Merge with develop

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

@@ -5,11 +5,11 @@
  */
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
-import nl.lumc.sasc.biopet.core.{ CommandLineResources, Reference, BiopetJavaCommandLineFunction }
+import nl.lumc.sasc.biopet.core.{ Version, CommandLineResources, Reference, BiopetJavaCommandLineFunction }
 import org.broadinstitute.gatk.engine.phonehome.GATKRunReport
 import org.broadinstitute.gatk.queue.extensions.gatk.CommandLineGATK
 
-trait GatkGeneral extends CommandLineGATK with CommandLineResources with Reference {
+trait GatkGeneral extends CommandLineGATK with CommandLineResources with Reference with Version {
   memoryLimit = Option(3)
 
   override def subPath = "gatk" :: super.subPath
@@ -35,9 +35,9 @@ trait GatkGeneral extends CommandLineGATK with CommandLineResources with Referen
   if (config.contains("gatk_key")) gatk_key = config("gatk_key")
   if (config.contains("pedigree")) pedigree = config("pedigree")
 
-  //override def versionRegex = """(.*)""".r
-  //override def versionExitcode = List(0, 1)
-  //override def versionCommand = executable + " -jar " + jarFile + " -version"
+  def versionRegex = """(.*)""".r
+  override def versionExitcode = List(0, 1)
+  def versionCommand = "java" + " -jar " + jarFile + " -version"
 
-  //override def getVersion = super.getVersion.collect { case v => "Gatk " + v }
+  override def getVersion = super.getVersion.collect { case v => "Gatk " + v }
 }

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

@@ -146,59 +146,6 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
       case Some(n) if n > 0 => n
       case _                => 1
     })
-    addJobReportBinding("version", getVersion)
-  }
-
-  /** Command to get version of executable */
-  protected[core] def versionCommand: String = null
-
-  /** Regex to get version from version command output */
-  protected[core] def versionRegex: Regex = null
-
-  /** Allowed exit codes for the version command */
-  protected[core] def versionExitcode = List(0)
-
-  /** Executes the version command */
-  private[core] def getVersionInternal: Option[String] = {
-    if (versionCommand == null || versionRegex == null) None
-    else getVersionInternal(versionCommand, versionRegex)
-  }
-
-  /** Executes the version command */
-  private[core] def getVersionInternal(versionCommand: String, versionRegex: Regex): Option[String] = {
-    if (versionCommand == null || versionRegex == null) return None
-    val exe = new File(versionCommand.trim.split(" ")(0))
-    if (!exe.exists()) return None
-    val stdout = new StringBuffer()
-    val stderr = new StringBuffer()
-    def outputLog = "Version command: \n" + versionCommand +
-      "\n output log: \n stdout: \n" + stdout.toString +
-      "\n stderr: \n" + stderr.toString
-    val process = Process(versionCommand).run(ProcessLogger(stdout append _ + "\n", stderr append _ + "\n"))
-    if (!versionExitcode.contains(process.exitValue())) {
-      logger.warn("getVersion give exit code " + process.exitValue + ", version not found \n" + outputLog)
-      return None
-    }
-    for (line <- stdout.toString.split("\n") ++ stderr.toString.split("\n")) {
-      line match {
-        case versionRegex(m) => return Some(m)
-        case _               =>
-      }
-    }
-    logger.warn("getVersion give a exit code " + process.exitValue + " but no version was found, executable correct? \n" + outputLog)
-    None
-  }
-
-  /** Get version from cache otherwise execute the version command  */
-  def getVersion: Option[String] = {
-    if (!BiopetCommandLineFunction.executableCache.contains(executable))
-      preProcessExecutable()
-    if (!BiopetCommandLineFunction.versionCache.contains(versionCommand))
-      getVersionInternal match {
-        case Some(version) => BiopetCommandLineFunction.versionCache += versionCommand -> version
-        case _             =>
-      }
-    BiopetCommandLineFunction.versionCache.get(versionCommand)
   }
 
   private[core] var _inputAsStdin = false
@@ -284,7 +231,6 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
 
