Merge branch 'patch-pipelines_test' into 'develop'

Patch pipelines test

This is a patch for the newly added pipeline tests to ensure that each pipeline test has a unique directory that is removed after the test. The curren behaviour is to use a named directory in the user's tmp directory, that may fail if a directory with that name already exist.

@p.j.van_t_hof , this is what we discussed earlier.

See merge request !96

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

@@ -2,15 +2,18 @@ package nl.lumc.sasc.biopet.pipelines.carp
 
 import java.io.File
 
+import com.google.common.io.Files
+import org.apache.commons.io.FileUtils
+import org.broadinstitute.gatk.queue.QSettings
+import org.testng.annotations.{ AfterClass, Test, DataProvider }
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+
 import nl.lumc.sasc.biopet.core.config.Config
 import nl.lumc.sasc.biopet.extensions.bwa.BwaMem
 import nl.lumc.sasc.biopet.extensions.macs2.Macs2CallPeak
 import nl.lumc.sasc.biopet.extensions.picard.{ MergeSamFiles, SortSam }
 import nl.lumc.sasc.biopet.utils.ConfigUtils
-import org.broadinstitute.gatk.queue.QSettings
-import org.testng.annotations.{ Test, DataProvider }
-import org.scalatest.Matchers
-import org.scalatest.testng.TestNGSuite
 
 /**
  * Created by pjvan_thof on 2/13/15.
@@ -69,10 +72,15 @@ class CarpTest extends TestNGSuite with Matchers {
       carp.functions.count(_.isInstanceOf[Macs2CallPeak]) shouldBe (numberSamples + (if (threatment) 1 else 0))
     }
   }
+
+  // remove temporary run directory all tests in the class have been run
+  @AfterClass def removeTempOutputDir() = {
+    FileUtils.deleteDirectory(CarpTest.outputDir)
+  }
 }
 
 object CarpTest {
-  val outputDir = System.getProperty("java.io.tmpdir") + File.separator + "flexiprep"
+  val outputDir = Files.createTempDir()
 
   val excutables = Map(
     "reference" -> "test",

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

@@ -2,15 +2,17 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
 
 import java.io.File
 
+import com.google.common.io.Files
+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.{ AfterClass, DataProvider, Test }
+
 import nl.lumc.sasc.biopet.core.config.Config
 import nl.lumc.sasc.biopet.extensions.{ Gzip, Zcat }
 import nl.lumc.sasc.biopet.tools.FastqSync
 import nl.lumc.sasc.biopet.utils.ConfigUtils
-import org.broadinstitute.gatk.queue.QSettings
-import org.broadinstitute.gatk.queue.function.QFunction
-import org.scalatest.Matchers
-import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.{ DataProvider, Test }
 
 /**
  * Created by pjvan_thof on 2/11/15.
@@ -67,9 +69,15 @@ class FlexiprepTest extends TestNGSuite with Matchers {
     flexiprep.functions.count(_.isInstanceOf[Sickle]) shouldBe (if (skipTrim) 0 else 1)
     flexiprep.functions.count(_.isInstanceOf[Gzip]) shouldBe (if (paired) 2 else 1)
   }
+
+  // remove temporary run directory all tests in the class have been run
+  @AfterClass def removeTempOutputDir() = {
+    FileUtils.deleteDirectory(FlexiprepTest.outputDir)
+  }
 }
+
 object FlexiprepTest {
-  val outputDir = System.getProperty("java.io.tmpdir") + File.separator + "flexiprep"
+  val outputDir = Files.createTempDir()
 
   val excutables = Map(
     "seqstat" -> Map("exe" -> "test"),

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

@@ -2,6 +2,13 @@ package nl.lumc.sasc.biopet.pipelines.mapping
 
 import java.io.File
 
+import com.google.common.io.Files
+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.{ AfterClass, DataProvider, Test }
+
 import nl.lumc.sasc.biopet.core.config.Config
 import nl.lumc.sasc.biopet.extensions.bwa.{ BwaSamse, BwaSampe, BwaAln, BwaMem }
 import nl.lumc.sasc.biopet.extensions.picard.{ MergeSamFiles, AddOrReplaceReadGroups, MarkDuplicates, SortSam }
@@ -12,10 +19,6 @@ import nl.lumc.sasc.biopet.pipelines.flexiprep.Sickle
 import nl.lumc.sasc.biopet.pipelines.flexiprep._
 import nl.lumc.sasc.biopet.tools.FastqSync
 import nl.lumc.sasc.biopet.utils.ConfigUtils
-import org.broadinstitute.gatk.queue.QSettings
-import org.scalatest.Matchers
-import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.{ DataProvider, Test }
 
 /**
  * Created by pjvan_thof on 2/12/15.
@@ -94,10 +97,15 @@ class MappingTest extends TestNGSuite with Matchers {
     mapping.functions.count(_.isInstanceOf[MergeSamFiles]) shouldBe (if (skipMarkDuplicate && chunks > 1) 1 else 0)
     mapping.functions.count(_.isInstanceOf[MarkDuplicates]) shouldBe (if (skipMarkDuplicate) 0 else 1)
   }
+
+  // remove temporary run directory all tests in the class have been run
+  @AfterClass def removeTempOutputDir() = {
+    FileUtils.deleteDirectory(MappingTest.outputDir)
+  }
 }
 
 object MappingTest {
-  val outputDir = System.getProperty("java.io.tmpdir") + File.separator + "flexiprep"
+  val outputDir = Files.createTempDir()
 
   val excutables = Map(
     "reference" -> "test",