Merge remote-tracking branch 'remotes/origin/develop' into fix-BIOPET-506

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

@@ -18,9 +18,8 @@ import java.io.File
 
 import htsjdk.samtools.reference.IndexedFastaSequenceFile
 import nl.lumc.sasc.biopet.core.summary.{ Summarizable, SummaryQScript }
-import nl.lumc.sasc.biopet.utils.{ LazyCheck, BamUtils, ConfigUtils, FastaUtils, Logging }
+import nl.lumc.sasc.biopet.utils._
 import nl.lumc.sasc.biopet.utils.config.{ Config, Configurable }
-import nl.lumc.sasc.biopet.utils.{ ConfigUtils, FastaUtils, Logging }
 
 import scala.collection.JavaConversions._
 
@@ -177,4 +176,33 @@ object Reference {
       if (!dict.exists()) Logging.addError("Reference is missing a dict file")
     }
   }
+
+  def askReference: Map[String, Any] = {
+    val warn = "If you use a non-standard reference, please make sure that you have generated all required indexes for this reference"
+    val globalSpecies = Config.global.defaults.getOrElse("references", Map()).asInstanceOf[Map[String, Any]]
+    val species = Question.string("species",
+      description = Some(if (globalSpecies.nonEmpty)
+        s"""Species found in general config:
+           |- ${globalSpecies.keys.toList.sorted.mkString("\n- ")}
+           |$warn
+           |""".stripMargin
+      else s"No references found in global config. $warn"))
+
+    val globalReferences = globalSpecies.getOrElse(species, Map()).asInstanceOf[Map[String, Any]]
+    val referenceName = Question.string("reference_name",
+      description = Some(if (globalReferences.nonEmpty)
+        s"""Reference for $species found in general config:
+            |- ${globalReferences.keys.toList.sorted.mkString("\n- ")}
+            |$warn
+            |""".stripMargin
+      else s"No references found in global config. $warn"))
+
+    val reference = globalReferences.getOrElse(referenceName, Map()).asInstanceOf[Map[String, Any]]
+    val referenceFasta: Option[String] = if (reference.contains("reference_fasta")) None else {
+      Some(Question.string("Reference Fasta", validation = List(TemplateTool.isAbsolutePath, TemplateTool.mustExist),
+        description = Some(s"No fasta file found for $species -> $referenceName")))
+    }
+
+    Map("species" -> species, "reference_name" -> referenceName) ++ referenceFasta.map("reference_fasta" -> _)
+  }
 }

