Merge branch 'feature-index_generation' into 'develop'

Reference index generation



See merge request !396

biopet-aggregate/pom.xml

@@ -17,6 +17,7 @@
 
     <modules>
         <module>../biopet-core</module>
+        <module>../generate-indexes</module>
         <module>../biopet-package</module>
         <module>../bammetrics</module>
         <module>../flexiprep</module>

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala

@@ -27,7 +27,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
  */
 class BiopetPipe(val commands: List[BiopetCommandLineFunction]) extends BiopetCommandLineFunction {
 
-  @Input
+  @Input(required = false)
   lazy val input: List[File] = try {
     commands.flatMap(_.inputs)
   } catch {

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Awk.scala

+package nl.lumc.sasc.biopet.extensions
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Version }
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+import scala.util.matching.Regex
+
+/**
+ * Created by pjvan_thof on 17-5-16.
+ */
+class Awk(val root: Configurable) extends BiopetCommandLineFunction with Version {
+  executable = config("exe", default = "awk", freeVar = false)
+
+  def versionCommand: String = executable + " --version"
+
+  def versionRegex: Regex = """(GNU Awk \d+\.\d+\.\d+)""".r
+
+  @Input(required = false)
+  var input: File = _
+
+  @Output
+  var output: File = _
+
+  var command: String = _
+
+  def cmdLine = executable +
+    required(command) +
+    (if (inputAsStdin) "" else required(input)) +
+    (if (outputAsStsout) "" else " > " + required(output))
+}
+
+object Awk {
+  def apply(root: Configurable, command: String): Awk = {
+    val awk = new Awk(root)
+    awk.command = command
+    awk
+  }
+}
\ No newline at end of file

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Curl.scala

@@ -34,5 +34,5 @@ class Curl(val root: Configurable) extends BiopetCommandLineFunction with Versio
   def versionCommand = executable + " --version"
   def versionRegex = """curl (\w+\.\w+\.\w+) .*""".r
 
-  def cmdLine: String = required(executable) + required(url) + " > " + required(output)
+  def cmdLine: String = required(executable) + required(url) + (if (outputAsStsout) "" else " > " + required(output))
 }

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/GtfToGenePred.scala

+package nl.lumc.sasc.biopet.extensions
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+/**
+ * Created by pjvan_thof on 17-5-16.
+ */
+class GtfToGenePred(val root: Configurable) extends BiopetCommandLineFunction {
+  executable = config("exe", default = "gtfToGenePred", freeVar = false)
+
+  @Input
+  var inputGtfs: List[File] = Nil
+
+  @Output
+  var outputGenePred: File = _
+
+  @Output
+  var infoOut: Option[File] = None
+
+  var genePredExt: Boolean = config("gene _pred _ext", default = false)
+  var allErrors: Boolean = config("all_errors", default = false)
+  var impliedStopAfterCds: Boolean = config("implied_stop_after_cds", default = false)
+  var simple: Boolean = config("simple", default = false)
+  var geneNameAsName2: Boolean = config("gene _name_as_name2", default = false)
+
+  def cmdLine = executable +
+    conditional(genePredExt, "-genePredExt") +
+    conditional(allErrors, "-allErrors") +
+    optional("-infoOut", infoOut) +
+    conditional(allErrors, "-allErrors") +
+    conditional(impliedStopAfterCds, "-impliedStopAfterCds") +
+    conditional(simple, "-simple") +
+    conditional(geneNameAsName2, "-geneNameAsName2") +
+    repeat(inputGtfs) +
+    (if (outputAsStsout) required("/dev/stdout") else required(outputGenePred))
+}

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala

@@ -75,7 +75,8 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction with Refere
   var genomeSAindexNbases: Option[Int] = config("genomesaindexnbases")
   var genomeSAsparseD: Option[Int] = config("genomesasparsed")
 
-  var sjdbGTFfile: Option[String] = config("sjdbgtfile")
+  @Input(required = false)
+  var sjdbGTFfile: Option[File] = config("sjdbgtfile")
   var sjdbGTFchrPrefix: Option[String] = config("sjdbgtfchrprefix")
   var sjdbGTFfeatureExon: Option[String] = config("sjdbgtffeatureexon")
   var sjdbGTFtagExonParentTranscript: Option[String] = config("sjdbgtftagexonparenttranscript")

