Merge branch 'develop' into feature-fix_missing_values

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 = executable.substring(0, executable.lastIndexOf("/"))
+
+    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/flexiprep/pom.xml

@@ -39,5 +39,17 @@
             <artifactId>BiopetFramework</artifactId>
             <version>${project.version}</version>
         </dependency>
+        <dependency>
+            <groupId>org.testng</groupId>
+            <artifactId>testng</artifactId>
+            <version>6.8</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.scalatest</groupId>
+            <artifactId>scalatest_2.11</artifactId>
+            <version>2.2.1</version>
+            <scope>test</scope>
+        </dependency>
     </dependencies>
 </project>

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

@@ -33,14 +33,14 @@ class Cutadapt(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Cutada
   override def beforeCmd() {
     super.beforeCmd
 
-    val foundAdapters = fastqc.getFoundAdapters.map(_.seq)
+    val foundAdapters = fastqc.foundAdapters.map(_.seq)
     if (default_clip_mode == "3") opt_adapter ++= foundAdapters
     else if (default_clip_mode == "5") opt_front ++= foundAdapters
     else if (default_clip_mode == "both") opt_anywhere ++= foundAdapters
   }
 
   override def cmdLine = {
-    if (!opt_adapter.isEmpty || !opt_anywhere.isEmpty || !opt_front.isEmpty) {
+    if (opt_adapter.nonEmpty || opt_anywhere.nonEmpty || opt_front.nonEmpty) {
       analysisName = getClass.getSimpleName
       super.cmdLine
     } else {

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

@@ -16,82 +16,154 @@
 
 package nl.lumc.sasc.biopet.pipelines.flexiprep
 
-import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import java.io.{ File, FileNotFoundException }
+
 import scala.io.Source
 
 import argonaut._, Argonaut._
 import scalaz._, Scalaz._
 
+import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.ConfigUtils
+
+/**
+ * FastQC wrapper with added functionality for the Flexiprep pipeline
+ *
+ * This wrapper implements additional methods for parsing FastQC output files and aggregating everything in a summary
+ * object. The current implementation is based on FastQC v0.10.1.
+ */
 class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(root) {
-  def getDataBlock(name: String): Array[String] = { // Based on Fastqc v0.10.1
-    val outputDir = output.getAbsolutePath.stripSuffix(".zip")
-    val dataFile = new File(outputDir + "/fastqc_data.txt")
-    if (!dataFile.exists) return null
-    val data = Source.fromFile(dataFile).mkString
-    for (block <- data.split(">>END_MODULE\n")) {
-      val b = if (block.startsWith("##FastQC")) block.substring(block.indexOf("\n") + 1) else block
-      if (b.startsWith(">>" + name))
-        return for (line <- b.split("\n"))
-          yield line
-    }
-    return null
-  }
 
-  def getEncoding: String = {
-    val block = getDataBlock("Basic Statistics")
-    if (block == null) return null
-    for (
-      line <- block if (line.startsWith("Encoding"))
-    ) return line.stripPrefix("Encoding\t")
-    return null // Could be default Sanger with a warning in the log
+  /** Class for storing a single FastQC module result */
+  protected case class FastQCModule(name: String, status: String, lines: Seq[String])
+
+  /** Default FastQC output directory containing actual results */
+  // this is a def instead of a val since the value depends on the variable `output`, which is null on class creation
+  def outputDir: File = new File(output.getAbsolutePath.stripSuffix(".zip"))
+
+  /** Default FastQC output data file */
+  // this is a def instead of a val since the value depends on the variable `output`, which is null on class creation
+  def dataFile: File = new File(outputDir, "fastqc_data.txt")
+
+  /**
+   * FastQC QC modules.
+   *
+   * @return Mapping of FastQC module names and its contents as array of strings (one item per line)
+   * @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 {
+        case (modString) =>
+          // module name is in the first line, without '>>' and before the tab character
+          val Array(firstLine, otherLines) = modString
+            // drop all '>>' character (start of module)
+            .dropWhile(_ == '>')
+            // split first line and others
+            .split("\n", 2)
+            // and slice them
+            .slice(0, 2)
+          // extract module name and module status
+          val Array(modName, modStatus) = firstLine
+            .split("\t", 2)
+            .slice(0, 2)
+          modName -> FastQCModule(modName, modStatus, otherLines.split("\n").toSeq)
+      }
+      .toMap
+
+    if (fqModules.isEmpty) throw new IllegalStateException("Empty FastQC data file " + dataFile.toString)
+    else fqModules
   }
 
