Adding separated outputDirs

basty/src/test/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTest.scala

@@ -14,19 +14,20 @@
  */
 package nl.lumc.sasc.biopet.pipelines.basty
 
-import java.io.{ File, FileOutputStream }
+import java.io.{File, FileOutputStream}
 
 import com.google.common.io.Files
-import nl.lumc.sasc.biopet.extensions.{ Raxml, RunGubbins }
-import nl.lumc.sasc.biopet.extensions.gatk.{ BaseRecalibrator, IndelRealigner, PrintReads, RealignerTargetCreator }
+import nl.lumc.sasc.biopet.extensions.{Raxml, RunGubbins}
+import nl.lumc.sasc.biopet.extensions.gatk.{BaseRecalibrator, IndelRealigner, PrintReads, RealignerTargetCreator}
 import nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates
-import nl.lumc.sasc.biopet.extensions.tools.{ BastyGenerateFasta, VcfStats }
-import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
+import nl.lumc.sasc.biopet.extensions.tools.{BastyGenerateFasta, VcfStats}
+import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
 import nl.lumc.sasc.biopet.utils.config.Config
+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.{ DataProvider, Test }
+import org.testng.annotations.{AfterClass, DataProvider, Test}
 
 /**
  * Created by pjvanthof on 27/09/16.
@@ -61,10 +62,14 @@ class BastyTest extends TestNGSuite with Matchers {
   def annotation = false
   def bootRuns: Option[Int] = None
 
+  private var dirs: List[File] = Nil
+
   @Test(dataProvider = "bastyOptions")
   def testBasty(f: String, sample1: Boolean, sample2: Boolean): Unit = {
+    val outputDir = BastyTest.outputDir
+    dirs :+= outputDir
     val map = {
-      var m: Map[String, Any] = BastyTest.config
+      var m: Map[String, Any] = BastyTest.config(outputDir)
       if (sample1) m = ConfigUtils.mergeMaps(BastyTest.sample1, m)
       if (sample2) m = ConfigUtils.mergeMaps(BastyTest.sample2, m)
       if (dbsnp) m = ConfigUtils.mergeMaps(Map("dbsnp_vcf" -> "test.vcf.gz"), m)
@@ -133,21 +138,26 @@ class BastyTest extends TestNGSuite with Matchers {
       pipeline.functions.count(_.isInstanceOf[RunGubbins]) shouldBe 2
     }
   }
+
+  // remove temporary run directory all tests in the class have been run
+  @AfterClass def removeTempOutputDir() = {
+    dirs.foreach(FileUtils.deleteDirectory)
+  }
 }
 
 object BastyTest {
-  val outputDir = Files.createTempDir()
-  outputDir.deleteOnExit()
-  new File(outputDir, "input").mkdirs()
+  def outputDir = Files.createTempDir()
+  val inputDir = Files.createTempDir()
+
   def inputTouch(name: String): String = {
-    val file = new File(outputDir, "input" + File.separator + name)
+    val file = new File(inputDir, name)
     Files.touch(file)
     file.getAbsolutePath
   }
 
   private def copyFile(name: String): Unit = {
     val is = getClass.getResourceAsStream("/" + name)
-    val os = new FileOutputStream(new File(outputDir, name))
+    val os = new FileOutputStream(new File(inputDir, name))
     org.apache.commons.io.IOUtils.copy(is, os)
     os.close()
   }
@@ -156,14 +166,14 @@ object BastyTest {
   copyFile("ref.dict")
   copyFile("ref.fa.fai")
 
-  val config = Map(
+  def config(outputDir: File) = Map(
     "skip_write_dependencies" -> true,
     "name_prefix" -> "test",
     "cache" -> true,
     "dir" -> "test",
     "vep_script" -> "test",
     "output_dir" -> outputDir,
-    "reference_fasta" -> (outputDir + File.separator + "ref.fa"),
+    "reference_fasta" -> (inputDir + File.separator + "ref.fa"),
     "gatk_jar" -> "test",
     "samtools" -> Map("exe" -> "test"),
     "bcftools" -> Map("exe" -> "test"),

carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala

@@ -50,10 +50,14 @@ class CarpTest extends TestNGSuite with Matchers {
     for (s1 <- bool; s2 <- bool; s3 <- bool; t <- bool; c <- bool) yield Array("", s1, s2, s3, t, c)
   }
 