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

+package nl.lumc.sasc.biopet.core
+
+import java.io.{ File, PrintWriter }
+
+import nl.lumc.sasc.biopet.utils.summary.Summary
+import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Question, ToolCommand }
+
+import scala.io.Source
+
+/**
+ * Created by pjvanthof on 17/12/2016.
+ */
+trait TemplateTool extends ToolCommand {
+  import TemplateTool._
+  case class Args(outputConfig: File = null,
+                  runScript: Option[File] = None,
+                  expert: Boolean = false,
+                  template: Option[File] = None) extends AbstractArgs
+
+  class OptParser extends AbstractOptParser {
+    opt[File]('o', "outputConfig") required () valueName "<file>" action { (x, c) =>
+      c.copy(outputConfig = x)
+    } text "Path to output config"
+    opt[File]('s', "outputScript") valueName "<file>" action { (x, c) =>
+      c.copy(runScript = Some(x))
+    } text "Path to output script"
+    opt[File]('t', "template") valueName "<file>" action { (x, c) =>
+      c.copy(template = Some(x))
+    } text "Path to template. By default it will try to fetch this from the ENV value 'BIOPET_SCRIPT_TEMPLATE'"
+    opt[Unit]("expert") action { (x, c) =>
+      c.copy(expert = true)
+    } text "This enables expert options / questions"
+  }
+
+  /**
+   * Program will split fastq file in multiple fastq files
+   *
+   * @param args the command line arguments
+   */
+  def main(args: Array[String]): Unit = {
+    val argsParser = new OptParser
+    val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
+
+    cmdArgs.runScript.foreach(writeScript(_, cmdArgs.outputConfig, sampleConfigs, cmdArgs.template))
+
+    val standard: Map[String, Any] = Map("output_dir" -> Question.string("Output directory",
+      validation = List(isAbsolutePath, parentIsWritable)))
+    val config = pipelineMap(standard, cmdArgs.expert)
+
+    val configWriter = new PrintWriter(cmdArgs.outputConfig)
+    configWriter.println(ConfigUtils.mapToYaml(config))
+    configWriter.close()
+  }
+
+  def writeScript(outputFile: File, config: File, samples: List[File], t: Option[File]): Unit = {
+    val template = t match {
+      case Some(f) => f
+      case _ => sys.env.get("BIOPET_SCRIPT_TEMPLATE") match {
+        case Some(file) => new File(file)
+        case _          => throw new IllegalArgumentException("No template found on argument or 'BIOPET_SCRIPT_TEMPLATE'")
+      }
+    }
+
+    val templateReader = Source.fromFile(template)
+    val scriptWriter = new PrintWriter(outputFile)
+
+    val biopetArgs: String = (config :: samples).map(_.getAbsolutePath).mkString("-config ", " \\\n-config ", "")
+    templateReader.getLines().mkString("\n").format(pipelineName, biopetArgs).foreach(scriptWriter.print)
+    templateReader.close()
+    scriptWriter.close()
+    outputFile.setExecutable(true, false)
+  }
+
+  def pipelineName: String
+
+  def pipelineMap(map: Map[String, Any], expert: Boolean): Map[String, Any]
+
+  def sampleConfigs: List[File] = Nil
+
+}
+
+object TemplateTool {
+  def isAbsolutePath(value: String): Boolean = {
+    if (new File(value).isAbsolute) true else {
+      println(s"'$value' must be a absulute path")
+      false
+    }
+  }
+
+  def mustExist(value: String): Boolean = {
+    if (new File(value).exists()) true else {
+      println(s"'$value' does not exist")
+      false
+    }
+  }
+
+  def parentIsWritable(value: String): Boolean = {
+    val parent = new File(value).getParentFile
+    if (!parent.exists()) {
+      println(s"$parent does not exist")
+      false
+    } else if (!parent.canRead) {
+      println(s"No permission to read $parent")
+      false
+    } else if (!parent.canWrite) {
+      println(s"No permission to write $parent")
+      false
+    } else true
+  }
+
+  def askSampleConfigs(currentList: List[File] = Nil): List[File] = {
+    val configFile = new File(Question.string("Sample config file", validation = List(mustExist, isAbsolutePath)))
+    val configMap = new Summary(configFile)
+    println(s"${configMap.samples.size} samples found in config " +
+      s"with in total ${configMap.libraries.map(_._2.size).sum} libraries for '$configFile'")
+    if (Question.boolean("Is this correct?")) {
+      if (Question.boolean("Add more sample configs?")) askSampleConfigs(configFile :: currentList)
+      else {
+        val files = configFile :: currentList
+        if (files.size > 1) {
+          val configs = files.map(f => new Summary(ConfigUtils.fileToConfigMap(f)))
+          val sizes = configs.map(x => (x.samples.size, x.libraries.map(_._2.size).sum))
+          val samples = configs.flatMap(_.samples.toList)
+          val libs = configs.flatMap(_.libraries.flatMap { case (s, libs) => libs.toList.map(l => (s, l)) })
+          val mergedConfig = new Summary(configs.foldLeft(Map[String, Any]())((a, b) => ConfigUtils.mergeMaps(a, b.map)))
+          val mergesSamples = mergedConfig.samples.size
+          val mergesLibraries = mergedConfig.libraries.map(_._2.size).sum
+          if (mergesSamples != samples.size) {
+            val overlappingSamples = samples.groupBy(s1 => samples.count(s2 => s1 == s2)).filter(_._1 > 1).flatMap(_._2).toList.distinct
+            println("WARNING: Overlapping samples detected:")
+            overlappingSamples.foreach(s => println(s"  - $s"))
+          }
+          if (mergesLibraries != libs.size) {
+            val overlappingLibs = libs.groupBy(l1 => libs.count(l2 => l1 == l2)).filter(_._1 > 1).flatMap(_._2).toList.distinct
+            println("WARNING: Overlapping libraries detected")
+            overlappingLibs.foreach(l => println(s"  - ${l._1} -> ${l._2}"))
+          }
+          println(s"$mergesSamples samples found in merged config with in total $mergesLibraries libraries")
+          if (Question.boolean("Is this correct?")) files
+          else {
+            println("Resetting sample configs")
+            askSampleConfigs()
+          }
+        } else files
+      }
+    } else askSampleConfigs(currentList)
+  }
+}
\ No newline at end of file

