diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/RscriptCommandLineFunction.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/RscriptCommandLineFunction.scala
index c773de6155b5a771f242dbbe83a4a21f98089eaa..0e4a29378a8a4334eeed795198c117431bdee8e2 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/RscriptCommandLineFunction.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/RscriptCommandLineFunction.scala
@@ -15,13 +15,9 @@
*/
package nl.lumc.sasc.biopet.core.extensions
-import java.io.{ File, FileOutputStream }
-
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.utils.rscript.Rscript
-import scala.sys.process._
-
/**
* General rscript extension
*
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
index 02c860fdb1719c8c4635d467bea752b74745f9b2..bb6e1bf5606f21e99ceb7d557a93b68b690c0c3d 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
@@ -184,6 +184,7 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
map.toMap
}
}
+
object WriteSummary {
/** Retrive checksum from file */
def parseChecksum(checksumFile: File): String = {
diff --git a/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/ReferenceTest.scala b/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/ReferenceTest.scala
index 31b70db9d1595f2dd5614c9abe4a5fa1047ed834..79741a2c2eb73a39cce67d8ad48b5680ba939163 100644
--- a/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/ReferenceTest.scala
+++ b/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/ReferenceTest.scala
@@ -19,6 +19,7 @@ class ReferenceTest extends TestNGSuite with Matchers with MockitoSugar {
@Test
def testDefault: Unit = {
+ Logging.errors.clear()
make(config :: testReferenceNoIndex :: Nil).referenceFasta()
Logging.checkErrors(true)
diff --git a/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/SummarizableTest.scala b/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/SummarizableTest.scala
new file mode 100644
index 0000000000000000000000000000000000000000..1be487ff6d1309685d004d4b2f8f8b5523a93d75
--- /dev/null
+++ b/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/SummarizableTest.scala
@@ -0,0 +1,32 @@
+package nl.lumc.sasc.biopet.core.summary
+
+import java.io.File
+
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+/**
+ * Created by pjvanthof on 14/01/16.
+ */
+class SummarizableTest extends TestNGSuite with Matchers {
+ @Test
+ def testDefaultMerge: Unit = {
+ val summarizable = new Summarizable {
+ def summaryFiles: Map[String, File] = ???
+ def summaryStats: Any = ???
+ }
+ intercept[IllegalStateException] {
+ summarizable.resolveSummaryConflict("1", "1", "key")
+ }
+ }
+
+ def testOverrideMerge: Unit = {
+ val summarizable = new Summarizable {
+ def summaryFiles: Map[String, File] = ???
+ def summaryStats: Any = ???
+ override def resolveSummaryConflict(v1: Any, v2: Any, key: String) = v1
+ }
+ summarizable.resolveSummaryConflict("1", "1", "key") shouldBe "1"
+ }
+}
diff --git a/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScriptTest.scala b/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScriptTest.scala
new file mode 100644
index 0000000000000000000000000000000000000000..a53fe068f9537cdce91a75f45ef9393631377d0d
--- /dev/null
+++ b/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScriptTest.scala
@@ -0,0 +1,126 @@
+package nl.lumc.sasc.biopet.core.summary
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.BiopetQScript.InputFile
+import nl.lumc.sasc.biopet.core.extensions.Md5sum
+import nl.lumc.sasc.biopet.utils.config.{ Config, Configurable }
+import org.broadinstitute.gatk.queue.QScript
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+import SummaryQScriptTest._
+
+/**
+ * Created by pjvanthof on 14/01/16.