+  private var dirs: List[File] = Nil
+
   @Test(dataProvider = "carpOptions")
   def testCarp(f: String, sample1: Boolean, sample2: Boolean, sample3: Boolean, threatment: Boolean, control: Boolean): Unit = {
+    val outputDir = CarpTest.outputDir
+    dirs :+= outputDir
     val map = {
-      var m = ConfigUtils.mergeMaps(Map("output_dir" -> CarpTest.outputDir
+      var m = ConfigUtils.mergeMaps(Map("output_dir" -> outputDir
       ), CarpTest.executables)
 
       if (sample1) m = ConfigUtils.mergeMaps(CarpTest.sample1, m)
@@ -92,22 +96,23 @@ class CarpTest extends TestNGSuite with Matchers {
 
   // remove temporary run directory all tests in the class have been run
   @AfterClass def removeTempOutputDir() = {
-    FileUtils.deleteDirectory(CarpTest.outputDir)
+    dirs.foreach(FileUtils.deleteDirectory)
   }
 }
 
 object CarpTest {
-  val outputDir = Files.createTempDir()
-  new File(outputDir, "input").mkdirs()
+  def outputDir = Files.createTempDir()
+  val inputDir = Files.createTempDir()
+
   def inputTouch(name: String): String = {
-    val file = new File(outputDir, "input" + File.separator + name)
+    val file = new File(inputDir, name)
     Files.touch(file)
     file.getAbsolutePath
   }
 
   private def copyFile(name: String): Unit = {
     val is = getClass.getResourceAsStream("/" + name)
-    val os = new FileOutputStream(new File(outputDir, name))
+    val os = new FileOutputStream(new File(inputDir, name))
     org.apache.commons.io.IOUtils.copy(is, os)
     os.close()
   }
@@ -118,7 +123,7 @@ object CarpTest {
 
   val executables = Map(
     "skip_write_dependencies" -> true,
-    "reference_fasta" -> (outputDir + File.separator + "ref.fa"),
+    "reference_fasta" -> (inputDir + File.separator + "ref.fa"),
     "fastqc" -> Map("exe" -> "test"),
     "seqtk" -> Map("exe" -> "test"),
     "sickle" -> Map("exe" -> "test"),

flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala

@@ -59,10 +59,14 @@ class FlexiprepTest extends TestNGSuite with Matchers {
     ) yield Array("", pair, skipTrim, skipClip, zip, abortOnCorruptFastq)
   }
 
+  private var dirs: List[File] = Nil
+
   @Test(dataProvider = "flexiprepOptions")
   def testFlexiprep(f: String, paired: Boolean, skipTrim: Boolean, skipClip: Boolean,
                     zipped: Boolean, abortOnCorruptFastq: Boolean) = {
-    val map = ConfigUtils.mergeMaps(Map("output_dir" -> FlexiprepTest.outputDir,
+    val outputDir = FlexiprepTest.outputDir
+    dirs :+= outputDir
+    val map = ConfigUtils.mergeMaps(Map("output_dir" -> outputDir,
       "skip_trim" -> skipTrim,
       "skip_clip" -> skipClip,
       "abort_on_corrupt_fastq" -> abortOnCorruptFastq
@@ -85,8 +89,10 @@ class FlexiprepTest extends TestNGSuite with Matchers {
 
   @Test
   def testNoSample: Unit = {
+    val outputDir = FlexiprepTest.outputDir
+    dirs :+= outputDir
     val map = ConfigUtils.mergeMaps(Map(
-      "output_dir" -> FlexiprepTest.outputDir
+      "output_dir" -> outputDir
     ), Map(FlexiprepTest.executables.toSeq: _*))
     val flexiprep: Flexiprep = initPipeline(map)
 