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala

@@ -24,7 +24,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 /** Extension for zcat */
 class Zcat(val root: Configurable) extends BiopetCommandLineFunction with Version {
   @Input(doc = "Zipped file", required = true)
-  var input: List[File] = _
+  var input: List[File] = Nil
 
   @Output(doc = "Unzipped file", required = true)
   var output: File = _

biopet-package/pom.xml

@@ -44,6 +44,11 @@
             <artifactId>BiopetCore</artifactId>
             <version>${project.version}</version>
         </dependency>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>GenerateIndexes</artifactId>
+            <version>${project.version}</version>
+        </dependency>
         <dependency>
             <groupId>nl.lumc.sasc</groupId>
             <artifactId>Flexiprep</artifactId>

biopet-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutableMain.scala

@@ -15,6 +15,7 @@
  */
 package nl.lumc.sasc.biopet
 
+import nl.lumc.sasc.biopet.pipelines.generateindexes.GenerateIndexes
 import nl.lumc.sasc.biopet.utils.{ BiopetExecutable, MainCommand }
 
 object BiopetExecutableMain extends BiopetExecutable {
@@ -36,7 +37,8 @@ object BiopetExecutableMain extends BiopetExecutable {
     nl.lumc.sasc.biopet.pipelines.gwastest.GwasTest,
     nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcalling,
     nl.lumc.sasc.biopet.pipelines.basty.Basty,
-    nl.lumc.sasc.biopet.pipelines.shiva.Shiva
+    nl.lumc.sasc.biopet.pipelines.shiva.Shiva,
+    GenerateIndexes
   )
 
   def tools: List[MainCommand] = BiopetToolsExecutable.tools

generate-indexes/pom.xml

@@ -45,6 +45,18 @@
             <artifactId>BiopetExtensions</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_2.10</artifactId>
+            <version>2.2.1</version>
+            <scope>test</scope>
+        </dependency>
     </dependencies>
 
 </project>
\ No newline at end of file

generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/FastaMerging.scala

+package nl.lumc.sasc.biopet.pipelines.generateindexes
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+/**
+ * Created by pjvan_thof on 13-5-16.
+ */
+class FastaMerging(val root: Configurable) extends BiopetCommandLineFunction {
+  @Input
+  var input: List[File] = Nil
+
+  @Output(required = true)
+  var output: File = _
+
+  var cmds: Array[BiopetCommandLineFunction] = Array()
+
+  def cmdLine = cmds.map(_.commandLine).mkString(" && ")
+
+}

generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/GenerateIndexes.scala → generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexes.scala

@@ -13,14 +13,13 @@
  * 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
+package nl.lumc.sasc.biopet.pipelines.generateindexes
 
-import java.io.PrintWriter
+import java.io.{ File, PrintWriter }
 import java.util
 
 import nl.lumc.sasc.biopet.core.extensions.Md5sum
-import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, BiopetQScript, PipelineCommand }
+import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
 import nl.lumc.sasc.biopet.extensions._
 import nl.lumc.sasc.biopet.extensions.bowtie.{ Bowtie2Build, BowtieBuild }
 import nl.lumc.sasc.biopet.extensions.bwa.BwaIndex
@@ -29,26 +28,26 @@ import nl.lumc.sasc.biopet.extensions.gmap.GmapBuild
 import nl.lumc.sasc.biopet.extensions.picard.CreateSequenceDictionary
 import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFaidx
 import nl.lumc.sasc.biopet.utils.ConfigUtils
+import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
 
-import scala.language.reflectiveCalls
 import scala.collection.JavaConversions._
+import scala.language.reflectiveCalls
 
 class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript {
   def this() = this(null)
 
-  @Argument
-  var referenceConfigFile: File = _
-
-  var referenceConfig: Map[String, Any] = Map()
+  @Argument(required = true)
+  var referenceConfigFiles: List[File] = Nil
 
-  var configDeps: List[File] = Nil
+  var referenceConfig: Map[String, Any] = null
 