-  protected case class Sequence(name: String, seq: String)
-  def getFoundAdapters: List[Sequence] = {
-    def getSeqs(file: File) = {
-      if (file != null) {
-        (for (
-          line <- Source.fromFile(file).getLines(); if line.startsWith("#");
-          values = line.split("\t*") if values.size >= 2
-        ) yield Sequence(values(0), values(1))).toList
-      } else Nil
-    }
+  /**
+   * Retrieves the FASTQ file encoding as computed by FastQC.
+   *
+   * @return encoding name
+   * @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")
+      .lines
+      .dropWhile(!_.startsWith("Encoding"))
+      .head
+      .stripPrefix("Encoding\t")
+      .stripSuffix("\t")
+
+  /** Case class representing a known adapter sequence */
+  protected case class AdapterSequence(name: String, seq: String)
 
-    val seqs = getSeqs(adapters) ::: getSeqs(contaminants)
+  /**
+   * Retrieves overrepresented sequences found by FastQ.
+   *
+   * @return a [[Set]] of [[AdapterSequence]] objects.
+   */
+  def foundAdapters: Set[AdapterSequence] = {
 
-    val block = getDataBlock("Overrepresented sequences")
-    if (block == null) return Nil
+    /** 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 = for (
-      line <- block if !line.startsWith("#");
-      values = line.split("\t") if values.size >= 4
-    ) yield values(3)
+    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)
+    }
 
-    seqs.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)))
   }
 
-  def getSummary: Json = {
-    val subfixs = Map("plot_duplication_levels" -> "Images/duplication_levels.png",
-      "plot_kmer_profiles" -> "Images/kmer_profiles.png",
-      "plot_per_base_gc_content" -> "Images/per_base_gc_content.png",
-      "plot_per_base_n_content" -> "Images/per_base_n_content.png",
-      "plot_per_base_quality" -> "Images/per_base_quality.png",
-      "plot_per_base_sequence_content" -> "Images/per_base_sequence_content.png",
-      "plot_per_sequence_gc_content" -> "Images/per_sequence_gc_content.png",
-      "plot_per_sequence_quality" -> "Images/per_sequence_quality.png",
-      "plot_sequence_length_distribution" -> "Images/sequence_length_distribution.png",
-      "fastqc_data" -> "fastqc_data.txt")
-    val dir = output.getAbsolutePath.stripSuffix(".zip") + "/"
-    var outputMap: Map[String, Map[String, String]] = Map()
-    for ((k, v) <- subfixs) outputMap += (k -> Map("path" -> (dir + v)))
-
-    val temp = ("" := outputMap) ->: jEmptyObject
-    return temp.fieldOrEmptyObject("")
+  /** Summary of the FastQC run, stored in a [[Json]] object */
+  def summary: Json = {
+
+    val outputMap =
+      Map("plot_duplication_levels" -> "Images/duplication_levels.png",
+        "plot_kmer_profiles" -> "Images/kmer_profiles.png",
+        "plot_per_base_gc_content" -> "Images/per_base_gc_content.png",
+        "plot_per_base_n_content" -> "Images/per_base_n_content.png",
+        "plot_per_base_quality" -> "Images/per_base_quality.png",
+        "plot_per_base_sequence_content" -> "Images/per_base_sequence_content.png",
+        "plot_per_sequence_gc_content" -> "Images/per_sequence_gc_content.png",
+        "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) =>
+            name -> Map("path" -> (outputDir + File.separator + relPath))
+        }
+
+    ConfigUtils.mapToJson(outputMap)
   }
 }
 
