Rename root to parent

bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala

@@ -27,7 +27,7 @@ import org.broadinstitute.gatk.queue.QScript
  *
  * Created by pjvan_thof on 1/29/15.
  */
-class Bam2Wig(val root: Configurable) extends QScript with BiopetQScript {
+class Bam2Wig(val parent: Configurable) extends QScript with BiopetQScript {
   def this() = this(null)
 
   @Input(doc = "Input bam file", required = true)

bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala

@@ -28,7 +28,7 @@ import scala.collection.JavaConversions._
  *
  * Created by pjvan_thof on 1/29/15.
  */
-class BamToChromSizes(val root: Configurable) extends InProcessFunction with Configurable {
+class BamToChromSizes(val parent: Configurable) extends InProcessFunction with Configurable {
   @Input
   var bamFile: File = _
 

bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

@@ -28,7 +28,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.utils.intervals.BedCheck
 import org.broadinstitute.gatk.queue.QScript
 
-class BamMetrics(val root: Configurable) extends QScript
+class BamMetrics(val parent: Configurable) extends QScript
   with SummaryQScript
   with SampleLibraryTag
   with Reference

bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala

@@ -21,7 +21,7 @@ import nl.lumc.sasc.biopet.core.report.{ ReportBuilderExtension, ReportBuilder,
 import nl.lumc.sasc.biopet.utils.summary.{ Summary, SummaryValue }
 import nl.lumc.sasc.biopet.utils.rscript.{ StackedBarPlot, LinePlot }
 
-class BammetricsReport(val root: Configurable) extends ReportBuilderExtension {
+class BammetricsReport(val parent: Configurable) extends ReportBuilderExtension {
   def builder = BammetricsReport
 }
 

bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/CoverageStats.scala

@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.core.summary.Summarizable
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
-class CoverageStats(val root: Configurable) extends PythonCommandLineFunction with Summarizable {
+class CoverageStats(val parent: Configurable) extends PythonCommandLineFunction with Summarizable {
   setPythonScript("bedtools_cov_stats.py")
 
   @Input(doc = "Input file", required = false)

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

@@ -28,7 +28,7 @@ import nl.lumc.sasc.biopet.extensions.tools.BastyGenerateFasta
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
 
-class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
+class Basty(val parent: Configurable) extends QScript with MultiSampleQScript {
   qscript =>
 
   def this() = this(null)

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetFifoPipe.scala

@@ -22,7 +22,7 @@ import org.broadinstitute.gatk.utils.commandline.Output
 /**
  * Created by pjvan_thof on 9/29/15.
  */
-class BiopetFifoPipe(val root: Configurable,
+class BiopetFifoPipe(val parent: Configurable,
                      protected var commands: List[BiopetCommandLineFunction]) extends BiopetCommandLineFunction {
 
   def fifos: List[File] = {

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala

@@ -72,7 +72,7 @@ class BiopetPipe(val commands: List[BiopetCommandLineFunction]) extends BiopetCo
   override def defaultCoreMemory = 0.0
   override def defaultThreads = 0
 
-  val root: Configurable = commands.head.root
+  val parent: Configurable = commands.head.parent
   override def configNamespace = commands.map(_.configNamespace).mkString("-")
   def cmdLine: String = {
     "(" + commands.head.cmdLine + (if (commands.head.stdinFile.isDefined) {

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala

@@ -33,7 +33,7 @@ trait Reference extends Configurable {
 
   /** Returns species, default to unknown_species */
   def referenceSpecies: String = {
-    root match {
+    parent match {
       case r: Reference if r.referenceSpecies != "unknown_species" => r.referenceSpecies
       case _ => config("species", default = "unknown_species", path = super.configPath)
     }
@@ -41,7 +41,7 @@ trait Reference extends Configurable {
 
   /** Return referencename, default to unknown_ref */
   def referenceName: String = {
-    root match {
+    parent match {
       case r: Reference if r.referenceName != "unknown_ref" => r.referenceName
       case _ =>
         val default: String = config("default", default = "unknown_ref", path = List("references", referenceSpecies))

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/SampleLibraryTag.scala

@@ -27,13 +27,13 @@ trait SampleLibraryTag extends Configurable {
   //FIXME: not possible to have required sample / lib
 
   @Argument(doc = "Sample ID", shortName = "sample", required = false)
-  var sampleId: Option[String] = root match {
+  var sampleId: Option[String] = parent match {
     case tag: SampleLibraryTag => tag.sampleId
     case _                     => None
   }
 
   @Argument(doc = "Library ID", shortName = "library", required = false)
-  var libId: Option[String] = root match {
+  var libId: Option[String] = parent match {
     case tag: SampleLibraryTag => tag.libId
     case _                     => None
   }

