Add test for Gentrap initialization with minimum config

public/gentrap/pom.xml

@@ -44,5 +44,17 @@
             <artifactId>Mapping</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_2.11</artifactId>
+            <version>2.2.1</version>
+            <scope>test</scope>
+        </dependency>
     </dependencies>
 </project>

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

+/**
+ * Copyright (c) 2015 Leiden University Medical Center - Sequencing Analysis Support Core <sasc@lumc.nl>
+ * @author Wibowo Arindrarto <w.arindrarto@lumc.nl>
+ */
+package nl.lumc.sasc.biopet.pipelines.gentrap
+
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+import nl.lumc.sasc.biopet.core.config.Config
+
+class GentrapTest extends TestNGSuite with Matchers {
+
+  /** Method to set test config */
+  // since the pipeline Config is a global value, we first store the
+  // initial config into a value, store the supplied value, then return
+  // the initial config for restoring later
+  private def setConfig(map: Map[String, Any]): Map[String, Any] = {
+    val oldMap: Map[String, Any] = Config.global.map.toMap
+    Config.global.map = map
+    oldMap
+  }
+
+  /** Method to set the global config */
+  private def restoreConfig(initConfig: Map[String, Any]): Unit = Config.global.map = initConfig
+
+  /** Minimum config required for Gentrap */
+  private val minimumConfig = Map(
+    "output_dir" -> "/tmp",
+    "aligner" -> "gsnap",
+    "reference" -> "mock",
+    "gsnap" -> Map("db" -> "fixt_gentrap_hg19"),
+    "samples" -> Map(
+      "sample_1" -> Map(
+        "libraries" -> Map(
+          "lib_1" -> Map(
+            "R1" -> "/tmp/mock.fq"
+          )
+        )
+      )
+    )
+  )
+
+  // Test pipeline initialization with minimum config -- there should be no exceptions raised
+  @Test def testInitMinimumConfig() = {
+    val initialConfig = setConfig(minimumConfig)
+    val gentrap = new Gentrap()
+    restoreConfig(initialConfig)
+  }
+}