-  def outputConfigFile = new File(outputDir, "reference.json")
+  protected var configDeps: List[File] = Nil
 
   /** This is executed before the script starts */
   def init(): Unit = {
-    referenceConfig = ConfigUtils.fileToConfigMap(referenceConfigFile)
+    if (referenceConfig == null)
+      referenceConfig = referenceConfigFiles.foldLeft(Map[String, Any]())((a, b) => ConfigUtils.mergeMaps(a, ConfigUtils.fileToConfigMap(b)))
   }
 
   /** Method where jobs must be added */
@@ -58,11 +57,13 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
       val speciesConfig = ConfigUtils.any2map(c)
       val speciesDir = new File(outputDir, speciesName)
       for ((genomeName, c) <- speciesConfig) yield genomeName -> {
+        var configDeps: List[File] = Nil
         val genomeConfig = ConfigUtils.any2map(c)
         val fastaUris = genomeConfig.getOrElse("fasta_uri",
           throw new IllegalArgumentException(s"No fasta_uri found for $speciesName - $genomeName")) match {
-            case a: Array[_] => a.map(_.toString)
-            case a           => Array(a.toString)
+            case a: Traversable[_]    => a.map(_.toString).toArray
+            case a: util.ArrayList[_] => a.map(_.toString).toArray
+            case a                    => Array(a.toString)
           }
 
         val genomeDir = new File(speciesDir, genomeName)
@@ -83,18 +84,10 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
           curl.output
         }
 
-        val fastaCat = new CommandLineFunction {
-          var cmds: Array[BiopetCommandLineFunction] = Array()
+        val fastaCat = new FastaMerging(this)
+        fastaCat.output = fastaFile
 
-          @Input
-          var input: List[File] = Nil
-
-          @Output
-          var output = fastaFile
-          def commandLine = cmds.mkString(" && ")
-        }
-
-        if (fastaUris.length > 1 || fastaFiles.filter(_.getName.endsWith(".gz")).nonEmpty) {
+        if (fastaUris.length > 1 || fastaFiles.exists(_.getName.endsWith(".gz"))) {
           fastaFiles.foreach { file =>
             if (file.getName.endsWith(".gz")) {
               val zcat = new Zcat(this)
@@ -159,14 +152,13 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
 
           val regex = """.*\/(.*)_vep_(\d*)_(.*)\.tar\.gz""".r
           vepCacheUri.toString match {
-            case regex(species, version, assembly) if (version.forall(_.isDigit)) => {
+            case regex(species, version, assembly) if version.forall(_.isDigit) =>
               outputConfig ++= Map("varianteffectpredictor" -> Map(
                 "species" -> species,
                 "assembly" -> assembly,
                 "cache_version" -> version.toInt,
                 "cache" -> vepDir,
                 "fasta" -> createLinks(vepDir)))
-            }
             case _ => throw new IllegalArgumentException("Cache found but no version was found")
           }
         }
@@ -183,13 +175,14 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
             add(curl)
             cv.variant :+= curl.output
 
-            val tabix = new Tabix(this)
-            tabix.input = curl.output
-            tabix.p = Some("vcf")
-            tabix.isIntermediate = true
-            add(tabix)
-            configDeps :+= tabix.outputIndex
-            cv.deps ::= tabix.outputIndex
+            if (curl.output.getName.endsWith(".vcf.gz")) {
+              val tabix = new Tabix(this)
+              tabix.input = curl.output
+              tabix.p = Some("vcf")
+              tabix.isIntermediate = true
+              add(tabix)
+              configDeps :+= tabix.outputIndex
+            }
           }
 
           dbsnpUri match {
@@ -200,6 +193,28 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
 
           cv.out = new File(annotationDir, "dbsnp.vcf.gz")
           add(cv)
+          outputConfig += "dbsnp" -> cv.out
+        }
+
+        val gtfFile: Option[File] = genomeConfig.get("gtf_uri").map { gtfUri =>
+          val outputFile = new File(annotationDir, new File(gtfUri.toString).getName.stripSuffix(".gz"))
+          val curl = new Curl(this)
+          curl.url = gtfUri.toString
+          if (gtfUri.toString.endsWith(".gz")) add(curl | Zcat(this) > outputFile)
+          else add(curl > outputFile)
+          outputConfig += "annotation_gtf" -> outputFile
+          outputFile
+        }
+
+        val refFlatFile: Option[File] = gtfFile.map { gtf =>
+          val refFlat = new File(gtf + ".refFlat")
+          val gtfToGenePred = new GtfToGenePred(this)
+          gtfToGenePred.inputGtfs :+= gtf
+
+          add(gtfToGenePred | Awk(this, """{ print $12"\t"$1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10 }""") > refFlat)
+
+          outputConfig += "annotation_refflat" -> refFlat
+          refFlat
         }
 