@@ -97,22 +103,27 @@ class FlexiprepTest extends TestNGSuite with Matchers {
 
   // remove temporary run directory all tests in the class have been run
   @AfterClass def removeTempOutputDir() = {
-    FileUtils.deleteDirectory(FlexiprepTest.outputDir)
+    dirs.foreach(FileUtils.deleteDirectory)
   }
 }
 
 object FlexiprepTest {
-  val outputDir = Files.createTempDir()
-  new File(outputDir, "input").mkdirs()
+  def outputDir = Files.createTempDir()
+
+  val inputDir = Files.createTempDir()
 
-  val r1 = new File(outputDir, "input" + File.separator + "R1.fq")
+  val r1 = new File(inputDir, "R1.fq")
   Files.touch(r1)
-  val r2 = new File(outputDir, "input" + File.separator + "R2.fq")
+  r1.deleteOnExit()
+  val r2 = new File(inputDir, "R2.fq")
   Files.touch(r2)
-  val r1Zipped = new File(outputDir, "input" + File.separator + "R1.fq.gz")
+  r2.deleteOnExit()
+  val r1Zipped = new File(inputDir, "R1.fq.gz")
   Files.touch(r1Zipped)
-  val r2Zipped = new File(outputDir, "input" + File.separator + "R2.fq.gz")
+  r1Zipped.deleteOnExit()
+  val r2Zipped = new File(inputDir, "R2.fq.gz")
   Files.touch(r2Zipped)
+  r2Zipped.deleteOnExit()
 
   val executables = Map(
     "skip_write_dependencies" -> true,

gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala

@@ -18,13 +18,14 @@ import java.io.File
 
 import com.google.common.io.Files
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import nl.lumc.sasc.biopet.extensions.centrifuge.{ Centrifuge, CentrifugeKreport }
-import nl.lumc.sasc.biopet.extensions.kraken.{ Kraken, KrakenReport }
+import nl.lumc.sasc.biopet.extensions.centrifuge.{Centrifuge, CentrifugeKreport}
+import nl.lumc.sasc.biopet.extensions.kraken.{Kraken, KrakenReport}
 import nl.lumc.sasc.biopet.extensions.picard.SamToFastq
 import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
 import nl.lumc.sasc.biopet.extensions.tools.KrakenReportToJson
-import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
+import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
 import nl.lumc.sasc.biopet.utils.config.Config
+import org.apache.commons.io.FileUtils
 import org.broadinstitute.gatk.queue.QSettings
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
@@ -60,15 +61,19 @@ abstract class TestGearsSingle extends TestNGSuite with Matchers {
 
   def inputMode: Option[String] = Some("fastq")
 
+  private var dirs: List[File] = Nil
+
   @Test
   def testGears(): Unit = {
+    val outputDir = TestGearsSingle.outputDir
+    dirs :+= outputDir
     val map = ConfigUtils.mergeMaps(Map(
       "gears_use_qiime_rtax" -> qiimeRtax,
       "gears_use_centrifuge" -> centrifuge,
       "gears_use_qiime_closed" -> qiimeClosed,
       "gears_use_qiime_open" -> qiimeOpen,
       "gears_use_seq_count" -> seqCount,
-      "output_dir" -> TestGearsSingle.outputDir
+      "output_dir" -> outputDir
     ) ++
       kraken.map("gears_use_kraken" -> _) ++
       downsample.map("downsample" -> _),
@@ -134,6 +139,11 @@ abstract class TestGearsSingle extends TestNGSuite with Matchers {
       pipesJobs.count(_.isInstanceOf[CentrifugeKreport]) shouldBe (if (centrifuge) 2 else 0)
     }
   }
+
+  @AfterClass
+  def removeDirs: Unit = {
+    dirs.foreach(FileUtils.deleteDirectory)
+  }
 }
 
 class GearsSingleNoInputTest extends TestGearsSingle {
@@ -219,17 +229,17 @@ class GearsSingleQiimeOpenDownsampleTest extends TestGearsSingle {
 }
 
 object TestGearsSingle {
-  val outputDir = Files.createTempDir()
-  outputDir.deleteOnExit()
-  new File(outputDir, "input").mkdirs()
+  def outputDir = Files.createTempDir()
+
+  val inputDir = Files.createTempDir()
 
