Added separated outputDirs

bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala

@@ -56,9 +56,13 @@ class BamMetricsTest extends TestNGSuite with Matchers {
     ) yield Array(rois, amplicon, rna, wgs)
   }
 
+  private var dirs: List[File] = Nil
+
   @Test(dataProvider = "bammetricsOptions")
   def testBamMetrics(rois: Int, amplicon: Boolean, rna: Boolean, wgs: Boolean) = {
-    val map = ConfigUtils.mergeMaps(Map("output_dir" -> BamMetricsTest.outputDir, "rna_metrics" -> rna, "wgs_metrics" -> wgs),
+    val outputDir = Files.createTempDir()
+    dirs :+= outputDir
+    val map = ConfigUtils.mergeMaps(Map("output_dir" -> outputDir, "rna_metrics" -> rna, "wgs_metrics" -> wgs),
       Map(BamMetricsTest.executables.toSeq: _*)) ++
       (if (amplicon) Map("amplicon_bed" -> BamMetricsTest.ampliconBed.getAbsolutePath) else Map()) ++
       (if (rna) Map("annotation_refflat" -> "transcripts.refFlat") else Map()) ++
@@ -81,30 +85,28 @@ class BamMetricsTest extends TestNGSuite with Matchers {
   }
 
   // remove temporary run directory all tests in the class have been run
-  @AfterClass
-  def removeTempOutputDir() = {
-    FileUtils.deleteDirectory(BamMetricsTest.outputDir)
+  @AfterClass def removeTempOutputDir() = {
+    dirs.foreach(FileUtils.deleteDirectory)
   }
 }
 
 object BamMetricsTest {
-  val outputDir = Files.createTempDir()
-  new File(outputDir, "input").mkdirs()
+  val inputDir = Files.createTempDir()
 
-  val bam = new File(outputDir, "input" + File.separator + "bla.bam")
+  val bam = new File(inputDir, "input" + File.separator + "bla.bam")
   Files.touch(bam)
-  val ampliconBed = new File(outputDir, "input" + File.separator + "amplicon_bed.bed")
+  val ampliconBed = new File(inputDir, "input" + File.separator + "amplicon_bed.bed")
   Files.touch(ampliconBed)
 
   def roi(i: Int): File = {
-    val roi = new File(outputDir, "input" + File.separator + s"roi${i}.bed")
+    val roi = new File(inputDir, "input" + File.separator + s"roi${i}.bed")
     Files.touch(roi)
     roi
   }
 
   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()
   }
@@ -116,7 +118,7 @@ object BamMetricsTest {
   val executables = Map(
     "skip_write_dependencies" -> true,
     "refFlat" -> "bla.refFlat",
-    "reference_fasta" -> (outputDir + File.separator + "ref.fa"),
+    "reference_fasta" -> (inputDir + File.separator + "ref.fa"),
     "samtools" -> Map("exe" -> "test"),
     "bedtools" -> Map("exe" -> "test"),
     "md5sum" -> Map("exe" -> "test")

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

@@ -14,58 +14,73 @@
  */
 package nl.lumc.sasc.biopet.pipelines.generateindexes
 
+import java.io.File
+
 import com.google.common.io.Files
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 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.Test
+import org.testng.annotations.{AfterClass, Test}
 
 /**
  * Created by pjvan_thof on 13-5-16.
  */
 class DownloadGenomesTest extends TestNGSuite with Matchers {
-  def initPipeline(map: Map[String, Any]): DownloadGenomes = {
+  def initPipeline(map: Map[String, Any], outputDir: File): DownloadGenomes = {
     new DownloadGenomes() {
       override def configNamespace = "generateindexes"
-      override def globalConfig = new Config(ConfigUtils.mergeMaps(map, DownloadGenomesTest.config))
+      override def globalConfig = new Config(ConfigUtils.mergeMaps(map, DownloadGenomesTest.config(outputDir)))
       qSettings = new QSettings
       qSettings.runName = "test"
     }
   }
 
+  private var dirs: List[File] = Nil
+
   @Test
   def testNoFastaUri(): Unit = {
-    val pipeline = initPipeline(Map())
+    val outputDir = Files.createTempDir()
+    dirs :+= outputDir
+    val pipeline = initPipeline(Map(), outputDir)
     pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("" -> "")))
     an[IllegalArgumentException] should be thrownBy pipeline.script()
   }
 
   @Test
   def testNcbiAssembly(): Unit = {
-    val pipeline = initPipeline(Map())
+    val outputDir = Files.createTempDir()
+    dirs :+= outputDir
+    val pipeline = initPipeline(Map(), outputDir)
     pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("ncbi_assembly_report" -> "id")))
     noException should be thrownBy pipeline.script()
   }
 
