Merge branch 'develop' into feature-unittest_core

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

docs/config.md

@@ -72,16 +72,16 @@ Global setting examples are:
 #### Example settings config
 ~~~
 {
-        "reference": "/data/LGTC/projects/vandoorn-melanoma/data/references/hg19_nohap/ucsc.hg19_nohap.fasta",
-        "dbsnp": "/data/LGTC/projects/vandoorn-melanoma/data/references/hg19_nohap/dbsnp_137.hg19_nohap.vcf",
+        "reference": "/references/hg19_nohap/ucsc.hg19_nohap.fasta",
+        "dbsnp": "/references/hg19_nohap/dbsnp_137.hg19_nohap.vcf",
         "joint_variantcalling": false,
         "haplotypecaller": { "scattercount": 100 },
         "multisample": { "haplotypecaller": { "scattercount": 1000 } },
         "picard": { "validationstringency": "LENIENT" },
         "library_variantcalling_temp": true,
-        "target_bed_temp": "/data/LGTC/projects/vandoorn-melanoma/analysis/target.bed",
+        "target_bed_temp": "analysis/target.bed",
         "min_dp": 5,
-        "bedtools": {"exe":"/share/isilon/system/local/BEDtools/bedtools-2.17.0/bin/bedtools"},
+        "bedtools": {"exe":"/BEDtools/bedtools-2.17.0/bin/bedtools"},
         "bam_to_fastq": true,
         "baserecalibrator": { "memory_limit": 8, "vmem":"16G" },
         "samtofastq": {"memory_limit": 8, "vmem": "16G"},
@@ -95,4 +95,4 @@ Global setting examples are:
 ### JSON validation
 
 To check if the JSON file created is correct we can use multiple options the simplest way is using [this](http://jsonformatter.curiousconcept.com/)
-website. It is also possible to use Python or Scala for validating but this requires some more knowledge.
\ No newline at end of file
+website. It is also possible to use Python or Scala for validating but this requires some more knowledge.

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

@@ -33,7 +33,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
   def makeSample(id: String) = new Sample(id)
   class Sample(sampleId: String) extends AbstractSample(sampleId) {
     def makeLibrary(id: String) = new Library(id)
-    class Library(libraryId: String) extends AbstractLibrary(libraryId) {
+    class Library(libId: String) extends AbstractLibrary(libId) {
       protected def addJobs(): Unit = {}
     }
 

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

@@ -13,13 +13,13 @@ trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction {
 
   override def subPath = "gatk" :: super.subPath
 
-  jarFile = config("gatk_jar", required = true)
+  jarFile = config("gatk_jar")
 
   override val defaultVmem = "7G"
 
   if (config.contains("intervals")) intervals = config("intervals").asFileList
   if (config.contains("exclude_intervals")) excludeIntervals = config("exclude_intervals").asFileList
-  reference_sequence = config("reference", required = true)
+  reference_sequence = config("reference")
   if (config.contains("gatk_key")) gatk_key = config("gatk_key")
   if (config.contains("pedigree")) pedigree = config("pedigree").asFileList
 }

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala

@@ -35,17 +35,17 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
   var jointGenotyping: Boolean = config("joint_genotyping", default = false)
 
   var singleSampleCalling = config("single_sample_calling", default = true)
-  var reference: File = config("reference", required = true)
+  var reference: File = config("reference")
   var useAllelesOption: Boolean = config("use_alleles_option", default = false)
   val externalGvcfs = config("external_gvcfs_files", default = Nil).asFileList
 
   def makeSample(id: String) = new Sample(id)
   class Sample(sampleId: String) extends AbstractSample(sampleId) {
     def makeLibrary(id: String) = new Library(id)
-    class Library(libraryId: String) extends AbstractLibrary(libraryId) {
+    class Library(libId: String) extends AbstractLibrary(libId) {
       val mapping = new Mapping(qscript)
       mapping.sampleId = sampleId
-      mapping.libraryId = libraryId
+      mapping.libId = libId
       mapping.outputDir = libDir + "/variantcalling/"
 
       /** Library variantcalling */
@@ -66,8 +66,8 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
           if (!bamFile.exists) throw new IllegalStateException("Bam in config does not exist, file: " + bamFile)
 
           if (config("bam_to_fastq", default = false).asBoolean) {
-            val samToFastq = SamToFastq(qscript, bamFile, libDir + sampleId + "-" + libraryId + ".R1.fastq",