 object Fastqc {
+
   def apply(root: Configurable, fastqfile: File, outDir: String): Fastqc = {
     val fastqcCommand = new Fastqc(root)
     fastqcCommand.fastqfile = fastqfile
@@ -102,6 +174,6 @@ object Fastqc {
     //if (filename.endsWith(".fq")) filename = filename.substring(0,filename.size - 3)
     fastqcCommand.output = new File(outDir + "/" + filename + "_fastqc.zip")
     fastqcCommand.afterGraph
-    return fastqcCommand
+    fastqcCommand
   }
 }

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

@@ -201,7 +201,7 @@ class FlexiprepSummary(val root: Configurable) extends InProcessFunction with Co
 
   def fastqcSummary(fastqc: Fastqc): Option[Json] = {
     if (fastqc == null) return None
-    else return Option(fastqc.getSummary)
+    else return Option(fastqc.summary)
   }
 
   def clipstatSummary(): Option[Json] = {

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

@@ -25,7 +25,7 @@ class SeqtkSeq(root: Configurable) extends nl.lumc.sasc.biopet.extensions.seqtk.
   override def beforeCmd {
     super.beforeCmd
     if (fastqc != null && Q == None) {
-      val encoding = fastqc.getEncoding
+      val encoding = fastqc.encoding
       Q = encoding match {
         case null                                       => None
         case s if (s.contains("Sanger / Illumina 1.9")) => None