+ */
+class SummaryQScriptTest extends TestNGSuite with Matchers {
+ @Test
+ def testNoJobs: Unit = {
+ SummaryQScript.md5sumCache.clear()
+ val script = makeQscript()
+ script.addSummaryJobs()
+ SummaryQScript.md5sumCache shouldBe empty
+ }
+
+ @Test
+ def testFiles: Unit = {
+ SummaryQScript.md5sumCache.clear()
+ val file = new File(s".${File.separator}bla")
+ val script = makeQscript(files = Map("file" -> file))
+ script.addSummaryJobs()
+ SummaryQScript.md5sumCache should not be empty
+ SummaryQScript.md5sumCache.toMap shouldBe Map(
+ new File(s".${File.separator}bla") -> new File(s".${File.separator}bla.md5"))
+ script.functions.size shouldBe 2
+ assert(script.functions
+ .filter(_.isInstanceOf[Md5sum])
+ .map(_.asInstanceOf[Md5sum])
+ .exists(_.cmdLine.contains(" || ")))
+ }
+
+ @Test
+ def testDuplicateFiles: Unit = {
+ SummaryQScript.md5sumCache.clear()
+ val file = new File(s".${File.separator}bla")
+ val script = makeQscript(files = Map("file" -> file, "file2" -> file))
+ script.addSummaryJobs()
+ SummaryQScript.md5sumCache should not be empty
+ SummaryQScript.md5sumCache.toMap shouldBe Map(
+ new File(s".${File.separator}bla") -> new File(s".${File.separator}bla.md5"))
+ script.functions.size shouldBe 2
+ assert(script.functions
+ .filter(_.isInstanceOf[Md5sum])
+ .map(_.asInstanceOf[Md5sum])
+ .exists(_.cmdLine.contains(" || ")))
+ }
+
+ @Test
+ def testAddSummarizable: Unit = {
+ SummaryQScript.md5sumCache.clear()
+ val file = new File(s".${File.separator}bla")
+ val script = makeQscript()
+ script.addSummarizable(makeSummarizable(files = Map("file" -> file, "file2" -> file)), "test")
+ script.summarizables.size shouldBe 1
+ script.addSummaryJobs()
+ SummaryQScript.md5sumCache should not be empty
+ SummaryQScript.md5sumCache.toMap shouldBe Map(
+ new File(s".${File.separator}bla") -> new File(s".${File.separator}bla.md5"))
+ script.functions.size shouldBe 2
+ assert(script.functions
+ .filter(_.isInstanceOf[Md5sum])
+ .map(_.asInstanceOf[Md5sum])
+ .exists(_.cmdLine.contains(" || ")))
+ }
+
+ @Test
+ def testInputFile: Unit = {
+ SummaryQScript.md5sumCache.clear()
+ val file = new File(s".${File.separator}bla")
+ val script = makeQscript()
+ script.addSummarizable(makeSummarizable(files = Map("file" -> file, "file2" -> file)), "test")
+ script.summarizables.size shouldBe 1
+ script.inputFiles :+= InputFile(file, Some("md5sum"))
+ script.inputFiles :+= InputFile(file, None)
+ script.addSummaryJobs()
+ SummaryQScript.md5sumCache should not be empty
+ SummaryQScript.md5sumCache.toMap shouldBe Map(
+ new File(s".${File.separator}bla") -> new File(s".${File.separator}bla.md5"))
+ script.functions.size shouldBe 3
+ assert(script.functions
+ .filter(_.isInstanceOf[Md5sum])
+ .map(_.asInstanceOf[Md5sum])
+ .exists(_.cmdLine.contains(" || ")))
+ }
+
+ @Test
+ def testAddQscript: Unit = {
+ SummaryQScript.md5sumCache.clear()
+ val script = makeQscript()
+ script.addSummaryQScript(script)
+ script.summaryQScripts.head shouldBe script
+ }
+}
+
+object SummaryQScriptTest {
+ def makeQscript(settings: Map[String, Any] = Map(),
+ files: Map[String, File] = Map(),
+ c: Map[String, Any] = Map()) =
+ new SummaryQScript with QScript {
+ outputDir = new File(".")
+ override def globalConfig = new Config(c)
+ def summarySettings: Map[String, Any] = settings
+ def summaryFiles: Map[String, File] = files
+ val tempFile = File.createTempFile("summary", ".json")
+ tempFile.deleteOnExit()
+ def summaryFile: File = tempFile
+ def init(): Unit = ???