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala

@@ -30,7 +30,7 @@ import scala.collection.mutable.ListBuffer
  * @author Peter van 't Hof <p.j.van_t_hof@lumc.nl>
  */
 object WriteDependencies extends Logging with Configurable {
-  val root: Configurable = null
+  val parent: Configurable = null
   private def createFunctionNames(functions: Seq[QFunction]): Map[QFunction, String] = {
     val cache: mutable.Map[String, Int] = mutable.Map()
     (for (function <- functions) yield {
@@ -113,7 +113,7 @@ object WriteDependencies extends Logging with Configurable {
           case _                        => None
         }), "main_job" -> (f match {
           case cmd: BiopetCommandLineFunction            => cmd.mainFunction
-          case s: WriteSummary if s.qscript.root == null => true
+          case s: WriteSummary if s.qscript.parent == null => true
           case _                                         => false
         }), "intermediate" -> f.isIntermediate,
           "depends_on_intermediate" -> BiopetQScript.safeInputs(f).getOrElse(Seq()).exists(files(_).isIntermediate),

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/Md5sum.scala

@@ -21,7 +21,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /** Extension for md5sum */
-class Md5sum(val root: Configurable) extends BiopetCommandLineFunction with Version {
+class Md5sum(val parent: Configurable) extends BiopetCommandLineFunction with Version {
   mainFunction = false
 
   @Input(doc = "Input")

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala

@@ -31,13 +31,13 @@ import scala.io.Source
  *
  * Created by pjvan_thof on 2/14/15.
  */
-class WriteSummary(val root: Configurable) extends InProcessFunction with Configurable {
+class WriteSummary(val parent: Configurable) extends InProcessFunction with Configurable {
   this.analysisName = getClass.getSimpleName
 
-  require(root.isInstanceOf[SummaryQScript], "root is not a SummaryQScript")
+  require(parent.isInstanceOf[SummaryQScript], "root is not a SummaryQScript")
 
   /** To access qscript for this summary */
-  val qscript = root.asInstanceOf[SummaryQScript]
+  val qscript = parent.asInstanceOf[SummaryQScript]
 
   @Input(doc = "deps", required = false)
   var deps: List[File] = Nil

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/BiopetPipeTest.scala

@@ -23,14 +23,14 @@ import org.testng.annotations.Test
  */
 class BiopetPipeTest extends TestNGSuite with Matchers {
   class Pipe1 extends BiopetCommandLineFunction {
-    val root = null
+    val parent = null
     def cmdLine = "pipe1" +
       (if (!inputAsStdin) " input1 " else "") +
       (if (!outputAsStsout) " output1 " + "")
   }
 
   class Pipe2 extends BiopetCommandLineFunction {
-    val root = null
+    val parent = null
     def cmdLine = "pipe2" +
       (if (!inputAsStdin) " input2 " else "") +
       (if (!outputAsStsout) " output2 " + "")

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/CommandLineResourcesTest.scala

@@ -28,7 +28,7 @@ class CommandLineResourcesTest extends TestNGSuite with Matchers {
   class CommandLineFunctionMock(c: Map[String, Any] = Map()) extends CommandLineFunction with Configurable {
     override def freezeFieldValues() {}
     def commandLine = "command"
-    val root = null
+    val parent = null
     override def globalConfig = new Config(c)
   }
 

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/MultiSampleQScriptTest.scala

@@ -214,7 +214,7 @@ object MultiSampleQScriptTest {
       override def globalConfig = new Config(configs
         .foldLeft(Map[String, Any]()) { case (a, b) => ConfigUtils.mergeMaps(a, b) })
 
-      val root = null
+      val parent = null
 
       def getLastLogMessage: String = {
         Logging.errors.toList.last.getMessage

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/ReferenceTest.scala

@@ -105,7 +105,7 @@ object ReferenceTest {
            r: Configurable = null,
            fai: Boolean = false,
            dict: Boolean = false) = new Reference {
-    val root = r
+    val parent = r
     override def globalConfig = new Config(configs
       .foldLeft(Map[String, Any]()) { case (a, b) => ConfigUtils.mergeMaps(a, b) })
     override def dictRequired = if (dict) true else super.dictRequired

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/SampleLibraryTagTest.scala

@@ -26,7 +26,7 @@ class SampleLibraryTagTest extends TestNGSuite with Matchers {
   @Test
   def testDefault: Unit = {
     val o = new SampleLibraryTag {
-      override def root: Configurable = null
+      override def parent: Configurable = null
       override def globalConfig = new Config(Map())
     }
     o.sampleId shouldBe None
@@ -36,7 +36,7 @@ class SampleLibraryTagTest extends TestNGSuite with Matchers {
   @Test
   def testInherit: Unit = {
     val o1 = new SampleLibraryTag {
-      override def root: Configurable = null
+      override def parent: Configurable = null
       override def globalConfig = new Config(Map())
     }
     o1.sampleId = Some("sampleName")
@@ -45,7 +45,7 @@ class SampleLibraryTagTest extends TestNGSuite with Matchers {
     o1.libId shouldBe Some("libName")
 
     val o2 = new SampleLibraryTag {
-      override def root: Configurable = o1
+      override def parent: Configurable = o1
       override def globalConfig = new Config(Map())
     }
     o2.sampleId shouldBe o1.sampleId