-  val r1 = new File(outputDir, "input" + File.separator + "R1.fq")
+  val r1 = new File(inputDir, "R1.fq")
   Files.touch(r1)
   r1.deleteOnExit()
-  val r2 = new File(outputDir, "input" + File.separator + "R2.fq")
+  val r2 = new File(inputDir, "R2.fq")
   Files.touch(r2)
   r2.deleteOnExit()
-  val bam = new File(outputDir, "input" + File.separator + "bamfile.bam")
+  val bam = new File(inputDir, "bamfile.bam")
   Files.touch(bam)
   bam.deleteOnExit()
 

gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala

@@ -17,12 +17,13 @@ package nl.lumc.sasc.biopet.pipelines.gears
 import java.io.File
 
 import com.google.common.io.Files
-import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
+import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
 import nl.lumc.sasc.biopet.utils.config.Config
+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.{ DataProvider, Test }
+import org.testng.annotations.{AfterClass, DataProvider, Test}
 
 /**
  * Created by pjvanthof on 04/02/16.
@@ -55,10 +56,14 @@ abstract class GearsTest extends TestNGSuite with Matchers {
     ) yield Array("", s1, s2)
   }
 
+  private var dirs: List[File] = Nil
+
   @Test(dataProvider = "gearsOptions")
   def testGears(dummy: String, sample1: Boolean, sample2: Boolean): Unit = {
+    val outputDir = GearsTest.outputDir
+    dirs :+= outputDir
     val map = {
-      var m: Map[String, Any] = GearsTest.config
+      var m: Map[String, Any] = GearsTest.config(outputDir)
       if (sample1) m = ConfigUtils.mergeMaps(GearsTest.sample1, m)
       if (sample2) m = ConfigUtils.mergeMaps(GearsTest.sample2, m)
       ConfigUtils.mergeMaps(Map(
@@ -82,6 +87,11 @@ abstract class GearsTest extends TestNGSuite with Matchers {
 
     }
   }
+
+  @AfterClass
+  def removeDirs: Unit = {
+    dirs.foreach(FileUtils.deleteDirectory)
+  }
 }
 
 class GearsDefaultTest extends GearsTest
@@ -101,18 +111,21 @@ class GearsLibraryTest extends GearsTest {
 }
 
 object GearsTest {
-  val outputDir = Files.createTempDir()
-  new File(outputDir, "input").mkdirs()
-  outputDir.deleteOnExit()
+  def outputDir = Files.createTempDir()
+
+  val inputDir = Files.createTempDir()
 
-  val r1 = new File(outputDir, "input" + File.separator + "R1.fq")
+  val r1 = new File(inputDir, "R1.fq")
   Files.touch(r1)
-  val r2 = new File(outputDir, "input" + File.separator + "R2.fq")
+  r1.deleteOnExit()
+  val r2 = new File(inputDir, "R2.fq")
   Files.touch(r2)
-  val bam = new File(outputDir, "input" + File.separator + "bamfile.bam")
+  r2.deleteOnExit()
+  val bam = new File(inputDir, "bamfile.bam")
   Files.touch(bam)
+  bam.deleteOnExit()
 
