }
 
   def addBedtoolsCounts(bamFile: File, outputPrefix: String, outputDir: String) {