         // Bwa index
@@ -220,11 +235,13 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
         outputConfig += "gsnap" -> Map("dir" -> gmapBuild.dir.getAbsolutePath, "db" -> genomeName)
         outputConfig += "gmap" -> Map("dir" -> gmapBuild.dir.getAbsolutePath, "db" -> genomeName)
 
+        // STAR index
         val starDir = new File(genomeDir, "star")
         val starIndex = new Star(this)
         starIndex.outputDir = starDir
         starIndex.reference = createLinks(starDir)
         starIndex.runmode = "genomeGenerate"
+        starIndex.sjdbGTFfile = gtfFile
         add(starIndex)
         configDeps :+= starIndex.jobOutputFile
         outputConfig += "star" -> Map(
@@ -232,6 +249,7 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
           "genomeDir" -> starDir.getAbsolutePath
         )
 
+        // Bowtie index
         val bowtieIndex = new BowtieBuild(this)
         bowtieIndex.reference = createLinks(new File(genomeDir, "bowtie"))
         bowtieIndex.baseName = "reference"
@@ -239,6 +257,7 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
         configDeps :+= bowtieIndex.jobOutputFile
         outputConfig += "bowtie" -> Map("reference_fasta" -> bowtieIndex.reference.getAbsolutePath)
 
+        // Bowtie2 index
         val bowtie2Index = new Bowtie2Build(this)
         bowtie2Index.reference = createLinks(new File(genomeDir, "bowtie2"))
         bowtie2Index.baseName = "reference"
@@ -249,19 +268,22 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
           "bowtie_index" -> bowtie2Index.reference.getAbsolutePath.stripSuffix(".fa").stripSuffix(".fasta")
         )
 
+        val writeConfig = new WriteConfig
+        writeConfig.deps = configDeps
+        writeConfig.out = new File(genomeDir, s"$speciesName-$genomeName.json")
+        writeConfig.config = Map("references" -> Map(speciesName -> Map(genomeName -> outputConfig)))
+        add(writeConfig)
+
+        this.configDeps :::= configDeps
         outputConfig
       }
     }
 
-    add(new InProcessFunction {
-      @Input val deps: List[File] = configDeps
-
-      def run: Unit = {
-        val writer = new PrintWriter(outputConfigFile)
-        writer.println(ConfigUtils.mapToJson(Map("references" -> outputConfig)).spaces2)
-        writer.close()
-      }
-    })
+    val writeConfig = new WriteConfig
+    writeConfig.deps = configDeps
+    writeConfig.out = new File(outputDir, "references.json")
+    writeConfig.config = Map("references" -> outputConfig)
+    add(writeConfig)
   }
 }
 

generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/WriteConfig.scala

+package nl.lumc.sasc.biopet.pipelines.generateindexes
+
+import java.io.{ File, PrintWriter }
+
+import nl.lumc.sasc.biopet.utils.ConfigUtils
+import org.broadinstitute.gatk.queue.function.InProcessFunction
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+/**
+ * Created by pjvanthof on 15/05/16.
+ */
+class WriteConfig extends InProcessFunction {
+  @Input
+  var deps: List[File] = Nil
+
+  @Output(required = true)
+  var out: File = _
+
+  var config: Map[String, Any] = _
+
+  def run: Unit = {
+    val writer = new PrintWriter(out)
+    writer.println(ConfigUtils.mapToJson(config).spaces2)
+    writer.close()
+  }
+}
\ No newline at end of file

generate-indexes/src/test/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexesTest.scala

