Fix fastqc dry run bug

public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala

@@ -52,19 +52,16 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
    * @throws FileNotFoundException if the FastQC data file can not be found.
    * @throws IllegalStateException if the module lines have no content or mapping is empty.
    */
-  @throws(classOf[FileNotFoundException])
-  @throws(classOf[IllegalStateException])
   def qcModules: Map[String, FastQCModule] = {
-
-    val fqModules = Source.fromFile(dataFile)
-      // drop all the characters before the first module delimiter (i.e. '>>')
-      .dropWhile(_ != '>')
-      // pull everything into a string
-      .mkString
-      // split into modules
-      .split(">>END_MODULE\n")
-      // make map of module name -> module lines
-      .map {
+      val fqModules = Source.fromFile(dataFile)
+        // drop all the characters before the first module delimiter (i.e. '>>')
+        .dropWhile(_ != '>')
+        // pull everything into a string
+        .mkString
+        // split into modules
+        .split(">>END_MODULE\n")
+        // make map of module name -> module lines
+        .map {
         case (modString) =>
           // module name is in the first line, without '>>' and before the tab character
           val Array(firstLine, otherLines) = modString
@@ -80,10 +77,10 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
             .slice(0, 2)
           modName -> FastQCModule(modName, modStatus, otherLines.split("\n").toSeq)
       }
-      .toMap
+        .toMap
 
-    if (fqModules.isEmpty) throw new IllegalStateException("Empty FastQC data file " + dataFile.toString)
-    else fqModules
+      if (fqModules.isEmpty) throw new IllegalStateException("Empty FastQC data file " + dataFile.toString)
+      else fqModules
   }
 
   /**
@@ -93,14 +90,16 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
    * @throws NoSuchElementException when the "Basic Statistics" key does not exist in the mapping or
    *                                when a line starting with "Encoding" does not exist.
    */
-  @throws(classOf[NoSuchElementException])
-  def encoding: String =
-    qcModules("Basic Statistics")
+  def encoding: String = {
+    if (dataFile.exists())
+      qcModules("Basic Statistics") //FIXME: not save
       .lines
       .dropWhile(!_.startsWith("Encoding"))
       .head
       .stripPrefix("Encoding\t")
       .stripSuffix("\t")
+    else ""
+  }
 
   /** Case class representing a known adapter sequence */
   protected case class AdapterSequence(name: String, seq: String)
@@ -111,32 +110,33 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
    * @return a [[Set]] of [[AdapterSequence]] objects.
    */
   def foundAdapters: Set[AdapterSequence] = {
+    if (dataFile.exists()) {
+      /** Returns a list of adapter and/or contaminant sequences known to FastQC */
+      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 => Seq.empty[String]
+        case Some(qcModule) =>
+          for (
+            line <- qcModule.lines if !(line.startsWith("#") || line.startsWith(">"));
+            values = line.split("\t") if values.size >= 4
+          ) yield values(3)
+      }
 
-    /** Returns a list of adapter and/or contaminant sequences known to FastQC */
-    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 => Seq.empty[String]
-      case Some(qcModule) =>
-        for (
-          line <- qcModule.lines if !(line.startsWith("#") || line.startsWith(">"));
-          values = line.split("\t") if values.size >= 4
-        ) yield values(3)
-    }
-
-    // select full sequences from known adapters and contaminants
-    // based on overrepresented sequences results
-    (getFastqcSeqs(adapters) ++ getFastqcSeqs(contaminants))
-      .filter(x => found.exists(_.startsWith(x.name)))
+      // select full sequences from known adapters and contaminants
+      // based on overrepresented sequences results
+      (getFastqcSeqs(adapters) ++ getFastqcSeqs(contaminants))
+        .filter(x => found.exists(_.startsWith(x.name)))
+    } else Set()
   }
 
   /** Summary of the FastQC run, stored in a [[Json]] object */

public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala

@@ -32,6 +32,7 @@ class SeqtkSeq(root: Configurable) extends nl.lumc.sasc.biopet.extensions.seqtk.
         case s if (s.contains("Illumina <1.3"))         => Option(64)
         case s if (s.contains("Illumina 1.3"))          => Option(64)
         case s if (s.contains("Illumina 1.5"))          => Option(64)
+        case _ => None
       }
       if (Q != None) V = true
     }