 /** stores global caches */
 object BiopetCommandLineFunction {
-  private[core] val versionCache: mutable.Map[String, String] = mutable.Map()
   private[core] val executableMd5Cache: mutable.Map[String, String] = mutable.Map()
   private[core] val executableCache: mutable.Map[String, String] = mutable.Map()
 }

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

@@ -51,6 +51,9 @@ class BiopetFifoPipe(val root: Configurable,
 
     deps :::= inputs.values.toList.flatten.filter(!fifoFiles.contains(_))
     deps = deps.distinct
+
+    pipesJobs :::= commands
+    pipesJobs = pipesJobs.distinct
   }
 
   override def beforeCmd(): Unit = {

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

@@ -55,12 +55,12 @@ trait BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetC
   def getJavaVersion: Option[String] = {
     if (!BiopetCommandLineFunction.executableCache.contains(executable))
       preProcessExecutable()
-    if (!BiopetCommandLineFunction.versionCache.contains(javaVersionCommand))
-      getVersionInternal(javaVersionCommand, """java version "(.*)"""".r) match {
-        case Some(version) => BiopetCommandLineFunction.versionCache += javaVersionCommand -> version
+    if (!Version.versionCache.contains(javaVersionCommand))
+      Version.getVersionInternal(javaVersionCommand, """java version "(.*)"""".r) match {
+        case Some(version) => Version.versionCache += javaVersionCommand -> version
         case _             =>
       }
-    BiopetCommandLineFunction.versionCache.get(javaVersionCommand)
+    Version.versionCache.get(javaVersionCommand)
   }
 
   override def setupRetry(): Unit = {

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

@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.core
 import java.io.File
 
 import nl.lumc.sasc.biopet.core.summary.{ Summarizable, SummaryQScript }
-import nl.lumc.sasc.biopet.utils.ConfigUtils
+import nl.lumc.sasc.biopet.utils.{ Logging, ConfigUtils }
 import org.broadinstitute.gatk.utils.commandline.Argument
 
 /** This trait creates a structured way of use multisample pipelines */
@@ -47,6 +47,8 @@ trait MultiSampleQScript extends SummaryQScript {
 
       /** Adds the library jobs */
       final def addAndTrackJobs(): Unit = {
+        if (nameRegex.findFirstIn(libId) == None)
+          Logging.addError(s"Library '$libId' $nameError")
         currentSample = Some(sampleId)
         currentLib = Some(libId)
         addJobs()
@@ -90,6 +92,8 @@ trait MultiSampleQScript extends SummaryQScript {
 
     /** Adds sample jobs */
     final def addAndTrackJobs(): Unit = {
+      if (nameRegex.findFirstIn(sampleId) == None)
+        Logging.addError(s"Sample '$sampleId' $nameError")
       currentSample = Some(sampleId)
       addJobs()
       qscript.addSummarizable(this, "pipeline", Some(sampleId))
@@ -129,6 +133,12 @@ trait MultiSampleQScript extends SummaryQScript {
   /** Returns a list of all sampleIDs */
   protected def sampleIds: Set[String] = ConfigUtils.any2map(globalConfig.map("samples")).keySet
 
+  protected lazy val nameRegex = """^[a-zA-Z0-9][a-zA-Z0-9-_]+[a-zA-Z0-9]$""".r
+  protected lazy val nameError = " name invalid." +
+    "Name must have at least 3 characters," +
+    "must begin and end with an alphanumeric character, " +
+    "and must not have whitespace."
+
   /** Runs addAndTrackJobs method for each sample */
   final def addSamplesJobs() {
     if (onlySamples.isEmpty || samples.forall(x => onlySamples.contains(x._1))) {

public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommandFuntion.scala → public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommandFunction.scala