   @Test
   def testSingleFasta(): Unit = {
-    val pipeline = initPipeline(Map())
+    val outputDir = Files.createTempDir()
+    dirs :+= outputDir
+    val pipeline = initPipeline(Map(), outputDir)
     pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri")))
     noException should be thrownBy pipeline.script()
   }
 
   @Test
   def testMultiFasta(): Unit = {
-    val pipeline = initPipeline(Map())
+    val outputDir = Files.createTempDir()
+    dirs :+= outputDir
+    val pipeline = initPipeline(Map(), outputDir)
     pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> List("uri", "uri2", "uri3.gz"))))
     noException should be thrownBy pipeline.script()
   }
 
   @Test
   def testSingleDbsnp(): Unit = {
-    val pipeline = initPipeline(Map("download_annotations" -> true))
+    val outputDir = Files.createTempDir()
+    dirs :+= outputDir
+    val pipeline = initPipeline(Map("download_annotations" -> true), outputDir)
     pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri",
       "dbsnp" -> Map("version" -> Map("vcf_uri" -> "uri.vcf.gz")))))
     noException should be thrownBy pipeline.script()
@@ -73,7 +88,9 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
 
   @Test
   def testContigMapDbsnp(): Unit = {
-    val pipeline = initPipeline(Map("download_annotations" -> true))
+    val outputDir = Files.createTempDir()
+    dirs :+= outputDir
+    val pipeline = initPipeline(Map("download_annotations" -> true), outputDir)
     pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri",
       "dbsnp" -> Map("version" -> Map("vcf_uri" -> "uri.vcf.gz", "contig_map" -> Map("1" -> "chr1"))))))
     noException should be thrownBy pipeline.script()
@@ -81,7 +98,9 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
 
   @Test
   def testUnzippedContigMapDbsnp(): Unit = {
-    val pipeline = initPipeline(Map("download_annotations" -> true))
+    val outputDir = Files.createTempDir()
+    dirs :+= outputDir
+    val pipeline = initPipeline(Map("download_annotations" -> true), outputDir)
     pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri",
       "dbsnp" -> Map("version" -> Map("vcf_uri" -> "uri.vcf", "contig_map" -> Map("1" -> "chr1"))))))
     noException should be thrownBy pipeline.script()
@@ -89,7 +108,9 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
 
   @Test
   def testSingleUnzippedDbsnp(): Unit = {
-    val pipeline = initPipeline(Map("download_annotations" -> true))
+    val outputDir = Files.createTempDir()
+    dirs :+= outputDir
+    val pipeline = initPipeline(Map("download_annotations" -> true), outputDir)
     pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri",
       "dbsnp" -> Map("version" -> Map(("vcf_uri" -> "uri.vcf"))))))
     noException should be thrownBy pipeline.script()
@@ -97,7 +118,9 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
 
   @Test
   def testMultiDbsnp(): Unit = {
-    val pipeline = initPipeline(Map("download_annotations" -> true))
+    val outputDir = Files.createTempDir()
+    dirs :+= outputDir
+    val pipeline = initPipeline(Map("download_annotations" -> true), outputDir)
     pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri",
       "dbsnp" -> Map("version" -> Map("vcf_uri" -> List("uri.vcf.gz", "uri2.vcf.gz"))))))
     noException should be thrownBy pipeline.script()
@@ -105,7 +128,9 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
 
   @Test
   def testVep(): Unit = {
-    val pipeline = initPipeline(Map("download_annotations" -> true))
+    val outputDir = Files.createTempDir()
+    dirs :+= outputDir
+    val pipeline = initPipeline(Map("download_annotations" -> true), outputDir)
     pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri",
       "vep" -> Map("version" -> Map("cache_uri" -> "something/human_vep_80_hg19.tar.gz")))))
     noException should be thrownBy pipeline.script()
@@ -113,7 +138,9 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
 
   @Test
   def testGtfZipped(): Unit = {
-    val pipeline = initPipeline(Map("download_annotations" -> true))
+    val outputDir = Files.createTempDir()
+    dirs :+= outputDir
+    val pipeline = initPipeline(Map("download_annotations" -> true), outputDir)
     pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri",
       "gene_annotation" -> Map("version" -> Map("gtf_uri" -> "bla.gf.gz")))))
     noException should be thrownBy pipeline.script()
@@ -121,7 +148,9 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
 
