Rename root to parent

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 {
+class HtseqCount(val parent: Configurable) extends BiopetCommandLineFunction with Version {
 
   /** default executable */
   executable = config("exe", default = "htseq-count")

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

@@ -25,7 +25,7 @@ import scala.sys.process.{ Process, ProcessLogger }
 /**
  * This class can execute ln as InProcessFunction or used to only generate the ln command
  */
-class Ln(val root: Configurable) extends InProcessFunction with Configurable {
+class Ln(val parent: Configurable) extends InProcessFunction with Configurable {
   this.analysisName = getClass.getSimpleName
 
   @Input(doc = "Input file")

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala

@@ -21,7 +21,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /** Extension for pbzip2 */
-class Pbzip2(val root: Configurable) extends BiopetCommandLineFunction {
+class Pbzip2(val parent: Configurable) extends BiopetCommandLineFunction {
   @Input(doc = "Zipped file")
   var input: File = _