-  val config = Map(
+  def config(outputDir: File) = Map(
     "skip_write_dependencies" -> true,
     "output_dir" -> outputDir,
     "kraken" -> Map("exe" -> "test", "db" -> "test"),

gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala

@@ -14,21 +14,22 @@
  */
 package nl.lumc.sasc.biopet.pipelines.gentrap
 
-import java.io.{ File, FileOutputStream }
+import java.io.{File, FileOutputStream}
 
 import com.google.common.io.Files
-import nl.lumc.sasc.biopet.core.{ BiopetFifoPipe, BiopetPipe }
+import nl.lumc.sasc.biopet.core.{BiopetFifoPipe, BiopetPipe}
 import nl.lumc.sasc.biopet.extensions._
 import nl.lumc.sasc.biopet.extensions.gmap.Gsnap
 import nl.lumc.sasc.biopet.extensions.hisat.Hisat2
-import nl.lumc.sasc.biopet.extensions.tools.{ BaseCounter, WipeReads }
-import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
+import nl.lumc.sasc.biopet.extensions.tools.{BaseCounter, WipeReads}
+import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
 import nl.lumc.sasc.biopet.utils.config.Config
 import nl.lumc.sasc.biopet.utils.camelize
+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.{ DataProvider, Test }
+import org.testng.annotations.{AfterClass, DataProvider, Test}
 
 abstract class GentrapTestAbstract(val expressionMeasures: List[String]) extends TestNGSuite with Matchers {
 
@@ -58,11 +59,14 @@ abstract class GentrapTestAbstract(val expressionMeasures: List[String]) extends
     } yield Array(strandProtocol)
   }
 
+  private var dirs: List[File] = Nil
+
   @Test(dataProvider = "expMeasuresstrandProtocol")
   def testGentrap(strandProtocol: String) = {
-
+    val outputDir = GentrapTest.outputDir
+    dirs :+= outputDir
     val settings = Map(
-      "output_dir" -> GentrapTest.outputDir,
+      "output_dir" -> outputDir,
       "gsnap" -> Map("db" -> "test", "dir" -> "test"),
       "expression_measures" -> expressionMeasures,
       "strand_protocol" -> strandProtocol
@@ -145,6 +149,10 @@ abstract class GentrapTestAbstract(val expressionMeasures: List[String]) extends
     }
   }
 
+  // remove temporary run directory all tests in the class have been run
+  @AfterClass def removeTempOutputDir() = {
+    dirs.foreach(FileUtils.deleteDirectory)
+  }
 }
 
 class GentrapFragmentsPerGeneTest extends GentrapTestAbstract(List("fragments_per_gene"))
@@ -166,18 +174,18 @@ class GentrapCallVariantsTest extends GentrapTestAbstract(List("fragments_per_ge
 }
 
 object GentrapTest {
-  val outputDir = Files.createTempDir()
-  outputDir.deleteOnExit()
-  new File(outputDir, "input").mkdirs()
+  def outputDir = Files.createTempDir()
+  val inputDir = Files.createTempDir()
+
   def inputTouch(name: String): String = {
-    val file = new File(outputDir, "input" + File.separator + name)
+    val file = new File(inputDir, name)
     Files.touch(file)
     file.getAbsolutePath
   }
 
   private def copyFile(name: String): Unit = {
     val is = getClass.getResourceAsStream("/" + name)
-    val os = new FileOutputStream(new File(outputDir, name))
+    val os = new FileOutputStream(new File(inputDir, name))
     org.apache.commons.io.IOUtils.copy(is, os)
     os.close()
   }
@@ -188,12 +196,12 @@ object GentrapTest {
 
   val executables: Map[String, Any] = Map(
     "skip_write_dependencies" -> true,
-    "reference_fasta" -> (outputDir + File.separator + "ref.fa"),
-    "refFlat" -> (outputDir + File.separator + "ref.fa"),
-    "annotation_gtf" -> (outputDir + File.separator + "ref.fa"),
-    "annotation_bed" -> (outputDir + File.separator + "ref.fa"),
-    "annotation_refflat" -> (outputDir + File.separator + "ref.fa"),
-    "ribosome_refflat" -> (outputDir + File.separator + "ref.fa"),
+    "reference_fasta" -> (inputDir + File.separator + "ref.fa"),
+    "refFlat" -> (inputDir + File.separator + "ref.fa"),
+    "annotation_gtf" -> (inputDir + File.separator + "ref.fa"),
+    "annotation_bed" -> (inputDir + File.separator + "ref.fa"),
+    "annotation_refflat" -> (inputDir + File.separator + "ref.fa"),
+    "ribosome_refflat" -> (inputDir + File.separator + "ref.fa"),
     "varscan_jar" -> "test",
     "rscript" -> Map("exe" -> "test"),
     "igvtools" -> Map("exe" -> "test", "igvtools_jar" -> "test"),

