Merge branch 'feature-more_unit_tests' into 'develop'

More unit tests



See merge request !403

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

@@ -132,7 +132,7 @@ trait ReportBuilder extends ToolCommand {
     logger.info("Start")
 
     val argsParser = new OptParser
-    val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse(throw new IllegalArgumentException)
+    val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
     require(cmdArgs.outputDir.exists(), "Output dir does not exist")
     require(cmdArgs.outputDir.isDirectory, "Output dir is not a directory")

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala

@@ -80,7 +80,7 @@ object AnnotateVcfWithBed extends ToolCommand {
     logger.info("Start")
 
     val argsParser = new OptParser
-    val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse(throw new IllegalArgumentException)
+    val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
     val fieldType = cmdArgs.fieldType match {
       case "Integer"   => VCFHeaderLineType.Integer

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala

@@ -53,7 +53,7 @@ object BaseCounter extends ToolCommand {
 
   def main(args: Array[String]): Unit = {
     val argsParser = new OptParser
-    val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse(throw new IllegalArgumentException)
+    val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
     //Sets picard logging level
     htsjdk.samtools.util.Log.setGlobalLogLevel(htsjdk.samtools.util.Log.LogLevel.valueOf(logger.getLevel.toString))

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala

@@ -113,7 +113,7 @@ object BastyGenerateFasta extends ToolCommand {
    */
   def main(args: Array[String]): Unit = {
     val argsParser = new OptParser
-    cmdArgs = argsParser.parse(args, Args()) getOrElse(throw new IllegalArgumentException)
+    cmdArgs = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
     if (cmdArgs.outputVariants != null) {
       writeVariantsOnly()

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala

@@ -47,7 +47,7 @@ object BedToInterval extends ToolCommand {
    */
   def main(args: Array[String]): Unit = {
     val argsParser = new OptParser
-    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse(throw new IllegalArgumentException)
+    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
     val writer = new PrintWriter(commandArgs.outputFile)
 

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala

@@ -39,7 +39,7 @@ object BedtoolsCoverageToCounts extends ToolCommand {
    */
   def main(args: Array[String]): Unit = {
     val argsParser = new OptParser
-    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse(throw new IllegalArgumentException)
+    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
     if (!commandArgs.input.exists) throw new IllegalStateException("Input file not found, file: " + commandArgs.input)
 

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala

@@ -50,7 +50,7 @@ object BiopetFlagstat extends ToolCommand {
    */
   def main(args: Array[String]): Unit = {
     val argsParser = new OptParser
-    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse(throw new IllegalArgumentException)
+    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
     val inputSam = SamReaderFactory.makeDefault.open(commandArgs.inputFile)
     val iterSam = if (commandArgs.region.isEmpty) inputSam.iterator else {

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala

@@ -71,7 +71,7 @@ object CheckAllelesVcfInBam extends ToolCommand {
 
   def main(args: Array[String]): Unit = {
     val argsParser = new OptParser
-    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse(throw new IllegalArgumentException)
+    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
     if (commandArgs.bamFiles.size != commandArgs.samples.size)
       logger.warn("Number of samples is different from number of bam files: additional samples or bam files will not be used")

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala

@@ -45,7 +45,7 @@ object FastqSplitter extends ToolCommand {
    */
   def main(args: Array[String]): Unit = {
     val argsParser = new OptParser
-    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse(throw new IllegalArgumentException)
+    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
     val groupSize = 100
     val output = for (file <- commandArgs.outputFile) yield new AsyncFastqWriter(new BasicFastqWriter(file), groupSize)

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala

@@ -46,7 +46,7 @@ object FindRepeatsPacBio extends ToolCommand {
   def main(args: Array[String]): Unit = {
 
     val argsParser = new OptParser
-    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse(throw new IllegalArgumentException)
+    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
     val bamReader = SamReaderFactory.makeDefault
       .validationStringency(ValidationStringency.SILENT)
       .open(commandArgs.inputBam)

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/GvcfToBed.scala

@@ -57,7 +57,7 @@ object GvcfToBed extends ToolCommand {
 
   def main(args: Array[String]): Unit = {
     val argsParser = new OptParser
-    val cmdArgs = argsParser.parse(args, Args()) getOrElse(throw new IllegalArgumentException)
+    val cmdArgs = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
     logger.debug("Opening reader")
     val reader = new VCFFileReader(cmdArgs.inputVcf, false)