biopet-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutableMain.scala

@@ -43,4 +43,10 @@ object BiopetExecutableMain extends BiopetExecutable {
   )
 
   def tools: List[MainCommand] = PipelineStatus :: BiopetToolsExecutable.tools
+
+  def templates: List[MainCommand] = List(
+    nl.lumc.sasc.biopet.pipelines.mapping.template.MultiSampleMapping,
+    nl.lumc.sasc.biopet.pipelines.shiva.template.Shiva,
+    nl.lumc.sasc.biopet.pipelines.gentrap.template.Gentrap
+  )
 }

biopet-tools-package/src/main/scala/nl/lumc/sasc/biopet/BiopetToolsExecutable.scala

@@ -53,4 +53,6 @@ object BiopetToolsExecutable extends BiopetExecutable {
     nl.lumc.sasc.biopet.tools.VepNormalizer,
     nl.lumc.sasc.biopet.tools.WipeReads,
     nl.lumc.sasc.biopet.tools.DownloadNcbiAssembly)
+
+  def templates: List[MainCommand] = List()
 }

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/BiopetExecutable.scala

@@ -30,9 +30,12 @@ trait BiopetExecutable extends Logging {
 
   def tools: List[MainCommand]
 
+  def templates: List[MainCommand]
+
   val modules: Map[String, List[MainCommand]] = Map(
     "pipeline" -> pipelines,
-    "tool" -> tools)
+    "tool" -> tools,
+    "template" -> templates)
 
   /**
    * @param args the command line arguments

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala

@@ -65,22 +65,20 @@ object ConfigUtils extends Logging {
    */
   def mergeMaps(map1: Map[String, Any], map2: Map[String, Any],
                 resolveConflict: (Any, Any, String) => Any = (m1, m2, key) => m1): Map[String, Any] = {
-    var newMap: Map[String, Any] = Map()
-    for (key <- map1.keySet.++(map2.keySet)) {
-      if (!map2.contains(key)) newMap += (key -> map1(key))
-      else if (!map1.contains(key)) newMap += (key -> map2(key))
+    (for (key <- map1.keySet.++(map2.keySet)) yield {
+      if (!map2.contains(key)) (key -> map1(key))
+      else if (!map1.contains(key)) (key -> map2(key))
       else {
         map1(key) match {
           case m1: Map[_, _] =>
             map2(key) match {
-              case m2: Map[_, _] => newMap += (key -> mergeMaps(any2map(m1), any2map(m2), resolveConflict))
-              case _             => newMap += (key -> map1(key))
+              case m2: Map[_, _] => (key -> mergeMaps(any2map(m1), any2map(m2), resolveConflict))
+              case _             => (key -> map1(key))
             }
-          case _ => newMap += (key -> resolveConflict(map1(key), map2(key), key))
+          case _ => (key -> resolveConflict(map1(key), map2(key), key))
         }
       }
-    }
-    newMap
+    }).toMap
   }
 