@@ -5,9 +5,12 @@ import nl.lumc.sasc.biopet.FullVersion
 /**
  * Created by pjvanthof on 11/09/15.
  */
-trait ToolCommandFuntion extends BiopetJavaCommandLineFunction {
+trait ToolCommandFunction extends BiopetJavaCommandLineFunction with Version {
   def toolObject: Object
 
+  def versionCommand = ""
+  def versionRegex = "".r
+
   override def getVersion = Some("Biopet " + FullVersion)
 
   override def beforeGraph(): Unit = {

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

+package nl.lumc.sasc.biopet.core
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.utils.Logging
+import org.broadinstitute.gatk.queue.function.QFunction
+
+import scala.collection.mutable
+import scala.sys.process.{ Process, ProcessLogger }
+import scala.util.matching.Regex
+
+/**
+ * Created by pjvan_thof on 10/13/15.
+ */
+trait Version extends QFunction {
+  /** Command to get version of executable */
+  def versionCommand: String
+
+  /** Regex to get version from version command output */
+  def versionRegex: Regex
+
+  /** Allowed exit codes for the version command */
+  protected[core] def versionExitcode = List(0)
+
+  /** Executes the version command */
+  private[core] def getVersionInternal: Option[String] = {
+    if (versionCommand == null || versionRegex == null) None
+    else Version.getVersionInternal(versionCommand, versionRegex, versionExitcode)
+  }
+
+  /** Get version from cache otherwise execute the version command  */
+  def getVersion: Option[String] = {
+    if (!Version.versionCache.contains(versionCommand))
+      getVersionInternal match {
+        case Some(version) => Version.versionCache += versionCommand -> version
+        case _             =>
+      }
+    Version.versionCache.get(versionCommand)
+  }
+
+  override def freezeFieldValues(): Unit = {
+    super.freezeFieldValues()
+    addJobReportBinding("version", getVersion.getOrElse("NA"))
+  }
+}
+
+object Version extends Logging {
+  private[core] val versionCache: mutable.Map[String, String] = mutable.Map()
+
+  /** Executes the version command */
+  private[core] def getVersionInternal(versionCommand: String,
+                                       versionRegex: Regex,
+                                       versionExitcode: List[Int] = List(0)): Option[String] = {
+    if (versionCache.contains(versionCommand)) return versionCache.get(versionCommand)
+    else if (versionCommand == null || versionRegex == null) return None
+    else {
+      val exe = new File(versionCommand.trim.split(" ")(0))
+      if (!exe.exists()) return None
+      val stdout = new StringBuffer()
+      val stderr = new StringBuffer()
+      def outputLog = "Version command: \n" + versionCommand +
+        "\n output log: \n stdout: \n" + stdout.toString +
+        "\n stderr: \n" + stderr.toString
+      val process = Process(versionCommand).run(ProcessLogger(stdout append _ + "\n", stderr append _ + "\n"))
+      if (!versionExitcode.contains(process.exitValue())) {
+        logger.warn("getVersion give exit code " + process.exitValue + ", version not found \n" + outputLog)
+        return None
+      }
+      for (line <- stdout.toString.split("\n") ++ stderr.toString.split("\n")) {
+        line match {
+          case versionRegex(m) => return Some(m)
+          case _               =>
+        }
+      }
+      logger.warn("getVersion give a exit code " + process.exitValue + " but no version was found, executable correct? \n" + outputLog)
+      None
+    }
+  }
+
+}
\ No newline at end of file

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

@@ -17,12 +17,12 @@ package nl.lumc.sasc.biopet.core.extensions
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction }
 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 {
+class Md5sum(val root: Configurable) extends BiopetCommandLineFunction with Version {
   @Input(doc = "Input")
   var input: File = _
 
@@ -31,8 +31,8 @@ class Md5sum(val root: Configurable) extends BiopetCommandLineFunction {
 
   executable = config("exe", default = "md5sum")
 