-              libDir + sampleId + "-" + libraryId + ".R2.fastq")
+            val samToFastq = SamToFastq(qscript, bamFile, libDir + sampleId + "-" + libId + ".R1.fastq",
+              libDir + sampleId + "-" + libId + ".R2.fastq")
             samToFastq.isIntermediate = true
             qscript.add(samToFastq)
             mapping.input_R1 = samToFastq.fastqR1
@@ -82,17 +82,17 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
             val header = inputSam.getFileHeader.getReadGroups
             for (readGroup <- inputSam.getFileHeader.getReadGroups) {
               if (readGroup.getSample != sampleId) logger.warn("Sample ID readgroup in bam file is not the same")
-              if (readGroup.getLibrary != libraryId) logger.warn("Library ID readgroup in bam file is not the same")
-              if (readGroup.getSample != sampleId || readGroup.getLibrary != libraryId) readGroupOke = false
+              if (readGroup.getLibrary != libId) logger.warn("Library ID readgroup in bam file is not the same")
+              if (readGroup.getSample != sampleId || readGroup.getLibrary != libId) readGroupOke = false
             }
             inputSam.close
 
             if (!readGroupOke) {
               if (config("correct_readgroups", default = false)) {
                 logger.info("Correcting readgroups, file:" + bamFile)
-                val aorrg = AddOrReplaceReadGroups(qscript, bamFile, new File(libDir + sampleId + "-" + libraryId + ".bam"))
-                aorrg.RGID = sampleId + "-" + libraryId
-                aorrg.RGLB = libraryId
+                val aorrg = AddOrReplaceReadGroups(qscript, bamFile, new File(libDir + sampleId + "-" + libId + ".bam"))
+                aorrg.RGID = sampleId + "-" + libId
+                aorrg.RGLB = libId
                 aorrg.RGSM = sampleId
                 aorrg.isIntermediate = true
                 qscript.add(aorrg)
@@ -105,7 +105,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
             Some(bamFile)
           }
         } else {
-          logger.error("Sample: " + sampleId + ": No R1 found for run: " + libraryId)
+          logger.error("Sample: " + sampleId + ": No R1 found for run: " + libId)
           None
         }
 

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala

@@ -30,7 +30,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
   var rawVcfInput: File = _
 
   @Argument(doc = "Reference", shortName = "R", required = false)
-  var reference: File = config("reference", required = true)
+  var reference: File = config("reference")
 
   @Argument(doc = "OutputName", required = false)
   var outputName: String = _

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

@@ -78,7 +78,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
   /**
    * Checks executable. Follow full CanonicalPath, checks if it is existing and do a md5sum on it to store in job report
    */
-  protected def checkExecutable {
+  protected[core] def checkExecutable {
     if (!BiopetCommandLineFunctionTrait.executableMd5Cache.contains(executable)) {
       try if (executable != null) {
         if (!BiopetCommandLineFunctionTrait.executableCache.contains(executable)) {
@@ -91,8 +91,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
             val file = new File(executable)
             executable = file.getCanonicalPath
           } else {
-            logger.error("executable: '" + executable + "' not found, please check config")
-            throw new QException("executable: '" + executable + "' not found, please check config")
+            BiopetQScript.addError("executable: '" + executable + "' not found, please check config")
           }
           BiopetCommandLineFunctionTrait.executableCache += oldExecutable -> executable
           BiopetCommandLineFunctionTrait.executableCache += executable -> executable
@@ -113,9 +112,8 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
         case ioe: java.io.IOException => logger.warn("Could not use 'which', check on executable skipped: " + ioe)
       }
     }
-    val md5 = BiopetCommandLineFunctionTrait.executableMd5Cache(executable)
-    if (md5 == null) addJobReportBinding("md5sum_exe", md5)
-    else addJobReportBinding("md5sum_exe", "None")
+    val md5 = BiopetCommandLineFunctionTrait.executableMd5Cache.get(executable)
+    addJobReportBinding("md5sum_exe", md5.getOrElse("None"))
   }
 
   /**
@@ -145,6 +143,8 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