+ def biopetScript(): Unit = ???
+ def root: Configurable = null
+ }
+
+ def makeSummarizable(files: Map[String, File] = Map(), stats: Map[String, Any] = Map()) = new Summarizable {
+ def summaryFiles: Map[String, File] = files
+ def summaryStats: Any = stats
+ }
+}
\ No newline at end of file
diff --git a/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala b/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala
new file mode 100644
index 0000000000000000000000000000000000000000..4bb196c162ddb93c85b19d1364d34789fb77e8b9
--- /dev/null
+++ b/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala
@@ -0,0 +1,346 @@
+package nl.lumc.sasc.biopet.core.summary
+
+import java.io.{ PrintWriter, File }
+
+import com.google.common.io.Files
+import nl.lumc.sasc.biopet.core._
+import nl.lumc.sasc.biopet.utils.config.{ Config, Configurable }
+import nl.lumc.sasc.biopet.utils.summary.Summary
+import org.broadinstitute.gatk.queue.function.CommandLineFunction
+import org.broadinstitute.gatk.queue.{ QScript, QSettings }
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import WriteSummaryTest._
+import org.testng.annotations.Test
+
+import scala.util.matching.Regex
+
+/**
+ * Created by pjvanthof on 15/01/16.
+ */
+class WriteSummaryTest extends TestNGSuite with Matchers {
+
+ @Test
+ def testWrongRoot(): Unit = {
+ intercept[IllegalArgumentException] {
+ makeWriter(null)
+ }
+ }
+
+ /** This is a basic summary test, no matter the content this should always be true */
+ def basicSummaryTest(summary: Summary,
+ name: String,
+ sampleId: Option[String] = None,
+ libId: Option[String] = None): Unit = {
+ summary.getValue(sampleId, libId, name) should not be None
+ summary.getValue(sampleId, libId, name, "files", "pipeline").get shouldBe a[Map[_, _]]
+ summary.getValue(sampleId, libId, name, "settings").get shouldBe a[Map[_, _]]
+ summary.getValue(sampleId, libId, name, "executables").get shouldBe a[Map[_, _]]
+
+ summary.getValue("meta") should not be None
+ summary.getValue("meta", "pipeline_name") shouldBe Some(name)
+ summary.getValue("meta", "last_commit_hash") shouldBe Some(nl.lumc.sasc.biopet.LastCommitHash)
+ summary.getValue("meta", "pipeline_version") shouldBe Some(nl.lumc.sasc.biopet.Version)
+ summary.getValue("meta", "output_dir") shouldBe Some(new File(".").getAbsolutePath)
+ summary.getValue("meta", "summary_creation") should not be None
+ }
+
+ def createFakeCheckSum(file: File): Unit = {
+ file.getParentFile.mkdirs()
+ val writer = new PrintWriter(file)
+ writer.println("checksum file")
+ writer.close()
+ file.deleteOnExit()
+ }
+
+ @Test
+ def testEmpty(): Unit = {
+ val qscript = makeQscript(name = "test")
+ val writer = makeWriter(qscript)
+ writer.freezeFieldValues()
+ writer.deps shouldBe empty
+ writer.run()
+
+ val summary = new Summary(writer.out)
+ basicSummaryTest(summary, "test")
+ }
+
+ @Test
+ def testMergeQscript(): Unit = {
+ val qscript = makeQscript(name = "test")
+ val qscript2 = makeQscript(name = "test2")
+ qscript.addSummaryQScript(qscript2)
+ val summaryWriter = new PrintWriter(qscript2.summaryFile)
+ summaryWriter.println("""{ "test2": "value" }""")
+ summaryWriter.close()
+ val writer = makeWriter(qscript)
+ writer.freezeFieldValues()
+ writer.run()
+
+ val summary = new Summary(writer.out)
+ basicSummaryTest(summary, "test")
+ summary.getValue("test2") shouldBe Some("value")
+ }
+
+ @Test
+ def testSingleJob(): Unit = {