-  override def versionRegex = """md5sum \(GNU coreutils\) (.*)""".r
-  override def versionCommand = executable + " --version"
+  def versionRegex = """md5sum \(GNU coreutils\) (.*)""".r
+  def versionCommand = executable + " --version"
 
   /** return commandline to execute */
   def cmdLine = required(executable) + required(input) + " > " + required(output)

public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala

@@ -16,7 +16,7 @@
 package nl.lumc.sasc.biopet.core.report
 
 import java.io._
-import nl.lumc.sasc.biopet.core.ToolCommandFuntion
+import nl.lumc.sasc.biopet.core.ToolCommandFunction
 import nl.lumc.sasc.biopet.utils.summary.Summary
 import nl.lumc.sasc.biopet.utils.{ ToolCommand, Logging, IoUtils }
 import org.broadinstitute.gatk.utils.commandline.Input
@@ -28,7 +28,7 @@ import scala.collection.mutable
  *
  * @author pjvan_thof
  */
-trait ReportBuilderExtension extends ToolCommandFuntion {
+trait ReportBuilderExtension extends ToolCommandFunction {
 
   /** Report builder object */
   val builder: ReportBuilder

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

@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.core.summary
 import java.io.{ File, PrintWriter }
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, BiopetJavaCommandLineFunction, SampleLibraryTag }
+import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction, BiopetJavaCommandLineFunction, SampleLibraryTag }
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import nl.lumc.sasc.biopet.{ LastCommitHash, Version }
 import org.broadinstitute.gatk.queue.function.{ InProcessFunction, QFunction }
@@ -71,21 +71,32 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
       val files = parseFiles(qscript.summaryFiles)
       val settings = qscript.summarySettings
       val executables: Map[String, Any] = {
-        (for (f <- qscript.functions if f.isInstanceOf[BiopetCommandLineFunction]) yield {
+
+        def fetchVersion(f: QFunction): Option[(String, Any)] = {
           f match {
-            case f: BiopetJavaCommandLineFunction =>
-              f.configName -> Map("version" -> f.getVersion.getOrElse(None),
+            case f: BiopetJavaCommandLineFunction with Version =>
+              Some(f.configName -> Map("version" -> f.getVersion.getOrElse(None),
                 "java_md5" -> BiopetCommandLineFunction.executableMd5Cache.getOrElse(f.executable, None),
                 "java_version" -> f.getJavaVersion,
-                "jar_path" -> f.jarFile)
-            case f: BiopetCommandLineFunction =>
-              f.configName -> Map("version" -> f.getVersion.getOrElse(None),
+                "jar_path" -> f.jarFile))
+            case f: BiopetCommandLineFunction with Version =>
+              Some(f.configName -> Map("version" -> f.getVersion.getOrElse(None),
                 "md5" -> BiopetCommandLineFunction.executableMd5Cache.getOrElse(f.executable, None),
-                "path" -> f.executable)
-            case _ => throw new IllegalStateException("This should not be possible")
+                "path" -> f.executable))
+            case f: Configurable with Version =>
+              Some(f.configName -> Map("version" -> f.getVersion.getOrElse(None)))
+            case _ => None
           }
-
-        }).toMap
+        }
+
+        (
+          qscript.functions.flatMap(fetchVersion(_)) ++
+          qscript.functions
+          .flatMap {
+            case f: BiopetCommandLineFunction => f.pipesJobs
+            case _                            => Nil
+          }.flatMap(fetchVersion(_))
+        ).toMap
       }
 
       val map = Map(qscript.summaryName -> ((if (settings.isEmpty) Map[String, Any]() else Map("settings" -> settings)) ++
@@ -113,7 +124,7 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
     }).foldRight(jobsMap)((a, b) => ConfigUtils.mergeMaps(a, b)) ++
       Map("meta" -> Map(
         "last_commit_hash" -> LastCommitHash,
-        "pipeline_version" -> Version,
+        "pipeline_version" -> nl.lumc.sasc.biopet.Version,
         "pipeline_name" -> qscript.summaryName,
         "output_dir" -> qscript.outputDir,
         "run_name" -> config("run_name", default = qSettings.runName).asString,