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/ToolCommandTest.scala

@@ -26,7 +26,7 @@ class ToolCommandTest extends TestNGSuite with Matchers {
   @Test
   def testToolCommand: Unit = {
     val tool = new ToolCommandFunction {
-      def root = null
+      def parent = null
       def toolObject = ToolCommandTest
     }
 

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/annotation/AnnotationTest.scala

@@ -78,7 +78,7 @@ class AnnotationTest extends TestNGSuite with Matchers {
 object AnnotationTest {
   class Script(c: Map[String, Any]) extends QScript with BiopetQScript {
     override def globalConfig: Config = new Config(c)
-    val root = null
+    val parent = null
 
     /** Init for pipeline */
     def init(): Unit = ???

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScriptTest.scala

@@ -130,7 +130,7 @@ object SummaryQScriptTest {
       def summaryFile: File = tempFile
       def init(): Unit = ???
       def biopetScript(): Unit = ???
-      def root: Configurable = null
+      def parent: Configurable = null
     }
 
   def makeSummarizable(files: Map[String, File] = Map(), stats: Map[String, Any] = Map()) = new Summarizable {

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala

@@ -238,7 +238,7 @@ object WriteSummaryTest {
       def summaryFile: File = tempFile
       def init(): Unit = {}
       def biopetScript(): Unit = {}
-      def root: Configurable = null
+      def parent: Configurable = null
     }
 
   def makeSampleLibraryQscript(name: String,
@@ -260,7 +260,7 @@ object WriteSummaryTest {
       def summaryFile: File = tempFile
       def init(): Unit = {}
       def biopetScript(): Unit = {}
-      def root: Configurable = null
+      def parent: Configurable = null
     }
 
   def makeMultisampleQscript(name: String,
@@ -278,7 +278,7 @@ object WriteSummaryTest {
       def summaryFile: File = tempFile
       def init(): Unit = {}
       def biopetScript(): Unit = {}
-      def root: Configurable = null
+      def parent: Configurable = null
 
       class Sample(id: String) extends AbstractSample(id) {
         class Library(id: String) extends AbstractLibrary(id) {
@@ -310,7 +310,7 @@ object WriteSummaryTest {
                       c: Map[String, Any] = Map()) = new BiopetJavaCommandLineFunction with Summarizable with Version {
     override def globalConfig = new Config(c)
     override def configNamespace = "java_command"
-    def root: Configurable = null
+    def parent: Configurable = null
     def summaryStats: Map[String, Any] = stats
     def summaryFiles: Map[String, File] = files
 
@@ -335,7 +335,7 @@ object WriteSummaryTest {
     new CommandLineFunction with Configurable with Summarizable with Version {
       override def globalConfig = new Config(c)
       override def configNamespace = "version_command"
-      def root: Configurable = null
+      def parent: Configurable = null
 
       def summaryFiles: Map[String, File] = files
       def summaryStats: Any = stats

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Awk.scala

@@ -25,7 +25,7 @@ import scala.util.matching.Regex
 /**
  * Created by pjvan_thof on 17-5-16.
  */
-class Awk(val root: Configurable) extends BiopetCommandLineFunction with Version {
+class Awk(val parent: Configurable) extends BiopetCommandLineFunction with Version {
   executable = config("exe", default = "awk", freeVar = false)
 
   def versionCommand: String = executable + " --version"

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala

@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /** Wrapper for the bgzip command */
-class Bgzip(val root: Configurable) extends BiopetCommandLineFunction {
+class Bgzip(val parent: Configurable) extends BiopetCommandLineFunction {
 
   @Input(doc = "Input files", required = false)
   var input: List[File] = Nil

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala

@@ -23,7 +23,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 /**
  * Extension for GNU cat
  */
-class Cat(val root: Configurable) extends BiopetCommandLineFunction {
+class Cat(val parent: Configurable) extends BiopetCommandLineFunction {
   @Input(doc = "Input file", required = true)
   var input: List[File] = Nil
 