+ val qscript = makeQscript("test")
+ val writer = makeWriter(qscript)
+ val summarizable = makeSummarizable(files = Map("file_1" -> new File("bla")), stats = Map("key" -> "value"))
+ qscript.addSummarizable(summarizable, "tool_1")
+ qscript.addSummaryJobs()
+ createFakeCheckSum(SummaryQScript.md5sumCache(new File("bla")))
+ writer.freezeFieldValues()
+ writer.run()
+
+ val summary = new Summary(writer.out)
+ basicSummaryTest(summary, "test")
+ summary.getValue("test", "stats", "tool_1", "key") shouldBe Some("value")
+ summary.getValue("test", "files", "tool_1", "file_1", "md5") shouldBe Some("checksum")
+ }
+
+ @Test
+ def testSingleJavaJob(): Unit = {
+ val qscript = makeQscript("test")
+ val writer = makeWriter(qscript)
+ val summarizable = makeJavaCommand(files = Map("file_1" -> new File("bla")), stats = Map("key" -> "value"))
+ qscript.add(summarizable)
+ qscript.addSummarizable(summarizable, "tool_1")
+ qscript.addSummaryJobs()
+ createFakeCheckSum(SummaryQScript.md5sumCache(new File("bla")))
+ writer.freezeFieldValues()
+ writer.run()
+
+ val summary = new Summary(writer.out)
+ basicSummaryTest(summary, "test")
+ summary.getValue("test", "stats", "tool_1", "key") shouldBe Some("value")
+ summary.getValue("test", "files", "tool_1", "file_1", "md5") shouldBe Some("checksum")
+ summary.getValue("test", "executables", "java_command", "version") shouldBe Some("test version")
+ }
+
+ @Test
+ def testVersion(): Unit = {
+ val qscript = makeQscript("test")
+ val writer = makeWriter(qscript)
+ val summarizable = makeVersionSummarizable(files = Map("file_1" -> new File("bla")), stats = Map("key" -> "value"))
+ qscript.add(summarizable)
+ qscript.addSummarizable(summarizable, "tool_1")
+ qscript.addSummaryJobs()
+ createFakeCheckSum(SummaryQScript.md5sumCache(new File("bla")))
+ writer.freezeFieldValues()
+ writer.run()
+
+ val summary = new Summary(writer.out)
+ basicSummaryTest(summary, "test")
+ summary.getValue("test", "stats", "tool_1", "key") shouldBe Some("value")
+ summary.getValue("test", "files", "tool_1", "file_1", "md5") shouldBe Some("checksum")
+ summary.getValue("test", "executables", "version_command", "version") shouldBe Some("test version")
+ }
+
+ @Test
+ def testSampleLibrary(): Unit = {
+ val qscript = makeSampleLibraryQscript("test", s = Some("sampleName"), l = Some("libName"))
+ val writer = makeWriter(qscript)
+ val summarizable = makeSummarizable(files = Map("file_1" -> new File("bla")), stats = Map("key" -> "value"))
+ qscript.addSummarizable(summarizable, "tool_1")
+ qscript.addSummaryJobs()
+ createFakeCheckSum(SummaryQScript.md5sumCache(new File("bla")))
+ writer.freezeFieldValues()
+ writer.deps shouldBe empty
+ writer.run()
+
+ val summary = new Summary(writer.out)
+ basicSummaryTest(summary, "test", sampleId = Some("sampleName"), libId = Some("libName"))
+ summary.getValue(Some("sampleName"), Some("libName"), "test", "stats", "tool_1", "key") shouldBe Some("value")
+ summary.getValue(Some("sampleName"), Some("libName"), "test", "files", "tool_1", "file_1", "md5") shouldBe Some("checksum")
+ }
+
+ @Test
+ def testSample(): Unit = {
+ val qscript = makeSampleLibraryQscript("test", s = Some("sampleName"))
+ val writer = makeWriter(qscript)
+ val summarizable = makeSummarizable(files = Map("file_1" -> new File("bla")), stats = Map("key" -> "value"))
+ qscript.addSummarizable(summarizable, "tool_1")
+ qscript.addSummaryJobs()