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

@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Reference }
+import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction, Reference }
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**
@@ -26,7 +26,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
  *
  * Based on version 1.1.1
  */
-class Bowtie(val root: Configurable) extends BiopetCommandLineFunction with Reference {
+class Bowtie(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version {
   @Input(doc = "Fastq file R1", shortName = "R1")
   var R1: File = null
 
@@ -40,9 +40,9 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction with Refe
   var output: File = null
 
   executable = config("exe", default = "bowtie", freeVar = false)
-  override def versionRegex = """.*[Vv]ersion:? (.*)""".r
+  def versionRegex = """.*[Vv]ersion:? (.*)""".r
   override def versionExitcode = List(0, 1)
-  override def versionCommand = executable + " --version"
+  def versionCommand = executable + " --version"
 
   override def defaultCoreMemory = 4.0
   override def defaultThreads = 8

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

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction }
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
@@ -25,7 +25,7 @@ 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 {
+class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction with Version {
 
   /** default executable */
   executable = config("exe", default = "cufflinks")
@@ -185,8 +185,8 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction {
   /** do not contact server to check for update availability [FALSE] */
   var no_update_check: Boolean = config("no_update_check", default = false)
 
-  override def versionRegex = """cufflinks v(.*)""".r
-  override def versionCommand = executable
+  def versionRegex = """cufflinks v(.*)""".r
+  def versionCommand = executable
   override def versionExitcode = List(0, 1)
 
   def cmdLine =

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

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction }
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
@@ -25,7 +25,7 @@ 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 {
+class Cuffquant(val root: Configurable) extends BiopetCommandLineFunction with Version {
 
   /** default executable */
   executable = config("exe", default = "cuffquant")
@@ -117,8 +117,8 @@ class Cuffquant(val root: Configurable) extends BiopetCommandLineFunction {
   /** Disable SCV correction */
   var no_scv_correction: Boolean = config("no_scv_correction", default = false)
 
-  override def versionRegex = """cuffquant v(.*)""".r
-  override def versionCommand = executable
+  def versionRegex = """cuffquant v(.*)""".r
+  def versionCommand = executable
   override def versionExitcode = List(0, 1)
 
   def cmdLine =

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

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction }
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.core.summary.Summarizable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
@@ -29,7 +29,7 @@ import scala.io.Source
  * Extension for cutadept
  * Based on version 1.5
  */
-class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Summarizable {
+class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Summarizable with Version {
   @Input(doc = "Input fastq file")
   var fastq_input: File = _
 
@@ -40,8 +40,8 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
   var stats_output: File = _
 
   executable = config("exe", default = "cutadapt")
-  override def versionCommand = executable + " --version"
-  override def versionRegex = """(.*)""".r
+  def versionCommand = executable + " --version"
+  def versionRegex = """(.*)""".r
 
   var default_clip_mode: String = config("default_clip_mode", default = "3")
   var opt_adapter: Set[String] = config("adapter", default = Nil)

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

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction }
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
@@ -25,7 +25,7 @@ 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 {
+class Fastqc(val root: Configurable) extends BiopetCommandLineFunction with Version {
 
   @Input(doc = "Contaminants", required = false)
   var contaminants: Option[File] = None
@@ -47,8 +47,8 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
   var nogroup: Boolean = config("nogroup", default = false)
   var extract: Boolean = config("extract", default = true)
 
-  override def versionRegex = """FastQC (.*)""".r
-  override def versionCommand = executable + " --version"
+  def versionRegex = """FastQC (.*)""".r
+  def versionCommand = executable + " --version"
   override def defaultThreads = 4
 