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala

@@ -50,7 +50,7 @@ object MergeAlleles extends ToolCommand {
    */
   def main(args: Array[String]): Unit = {
     val argsParser = new OptParser
-    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse(throw new IllegalArgumentException)
+    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
     val readers = commandArgs.inputFiles.map(new VCFFileReader(_, true))
     val referenceFile = new FastaSequenceFile(commandArgs.reference, true)

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeOtuMaps.scala

@@ -41,7 +41,7 @@ object MergeOtuMaps extends ToolCommand {
    */
   def main(args: Array[String]): Unit = {
     val argsParser = new OptParser
-    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse(throw new IllegalArgumentException)
+    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
     var map: Map[Long, String] = Map()
 

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala

@@ -62,7 +62,7 @@ object MpileupToVcf extends ToolCommand {
    */
   def main(args: Array[String]): Unit = {
     val argsParser = new OptParser
-    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse(throw new IllegalArgumentException)
+    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
     if (commandArgs.input != null && !commandArgs.input.exists) throw new IllegalStateException("Input file does not exist")
 
     val writer = new PrintWriter(commandArgs.output)

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala

@@ -52,7 +52,7 @@ object PrefixFastq extends ToolCommand {
     logger.info("Start")
 
     val argsParser = new OptParser
-    val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse(throw new IllegalArgumentException)
+    val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
     val writer = new AsyncFastqWriter(new BasicFastqWriter(cmdArgs.output), 3000)
     val reader = new FastqReader(cmdArgs.input)

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala

@@ -49,7 +49,7 @@ object RegionAfCount extends ToolCommand {
 
   def main(args: Array[String]): Unit = {
     val argsParser = new OptParser
-    val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse(throw new IllegalArgumentException)
+    val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
     logger.info("Start")
     logger.info("Reading bed file")

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala

@@ -41,7 +41,7 @@ object SageCountFastq extends ToolCommand {
    */
   def main(args: Array[String]): Unit = {
     val argsParser = new OptParser
-    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse(throw new IllegalArgumentException)
+    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
     if (!commandArgs.input.exists) throw new IllegalStateException("Input file not found, file: " + commandArgs.input)
 

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala

@@ -74,7 +74,7 @@ object SageCreateLibrary extends ToolCommand {
    */
   def main(args: Array[String]): Unit = {
     val argsParser = new OptParser
-    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse(throw new IllegalArgumentException)
+    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
     if (!commandArgs.input.exists) throw new IllegalStateException("Input file not found, file: " + commandArgs.input)
 

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala

@@ -52,7 +52,7 @@ object SageCreateTagCounts extends ToolCommand {
    */
   def main(args: Array[String]): Unit = {
     val argsParser = new OptParser
-    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse(throw new IllegalArgumentException)
+    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
     if (!commandArgs.input.exists) throw new IllegalStateException("Input file not found, file: " + commandArgs.input)
 

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala

@@ -46,7 +46,7 @@ object SamplesTsvToJson extends ToolCommand {
   /** Executes SamplesTsvToJson */
   def main(args: Array[String]): Unit = {
     val argsParser = new OptParser
-    val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse(throw new IllegalArgumentException)
+    val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
     val jsonString = stringFromInputs(cmdArgs.inputFiles, cmdArgs.tagFiles)
     cmdArgs.outputFile match {

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala

@@ -46,7 +46,7 @@ object SquishBed extends ToolCommand {
    */
   def main(args: Array[String]): Unit = {
     val argsParser = new OptParser
-    val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse(throw new IllegalArgumentException)
+    val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
     if (!cmdArgs.input.exists) throw new IllegalStateException("Input file not found, file: " + cmdArgs.input)
 

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SummaryToTsv.scala

@@ -61,7 +61,7 @@ object SummaryToTsv extends ToolCommand {
 
   def main(args: Array[String]): Unit = {
     val argsParser = new OptParser
-    val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse(throw new IllegalArgumentException)
+    val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
     val summary = new Summary(cmdArgs.summary)
 

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ValidateFastq.scala

@@ -51,7 +51,7 @@ object ValidateFastq extends ToolCommand {
 
     //parse all possible options into OptParser
     val argsParser = new OptParser
-    val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse(throw new IllegalArgumentException)
+    val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
     //read in fastq file 1 and if present fastq file 2
     val readFq1 = new FastqReader(cmdArgs.input)