+ createFakeCheckSum(SummaryQScript.md5sumCache(new File("bla")))
+ writer.freezeFieldValues()
+ writer.deps shouldBe empty
+ writer.run()
+
+ val summary = new Summary(writer.out)
+ basicSummaryTest(summary, "test", sampleId = Some("sampleName"), libId = None)
+ summary.getValue(Some("sampleName"), None, "test", "stats", "tool_1", "key") shouldBe Some("value")
+ summary.getValue(Some("sampleName"), None, "test", "files", "tool_1", "file_1", "md5") shouldBe Some("checksum")
+ }
+
+ @Test
+ def testMultisampleQscript(): Unit = {
+ val qscript = makeMultisampleQscript("test", multisampleConfig)
+ val writer = makeWriter(qscript)
+ val summarizable = makeSummarizable(files = Map("file_1" -> new File("bla")), stats = Map("key" -> "value"))
+ qscript.addSummarizable(summarizable, "tool_1")
+ qscript.addSummaryJobs()
+ createFakeCheckSum(SummaryQScript.md5sumCache(new File("bla")))
+ writer.freezeFieldValues()
+ writer.deps shouldBe empty
+ writer.run()
+
+ val summary = new Summary(writer.out)
+ basicSummaryTest(summary, "test")
+ summary.getValue("test", "stats", "tool_1", "key") shouldBe Some("value")
+ summary.getValue("test", "files", "tool_1", "file_1", "md5") shouldBe Some("checksum")
+
+ summary.getValue(Some("sampleName"), Some("libName"), "test") should not be None
+ }
+
+}
+
+object WriteSummaryTest {
+ def makeWriter(root: Configurable, c: Map[String, Any] = Map()) = new WriteSummary(root) {
+ override def globalConfig = new Config(c)
+ override def outputs = Seq()
+ override def inputs = Seq()
+ qSettings = new QSettings {
+ jobName = "test"
+ jobTempDir = Files.createTempDir()
+ jobTempDir.deleteOnExit()
+ jobPriority = Some(1)
+ }
+ override def absoluteCommandDirectory() {}
+ }
+
+ def makeQscript(name: String,
+ settings: Map[String, Any] = Map(),
+ files: Map[String, File] = Map(),
+ c: Map[String, Any] = Map()) =
+ new SummaryQScript with QScript {
+ summaryName = name
+ outputDir = new File(".").getAbsoluteFile
+ override def globalConfig = new Config(c)
+ def summarySettings: Map[String, Any] = settings
+ def summaryFiles: Map[String, File] = files
+ val tempFile = File.createTempFile("summary", ".json")
+ tempFile.deleteOnExit()
+ def summaryFile: File = tempFile
+ def init(): Unit = {}
+ def biopetScript(): Unit = {}
+ def root: Configurable = null
+ }
+
+ def makeSampleLibraryQscript(name: String,
+ settings: Map[String, Any] = Map(),
+ files: Map[String, File] = Map(),
+ c: Map[String, Any] = Map(),
+ s: Option[String] = None,
+ l: Option[String] = None) =
+ new SummaryQScript with QScript with SampleLibraryTag {
+ sampleId = s
+ libId = l
+ summaryName = "test"
+ outputDir = new File(".").getAbsoluteFile
+ override def globalConfig = new Config(c)
+ def summarySettings: Map[String, Any] = settings
+ def summaryFiles: Map[String, File] = files
+ val tempFile = File.createTempFile("summary", ".json")
+ tempFile.deleteOnExit()
+ def summaryFile: File = tempFile
+ def init(): Unit = {}
+ def biopetScript(): Unit = {}
+ def root: Configurable = null
+ }
+
+ def makeMultisampleQscript(name: String,
+ c: Map[String, Any],
+ settings: Map[String, Any] = Map(),
+ files: Map[String, File] = Map()) =
+ new MultiSampleQScript with QScript {
+ summaryName = "test"
+ outputDir = new File(".").getAbsoluteFile
+ override def globalConfig = new Config(c)
+ def summarySettings: Map[String, Any] = settings
+ def summaryFiles: Map[String, File] = files