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cnmops.scala

@@ -27,7 +27,7 @@ import nl.lumc.sasc.biopet.utils.getSemanticVersion
  * Wrapper for the Cnmops command line tool.
  * Written based on Cnmops version v2.2.1.
  */
-class Cnmops(val root: Configurable) extends RscriptCommandLineFunction with Version {
+class Cnmops(val parent: Configurable) extends RscriptCommandLineFunction with Version {
 
   override def defaultThreads = 4
   override def defaultCoreMemory: Double = 4.0

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala

@@ -24,7 +24,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
  * Wrapper for the cufflinks command line tool.
  * Written based on cufflinks version v2.2.1 (md5: 07c831c4f8b4e161882731ea5694ff80)
  */
-class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction with Version {
+class Cufflinks(val parent: Configurable) extends BiopetCommandLineFunction with Version {
 
   /** default executable */
   executable = config("exe", default = "cufflinks")

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala

@@ -24,7 +24,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
  * Wrapper for the cuffquant command line tool.
  * Written based on cuffquant version v2.2.1 (md5: 0765b82b11db9256f5be341a7da884d6)
  */
-class Cuffquant(val root: Configurable) extends BiopetCommandLineFunction with Version {
+class Cuffquant(val parent: Configurable) extends BiopetCommandLineFunction with Version {
 
   /** default executable */
   executable = config("exe", default = "cuffquant")

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Curl.scala

@@ -23,7 +23,7 @@ import org.broadinstitute.gatk.utils.commandline.Output
 /**
  * Created by pjvan_thof on 8/11/15.
  */
-class Curl(val root: Configurable) extends BiopetCommandLineFunction with Version {
+class Curl(val parent: Configurable) extends BiopetCommandLineFunction with Version {
   @Output
   var output: File = _
 

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala

@@ -30,7 +30,7 @@ import scala.util.matching.Regex
  * Started with version 1.5
  * Updated to version 1.9 (18-01-2016 by wyleung)
  */
-class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Summarizable with Version {
+class Cutadapt(val parent: Configurable) extends BiopetCommandLineFunction with Summarizable with Version {
   @Input(doc = "Input fastq file")
   var fastqInput: File = _
 

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

@@ -24,7 +24,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
  * Extension for fastqc
  * Based on version 0.10.1 and 0.11.2
  */
-class Fastqc(val root: Configurable) extends BiopetCommandLineFunction with Version {
+class Fastqc(val parent: Configurable) extends BiopetCommandLineFunction with Version {
 
   @Input(doc = "Contaminants", required = false)
   var contaminants: Option[File] = None

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Flash.scala

@@ -25,7 +25,7 @@ import scala.util.matching.Regex
 /**
  * Created by pjvanthof on 16/12/15.
  */
-class Flash(val root: Configurable) extends BiopetCommandLineFunction with Version {
+class Flash(val parent: Configurable) extends BiopetCommandLineFunction with Version {
   executable = config("exe", default = "flash", freeVar = false)
 
   /** Command to get version of executable */

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala

@@ -25,7 +25,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
  *
  * Created by pjvan_thof on 3/3/15.
  */
-class Freebayes(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version {
+class Freebayes(val parent: Configurable) extends BiopetCommandLineFunction with Reference with Version {
 
   @Input(required = true)
   var bamfiles: List[File] = Nil

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/GffRead.scala

@@ -23,7 +23,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 /**
  * Created by pjvanthof on 20/06/16.
  */
-class GffRead(val root: Configurable) extends BiopetCommandLineFunction {
+class GffRead(val parent: Configurable) extends BiopetCommandLineFunction {
 
   executable = config("exe", default = "gffread", freeVar = false)
 

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Grep.scala

@@ -23,7 +23,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 /**
  * Created by pjvanthof on 30/03/16.
  */
-class Grep(val root: Configurable) extends BiopetCommandLineFunction {
+class Grep(val parent: Configurable) extends BiopetCommandLineFunction {
   @Input(doc = "Input file", required = true)
   var input: File = _
 

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/GtfToGenePred.scala

@@ -23,7 +23,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 /**
  * Created by pjvan_thof on 17-5-16.
  */
-class GtfToGenePred(val root: Configurable) extends BiopetCommandLineFunction {
+class GtfToGenePred(val parent: Configurable) extends BiopetCommandLineFunction {
   executable = config("exe", default = "gtfToGenePred", freeVar = false)
 
   @Input

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala

@@ -20,7 +20,7 @@ import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction }
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
-class Gzip(val root: Configurable) extends BiopetCommandLineFunction with Version {
+class Gzip(val parent: Configurable) extends BiopetCommandLineFunction with Version {
   @Input(doc = "Input file", required = true)
   var input: List[File] = Nil
 

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala

@@ -24,7 +24,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
  * Wrapper for the htseq-count command line tool
  * Written based on htseq-count version 0.6.1p1
  */
-class HtseqCount(val root: Configurable) extends BiopetCommandLineFunction with Version {