public/flexiprep/src/test/resources/fqc_contaminants_v0101.txt

+# This file contains a list of potential contaminants which are
+# frequently found in high throughput sequencing reactions.  These
+# are mostly sequences of adapters / primers used in the various
+# sequencing chemistries.
+# 
+# Please DO NOT rely on these sequences to design your own oligos, some
+# of them are truncated at ambiguous positions, and none of them are
+# definitive sequences from the manufacturers so don't blame us if you
+# try to use them and they don't work.
+#
+# You can add more sequences to the file by putting one line per entry
+# and specifying a name[tab]sequence.  If the contaminant you add is 
+# likely to be of use to others please consider sending it to the FastQ
+# authors, either via a bug report at www.bioinformatics.bbsrc.ac.uk/bugzilla/
+# or by directly emailing simon.andrews@bbsrc.ac.uk so other users of
+# the program can benefit.
+
+Illumina Single End Adapter 1					GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG
+Illumina Single End Adapter 2					CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT
+Illumina Single End PCR Primer 1				AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
+Illumina Single End PCR Primer 2				CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT
+Illumina Single End Sequencing Primer			ACACTCTTTCCCTACACGACGCTCTTCCGATCT
+
+Illumina Paired End Adapter 1					ACACTCTTTCCCTACACGACGCTCTTCCGATCT
+Illumina Paired End Adapter 2					GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG
+Illumina Paried End PCR Primer 1				AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
+Illumina Paired End PCR Primer 2				CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
+Illumina Paried End Sequencing Primer 1			ACACTCTTTCCCTACACGACGCTCTTCCGATCT
+Illumina Paired End Sequencing Primer 2			CGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
+
+Illumina DpnII expression Adapter 1				ACAGGTTCAGAGTTCTACAGTCCGAC
+Illumina DpnII expression Adapter 2				CAAGCAGAAGACGGCATACGA
+Illumina DpnII expression PCR Primer 1			CAAGCAGAAGACGGCATACGA
+Illumina DpnII expression PCR Primer 2			AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
+Illumina DpnII expression Sequencing Primer		CGACAGGTTCAGAGTTCTACAGTCCGACGATC
+
+Illumina NlaIII expression Adapter 1			ACAGGTTCAGAGTTCTACAGTCCGACATG
+Illumina NlaIII expression Adapter 2			CAAGCAGAAGACGGCATACGA
+Illumina NlaIII expression PCR Primer 1			CAAGCAGAAGACGGCATACGA
+Illumina NlaIII expression PCR Primer 2			AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
+Illumina NlaIII expression Sequencing Primer	CCGACAGGTTCAGAGTTCTACAGTCCGACATG
+
+Illumina Small RNA Adapter 1					GTTCAGAGTTCTACAGTCCGACGATC
+Illumina Small RNA Adapter 2					TGGAATTCTCGGGTGCCAAGG
+Illumina Small RNA RT Primer					CAAGCAGAAGACGGCATACGA
+Illumina Small RNA PCR Primer 1					CAAGCAGAAGACGGCATACGA
+Illumina Small RNA PCR Primer 2					AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
+Illumina Small RNA Sequencing Primer			CGACAGGTTCAGAGTTCTACAGTCCGACGATC
+
+Illumina Multiplexing Adapter 1					GATCGGAAGAGCACACGTCT
+Illumina Multiplexing Adapter 2					ACACTCTTTCCCTACACGACGCTCTTCCGATCT
+Illumina Multiplexing PCR Primer 1.01			AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
+Illumina Multiplexing PCR Primer 2.01			GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
+Illumina Multiplexing Read1 Sequencing Primer	ACACTCTTTCCCTACACGACGCTCTTCCGATCT
+Illumina Multiplexing Index Sequencing Primer	GATCGGAAGAGCACACGTCTGAACTCCAGTCAC
+Illumina Multiplexing Read2 Sequencing Primer	GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
+
+Illumina PCR Primer Index 1						CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTC
+Illumina PCR Primer Index 2						CAAGCAGAAGACGGCATACGAGATACATCGGTGACTGGAGTTC
+Illumina PCR Primer Index 3						CAAGCAGAAGACGGCATACGAGATGCCTAAGTGACTGGAGTTC
+Illumina PCR Primer Index 4						CAAGCAGAAGACGGCATACGAGATTGGTCAGTGACTGGAGTTC
+Illumina PCR Primer Index 5						CAAGCAGAAGACGGCATACGAGATCACTGTGTGACTGGAGTTC
+Illumina PCR Primer Index 6						CAAGCAGAAGACGGCATACGAGATATTGGCGTGACTGGAGTTC
+Illumina PCR Primer Index 7						CAAGCAGAAGACGGCATACGAGATGATCTGGTGACTGGAGTTC
+Illumina PCR Primer Index 8						CAAGCAGAAGACGGCATACGAGATTCAAGTGTGACTGGAGTTC
+Illumina PCR Primer Index 9						CAAGCAGAAGACGGCATACGAGATCTGATCGTGACTGGAGTTC
+Illumina PCR Primer Index 10					CAAGCAGAAGACGGCATACGAGATAAGCTAGTGACTGGAGTTC
+Illumina PCR Primer Index 11					CAAGCAGAAGACGGCATACGAGATGTAGCCGTGACTGGAGTTC
+Illumina PCR Primer Index 12					CAAGCAGAAGACGGCATACGAGATTACAAGGTGACTGGAGTTC
+
+Illumina DpnII Gex Adapter 1					GATCGTCGGACTGTAGAACTCTGAAC
+Illumina DpnII Gex Adapter 1.01					ACAGGTTCAGAGTTCTACAGTCCGAC
+Illumina DpnII Gex Adapter 2					CAAGCAGAAGACGGCATACGA
+Illumina DpnII Gex Adapter 2.01					TCGTATGCCGTCTTCTGCTTG
+Illumina DpnII Gex PCR Primer 1					CAAGCAGAAGACGGCATACGA
+Illumina DpnII Gex PCR Primer 2					AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
+Illumina DpnII Gex Sequencing Primer			CGACAGGTTCAGAGTTCTACAGTCCGACGATC
+
+Illumina NlaIII Gex Adapter 1.01				TCGGACTGTAGAACTCTGAAC
+Illumina NlaIII Gex Adapter 1.02				ACAGGTTCAGAGTTCTACAGTCCGACATG
+Illumina NlaIII Gex Adapter 2.01				CAAGCAGAAGACGGCATACGA
+Illumina NlaIII Gex Adapter 2.02				TCGTATGCCGTCTTCTGCTTG
+Illumina NlaIII Gex PCR Primer 1				CAAGCAGAAGACGGCATACGA
+Illumina NlaIII Gex PCR Primer 2				AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
+Illumina NlaIII Gex Sequencing Primer			CCGACAGGTTCAGAGTTCTACAGTCCGACATG
+
+Illumina Small RNA RT Primer					CAAGCAGAAGACGGCATACGA
+Illumina 5p RNA Adapter							GTTCAGAGTTCTACAGTCCGACGATC
+Illumina RNA Adapter1							TGGAATTCTCGGGTGCCAAGG
+
+Illumina Small RNA 3p Adapter 1					ATCTCGTATGCCGTCTTCTGCTTG
+Illumina Small RNA PCR Primer 1					CAAGCAGAAGACGGCATACGA
+Illumina Small RNA PCR Primer 2					AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
+Illumina Small RNA Sequencing Primer			CGACAGGTTCAGAGTTCTACAGTCCGACGATC