   /** Executes the version command */
   private def getVersionInternal: String = {
     if (versionCommand == null || versionRegex == null) return "N/A"
+    val exe = new File(versionCommand.trim.split(" ")(0))
+    if (!exe.exists()) return "N/A"
     val stdout = new StringBuffer()
     val stderr = new StringBuffer()
     def outputLog = "Version command: \n" + versionCommand +
@@ -206,4 +206,4 @@ object BiopetCommandLineFunctionTrait {
   private val versionCache: Map[String, String] = Map()
   private val executableMd5Cache: Map[String, String] = Map()
   private val executableCache: Map[String, String] = Map()
-}
\ No newline at end of file
+}

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

@@ -23,6 +23,7 @@ import org.broadinstitute.gatk.queue.QSettings
 import org.broadinstitute.gatk.queue.function.QFunction
 import org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction
 import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging }
+import scala.collection.mutable.ListBuffer
 
 /**
  * Base for biopet pipeline
@@ -33,8 +34,8 @@ trait BiopetQScript extends Configurable with GatkLogging {
   val configfiles: List[File] = Nil
 
   var outputDir: String = {
-    val temp = Config.getValueFromMap(Config.global.map, ConfigValueIndex(this.configName, configPath, "output_dir"))
-    if (temp.isEmpty) throw new IllegalArgumentException("No output_dir defined in config")
+    val temp = Config.getValueFromMap(globalConfig.map, ConfigValueIndex(this.configName, configPath, "output_dir"))
+    if (temp.isEmpty) ""
     else {
       val t = temp.get.value.toString
       if (!t.endsWith("/")) t + "/" else t
@@ -62,8 +63,9 @@ trait BiopetQScript extends Configurable with GatkLogging {
    * Script from queue itself, final to force some checks for each pipeline and write report
    */
   final def script() {
-    outputDir = config("output_dir", required = true)
-    if (!outputDir.endsWith("/")) outputDir += "/"
+    outputDir = config("output_dir")
+    if (outputDir.isEmpty) outputDir = new File(".").getAbsolutePath()
+    else if (!outputDir.endsWith("/")) outputDir += "/"
     init
     biopetScript
 
@@ -72,11 +74,17 @@ trait BiopetQScript extends Configurable with GatkLogging {
       case _                            =>
     }
     for (function <- functions) function match {
-      case f: BiopetCommandLineFunctionTrait => f.afterGraph
-      case _                                 =>
+      case f: BiopetCommandLineFunctionTrait => {
+        f.checkExecutable
+        f.afterGraph
+      }
+      case _ =>
     }
 
-    Config.global.writeReport(qSettings.runName, outputDir + ".log/" + qSettings.runName)
+    if (new File(outputDir).canWrite) globalConfig.writeReport(qSettings.runName, outputDir + ".log/" + qSettings.runName)
+    else BiopetQScript.addError("Output dir: '" + outputDir + "' is not writeable")
+
+    BiopetQScript.checkErrors
   }
 
   /** Get implemented from org.broadinstitute.gatk.queue.QScript */
@@ -92,3 +100,28 @@ trait BiopetQScript extends Configurable with GatkLogging {
     add(function)
   }
 }
+
+object BiopetQScript extends Logging {
+  private val errors: ListBuffer[Exception] = ListBuffer()
+
+  def addError(error: String, debug: String = null): Unit = {
+    val msg = error + (if (debug != null && logger.isDebugEnabled) "; " + debug else "")
+    errors.append(new Exception(msg))
+  }
+
+  protected def checkErrors: Unit = {
+    if (!errors.isEmpty) {
+      logger.error("*************************")
+      logger.error("Biopet found some errors:")
+      if (logger.isDebugEnabled) {
+        for (e <- errors) {
+          logger.error(e.getMessage)
+          logger.debug(e.getStackTrace.mkString("Stack trace:\n", "\n", "\n"))
+        }
+      } else {
+        errors.map(_.getMessage).sorted.distinct.foreach(logger.error(_))
+      }
+      throw new IllegalStateException("Biopet found errors")
+    }
+  }
+}

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

@@ -28,7 +28,7 @@ trait MultiSampleQScript extends BiopetQScript {
   @Argument(doc = "Only Sample", shortName = "sample", required = false)
   private val onlySamples: List[String] = Nil
 
-  require(Config.global.map.contains("samples"), "No Samples found in config")
+  require(globalConfig.map.contains("samples"), "No Samples found in config")
 
   /**
    * Sample class with basic functions build in
@@ -40,26 +40,26 @@ trait MultiSampleQScript extends BiopetQScript {
 
     /**
