Use Option[File] for optional files and fix bug with adapter sequence from fastqc capture

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

@@ -25,10 +25,10 @@ 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 = _
@@ -50,17 +50,19 @@ 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)
+    contaminants = contaminants match {
+      case None =>
+        val fastqcDir = executable.substring(0, executable.lastIndexOf("/"))
+        val defaultContams = getVersion match {
+          case "v0.11.2" => Option(new File(fastqcDir + "/Configuration/contaminant_list.txt"))
+          case _         => Option(new File(fastqcDir + "/Contaminants/contaminant_list.txt"))
+        }
+        val defaultAdapters = getVersion match {
+          case "v0.11.2" => Option(new File(fastqcDir + "/Configuration/adapter_list.txt"))
+          case _         => None
+        }
+        config("contaminants", default = defaultContams)
+      case wrapped @ Some(_) => wrapped
     }
   }
 
@@ -74,6 +76,6 @@ 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/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala

@@ -99,13 +99,16 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
   def foundAdapters: Set[AdapterSequence] = {
 
     /** Returns a list of adapter and/or contaminant sequences known to FastQC */
-    def getFastqcSeqs(file: File): Set[AdapterSequence] =
-      if (file != null) {
-        (for (
-          line <- Source.fromFile(file).getLines(); if line.startsWith("#");
-          values = line.split("\t*") if values.size >= 2
-        ) yield AdapterSequence(values(0), values(1))).toSet
-      } else Set.empty[AdapterSequence]
+    def getFastqcSeqs(file: Option[File]): Set[AdapterSequence] = file match {
+      case None => Set.empty[AdapterSequence]
+      case Some(f) =>
+        (for {
+          line <- Source.fromFile(f).getLines()
+          if !line.startsWith("#")
+          values = line.split("\t*")
+          if values.size >= 2
+        } yield AdapterSequence(values(0), values(1))).toSet
+    }
 
     val found = qcModules.get("Overrepresented sequences") match {
       case None => Array.empty[String]
@@ -137,7 +140,8 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
         "plot_per_sequence_quality" -> "Images/per_sequence_quality.png",
         "plot_sequence_length_distribution" -> "Images/sequence_length_distribution.png",
         "fastqc_data" -> "fastqc_data.txt")
-        .map { case (name, relPath) =>
+        .map {
+          case (name, relPath) =>
             name -> Map("path" -> (outputDir + relPath))
         }