+package nl.lumc.sasc.biopet.pipelines.generateindexes
+
+import com.google.common.io.Files
+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.Test
+
+/**
+ * Created by pjvan_thof on 13-5-16.
+ */
+class GenerateIndexesTest extends TestNGSuite with Matchers {
+  def initPipeline(map: Map[String, Any]): GenerateIndexes = {
+    new GenerateIndexes() {
+      override def configNamespace = "generateindexes"
+      override def globalConfig = new Config(ConfigUtils.mergeMaps(map, GenerateIndexesTest.config))
+      qSettings = new QSettings
+      qSettings.runName = "test"
+    }
+  }
+
+  @Test
+  def testNoFastaUri: Unit = {
+    val pipeline = initPipeline(Map())
+    pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("" -> "")))
+    intercept[IllegalArgumentException] {
+      pipeline.script()
+    }
+  }
+
+  @Test
+  def testSingleFasta: Unit = {
+    val pipeline = initPipeline(Map())
+    pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri")))
+    pipeline.script()
+  }
+
+  @Test
+  def testMultiFasta: Unit = {
+    val pipeline = initPipeline(Map())
+    pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> List("uri", "uri2", "uri3.gz"))))
+    pipeline.script()
+  }
+
+  @Test
+  def testSingleDbsnp: Unit = {
+    val pipeline = initPipeline(Map())
+    pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri", "dbsnp_vcf_uri" -> "uri.vcf.gz")))
+    pipeline.script()
+  }
+
+  @Test
+  def testMultiDbsnp: Unit = {
+    val pipeline = initPipeline(Map())
+    pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri", "dbsnp_vcf_uri" -> List("uri.vcf.gz", "uri2.vcf.gz"))))
+    pipeline.script()
+  }
+
+  @Test
+  def testVep: Unit = {
+    val pipeline = initPipeline(Map())
+    pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri", "vep_cache_uri" -> "something/human_vep_80_hg19.tar.gz")))
+    pipeline.script()
+  }
+
+  @Test
+  def testGtfZipped: Unit = {
+    val pipeline = initPipeline(Map())
+    pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri", "gtf_uri" -> "bla.gf.gz")))
+    pipeline.script()
+  }
+
+  @Test
+  def testGtf: Unit = {
+    val pipeline = initPipeline(Map())
+    pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri", "gtf_uri" -> "bla.gf")))
+    pipeline.script()
+  }
+
+}
+
+object GenerateIndexesTest {
+  val outputDir = Files.createTempDir()
+  outputDir.deleteOnExit()
+
+  val config = Map("output_dir" -> outputDir,
+    "bwa" -> Map("exe" -> "test"),
+    "star" -> Map("exe" -> "test"),
+    "bowtiebuild" -> Map("exe" -> "test"),
+    "bowtie2build" -> Map("exe" -> "test"),
+    "gmapbuild" -> Map("exe" -> "test"),
+    "samtools" -> Map("exe" -> "test"),
+    "md5sum" -> Map("exe" -> "test"),
+    "gatk_jar" -> "test",
+    "tabix" -> Map("exe" -> "test")
+  )
+}

generate-indexes/src/test/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/WriteConfigTest.scala

+package nl.lumc.sasc.biopet.pipelines.generateindexes
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.utils.ConfigUtils
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+/**
+ * Created by pjvanthof on 17/05/16.
+ */
+class WriteConfigTest extends TestNGSuite with Matchers {
+  @Test
+  def testWriteConfig: Unit = {
+    val writeConfig = new WriteConfig
+    writeConfig.config = Map("test" -> "bla")
+    writeConfig.out = File.createTempFile("config.", ".json")
+    writeConfig.out.deleteOnExit()
+    writeConfig.run
+
+    ConfigUtils.fileToConfigMap(writeConfig.out) shouldBe Map("test" -> "bla")
+  }
+}

shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala

@@ -171,6 +171,7 @@ class ShivaWithAnnotationTest extends ShivaTestTrait {
 
 object ShivaTest {
   val outputDir = Files.createTempDir()
+  outputDir.deleteOnExit()
   new File(outputDir, "input").mkdirs()
   def inputTouch(name: String): String = {
     val file = new File(outputDir, "input" + File.separator + name)