   @Test
   def testGtf(): Unit = {
-    val pipeline = initPipeline(Map("download_annotations" -> true))
+    val outputDir = Files.createTempDir()
+    dirs :+= outputDir
+    val pipeline = initPipeline(Map("download_annotations" -> true), outputDir)
     pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri",
       "gene_annotation" -> Map("version" -> Map("gtf_uri" -> "bla.gf")))))
     noException should be thrownBy pipeline.script()
@@ -129,19 +158,22 @@ class DownloadGenomesTest extends TestNGSuite with Matchers {
 
   @Test
   def testGff(): Unit = {
-    val pipeline = initPipeline(Map("download_annotations" -> true))
+    val outputDir = Files.createTempDir()
+    dirs :+= outputDir
+    val pipeline = initPipeline(Map("download_annotations" -> true), outputDir)
     pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri",
       "gene_annotation" -> Map("version" -> Map("gff_uri" -> "bla.gf")))))
     noException should be thrownBy pipeline.script()
   }
 
+  // remove temporary run directory all tests in the class have been run
+  @AfterClass def removeTempOutputDir() = {
+    dirs.foreach(FileUtils.deleteDirectory)
+  }
 }
 
 object DownloadGenomesTest {
-  val outputDir = Files.createTempDir()
-  outputDir.deleteOnExit()
-
-  val config = Map(
+  def config(outputDir: File) = Map(
     "skip_write_dependencies" -> true,
     "output_dir" -> outputDir,
     "bwa" -> Map("exe" -> "test"),

gwas-test/src/test/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTestTest.scala

@@ -20,10 +20,11 @@ import java.nio.file.Paths
 import com.google.common.io.Files
 import nl.lumc.sasc.biopet.utils.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.Test
+import org.testng.annotations.{AfterClass, Test}
 
 /**
  * Created by pjvan_thof on 4/11/16.
@@ -38,10 +39,14 @@ class GwasTestTest extends TestNGSuite with Matchers {
     }
   }
 
+  private var dirs: List[File] = Nil
+
   @Test
   def testFromVcf: Unit = {
+    val outputDir = Files.createTempDir()
+    dirs :+= outputDir
     Logging.errors.clear()
-    val pipeline = initPipeline(GwasTestTest.config ++
+    val pipeline = initPipeline(GwasTestTest.config(outputDir) ++
       Map("input_vcf" -> GwasTestTest.vcfFile.toString
       )
     )
@@ -50,11 +55,18 @@ class GwasTestTest extends TestNGSuite with Matchers {
 
   @Test
   def testEmpty: Unit = {
-    val pipeline = initPipeline(GwasTestTest.config)
+    val outputDir = Files.createTempDir()
+    dirs :+= outputDir
+    val pipeline = initPipeline(GwasTestTest.config(outputDir))
     intercept[IllegalArgumentException] {
       pipeline.script()
     }
   }
+
+  // remove temporary run directory all tests in the class have been run
+  @AfterClass def removeTempOutputDir() = {
+    dirs.foreach(FileUtils.deleteDirectory)
+  }
 }
 
 object GwasTestTest {
@@ -65,16 +77,13 @@ object GwasTestTest {
   val phenotypeFile = File.createTempFile("gwas.", ".txt")
   phenotypeFile.deleteOnExit()
 
-  val outputDir = Files.createTempDir()
-  outputDir.deleteOnExit()
-
   val reference = new File(resourcePath("/fake_chrQ.fa"))
 
   private def resourcePath(p: String): String = {
     Paths.get(getClass.getResource(p).toURI).toString
   }
 
-  val config = Map(
+  def config(outputDir: File) = Map(
     "skip_write_dependencies" -> true,
     "reference_fasta" -> reference.toString,
     "phenotype_file" -> phenotypeFile.toString,

gwas-test/src/test/scala/nl/lumc/sasc/biopet/pipelines/gwastest/impute/Impute2VcfTest.scala

@@ -19,10 +19,11 @@ import java.nio.file.Paths
 
 import com.google.common.io.Files
 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.Test
+import org.testng.annotations.{AfterClass, Test}
 
 /**
  * Created by pjvan_thof on 31-5-16.
@@ -37,9 +38,13 @@ class Impute2VcfTest extends TestNGSuite with Matchers {
     }
   }
 
+  private var dirs: List[File] = Nil
+
   @Test
   def testFromGens: Unit = {
-    val pipeline = initPipeline(Impute2VcfTest.config ++
+    val outputDir = Files.createTempDir()
+    dirs :+= outputDir
+    val pipeline = initPipeline(Impute2VcfTest.config(outputDir) ++
       Map("input_gens" -> List(Map("genotypes" -> Impute2VcfTest.vcfFile, "contig" -> "chrQ"))
       )
     )
@@ -48,7 +53,9 @@ class Impute2VcfTest extends TestNGSuite with Matchers {
 