+
+TruSeq Universal Adapter						AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
+TruSeq Adapter, Index 1							GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 2							GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 3							GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 4							GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 5							GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 6							GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 7							GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 8							GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 9							GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 10						GATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 11						GATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 12						GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCTTCTGCTTG
+
+Illumina RNA RT Primer							GCCTTGGCACCCGAGAATTCCA
+Illumina RNA PCR Primer							AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA
+
+RNA PCR Primer, Index 1							CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 2							CAAGCAGAAGACGGCATACGAGATACATCGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 3							CAAGCAGAAGACGGCATACGAGATGCCTAAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 4							CAAGCAGAAGACGGCATACGAGATTGGTCAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 5							CAAGCAGAAGACGGCATACGAGATCACTGTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 6							CAAGCAGAAGACGGCATACGAGATATTGGCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 7							CAAGCAGAAGACGGCATACGAGATGATCTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 8							CAAGCAGAAGACGGCATACGAGATTCAAGTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 9							CAAGCAGAAGACGGCATACGAGATCTGATCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 10						CAAGCAGAAGACGGCATACGAGATAAGCTAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 11						CAAGCAGAAGACGGCATACGAGATGTAGCCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 12						CAAGCAGAAGACGGCATACGAGATTACAAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 13						CAAGCAGAAGACGGCATACGAGATTTGACTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 14						CAAGCAGAAGACGGCATACGAGATGGAACTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 15						CAAGCAGAAGACGGCATACGAGATTGACATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 16						CAAGCAGAAGACGGCATACGAGATGGACGGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 17						CAAGCAGAAGACGGCATACGAGATCTCTACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 18						CAAGCAGAAGACGGCATACGAGATGCGGACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 19						CAAGCAGAAGACGGCATACGAGATTTTCACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 20						CAAGCAGAAGACGGCATACGAGATGGCCACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 21						CAAGCAGAAGACGGCATACGAGATCGAAACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 22						CAAGCAGAAGACGGCATACGAGATCGTACGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 23						CAAGCAGAAGACGGCATACGAGATCCACTCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 24						CAAGCAGAAGACGGCATACGAGATGCTACCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 25						CAAGCAGAAGACGGCATACGAGATATCAGTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 26						CAAGCAGAAGACGGCATACGAGATGCTCATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 27						CAAGCAGAAGACGGCATACGAGATAGGAATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 28						CAAGCAGAAGACGGCATACGAGATCTTTTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 29						CAAGCAGAAGACGGCATACGAGATTAGTTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 30						CAAGCAGAAGACGGCATACGAGATCCGGTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 31						CAAGCAGAAGACGGCATACGAGATATCGTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 32						CAAGCAGAAGACGGCATACGAGATTGAGTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 33						CAAGCAGAAGACGGCATACGAGATCGCCTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 34						CAAGCAGAAGACGGCATACGAGATGCCATGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 35						CAAGCAGAAGACGGCATACGAGATAAAATGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 36						CAAGCAGAAGACGGCATACGAGATTGTTGGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 37						CAAGCAGAAGACGGCATACGAGATATTCCGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 38						CAAGCAGAAGACGGCATACGAGATAGCTAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 39						CAAGCAGAAGACGGCATACGAGATGTATAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 40						CAAGCAGAAGACGGCATACGAGATTCTGAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 41						CAAGCAGAAGACGGCATACGAGATGTCGTCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 42						CAAGCAGAAGACGGCATACGAGATCGATTAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 43						CAAGCAGAAGACGGCATACGAGATGCTGTAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 44						CAAGCAGAAGACGGCATACGAGATATTATAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 45						CAAGCAGAAGACGGCATACGAGATGAATGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 46						CAAGCAGAAGACGGCATACGAGATTCGGGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 47						CAAGCAGAAGACGGCATACGAGATCTTCGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 48						CAAGCAGAAGACGGCATACGAGATTGCCGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+
+ABI Dynabead EcoP Oligo							CTGATCTAGAGGTACCGGATCCCAGCAGT
+ABI Solid3 Adapter A							CTGCCCCGGGTTCCTCATTCTCTCAGCAGCATG
+ABI Solid3 Adapter B							CCACTACGCCTCCGCTTTCCTCTCTATGGGCAGTCGGTGAT
+ABI Solid3 5' AMP Primer						CCACTACGCCTCCGCTTTCCTCTCTATG
+ABI Solid3 3' AMP Primer						CTGCCCCGGGTTCCTCATTCT
+ABI Solid3 EF1 alpha Sense Primer				CATGTGTGTTGAGAGCTTC
+ABI Solid3 EF1 alpha Antisense Primer			GAAAACCAAAGTGGTCCAC
+ABI Solid3 GAPDH Forward Primer					TTAGCACCCCTGGCCAAGG
+ABI Solid3 GAPDH Reverse Primer					CTTACTCCTTGGAGGCCATG