sage/src/test/scala/nl/lumc/sasc/biopet/pipelines/sage/SageTest.scala

@@ -14,15 +14,16 @@
  */
 package nl.lumc.sasc.biopet.pipelines.sage
 
-import java.io.{ File, FileOutputStream }
+import java.io.{File, FileOutputStream}
 
 import com.google.common.io.Files
-import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
+import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
 import nl.lumc.sasc.biopet.utils.config.Config
+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.{ DataProvider, Test }
+import org.testng.annotations.{AfterClass, DataProvider, Test}
 
 /**
  * Created by pjvanthof on 28/09/16.
@@ -53,10 +54,14 @@ class SageTest extends TestNGSuite with Matchers {
   def tagsLibrary = false
   def libraryCounts: Option[Boolean] = None
 
+  private var dirs: List[File] = Nil
+
   @Test(dataProvider = "sageOptions")
   def testSage(f: String, sample1: Boolean, sample2: Boolean): Unit = {
+    val outputDir = SageTest.outputDir
+    dirs :+= outputDir
     val map = {
-      var m: Map[String, Any] = SageTest.config
+      var m: Map[String, Any] = SageTest.config(outputDir)
       if (sample1) m = ConfigUtils.mergeMaps(SageTest.sample1, m)
       if (sample2) m = ConfigUtils.mergeMaps(SageTest.sample2, m)
       ConfigUtils.mergeMaps(
@@ -99,6 +104,11 @@ class SageTest extends TestNGSuite with Matchers {
 
     }
   }
+
+  // remove temporary run directory all tests in the class have been run
+  @AfterClass def removeTempOutputDir() = {
+    dirs.foreach(FileUtils.deleteDirectory)
+  }
 }
 
 class SageNoBedTest extends SageTest {
@@ -121,11 +131,11 @@ class SageLibraryCountsTest extends SageTest {
 }
 
 object SageTest {
-  val outputDir = Files.createTempDir()
-  outputDir.deleteOnExit()
-  new File(outputDir, "input").mkdirs()
+  def outputDir = Files.createTempDir()
+  val intputDir = Files.createTempDir()
+
   def inputTouch(name: String): String = {
-    val file = new File(outputDir, "input" + File.separator + name)
+    val file = new File(intputDir, name)
     Files.touch(file)
     file.getAbsolutePath
   }
@@ -134,7 +144,7 @@ object SageTest {
 
   private def copyFile(name: String): Unit = {
     val is = getClass.getResourceAsStream("/" + name)
-    val os = new FileOutputStream(new File(outputDir, name))
+    val os = new FileOutputStream(new File(intputDir, name))
     org.apache.commons.io.IOUtils.copy(is, os)
     os.close()
   }
@@ -143,9 +153,9 @@ object SageTest {
   copyFile("ref.dict")
   copyFile("ref.fa.fai")
 
-  val config: Map[String, Any] = Map(
+  def config(outputDir: File): Map[String, Any] = Map(
     "skip_write_dependencies" -> true,
-    "reference_fasta" -> (outputDir + File.separator + "ref.fa"),
+    "reference_fasta" -> (intputDir + File.separator + "ref.fa"),
     "output_dir" -> outputDir.getAbsolutePath,
     "fastqc" -> Map("exe" -> "test"),
     "seqtk" -> Map("exe" -> "test"),