   /**

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/Question.scala

+package nl.lumc.sasc.biopet.utils
+
+/**
+ * Created by pjvanthof on 16/12/2016.
+ */
+object Question {
+
+  def string(name: String,
+             default: Option[String] = None,
+             description: Option[String] = None,
+             posibleValues: List[String] = Nil,
+             validation: List[(String) => Boolean] = Nil): String = {
+    description.foreach(println)
+    if (posibleValues.nonEmpty) println(s"possible values: ${posibleValues.mkString(", ")}")
+    default.foreach(x => println(s"Default value: $x"))
+    print(s"$name > ")
+    (Console.readLine.trim, default) match {
+      case (a, Some(d)) if a.isEmpty => d
+      case (a, None) if a.isEmpty =>
+        println("ERROR: Value is required")
+        string(name, default, description, posibleValues, validation)
+      case (a, _) =>
+        if (!validation.forall(_(a))) {
+          println("ERROR: Validation of failed")
+          string(name, default, description, posibleValues, validation)
+        } else if (posibleValues.nonEmpty && !posibleValues.contains(a)) {
+          println("ERROR: Value not allowed")
+          string(name, default, description, posibleValues, validation)
+        } else a
+    }
+  }
+
+  def boolean(name: String,
+              default: Option[Boolean] = None,
+              description: Option[String] = None): Boolean = {
+    description.foreach(println)
+    default.foreach(x => println(s"Default value: $x"))
+    print(s"$name (y/n) > ")
+    Console.readLine.trim.toLowerCase match {
+      case "" => default match {
+        case Some(d) => d
+        case _ =>
+          println("ERROR: Value is required")
+          boolean(name, default, description)
+      }
+      case "y" | "yes" | "true" => true
+      case "n" | "no" | "false" => false
+      case _ =>
+        println("ERROR: Value is a boolean value, please select 'y' of 'n'")
+        boolean(name, default, description)
+    }
+  }
+
+  def list(name: String,
+           default: Option[List[String]] = None,
+           description: Option[String] = None,
+           posibleValues: List[String] = Nil,
+           validation: (String) => Boolean = String => true): List[String] = {
+    description.foreach(println)
+    if (posibleValues.nonEmpty) println(s"possible values: ${posibleValues.mkString(", ")}")
+    default.foreach(x => println(s"Default value: $x"))
+    print(s"$name > ")
+    (Console.readLine.split(",").toList.map(_.trim), default) match {
+      case (List(""), Some(d)) => d
+      case (List(""), None) =>
+        println("ERROR: Value is required")
+        list(name, default, description, posibleValues, validation)
+      case (a, _) =>
+        if (!a.forall(validation)) {
+          println("ERROR: Validation of failed")
+          list(name, default, description, posibleValues, validation)
+        } else if (posibleValues.nonEmpty && !a.forall(posibleValues.contains)) {
+          println("ERROR: Value not allowed")
+          list(name, default, description, posibleValues, validation)
+        } else a
+    }
+  }
+}

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Config.scala

@@ -47,11 +47,11 @@ class Config(protected var _map: Map[String, Any],
         for (globalFile <- globalFiles.split(":")) {
           val file: File = new File(globalFile)
           if (file.exists) {
-            logger.info("Loading config file: " + file)
+            logger.debug("Loading config file: " + file)
             loadConfigFile(file, default)
           } else logger.warn(valueName + " value found but file '" + file + "' does not exist, no global config is loaded")
         }
-      case _ => logger.info(valueName + " value not found, no global config is loaded")
+      case _ => logger.debug(valueName + " value not found, no global config is loaded")
     }
   }
 

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/package.scala

@@ -101,6 +101,30 @@ package object utils {
     }
   }
 
+  /** Converts string with underscores into camel-case strings */
+  def camelize(ustring: String): String = ustring
+    .split("_")
+    .map(_.toLowerCase.capitalize)
+    .mkString("")
+
+  /** Split camelcase to separated words */
+  def camelizeToWords(string: String, current: List[String] = Nil): List[String] = {
+    if (string.nonEmpty) {
+      val char = string.tail.find(!_.isLower)
+      char match {
+        case Some(c) =>
+          val index = string.indexOf(c, 1)
+          camelizeToWords(string.drop(index), current ::: List(string.take(index)))
+        case _ => current ::: List(string)
+      }
+    } else current
+  }
+
+  /** Convert camelcase to underscores */
+  def unCamelize(string: String): String = {
+    camelizeToWords(string).map(_.toLowerCase).mkString("_")
+  }
+
   /** Function to sort Any values */
   def sortAnyAny(a: Any, b: Any): Boolean = {
     a match {

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/Summary.scala

@@ -23,8 +23,9 @@ import nl.lumc.sasc.biopet.utils.ConfigUtils
  *
  * Created by pjvan_thof on 3/26/15.
  */
-class Summary(file: File) {
-  val map = ConfigUtils.fileToConfigMap(file)
+class Summary(val map: Map[String, Any]) {
+
+  def this(file: File) = this(ConfigUtils.fileToConfigMap(file))
 
   /** List of all samples in the summary */
   lazy val samples: Set[String] = {

external-example/src/main/scala/org/example/group/ExecutableExample.scala

@@ -30,4 +30,6 @@ object ExecutableExample extends BiopetExecutable {
 
   /** This list defines the (biopet)tools that are usable from the executable */
   def tools: List[MainCommand] = Nil
+
+  def templates: List[MainCommand] = List()
 }

