Adding testing on number of jobs

public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala

@@ -140,8 +140,8 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
 
   /**
    * Performs the varda import and activate for one sample
-    *
-    * @param sampleID the sampleID to be used
+   *
+   * @param sampleID the sampleID to be used
    * @param inputVcf the input VCF
    * @param gVCF the gVCF for coverage
    * @param annotation: ManweDownloadAnnotateVcf object of annotated vcf
@@ -210,8 +210,8 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
 
   /**
    * Perform varda analysis
-    *
-    * @param vcf input vcf
+   *
+   * @param vcf input vcf
    * @param gVcf The gVCF to be used for coverage calculations
    * @return return vcf
    */

public/toucan/src/main/test/scala/nl/lumc/sasc/biopet/pipelines/toucan/ToucanTest.scala

@@ -4,6 +4,8 @@ import java.io.File
 import java.nio.file.Paths
 
 import com.google.common.io.Files
+import nl.lumc.sasc.biopet.extensions.VariantEffectPredictor
+import nl.lumc.sasc.biopet.extensions.tools.VcfWithVcf
 import nl.lumc.sasc.biopet.utils.config.Config
 import org.broadinstitute.gatk.queue.QSettings
 import org.scalatest.Matchers
@@ -11,8 +13,8 @@ import org.scalatest.testng.TestNGSuite
 import org.testng.annotations.Test
 
 /**
-  * Created by pjvan_thof on 4/11/16.
-  */
+ * Created by pjvan_thof on 4/11/16.
+ */
 class ToucanTest extends TestNGSuite with Matchers {
   def initPipeline(map: Map[String, Any]): Toucan = {
     new Toucan {
@@ -28,6 +30,19 @@ class ToucanTest extends TestNGSuite with Matchers {
     val pipeline = initPipeline(ToucanTest.config)
     pipeline.inputVcf = new File(ToucanTest.resourcePath("/chrQ2.vcf.gz"))
     pipeline.script()
+
+    pipeline.functions.count(_.isInstanceOf[VariantEffectPredictor]) shouldBe 1
+    pipeline.functions.count(_.isInstanceOf[VcfWithVcf]) shouldBe 0
+  }
+
+  @Test
+  def testBinning(): Unit = {
+    val pipeline = initPipeline(ToucanTest.config ++ Map("bin_size" -> 4000))
+    pipeline.inputVcf = new File(ToucanTest.resourcePath("/chrQ2.vcf.gz"))
+    pipeline.script()
+
+    pipeline.functions.count(_.isInstanceOf[VariantEffectPredictor]) shouldBe 4
+    pipeline.functions.count(_.isInstanceOf[VcfWithVcf]) shouldBe 0
   }
 
   @Test
@@ -35,6 +50,9 @@ class ToucanTest extends TestNGSuite with Matchers {
     val pipeline = initPipeline(ToucanTest.config ++ Map("gonl_vcf" -> ToucanTest.gonlVcfFile))
     pipeline.inputVcf = new File(ToucanTest.resourcePath("/chrQ2.vcf.gz"))
     pipeline.script()
+
+    pipeline.functions.count(_.isInstanceOf[VariantEffectPredictor]) shouldBe 1
+    pipeline.functions.count(_.isInstanceOf[VcfWithVcf]) shouldBe 1
   }
 
   @Test
@@ -42,6 +60,9 @@ class ToucanTest extends TestNGSuite with Matchers {
     val pipeline = initPipeline(ToucanTest.config ++ Map("exac_vcf" -> ToucanTest.exacVcfFile))
     pipeline.inputVcf = new File(ToucanTest.resourcePath("/chrQ2.vcf.gz"))
     pipeline.script()
+
+    pipeline.functions.count(_.isInstanceOf[VariantEffectPredictor]) shouldBe 1
+    pipeline.functions.count(_.isInstanceOf[VcfWithVcf]) shouldBe 1
   }
 
   @Test
@@ -51,6 +72,9 @@ class ToucanTest extends TestNGSuite with Matchers {
     pipeline.inputVcf = new File(ToucanTest.resourcePath("/chrQ2.vcf.gz"))
     pipeline.inputGvcf = Some(gvcfFile)
     pipeline.script()
+
+    pipeline.functions.count(_.isInstanceOf[VariantEffectPredictor]) shouldBe 1
+    pipeline.functions.count(_.isInstanceOf[VcfWithVcf]) shouldBe 0
   }
 
 }
@@ -68,7 +92,6 @@ object ToucanTest {
   val exacVcfFile: File = File.createTempFile("exac.", ".vcf.gz")
   exacVcfFile.deleteOnExit()
 
-
   val config = Map(
     "reference_fasta" -> resourcePath("/fake_chrQ.fa"),
     "output_dir" -> outputDir,