   @Test
   def testWrongContig: Unit = {
-    val pipeline = initPipeline(Impute2VcfTest.config ++
+    val outputDir = Files.createTempDir()
+    dirs :+= outputDir
+    val pipeline = initPipeline(Impute2VcfTest.config(outputDir) ++
       Map("input_gens" -> List(Map("genotypes" -> Impute2VcfTest.vcfFile, "contig" -> "chrBla"))
       )
     )
@@ -59,7 +66,9 @@ class Impute2VcfTest extends TestNGSuite with Matchers {
 
   @Test
   def testFromSpecs: Unit = {
-    val pipeline = initPipeline(Impute2VcfTest.config ++
+    val outputDir = Files.createTempDir()
+    dirs :+= outputDir
+    val pipeline = initPipeline(Impute2VcfTest.config(outputDir) ++
       Map("imute_specs_file" -> Impute2VcfTest.resourcePath("/specs/files.specs"))
     )
     pipeline.script()
@@ -67,12 +76,18 @@ class Impute2VcfTest extends TestNGSuite with Matchers {
 
   @Test
   def testEmpty: Unit = {
-    val pipeline = initPipeline(Impute2VcfTest.config)
+    val outputDir = Files.createTempDir()
+    dirs :+= outputDir
+    val pipeline = initPipeline(Impute2VcfTest.config(outputDir))
     intercept[IllegalArgumentException] {
       pipeline.script()
     }
   }
 
+  // remove temporary run directory all tests in the class have been run
+  @AfterClass def removeTempOutputDir() = {
+    dirs.foreach(FileUtils.deleteDirectory)
+  }
 }
 
 object Impute2VcfTest {
@@ -83,16 +98,13 @@ object Impute2VcfTest {
   val phenotypeFile = File.createTempFile("gwas.", ".txt")
   phenotypeFile.deleteOnExit()
 
-  val outputDir = Files.createTempDir()
-  outputDir.deleteOnExit()
-
   val reference = new File(resourcePath("/fake_chrQ.fa"))
 
   private def resourcePath(p: String): String = {
     Paths.get(getClass.getResource(p).toURI).toString
   }
 
-  val config = Map(
+  def config(outputDir: File) = Map(
     "skip_write_dependencies" -> true,
     "reference_fasta" -> reference.toString,
     "phenotype_file" -> phenotypeFile.toString,

kopisu/src/test/scala/nl/lumc/sasc/biopet/pipelines/kopisu/KopisuTest.scala

@@ -14,16 +14,17 @@
  */
 package nl.lumc.sasc.biopet.pipelines.kopisu
 
-import java.io.{ File, FileOutputStream }
+import java.io.{File, FileOutputStream}
 
 import com.google.common.io.Files
-import nl.lumc.sasc.biopet.extensions.freec.{ FreeC, FreeCAssessSignificancePlot, FreeCCNVPlot }
+import nl.lumc.sasc.biopet.extensions.freec.{FreeC, FreeCAssessSignificancePlot, FreeCCNVPlot}
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 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
 
@@ -33,15 +34,17 @@ import scala.collection.mutable.ListBuffer
  * Created by pjvan_thof on 3/2/15.
  */
 class KopisuTest extends TestNGSuite with Matchers {
-  def initPipeline(map: Map[String, Any]): Kopisu = {
+  def initPipeline(map: Map[String, Any], outputDir: File): Kopisu = {
     new Kopisu() {
       override def configNamespace = "kopisu"
-      override def globalConfig = new Config(ConfigUtils.mergeMaps(map, KopisuTest.config))
+      override def globalConfig = new Config(ConfigUtils.mergeMaps(map, KopisuTest.config(outputDir)))
       qSettings = new QSettings
       qSettings.runName = "test"
     }
   }
 
+  private var dirs: List[File] = Nil
+
   @DataProvider(name = "shivaSvCallingOptions")
   def shivaSvCallingOptions = {
     val bool = Array(true, false)
@@ -56,12 +59,15 @@ class KopisuTest extends TestNGSuite with Matchers {
   def testShivaSvCalling(bams: Int,
                          freec: Boolean,
                          conifer: Boolean) = {
+    val outputDir = Files.createTempDir()
+    dirs :+= outputDir
+
     val callers: ListBuffer[String] = ListBuffer()
     val map = Map("sv_callers" -> callers.toList)
     val pipeline = initPipeline(map ++ Map(
       "use_freec_method" -> freec,
       "use_conifer_method" -> conifer
-    ))
+    ), outputDir)
 
     pipeline.inputBams = (for (n <- 1 to bams) yield n.toString -> KopisuTest.inputTouch("bam_" + n + ".bam")).toMap
 