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

@@ -203,7 +203,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
       fqSync.outputFastq2 = new File(outDir, fastqR2Qc.get.getName)
       fqSync.outputStats = new File(outDir, s"${sampleId.getOrElse("x")}-${libId.getOrElse("x")}.sync.stats")
 
-      val pipe = new BiopetFifoPipe(this, fqSync :: Nil) with Summarizable {
+      val pipe = new BiopetFifoPipe(this, fqSync :: qcCmdR1.jobs ::: qcCmdR2.jobs) with Summarizable {
         override def configNamespace = "qc_cmd"
 
         override def beforeGraph(): Unit = {
@@ -232,6 +232,8 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
 
       pipe.deps ::= fastqcR1.output
       pipe.deps ::= fastqcR2.output
+      pipe.deps ::= R1_in
+      pipe.deps ::= R2_in.get
       pipe.isIntermediate = !keepQcFastqFiles
       addSummarizable(pipe, "qc_cmd")
       add(pipe)

gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala

@@ -24,6 +24,7 @@ import nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingTrait
 import nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcalling
 import nl.lumc.sasc.biopet.utils.{ LazyCheck, Logging }
 import nl.lumc.sasc.biopet.utils.config._
+import nl.lumc.sasc.biopet.utils.camelize
 import org.broadinstitute.gatk.queue.QScript
 import picard.analysis.directed.RnaSeqMetricsCollector.StrandSpecificity
 import java.io.File
@@ -54,7 +55,7 @@ class Gentrap(val root: Configurable) extends QScript
   // see the enumeration below for valid modes
   lazy val expMeasures = new LazyCheck({
     config("expression_measures", default = Nil).asStringList.map(value =>
-      ExpMeasures.values.find(_.toString == Gentrap.camelize(value)) match {
+      ExpMeasures.values.find(_.toString == camelize(value)) match {
         case Some(v) => v
         case _       => throw new IllegalArgumentException(s"'$value' is not a valid Expression measurement")
       }
@@ -64,7 +65,7 @@ class Gentrap(val root: Configurable) extends QScript
   /** Strandedness modes */
   lazy val strandProtocol = new LazyCheck({
     val value: String = config("strand_protocol")
-    StrandProtocol.values.find(_.toString == Gentrap.camelize(value)) match {
+    StrandProtocol.values.find(_.toString == camelize(value)) match {
       case Some(v) => v
       case other =>
         Logging.addError(s"'$other' is no strand_protocol or strand_protocol is not given")
@@ -240,7 +241,7 @@ object Gentrap extends PipelineCommand {
 
   /** Enumeration of available expression measures */
   object ExpMeasures extends Enumeration {
-    val FragmentsPerGene, FragmentsPerExon, BaseCounts, CufflinksStrict, CufflinksGuided, CufflinksBlind = Value
+    val FragmentsPerGene, BaseCounts, CufflinksStrict, CufflinksGuided, CufflinksBlind = Value
   }
 
   /** Enumeration of available strandedness */
@@ -248,10 +249,4 @@ object Gentrap extends PipelineCommand {
     // for now, only non-strand specific and dUTP stranded protocol is supported
     val NonSpecific, Dutp = Value
   }
-
-  /** Converts string with underscores into camel-case strings */
-  private[gentrap] def camelize(ustring: String): String = ustring
-    .split("_")
-    .map(_.toLowerCase.capitalize)
-    .mkString("")
 }

gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/template/Gentrap.scala

+package nl.lumc.sasc.biopet.pipelines.gentrap.template
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.TemplateTool
+import nl.lumc.sasc.biopet.pipelines.gentrap.Gentrap.{ ExpMeasures, StrandProtocol }
+import nl.lumc.sasc.biopet.pipelines.mapping.template.MultiSampleMapping
+import nl.lumc.sasc.biopet.pipelines.shiva.template.Shiva
+import nl.lumc.sasc.biopet.utils._
+
+/**
+ * Created by pjvanthof on 17/12/2016.
+ */
+object Gentrap extends TemplateTool {
+
+  def pipelineName = "Gentrap"
+
+  override def sampleConfigs: List[File] = TemplateTool.askSampleConfigs()
+
+  def pipelineMap(map: Map[String, Any], expert: Boolean): Map[String, Any] = {
+    val aligner = Question.string("Aligner", posibleValues = MultiSampleMapping.possibleAligners,
+      default = Some("gsnap"))
+
+    val mappingConfig = MultiSampleMapping.pipelineMap(map ++ Map("aligner" -> aligner), expert)
+
+    val expressionMeasures = Question.list("ExpressionMeasures",
+      posibleValues = ExpMeasures.values.map(x => unCamelize(x.toString)).toList)
+
+    val strandProtocol = Question.list("StrandProtocol",
+      posibleValues = StrandProtocol.values.map(x => unCamelize(x.toString)).toList)
+
+    val annotationRefFlat = Question.string("annotationRefFlat",
+      validation = List(TemplateTool.isAbsolutePath, TemplateTool.mustExist))
+
+    val annotationGtf = if (expressionMeasures.contains(unCamelize(ExpMeasures.FragmentsPerGene.toString)) ||
+      expressionMeasures.exists(_.startsWith("cufflinks")))
+      Some(Question.string("annotationGtf",
+        validation = List(TemplateTool.isAbsolutePath, TemplateTool.mustExist)))
+    else None
+
+    mappingConfig ++ annotationGtf.map("annotation_gtf" -> _) ++ Map(
+      "expression_measures" -> expressionMeasures,
+      "strand_protocol" -> strandProtocol,
+      "annotation_refflat" -> annotationRefFlat
+    ) ++ (if (Question.boolean("Call variants")) {
+        val variantCallers = Question.list("Variantcallers", posibleValues = Shiva.possibleVariantcallers,
+          default = Some(List("varscan_cns_singlesample")))
+
+        Map("call_variants" -> true, "variantcallers" -> variantCallers)
+      } else Map("call_variants" -> false))
+  }
+}

gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala

@@ -24,6 +24,7 @@ import nl.lumc.sasc.biopet.extensions.hisat.Hisat2
 import nl.lumc.sasc.biopet.extensions.tools.{ BaseCounter, WipeReads }
 import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
 import nl.lumc.sasc.biopet.utils.config.Config
+import nl.lumc.sasc.biopet.utils.camelize
 import org.broadinstitute.gatk.queue.QSettings
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
@@ -97,10 +98,10 @@ abstract class GentrapTestAbstract(val expressionMeasures: List[String]) extends
       gentrap.shivaVariantcalling.isDefined shouldBe callVariants.getOrElse(false)
 
       gentrap.summarySettings.getOrElse("expression_measures", List()).asInstanceOf[List[String]].sorted shouldBe
-        expressionMeasures.map(Gentrap.camelize(_)).sorted
+        expressionMeasures.map(camelize(_)).sorted
       gentrap.summarySettings.get("call_variants") shouldBe Some(callVariants.getOrElse(false))
       gentrap.summarySettings.get("remove_ribosomal_reads") shouldBe Some(removeRiboReads.getOrElse(false))
-      gentrap.summarySettings.get("strand_protocol") shouldBe Some(Gentrap.camelize(strandProtocol))
+      gentrap.summarySettings.get("strand_protocol") shouldBe Some(camelize(strandProtocol))
 
       if (expressionMeasures.contains("fragments_per_gene"))
         assert(gentrap.functions.exists(_.isInstanceOf[HtseqCount]))

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

@@ -19,11 +19,11 @@ import java.util.Date
 
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.extensions.bowtie.{ Bowtie, Bowtie2 }
-import nl.lumc.sasc.biopet.extensions.bwa.{ BwaAln, BwaMem, BwaSampe, BwaSamse }
+import nl.lumc.sasc.biopet.extensions.bowtie.{Bowtie, Bowtie2}
+import nl.lumc.sasc.biopet.extensions.bwa.{BwaAln, BwaMem, BwaSampe, BwaSamse}
 import nl.lumc.sasc.biopet.extensions.gmap.Gsnap
 import nl.lumc.sasc.biopet.extensions.hisat.Hisat2
-import nl.lumc.sasc.biopet.extensions.picard.{ AddOrReplaceReadGroups, MarkDuplicates, MergeSamFiles, ReorderSam, SortSam }