+ val tempFile = File.createTempFile("summary", ".json")
+ tempFile.deleteOnExit()
+ def summaryFile: File = tempFile
+ def init(): Unit = {}
+ def biopetScript(): Unit = {}
+ def root: Configurable = null
+
+ class Sample(id: String) extends AbstractSample(id) {
+ class Library(id: String) extends AbstractLibrary(id) {
+ protected def addJobs(): Unit = {}
+ def summaryFiles: Map[String, File] = files
+ def summaryStats: Any = Map()
+ }
+
+ def makeLibrary(id: String): Library = new Library(id)
+ protected def addJobs(): Unit = {}
+ def summaryFiles: Map[String, File] = files
+ def summaryStats: Any = Map()
+ }
+
+ def makeSample(id: String): Sample = new Sample(id)
+
+ def addMultiSampleJobs(): Unit = {}
+ }
+
+ val multisampleConfig = Map("samples" -> Map("sampleName" -> Map("libraries" -> Map("libName" -> Map()))))
+
+ def makeSummarizable(files: Map[String, File] = Map(), stats: Map[String, Any] = Map()) = new Summarizable {
+ def summaryFiles: Map[String, File] = files
+ def summaryStats: Any = stats
+ }
+
+ def makeJavaCommand(files: Map[String, File] = Map(),
+ stats: Map[String, Any] = Map(),
+ c: Map[String, Any] = Map()) = new BiopetJavaCommandLineFunction with Summarizable with Version {
+ override def globalConfig = new Config(c)
+ override def configName = "java_command"
+ def root: Configurable = null
+ def summaryStats: Map[String, Any] = stats
+ def summaryFiles: Map[String, File] = files
+
+ def versionCommand: String = "echo test version"
+ def versionRegex: Regex = """(.*)""".r
+ override def getVersion = Some("test version")
+
+ override def outputs = Seq()
+ override def inputs = Seq()
+ qSettings = new QSettings {
+ jobName = "test"
+ jobTempDir = Files.createTempDir()
+ jobTempDir.deleteOnExit()
+ jobPriority = Some(1)
+ }
+ override def absoluteCommandDirectory() {}
+ }
+
+ def makeVersionSummarizable(files: Map[String, File] = Map(),
+ stats: Map[String, Any] = Map(),
+ c: Map[String, Any] = Map()) =
+ new CommandLineFunction with Configurable with Summarizable with Version {
+ override def globalConfig = new Config(c)
+ override def configName = "version_command"
+ def root: Configurable = null
+
+ def summaryFiles: Map[String, File] = files
+ def summaryStats: Any = stats
+
+ def versionCommand: String = "echo test version"
+ def versionRegex: Regex = """(.*)""".r
+ override def getVersion = Some("test version")
+
+ def commandLine: String = ""
+
+ override def outputs = Seq()
+ override def inputs = Seq()
+ qSettings = new QSettings {
+ jobName = "test"
+ jobTempDir = Files.createTempDir()
+ jobTempDir.deleteOnExit()
+ jobPriority = Some(1)
+ }
+ override def absoluteCommandDirectory() {}
+ }
+
+}
\ No newline at end of file
diff --git a/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/Logging.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/Logging.scala
index d01755e07300cf09f874bc36f07d640d6567c84e..9d4b9dc2bf84bcda084ce5de9647620e1a130658 100644
--- a/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/Logging.scala
+++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/Logging.scala
@@ -36,7 +36,7 @@ trait Logging {
object Logging {
val logger = Logger.getRootLogger
- private val errors: ListBuffer[Exception] = ListBuffer()
+ private[biopet] val errors: ListBuffer[Exception] = ListBuffer()
def addError(error: String, debug: String = null): Unit = {
val msg = error + (if (debug != null && logger.isDebugEnabled) "; " + debug else "")