public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FastqcV0101Test.scala

+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+package nl.lumc.sasc.biopet.pipelines.flexiprep
+
+import java.io.File
+import java.nio.file.Paths
+
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+class FastqcV0101Test extends TestNGSuite with Matchers {
+
+  /** Returns the absolute path to test resource directory as a File object */
+  private val resourceDir: File = new File(Paths.get(getClass.getResource("/").toURI).toString)
+
+  /** Given a resource file name, returns the the absolute path to it as a File object */
+  private def resourceFile(p: String): File = new File(resourceDir, p)
+
+  /** Mock output file of a FastQC v0.10.1 run */
+  // the file doesn't actually exist, we just need it so the outputDir value can be computed correctly
+  private val outputv0101: File = resourceFile("v0101.fq_fastqc.zip")
+
+  @Test def testOutputDir() = {
+    val fqc = new Fastqc(null)
+    fqc.output = outputv0101
+    fqc.outputDir shouldBe new File(resourceDir, "v0101.fq_fastqc")
+  }
+
+  @Test def testQcModules() = {
+    val fqc = new Fastqc(null)
+    fqc.output = outputv0101
+    // 11 QC modules
+    fqc.qcModules.size shouldBe 11
+    // first module
+    fqc.qcModules.keySet should contain("Basic Statistics")
+    // mid (6th module)
+    fqc.qcModules.keySet should contain("Per sequence GC content")
+    // last module
+    fqc.qcModules.keySet should contain("Kmer Content")
+  }
+
+  @Test def testSingleQcModule() = {