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala

@@ -137,7 +137,7 @@ object VcfFilter extends ToolCommand {
   def main(args: Array[String]): Unit = {
     logger.info("Start")
     val argsParser = new OptParser
-    val cmdArgs = argsParser.parse(args, Args()) getOrElse(throw new IllegalArgumentException)
+    val cmdArgs = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
     val reader = new VCFFileReader(cmdArgs.inputVcf, false)
     val header = reader.getFileHeader

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala

@@ -206,7 +206,7 @@ object VcfStats extends ToolCommand {
   def main(args: Array[String]): Unit = {
     logger.info("Started")
     val argsParser = new OptParser
-    cmdArgs = argsParser.parse(args, Args()) getOrElse(throw new IllegalArgumentException)
+    cmdArgs = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
     val reader = new VCFFileReader(cmdArgs.inputFile, true)
     val header = reader.getFileHeader

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala

@@ -72,7 +72,7 @@ object VcfToTsv extends ToolCommand {
 
   def main(args: Array[String]): Unit = {
     val argsParser = new OptParser
-    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse(throw new IllegalArgumentException)
+    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
     // Throw exception if separator and listSeparator are identical
     if (commandArgs.separator == commandArgs.listSeparator) throw new IllegalArgumentException(

mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTrait.scala → mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala

@@ -43,7 +43,7 @@ trait MultisampleMappingTrait extends MultiSampleQScript
   /** With this method the merge strategy for libraries to samples is defined. This can be overriden to fix the merge strategy. */
   def mergeStrategy: MergeStrategy.Value = {
     val value: String = config("merge_strategy", default = "preprocessmarkduplicates")
-    MergeStrategy.values.find(_.toString.toLowerCase == value) match {
+    MergeStrategy.values.find(_.toString.toLowerCase == value.toLowerCase) match {
       case Some(v) => v
       case _       => throw new IllegalArgumentException(s"merge_strategy '$value' does not exist")
     }
@@ -151,10 +151,9 @@ trait MultisampleMappingTrait extends MultiSampleQScript
               try {
                 header.getSequenceDictionary.assertSameDictionary(referenceFile.getSequenceDictionary)
               } catch {
-                case e: AssertionError => {
+                case e: AssertionError =>
                   logger.error(e.getMessage)
                   oke = false
-                }
               }
               oke
             }
@@ -172,8 +171,7 @@ trait MultisampleMappingTrait extends MultiSampleQScript
                 "Sample readgroup and/or library of input bamfile is not correct, file: " + bamFile +
                   "\nPlease note that it is possible to set 'correct_readgroups' to true in the config to automatic fix this")
               if (!dictOke) Logging.addError(
-                "Sequence dictionary in the bam file is not the same as the reference, file: " + bamFile +
-                  "\nPlease note that it is possible to set 'correct_dict' to true in the config to automatic fix this")
+                "Sequence dictionary in the bam file is not the same as the reference, file: " + bamFile)
 
               if (!readGroupOke && correctReadgroups) {
                 logger.info("Correcting readgroups, file:" + inputBam.get)

mapping/src/test/resources/empty.sam

+@HD	VN:1.5	SO:coordinate
+@SQ	SN:chr1	LN:9	UR:file:/home/pjvan_thof/pipelines/biopet/public/mapping/src/test/resources/ref.fa	M5:fe15dbbd0900310caf32827f6da57550
+@RG	ID:001	SM:sample3	LB:lib1
+r02	0	chr1	210	60	10M	*	0	0	TACGTACGTA	EEFFGGHHII	RG:Z:001

mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala

@@ -18,6 +18,7 @@ package nl.lumc.sasc.biopet.pipelines.mapping
 import java.io.{ File, FileOutputStream }
 
 import com.google.common.io.Files
+import nl.lumc.sasc.biopet.extensions.kraken.Kraken
 import nl.lumc.sasc.biopet.pipelines.flexiprep.Fastqc
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import nl.lumc.sasc.biopet.utils.config.Config
@@ -25,7 +26,7 @@ import org.apache.commons.io.FileUtils
 import org.broadinstitute.gatk.queue.QSettings
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.{ BeforeClass, AfterClass, DataProvider, Test }
+import org.testng.annotations.{ AfterClass, BeforeClass, DataProvider, Test }
 
 /**
  * Test class for [[Mapping]]
@@ -42,14 +43,15 @@ abstract class AbstractTestMapping(val aligner: String) extends TestNGSuite with
     }
   }
 