      * Library class with basic functions build in
-     * @param libraryId
+     * @param libId
      */
-    abstract class AbstractLibrary(val libraryId: String) {
+    abstract class AbstractLibrary(val libId: String) {
       /** Overrules config of qscript with default sample and default library */
-      val config = new ConfigFunctions(defaultSample = sampleId, defaultLibrary = libraryId)
+      val config = new ConfigFunctions(defaultSample = sampleId, defaultLibrary = libId)
 
       /** Adds the library jobs */
       final def addAndTrackJobs(): Unit = {
         currentSample = Some(sampleId)
-        currentLib = Some(libraryId)
+        currentLib = Some(libId)
         addJobs()
         currentLib = None
         currentSample = None
       }
 
       /** Creates a library file with given suffix */
-      def createFile(suffix: String): File = new File(libDir, sampleId + "-" + libraryId + suffix)
+      def createFile(suffix: String): File = new File(libDir, sampleId + "-" + libId + suffix)
 
       /** Returns library directory */
-      def libDir = sampleDir + "lib_" + libraryId + File.separator
+      def libDir = sampleDir + "lib_" + libId + File.separator
 
       /** Function that add library jobs */
       protected def addJobs()
@@ -80,7 +80,7 @@ trait MultiSampleQScript extends BiopetQScript {
 
     /** returns a set with library names */
     protected def libIds: Set[String] = {
-      ConfigUtils.getMapFromPath(Config.global.map, List("samples", sampleId, "libraries")).getOrElse(Map()).keySet
+      ConfigUtils.getMapFromPath(globalConfig.map, List("samples", sampleId, "libraries")).getOrElse(Map()).keySet
     }
 
     /** Adds sample jobs */
@@ -95,7 +95,7 @@ trait MultiSampleQScript extends BiopetQScript {
 
     /** function add all libraries in one call */
     protected final def addPerLibJobs(): Unit = {
-      for ((libraryId, library) <- libraries) {
+      for ((libId, library) <- libraries) {
         library.addAndTrackJobs()
       }
     }
@@ -125,7 +125,7 @@ trait MultiSampleQScript extends BiopetQScript {
   val samples: Map[String, Sample] = sampleIds.map(id => id -> makeSample(id)).toMap
 
   /** Returns a list of all sampleIDs */
-  protected def sampleIds: Set[String] = ConfigUtils.any2map(Config.global.map("samples")).keySet
+  protected def sampleIds: Set[String] = ConfigUtils.any2map(globalConfig.map("samples")).keySet
 
   /** Runs addAndTrackJobs method for each sample */
   final def addSamplesJobs() {

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

@@ -133,11 +133,11 @@ class Config(var map: Map[String, Any]) extends Logging {
    */
   protected[config] def apply(module: String, path: List[String], key: String, default: Any = null, freeVar: Boolean = true): ConfigValue = {
     val requestedIndex = ConfigValueIndex(module, path, key, freeVar)
-    if (contains(requestedIndex)) return foundCache(requestedIndex)
+    if (contains(requestedIndex)) foundCache(requestedIndex)
     else if (default != null) {
       defaultCache += (requestedIndex -> ConfigValue(requestedIndex, null, default, freeVar))
-      return defaultCache(requestedIndex)
-    } else throw new IllegalStateException("Value in config could not be found but it seems required, index: " + requestedIndex)
+      defaultCache(requestedIndex)
+    } else ConfigValue(requestedIndex, null, null, freeVar)
   }
 
   def writeReport(id: String, directory: String): Unit = {
@@ -174,7 +174,7 @@ class Config(var map: Map[String, Any]) extends Logging {
     val fullEffective = ConfigUtils.mergeMaps(effectiveFound, effectiveDefaultFound)
     val fullEffectiveWithNotFound = ConfigUtils.mergeMaps(fullEffective, notFound)
 
-    writeMapToJsonFile(Config.global.map, "input")
+    writeMapToJsonFile(this.map, "input")
     writeMapToJsonFile(found, "found")
     writeMapToJsonFile(effectiveFound, "effective.found")
     writeMapToJsonFile(effectiveDefaultFound, "effective.defaults")

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

@@ -21,6 +21,7 @@ import nl.lumc.sasc.biopet.utils.ConfigUtils.ImplicitConversions
 trait Configurable extends ImplicitConversions {
   /** Should be object of parant object */
   val root: Configurable
+  val globalConfig: Config = if (root != null) root.globalConfig else Config.global
 
   /** subfix to the path */
   def subPath: List[String] = Nil
@@ -79,7 +80,6 @@ trait Configurable extends ImplicitConversions {
      * @param key Name of value
