Rename afterGraph to beforeGraph

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

@@ -11,8 +11,8 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 class ApplyRecalibration(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.ApplyRecalibration with GatkGeneral {
   scatterCount = config("scattercount", default = 0)
 
-  override def afterGraph {
-    super.afterGraph
+  override def beforeGraph {
+    super.beforeGraph
 
     nt = Option(getThreads(3))
     memoryLimit = Option(nt.getOrElse(1) * 2)

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

@@ -22,7 +22,7 @@ object BaseRecalibrator {
     val br = new BaseRecalibrator(root)
     br.input_file :+= input
     br.out = output
-    br.afterGraph
+    br.beforeGraph
     return br
   }
 }
\ No newline at end of file

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

@@ -35,8 +35,8 @@ class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.qu
     stand_emit_conf = config("stand_emit_conf", default = 0)
   }
 
-  override def afterGraph {
-    super.afterGraph
+  override def beforeGraph {
+    super.beforeGraph
     if (bamOutput != null && nct.getOrElse(1) > 1) {
       threads = 1
       logger.warn("BamOutput is on, nct/threads is forced to set on 1, this option is only for debug")

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

@@ -8,8 +8,8 @@ package nl.lumc.sasc.biopet.extensions.gatk
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class UnifiedGenotyper(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.UnifiedGenotyper with GatkGeneral {
-  override def afterGraph {
-    super.afterGraph
+  override def beforeGraph {
+    super.beforeGraph
 
     genotype_likelihoods_model = org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.BOTH
     if (config.contains("scattercount")) scatterCount = config("scattercount")

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

@@ -9,8 +9,8 @@ import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class VariantEval(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.VariantEval with GatkGeneral {
-  override def afterGraph {
-    super.afterGraph
+  override def beforeGraph {
+    super.beforeGraph
   }
 }
 
@@ -21,7 +21,7 @@ object VariantEval {
     vareval.eval = Seq(sample)
     vareval.comp = Seq(compareWith)
     vareval.out = output
-    vareval.afterGraph
+    vareval.beforeGraph
     return vareval
   }
 
@@ -35,7 +35,7 @@ object VariantEval {
     vareval.ST = ST
     vareval.noEV = true
     vareval.EV = EV
-    vareval.afterGraph
+    vareval.beforeGraph
     return vareval
   }
 

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

@@ -51,15 +51,14 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
    * Can overr
    * ide this method. This is executed after the script is done en queue starts to generate the graph
    */
-  protected[core] def afterGraph {}
-  //TODO: function need rename to beforeGraph
+  protected[core] def beforeGraph {}
 
   /**
    * Set default output file, threads and vmem for current job
    */
   override def freezeFieldValues() {
     checkExecutable
-    afterGraph
+    beforeGraph
     if (jobOutputFile == null) jobOutputFile = new File(firstOutput.getParent + "/." + firstOutput.getName + "." + configName + ".out")
 
     if (threads == 0) threads = getThreads(defaultThreads)
@@ -126,7 +125,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
 
     addJobReportBinding("cores", nCoresRequest match {
       case Some(n) if n > 0 => n
-      case _ => 1
+      case _                => 1
     })
     addJobReportBinding("version", getVersion)
   }

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

@@ -37,8 +37,8 @@ trait BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetC
   /**
    * Sets memory limit
    */
-  override def afterGraph {
-    super.afterGraph
+  override def beforeGraph {
+    super.beforeGraph
     memoryLimit = config("memory_limit")
   }
 

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

@@ -72,7 +72,7 @@ trait BiopetQScript extends Configurable with GatkLogging {
     for (function <- functions) function match {
       case f: BiopetCommandLineFunctionTrait => {
         f.checkExecutable
-        f.afterGraph
+        f.beforeGraph
         f.commandLine
       }
       case _ =>

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala

@@ -48,7 +48,7 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
   override def versionCommand = executable + " --version"
   override val defaultThreads = 4
 
-  override def afterGraph {
+  override def beforeGraph {
     this.checkExecutable
 
     val fastqcDir = new File(executable).getParent

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala

@@ -64,10 +64,10 @@ class Raxml(val root: Configurable) extends BiopetCommandLineFunction {
   var executableNonThreads: String = config("exe", default = "raxmlHPC")
   var executableThreads: Option[String] = config("exe_pthreads")
 
-  override def afterGraph {
+  override def beforeGraph {
     if (threads == 0) threads = getThreads(defaultThreads)
     executable = if (threads > 1 && executableThreads.isDefined) executableThreads.get else executableNonThreads
-    super.afterGraph
+    super.beforeGraph
     out +:= getInfoFile
     f match {
       case "d" if b.isEmpty => {

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala

@@ -47,8 +47,8 @@ class RunGubbins(val root: Configurable) extends BiopetCommandLineFunction {
   var verbose: Boolean = config("verbose", default = false)
   var noCleanup: Boolean = config("no_cleanup", default = false)
 
-  override def afterGraph: Unit = {
-    super.afterGraph
+  override def beforeGraph: Unit = {
+    super.beforeGraph
     jobLocalDir = new File(outputDirectory)
     if (prefix.isEmpty) prefix = Some(fastafile.getName)
     val out: List[String] = List(".recombination_predictions.embl",

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala

@@ -53,7 +53,7 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction {
   override val versionRegex = """sickle version (.*)""".r
   override def versionCommand = executable + " --version"
 