+  def paired = Array(true, false)
+  def chunks = Array(1, 5)
+  def skipMarkDuplicates = Array(true, false)
+  def skipFlexipreps = Array(true, false)
+  def zipped = Array(true, false)
+  def unmappedToGears = false
+
   @DataProvider(name = "mappingOptions")
   def mappingOptions = {
-    val paired = Array(true, false)
-    val chunks = Array(1, 5)
-    val skipMarkDuplicates = Array(true, false)
-    val skipFlexipreps = Array(true, false)
-    val zipped = Array(true, false)
-
     for (
       pair <- paired;
       chunk <- chunks;
@@ -68,7 +70,8 @@ abstract class AbstractTestMapping(val aligner: String) extends TestNGSuite with
       "aligner" -> aligner,
       "number_chunks" -> chunks,
       "skip_markduplicates" -> skipMarkDuplicate,
-      "skip_flexiprep" -> skipFlexiprep
+      "skip_flexiprep" -> skipFlexiprep,
+      "unmapped_to_gears" -> unmappedToGears
     ), Map(executables.toSeq: _*))
     val mapping: Mapping = initPipeline(map)
 
@@ -85,6 +88,8 @@ abstract class AbstractTestMapping(val aligner: String) extends TestNGSuite with
 
     //Flexiprep
     mapping.functions.count(_.isInstanceOf[Fastqc]) shouldBe (if (skipFlexiprep) 0 else if (paired) 4 else 2)
+
+    mapping.functions.count(_.isInstanceOf[Kraken]) shouldBe (if (unmappedToGears) 1 else 0)
   }
 
   val outputDir = Files.createTempDir()
@@ -133,6 +138,8 @@ abstract class AbstractTestMapping(val aligner: String) extends TestNGSuite with
     "bowtie2" -> Map("exe" -> "test"),
     "stampy" -> Map("exe" -> "test", "genome" -> "test", "hash" -> "test"),
     "samtools" -> Map("exe" -> "test"),
+    "kraken" -> Map("exe" -> "test", "db" -> "test"),
+    "krakenreport" -> Map("exe" -> "test", "db" -> "test"),
     "md5sum" -> Map("exe" -> "test")
   )
 
@@ -151,3 +158,13 @@ class MappingBowtie2Test extends AbstractTestMapping("bowtie2")
 class MappingStampyTest extends AbstractTestMapping("stampy")
 class MappingGsnapTest extends AbstractTestMapping("gsnap")
 class MappingTophatTest extends AbstractTestMapping("tophat")
+
+class MappingGearsTest extends AbstractTestMapping("bwa-mem") {
+  override def unmappedToGears = true
+
+  override def paired = Array(true)
+  override def chunks = Array(1)
+  override def skipMarkDuplicates = Array(true)
+  override def skipFlexipreps = Array(true)
+  override def zipped = Array(true)
+}

mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTest.scala

+package nl.lumc.sasc.biopet.pipelines.mapping
+
+import java.io.{ File, FileOutputStream }
+
+import com.google.common.io.Files
+import nl.lumc.sasc.biopet.extensions.kraken.Kraken
+import nl.lumc.sasc.biopet.extensions.picard.{ MarkDuplicates, MergeSamFiles }
+import nl.lumc.sasc.biopet.utils.ConfigUtils
+import nl.lumc.sasc.biopet.utils.config.Config
+import org.broadinstitute.gatk.queue.QSettings
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.{ DataProvider, Test }
+
+/**
+ * Created by pjvanthof on 15/05/16.
+ */
+trait MultisampleMappingTestTrait extends TestNGSuite with Matchers {
+  def initPipeline(map: Map[String, Any]): MultisampleMapping = {
+    new MultisampleMapping() {
+      override def configNamespace = "multisamplemapping"
+      override def globalConfig = new Config(ConfigUtils.mergeMaps(map, MultisampleMappingTestTrait.config))
+      qSettings = new QSettings
+      qSettings.runName = "test"
+    }
+  }
+
+  def mergeStrategies = MultisampleMapping.MergeStrategy.values
+  def bamToFastq = false
+  def correctReadgroups = false
+  def unmappedToGears = false
+  def sample1 = Array(true, false)
+  def sample2 = Array(true, false)
+  def sample3 = false
+  def sample4 = false
+
+  @DataProvider(name = "mappingOptions")
+  def mappingOptions = {
+    for (
+      merge <- mergeStrategies.toArray; s1 <- sample1; s2 <- sample2
+    ) yield Array(merge, s1, s2)
+  }
+
+  @Test(dataProvider = "mappingOptions")
+  def testMultisampleMapping(merge: MultisampleMapping.MergeStrategy.Value, sample1: Boolean, sample2: Boolean): Unit = {
+    val map: Map[String, Any] = {
+      var m: Map[String, Any] = MultisampleMappingTestTrait.config
+      if (sample1) m = ConfigUtils.mergeMaps(MultisampleMappingTestTrait.sample1, m)
+      if (sample2) m = ConfigUtils.mergeMaps(MultisampleMappingTestTrait.sample2, m)
+      if (sample3) m = ConfigUtils.mergeMaps(MultisampleMappingTestTrait.sample3, m)
+      if (sample4) m = ConfigUtils.mergeMaps(MultisampleMappingTestTrait.sample4, m)
+      m ++ Map(
+        "merge_strategy" -> merge.toString,
+        "bam_to_fastq" -> bamToFastq,
+        "correct_readgroups" -> correctReadgroups,
+        "unmapped_to_gears" -> unmappedToGears
+      )
+    }
+
+    if (!sample1 && !sample2 && !sample3 && !sample4) { // When no samples
+      intercept[IllegalArgumentException] {
+        initPipeline(map).script()
+      }
+    } else if (sample4 && !bamToFastq && !correctReadgroups) {
+      intercept[IllegalStateException] {
+        initPipeline(map).script()
+      }
+    } else {
+      val pipeline = initPipeline(map)
+      pipeline.script()
+
+      val numberFastqLibs = (if (sample1) 1 else 0) + (if (sample2) 2 else 0) + (if (sample3 && bamToFastq) 1 else 0) + (if (sample4 && bamToFastq) 1 else 0)
+      val numberSamples = (if (sample1) 1 else 0) + (if (sample2) 1 else 0)
+
+      import MultisampleMapping.MergeStrategy
+      pipeline.functions.count(_.isInstanceOf[MarkDuplicates]) shouldBe (numberFastqLibs +
+        (if (sample2 && (merge == MergeStrategy.MarkDuplicates || merge == MergeStrategy.PreProcessMarkDuplicates)) 1 else 0))
+      pipeline.functions.count(_.isInstanceOf[MergeSamFiles]) shouldBe (
+        (if (sample2 && (merge == MergeStrategy.MergeSam || merge == MergeStrategy.PreProcessMergeSam)) 1 else 0))
+      pipeline.samples.foreach {
+        case (sampleName, sample) =>
+          if (merge == MergeStrategy.None) sample.bamFile shouldBe None
+          sample.summaryStats shouldBe Map()
+          sample.libraries.foreach {
+            case (libraryId, library) =>
+              library.summaryStats shouldBe Map()
+          }
+      }
+
+      pipeline.functions.count(_.isInstanceOf[Kraken]) shouldBe (if (unmappedToGears) (numberFastqLibs + numberSamples) else 0)
+
+      pipeline.summarySettings.get("merge_strategy") shouldBe Some(merge.toString)
+    }
+  }
+}
+
+class MultisampleMappingTest extends MultisampleMappingTestTrait {
+  override def sample1 = Array(true)
+}
+
+class MultisampleMappingNoSamplesTest extends MultisampleMappingTestTrait {
+  override def sample1 = Array(false)
+  override def sample2 = Array(false)
+  override def mergeStrategies = MultisampleMapping.MergeStrategy.values.filter(_ == MultisampleMapping.MergeStrategy.PreProcessMarkDuplicates)
+}
+
+class MultisampleMappingGearsTest extends MultisampleMappingTestTrait {