      * @param default Default value if not found
      * @param submodule Adds to the path
-     * @param required Default false, if true and value is not found this function will raise an exception
      * @param freeVar Default true, if set false value must exist in module
      * @param sample Default null, when set path is prefixed with "samples" -> "sampleID"
      * @param library Default null, when set path is prefixed with "libraries" -> "libraryID"
@@ -88,7 +88,6 @@ trait Configurable extends ImplicitConversions {
     def apply(key: String,
               default: Any = null,
               submodule: String = null,
-              required: Boolean = false,
               freeVar: Boolean = true,
               sample: String = null,
               library: String = null): ConfigValue = {
@@ -100,14 +99,8 @@ trait Configurable extends ImplicitConversions {
         val value = Config.getValueFromMap(defaults.toMap, ConfigValueIndex(m, p, key, freeVar))
         if (value.isDefined) value.get.value else default
       }
-      if (!contains(key, submodule, freeVar, sample = s, library = l) && d == null) {
-        if (required) {
-          Logging.logger.error("Value in config could not be found but it is required, key: " + key + "   module: " + m + "   path: " + p)
-          throw new IllegalStateException("Value in config could not be found but it is required, key: " + key + "   module: " + m + "   path: " + p)
-        } else return null
-      }
-      if (d == null) return Config.global(m, p, key, freeVar = freeVar)
-      else return Config.global(m, p, key, d, freeVar)
+      if (d == null) globalConfig(m, p, key, freeVar = freeVar)
+      else globalConfig(m, p, key, d, freeVar)
     }
 
     /**
@@ -129,7 +122,7 @@ trait Configurable extends ImplicitConversions {
       val m = if (submodule != null) submodule else configName
       val p = path(s, l, submodule)
 
-      Config.global.contains(m, p, key, freeVar) || !(Config.getValueFromMap(defaults.toMap, ConfigValueIndex(m, p, key, freeVar)) == None)
+      globalConfig.contains(m, p, key, freeVar) || !(Config.getValueFromMap(defaults.toMap, ConfigValueIndex(m, p, key, freeVar)) == None)
     }
   }
 }

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

@@ -83,19 +83,15 @@ object BiopetQCommandLine extends GatkLogging {
 
     Runtime.getRuntime.addShutdownHook(shutdownHook)
 
+    CommandLineProgram.start(qCommandLine, argv)
     try {
-      CommandLineProgram.start(qCommandLine, argv)
-      try {
-        Runtime.getRuntime.removeShutdownHook(shutdownHook)
-        qCommandLine.shutdown()
-      } catch {
-        case e: Exception => /* ignore, example 'java.lang.IllegalStateException: Shutdown in progress' */
-      }
-      if (CommandLineProgram.result != 0)
-        System.exit(CommandLineProgram.result)
+      Runtime.getRuntime.removeShutdownHook(shutdownHook)
+      qCommandLine.shutdown()
     } catch {
-      case e: Exception => CommandLineProgram.exitSystemWithError(e)
+      case e: Exception => /* ignore, example 'java.lang.IllegalStateException: Shutdown in progress' */
     }
+    if (CommandLineProgram.result != 0)
+      System.exit(CommandLineProgram.result)
   }
 }
 
@@ -116,21 +112,28 @@ class BiopetQCommandLine extends CommandLineProgram with Logging {
   private var qScriptClasses: File = _
   private var shuttingDown = false
 
+  /**
+   * we modified this in Biopet to skip compiling and show full stacktrace again
+   */
   private lazy val qScriptPluginManager = {
     qScriptClasses = IOUtils.tempDir("Q-Classes-", "", settings.qSettings.tempDirectory)
-    //qScriptManager.loadScripts(scripts, qScriptClasses)
-    //var temp: Seq[URL] = Seq()
     for (t <- scripts) {
       val is = getClass.getResourceAsStream(t.getAbsolutePath)
       val os = new FileOutputStream(qScriptClasses.getAbsolutePath + "/" + t.getName)
       org.apache.commons.io.IOUtils.copy(is, os)
       os.close()
-      //temp :+= this.getClass.getResource(t.toString)
-      //logger.info(this.getClass.getResource(t.toString))
       val s = if (t.getName.endsWith("/")) t.getName.substring(0, t.getName.length - 1) else t.getName
       pipelineName = s.substring(0, s.lastIndexOf(".")) + "." + System.currentTimeMillis
     }
-    new PluginManager[QScript](qPluginType, List(qScriptClasses.toURI.toURL))
+
+    // override createByType to pass the correct exceptions
+    new PluginManager[QScript](qPluginType, List(qScriptClasses.toURI.toURL)) {