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

@@ -14,20 +14,21 @@
  */
 package nl.lumc.sasc.biopet.pipelines.shiva
 
-import java.io.{ File, FileOutputStream }
+import java.io.{File, FileOutputStream}
 import java.nio.file.Paths
 
 import com.google.common.io.Files
-import nl.lumc.sasc.biopet.extensions.breakdancer.{ BreakdancerCaller, BreakdancerConfig, BreakdancerVCF }
+import nl.lumc.sasc.biopet.extensions.breakdancer.{BreakdancerCaller, BreakdancerConfig, BreakdancerVCF}
 import nl.lumc.sasc.biopet.extensions.clever.CleverCaller
 import nl.lumc.sasc.biopet.extensions.delly.DellyCaller
-import nl.lumc.sasc.biopet.extensions.pindel.{ PindelCaller, PindelConfig, PindelVCF }
-import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
+import nl.lumc.sasc.biopet.extensions.pindel.{PindelCaller, PindelConfig, PindelVCF}
+import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
 import nl.lumc.sasc.biopet.utils.config.Config
+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.{ DataProvider, Test }
+import org.testng.annotations.{AfterClass, DataProvider, Test}
 
 import scala.collection.mutable.ListBuffer
 
@@ -37,15 +38,17 @@ import scala.collection.mutable.ListBuffer
  * Created by pjvan_thof on 3/2/15.
  */
 class ShivaSvCallingTest extends TestNGSuite with Matchers {
-  def initPipeline(map: Map[String, Any]): ShivaSvCalling = {
+  def initPipeline(map: Map[String, Any], outputDir: File): ShivaSvCalling = {
     new ShivaSvCalling {
       override def configNamespace = "shivasvcalling"
-      override def globalConfig = new Config(ConfigUtils.mergeMaps(map, ShivaSvCallingTest.config))
+      override def globalConfig = new Config(ConfigUtils.mergeMaps(map, ShivaSvCallingTest.config(outputDir)))
       qSettings = new QSettings
       qSettings.runName = "test"
     }
   }
 
+  private var dirs: List[File] = Nil
+
   @DataProvider(name = "shivaSvCallingOptions")
   def shivaSvCallingOptions = {
     val bool = Array(true, false)
@@ -64,13 +67,15 @@ class ShivaSvCallingTest extends TestNGSuite with Matchers {
                          clever: Boolean,
                          breakdancer: Boolean,
                          pindel: Boolean) = {
+    val outputDir = ShivaSvCallingTest.outputDir
+    dirs :+= outputDir
     val callers: ListBuffer[String] = ListBuffer()
     if (delly) callers.append("delly")
     if (clever) callers.append("clever")
     if (breakdancer) callers.append("breakdancer")
     if (pindel) callers.append("pindel")
     val map = Map("sv_callers" -> callers.toList)
-    val pipeline = initPipeline(map)
+    val pipeline = initPipeline(map, outputDir)
 
     pipeline.inputBams = (for (n <- 1 to bams) yield n.toString -> ShivaSvCallingTest.inputTouch("bam_" + n + ".bam")).toMap
 
@@ -122,11 +127,13 @@ class ShivaSvCallingTest extends TestNGSuite with Matchers {
 
   @Test(dataProvider = "dellyOptions")
   def testShivaDelly(bams: Int, del: Boolean, dup: Boolean, inv: Boolean, tra: Boolean): Unit = {
+    val outputDir = ShivaSvCallingTest.outputDir
+    dirs :+= outputDir
 
     val map = Map("sv_callers" -> List("delly"), "delly" ->
       Map("DEL" -> del, "DUP" -> dup, "INV" -> inv, "TRA" -> tra)
     )
-    val pipeline = initPipeline(map)
+    val pipeline = initPipeline(map, outputDir)
 
     pipeline.inputBams = Map("bam" -> ShivaSvCallingTest.inputTouch("bam" + ".bam"))
 
@@ -145,8 +152,11 @@ class ShivaSvCallingTest extends TestNGSuite with Matchers {
 
   @Test
   def testWrongCaller(): Unit = {
+    val outputDir = ShivaSvCallingTest.outputDir
+    dirs :+= outputDir
+
     val map = Map("sv_callers" -> List("this is not a caller"))
-    val pipeline = initPipeline(map)
+    val pipeline = initPipeline(map, outputDir)
 
     pipeline.inputBams =