@@ -84,21 +90,26 @@ class KopisuTest extends TestNGSuite with Matchers {
       pipeline.functions.count(_.isInstanceOf[FreeCCNVPlot]) shouldBe (if (freec) bams else 0)
     }
   }
+
+  // remove temporary run directory all tests in the class have been run
+  @AfterClass def removeTempOutputDir() = {
+    dirs.foreach(FileUtils.deleteDirectory)
+  }
 }
 
 object KopisuTest {
-  val outputDir = Files.createTempDir()
-  outputDir.deleteOnExit()
-  new File(outputDir, "input").mkdirs()
+  def outputDir = Files.createTempDir()
+  val inputDir = Files.createTempDir()
+
   private def inputTouch(name: String): File = {
-    val file = new File(outputDir, "input" + File.separator + name).getAbsoluteFile
+    val file = new File(inputDir, 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))
+    val os = new FileOutputStream(new File(inputDir, name))
     org.apache.commons.io.IOUtils.copy(is, os)
     os.close()
   }
@@ -108,14 +119,13 @@ object KopisuTest {
   copyFile("ref.fa.fai")
 
   val controlDir = Files.createTempDir()
-  controlDir.deleteOnExit()
   Files.touch(new File(controlDir, "test.txt"))
 
-  val config = Map(
+  def config(outputDir: File) = Map(
     "skip_write_dependencies" -> true,
     "name_prefix" -> "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"),
     "md5sum" -> Map("exe" -> "test"),

tinycap/src/test/scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCapTest.scala

@@ -47,6 +47,8 @@ import org.testng.annotations.{ AfterClass, DataProvider, Test }
 
 class TinyCapTest extends TestNGSuite with Matchers {
 
+  private var dirs: List[File] = Nil
+
   def initPipeline(map: Map[String, Any]): TinyCap = {
     new TinyCap() {
       override def configNamespace = "tinycap"
@@ -69,8 +71,10 @@ class TinyCapTest extends TestNGSuite with Matchers {
 
   @Test(dataProvider = "tinyCapOptions")
   def testTinyCap(dummy: String, sample1: Boolean): Unit = {
+    val outputDir = TinyCapTest.outputDir
+    dirs :+= outputDir
     val map = {
-      var m: Map[String, Any] = TinyCapTest.config
+      var m: Map[String, Any] = TinyCapTest.config(outputDir)
       if (sample1) m = ConfigUtils.mergeMaps(TinyCapTest.sample1, m)
       m
     }
@@ -90,35 +94,34 @@ class TinyCapTest extends TestNGSuite with Matchers {
 
   // remove temporary run directory all tests in the class have been run
   @AfterClass def removeTempOutputDir() = {
-    FileUtils.deleteDirectory(TinyCapTest.outputDir)
+    dirs.foreach(FileUtils.deleteDirectory)
   }
-
 }
 
 object TinyCapTest {
-  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.gz")
+  val r1 = new File(inputDir, "input" + File.separator + "R1.fq.gz")
   Files.touch(r1)
-  val bam = new File(outputDir, "input" + File.separator + "bamfile.bam")
+  val bam = new File(inputDir, "input" + File.separator + "bamfile.bam")
   Files.touch(bam)
 
-  val referenceFasta = new File(outputDir, "ref.fa")
+  val referenceFasta = new File(inputDir, "ref.fa")
   Files.touch(referenceFasta)
-  val referenceFastaDict = new File(outputDir, "ref.dict")
+  val referenceFastaDict = new File(inputDir, "ref.dict")
   Files.touch(referenceFastaDict)
-  val bowtieIndex = new File(outputDir, "ref.1.ebwt")
+  val bowtieIndex = new File(inputDir, "ref.1.ebwt")
   Files.touch(bowtieIndex)
 
-  val annotationGFF = new File(outputDir, "annot.gff")
-  val annotationGTF = new File(outputDir, "annot.gtf")
-  val annotationRefflat = new File(outputDir, "annot.refflat")
+  val annotationGFF = new File(inputDir, "annot.gff")
+  val annotationGTF = new File(inputDir, "annot.gtf")
+  val annotationRefflat = new File(inputDir, "annot.refflat")
   Files.touch(annotationGFF)
   Files.touch(annotationGTF)