-  override def afterGraph {
+  override def beforeGraph {
     if (qualityType.isEmpty) qualityType = Some(defaultQualityType)
   }
 

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala

@@ -62,7 +62,7 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction {
   override val defaultVmem = "6G"
   override val defaultThreads = 8
 
-  override def afterGraph() {
+  override def beforeGraph() {
     if (outFileNamePrefix != null && !outFileNamePrefix.endsWith(".")) outFileNamePrefix += "."
     val prefix = if (outFileNamePrefix != null) outputDir + outFileNamePrefix else outputDir
     if (runmode == null) {
@@ -103,7 +103,7 @@ object Star {
     star.outputDir = outputDir
     star.isIntermediate = isIntermediate
     star.deps = deps
-    star.afterGraph
+    star.beforeGraph
     return star
   }
 
@@ -111,20 +111,20 @@ object Star {
     val starCommand_pass1 = Star(configurable, R1, if (R2 != null) R2 else null, new File(outputDir, "aln-pass1"))
     starCommand_pass1.isIntermediate = isIntermediate
     starCommand_pass1.deps = deps
-    starCommand_pass1.afterGraph
+    starCommand_pass1.beforeGraph
 
     val starCommand_reindex = new Star(configurable)
     starCommand_reindex.sjdbFileChrStartEnd = starCommand_pass1.outputTab
     starCommand_reindex.outputDir = new File(outputDir, "re-index")
     starCommand_reindex.runmode = "genomeGenerate"
     starCommand_reindex.isIntermediate = isIntermediate
-    starCommand_reindex.afterGraph
+    starCommand_reindex.beforeGraph
 
     val starCommand_pass2 = Star(configurable, R1, if (R2 != null) R2 else null, new File(outputDir, "aln-pass2"))
     starCommand_pass2.genomeDir = starCommand_reindex.outputDir
     starCommand_pass2.isIntermediate = isIntermediate
     starCommand_pass2.deps = deps
-    starCommand_pass2.afterGraph
+    starCommand_pass2.beforeGraph
 
     return (starCommand_pass2.outputSam, List(starCommand_pass1, starCommand_reindex, starCommand_pass2))
   }

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala

@@ -64,7 +64,7 @@ class TopHat(val root: Configurable) extends BiopetCommandLineFunction {
 
   override def versionCommand = executable + " --version"
 
-  override def afterGraph() {
+  override def beforeGraph() {
     if (!outputDir.endsWith("/")) outputDir += "/"
     output = new File(outputDir + "accepted_hits.bam")
   }

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala

@@ -28,7 +28,7 @@ class ConiferExport(val root: Configurable) extends Conifer {
   @Output(doc = "Output <sample>.svdzrpkm.bed", shortName = "out", required = true)
   var output: File = _
 
-  override def afterGraph {
+  override def beforeGraph {
     this.checkExecutable
   }
 

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala

@@ -44,8 +44,8 @@ class IGVToolsCount(val root: Configurable) extends IGVTools {
 
   var pairs: Boolean = config("pairs", default = false)
 
-  override def afterGraph {
-    super.afterGraph
+  override def beforeGraph {
+    super.beforeGraph
     if (!input.exists()) throw new FileNotFoundException("Input bam is required for IGVToolsCount")
 
     if (!wig.isEmpty && !wig.get.getAbsolutePath.endsWith(".wig")) throw new IllegalArgumentException("Wiggle file should have a .wig file-extension")

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala

@@ -55,7 +55,7 @@ class Macs2CallPeak(val root: Configurable) extends Macs2 {
   var broadcutoff: Option[Int] = config("broadcutoff")
   var callsummits: Boolean = config("callsummits", default = false)
 
-  override def afterGraph: Unit = {
+  override def beforeGraph: Unit = {
     if (name.isEmpty) throw new IllegalArgumentException("Name is not defined")
     if (outputdir == null) throw new IllegalArgumentException("Outputdir is not defined")
     output_narrow = new File(outputdir + name.get + ".narrowPeak")

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala

@@ -49,7 +49,7 @@ class CollectGcBiasMetrics(val root: Configurable) extends Picard {
   @Argument(doc = "IS_BISULFITE_SEQUENCED", required = false)
   var isBisulfiteSequinced: Option[Boolean] = config("isbisulfitesequinced")
 
-  override def afterGraph {
+  override def beforeGraph {
     if (outputChart == null) outputChart = new File(output + ".pdf")
     //require(reference.exists)
   }

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala

@@ -54,7 +54,7 @@ class CollectInsertSizeMetrics(val root: Configurable) extends Picard {
   @Argument(doc = "HISTOGRAM_WIDTH", required = false)
   var histogramWidth: Option[Int] = config("histogramWidth")
 
-  override def afterGraph {
+  override def beforeGraph {
     if (outputHistogram == null) outputHistogram = new File(output + ".pdf")
     //require(reference.exists)
   }

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala

@@ -70,8 +70,8 @@ class MarkDuplicates(val root: Configurable) extends Picard {
   @Output(doc = "Bam Index", required = true)
   private var outputIndex: File = _
 
-  override def afterGraph {
-    super.afterGraph
+  override def beforeGraph {
+    super.beforeGraph
     if (createIndex) outputIndex = new File(output.getAbsolutePath.stripSuffix(".bam") + ".bai")
   }