   /** Sets contaminants and adapters when not yet set */

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

@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Reference }
+import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction, Reference }
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**
@@ -26,7 +26,7 @@ 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 {
+class Freebayes(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version {
 
   @Input(required = true)
   var bamfiles: List[File] = Nil
@@ -41,8 +41,8 @@ class Freebayes(val root: Configurable) extends BiopetCommandLineFunction with R
   var haplotypeLength: Option[Int] = config("haplotype_length")
 
   executable = config("exe", default = "freebayes")
-  override def versionRegex = """version:  (.*)""".r
-  override def versionCommand = executable + " --version"
+  def versionRegex = """version:  (.*)""".r
+  def versionCommand = executable + " --version"
 
   override def beforeGraph(): Unit = {
     super.beforeGraph()

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

@@ -18,14 +18,14 @@ package nl.lumc.sasc.biopet.extensions
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Reference }
+import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction, Reference }
 import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
 
 /**
  * Wrapper for the gsnap command line tool
  * Written based on gsnap version 2014-05-15
  */
-class Gsnap(val root: Configurable) extends BiopetCommandLineFunction with Reference {
+class Gsnap(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version {
 
   /** default executable */
   executable = config("exe", default = "gsnap", freeVar = false)
@@ -328,8 +328,8 @@ class Gsnap(val root: Configurable) extends BiopetCommandLineFunction with Refer
   /** value to put into read-group library (rg-pl) field */
   var read_group_platform: Option[String] = config("read_group_platform")
 
-  override def versionRegex = """.* version (.*)""".r
-  override def versionCommand = executable + " --version"
+  def versionRegex = """.* version (.*)""".r
+  def versionCommand = executable + " --version"
 
   def cmdLine = {
     required(executable) +

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

@@ -17,11 +17,11 @@ package nl.lumc.sasc.biopet.extensions
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+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 {
+class Gzip(val root: Configurable) extends BiopetCommandLineFunction with Version {
   @Input(doc = "Input file", required = true)
   var input: List[File] = Nil
 
@@ -30,8 +30,8 @@ class Gzip(val root: Configurable) extends BiopetCommandLineFunction {
 
   executable = config("exe", default = "gzip", freeVar = false)
 
-  override def versionRegex = """gzip (.*)""".r
-  override def versionCommand = executable + " --version"
+  def versionRegex = """gzip (.*)""".r
+  def versionCommand = executable + " --version"
 
   def cmdLine = required(executable) + " -c " +
     (if (inputAsStdin) "" else repeat(input)) +

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

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction }
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
@@ -25,7 +25,7 @@ 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 {
+class HtseqCount(val root: Configurable) extends BiopetCommandLineFunction with Version {
 
   /** default executable */
   executable = config("exe", default = "htseq-count")
@@ -70,8 +70,8 @@ class HtseqCount(val root: Configurable) extends BiopetCommandLineFunction {
   /** suppress progress report */
   var quiet: Boolean = config("quiet", default = false)
 
-  override def versionRegex = """.*, version (.*)\.""".r
-  override def versionCommand = executable + " --help"
+  def versionRegex = """.*, version (.*)\.""".r
+  def versionCommand = executable + " --help"
 
   def cmdLine = {
     required(executable) +

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

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction }
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
 
@@ -27,11 +27,11 @@ import scalaz.std.boolean.option
  * extension for raxml
  * based on version 8.1.3
  */
-class Raxml(val root: Configurable) extends BiopetCommandLineFunction {
+class Raxml(val root: Configurable) extends BiopetCommandLineFunction with Version {
 
   override def defaultThreads = 1
-  override def versionCommand = executable + " -v"
-  override def versionRegex = """.*version ([\w\.]*) .*""".r
+  def versionCommand = executable + " -v"
+  def versionRegex = """.*version ([\w\.]*) .*""".r
 
   @Input(doc = "Input phy/fasta file", required = true)
   var input: File = _