+  override def sample1 = Array(true)
+  override def sample2 = Array(false)
+  override def unmappedToGears = true
+  override def mergeStrategies = MultisampleMapping.MergeStrategy.values.filter(_ == MultisampleMapping.MergeStrategy.PreProcessMarkDuplicates)
+}
+
+class MultisampleMappingBamTest extends MultisampleMappingTestTrait {
+  override def sample1 = Array(false)
+  override def sample2 = Array(false)
+  override def sample3 = true
+  override def mergeStrategies = MultisampleMapping.MergeStrategy.values.filter(_ == MultisampleMapping.MergeStrategy.PreProcessMarkDuplicates)
+}
+
+class MultisampleMappingWrongBamTest extends MultisampleMappingTestTrait {
+  override def sample1 = Array(false)
+  override def sample2 = Array(false)
+  override def sample4 = true
+  override def mergeStrategies = MultisampleMapping.MergeStrategy.values.filter(_ == MultisampleMapping.MergeStrategy.PreProcessMarkDuplicates)
+}
+
+class MultisampleMappingCorrectBamTest extends MultisampleMappingTestTrait {
+  override def sample1 = Array(false)
+  override def sample2 = Array(false)
+  override def correctReadgroups = true
+  override def sample4 = true
+  override def mergeStrategies = MultisampleMapping.MergeStrategy.values.filter(_ == MultisampleMapping.MergeStrategy.PreProcessMarkDuplicates)
+}
+
+class MultisampleMappingBamToFastqTest extends MultisampleMappingTestTrait {
+  override def sample1 = Array(false)
+  override def sample2 = Array(false)
+  override def bamToFastq = true
+  override def sample3 = true
+  override def sample4 = true
+  override def mergeStrategies = MultisampleMapping.MergeStrategy.values.filter(_ == MultisampleMapping.MergeStrategy.PreProcessMarkDuplicates)
+}
+
+object MultisampleMappingTestTrait {
+  val outputDir = Files.createTempDir()
+  outputDir.deleteOnExit()
+  new File(outputDir, "input").mkdirs()
+  def inputTouch(name: String): File = {
+    val file = new File(outputDir, "input" + File.separator + name).getAbsoluteFile
+    Files.touch(file)
+    file
+  }
+
+  private def copyFile(name: String): Unit = {
+    val is = getClass.getResourceAsStream("/" + name)
+    val os = new FileOutputStream(new File(outputDir, name))
+    org.apache.commons.io.IOUtils.copy(is, os)
+    os.close()
+  }
+
+  copyFile("ref.fa")
+  copyFile("ref.dict")
+  copyFile("ref.fa.fai")
+  copyFile("empty.sam")
+
+  val config = Map(
+    "name_prefix" -> "test",
+    "cache" -> true,
+    "dir" -> "test",
+    "vep_script" -> "test",
+    "output_dir" -> outputDir,
+    "reference_fasta" -> (outputDir + File.separator + "ref.fa"),
+    "fastqc" -> Map("exe" -> "test"),
+    "input_alleles" -> "test",
+    "fastqc" -> Map("exe" -> "test"),
+    "seqtk" -> Map("exe" -> "test"),
+    "sickle" -> Map("exe" -> "test"),
+    "cutadapt" -> Map("exe" -> "test"),
+    "bwa" -> Map("exe" -> "test"),
+    "samtools" -> Map("exe" -> "test"),
+    "igvtools" -> Map("exe" -> "test"),
+    "wigtobigwig" -> Map("exe" -> "test"),
+    "kraken" -> Map("exe" -> "test", "db" -> "test"),
+    "krakenreport" -> Map("exe" -> "test", "db" -> "test"),
+    "md5sum" -> Map("exe" -> "test")
+  )
+
+  val sample1 = Map(
+    "samples" -> Map("sample1" -> Map("libraries" -> Map(
+      "lib1" -> Map(
+        "R1" -> inputTouch("1_1_R1.fq"),
+        "R2" -> inputTouch("1_1_R2.fq")
+      )
+    )
+    )))
+
+  val sample2 = Map(
+    "samples" -> Map("sample3" -> Map("libraries" -> Map(
+      "lib1" -> Map(
+        "R1" -> inputTouch("2_1_R1.fq"),
+        "R2" -> inputTouch("2_1_R2.fq")
+      ),
+      "lib2" -> Map(
+        "R1" -> inputTouch("2_2_R1.fq"),
+        "R2" -> inputTouch("2_2_R2.fq")
+      )
+    )
+    )))
+
+  val sample3 = Map(
+    "samples" -> Map("sample3" -> Map("libraries" -> Map(
+      "lib1" -> Map(
+        "bam" -> (outputDir + File.separator + "empty.sam")
+      )
+    )
+    )))
+
+  val sample4 = Map(
+    "samples" -> Map("sample4" -> Map("libraries" -> Map(
+      "lib1" -> Map(
+        "bam" -> (outputDir + File.separator + "empty.sam")
+      )
+    )
+    )))
+}

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala

@@ -179,8 +179,8 @@ class ShivaVariantcalling(val root: Configurable) extends QScript
   /** Settings for the summary */
   def summarySettings = Map(
     "variantcallers" -> configCallers.toList,
-    "regions_of_interest" -> roiBedFiles.map(_.getName.stripSuffix(".bed")),
-    "amplicon_bed" -> ampliconBedFile.map(_.getName.stripSuffix(