+      override def createByType(plugintype: Class[_ <: QScript]) = {
+        val noArgsConstructor = plugintype.getDeclaredConstructor()
+        noArgsConstructor.setAccessible(true)
+        noArgsConstructor.newInstance()
+      }
+    }
   }
 
   private lazy val qCommandPlugin = {
@@ -188,12 +191,7 @@ class BiopetQCommandLine extends CommandLineProgram with Logging {
         //if (settings.run)
         script.pullInputs()
         script.qSettings = settings.qSettings
-        try {
-          script.script()
-        } catch {
-          case e: Exception =>
-            throw new UserException.CannotExecuteQScript(script.getClass.getSimpleName + ".script() threw the following exception: " + e, e)
-        }
+        script.script()
 
         if (remoteFileConverter != null) {
           if (remoteFileConverter.convertToRemoteEnabled)

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

@@ -29,7 +29,7 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction {
   var R2: File = _
 
   @Input(doc = "The reference file for the bam files.", shortName = "R")
-  var reference: File = config("reference", required = true)
+  var reference: File = config("reference")
 
   @Output(doc = "Output file SAM", shortName = "output")
   var output: File = _

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

@@ -25,16 +25,16 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
 
   @Input(doc = "Contaminants", required = false)
-  var contaminants: File = _
+  var contaminants: Option[File] = None
 
   @Input(doc = "Adapters", required = false)
-  var adapters: File = _
+  var adapters: Option[File] = None
 
   @Input(doc = "Fastq file", shortName = "FQ")
-  var fastqfile: File = _
+  var fastqfile: File = null
 
   @Output(doc = "Output", shortName = "out")
-  var output: File = _
+  var output: File = null
 
   executable = config("exe", default = "fastqc")
   var java_exe: String = config("exe", default = "java", submodule = "java", freeVar = false)
@@ -50,17 +50,31 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
 
   override def afterGraph {
     this.checkExecutable
-    if (contaminants == null) {
-      val fastqcDir = executable.substring(0, executable.lastIndexOf("/"))
-      val defaultContams = getVersion match {
-        case "v0.11.2" => new File(fastqcDir + "/Configuration/contaminant_list.txt")
-        case _         => new File(fastqcDir + "/Contaminants/contaminant_list.txt")
-      }
-      val defaultAdapters = getVersion match {
-        case "v0.11.2" => new File(fastqcDir + "/Configuration/adapter_list.txt")
-        case _         => null
-      }
-      contaminants = config("contaminants", default = defaultContams)
+
+    val fastqcDir = new File(executable).getParent
+
+    contaminants = contaminants match {
+      // user-defined contaminants file take precedence
+      case userDefinedValue @ Some(_) => userDefinedValue
+      // otherwise, use default contaminants file (depending on FastQC version)
+      case None =>
+        val defaultContams = getVersion match {
+          case "v0.11.2" => new File(fastqcDir + "/Configuration/contaminant_list.txt")
+          case _         => new File(fastqcDir + "/Contaminants/contaminant_list.txt")
+        }
+        config("contaminants", default = defaultContams)
+    }
+
+    adapters = adapters match {
+      // user-defined contaminants file take precedence
+      case userDefinedValue @ Some(_) => userDefinedValue
+      // otherwise, check if adapters are already present (depending on FastQC version)
+      case None =>
+        val defaultAdapters = getVersion match {
+          case "v0.11.2" => Option(new File(fastqcDir + "/Configuration/adapter_list.txt"))
+          case _         => None
+        }
+        defaultAdapters.collect { case adp => config("adapters", default = adp) }
     }
   }
 
@@ -74,6 +88,6 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
     conditional(noextract, "--noextract") +
     conditional(extract, "--extract") +
     conditional(quiet, "--quiet") +
-    required("-o", output.getParent()) +
+    required("-o", output.getParent) +
     required(fastqfile)
 }

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

@@ -50,6 +50,8 @@ class Raxml(val root: Configurable) extends BiopetCommandLineFunction {
   @Argument(doc = "Output directory", required = true)
   var w: String = _
 
+  var noBfgs: Boolean = config("no_bfgs", default = false)
+
   @Input(required = false)
   var t: File = _