Fixed unit tests

public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala

@@ -83,13 +83,14 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
   /** Set default output file, threads and vmem for current job */
   final def internalBeforeGraph(): Unit = {
 
-    pipesJobs.foreach(_.beforeGraph())
-    pipesJobs.foreach(_.internalBeforeGraph())
+    _pipesJobs.foreach(_.beforeGraph())
+    _pipesJobs.foreach(_.internalBeforeGraph())
 
   }
 
   /**
    * Can override this value is executable may not be converted to CanonicalPath
+   *
    * @deprecated
    */
   val executableToCanonicalPath = true
@@ -121,6 +122,7 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
 
   /**
    * This operator sends stdout to `that` and combine this into 1 command line function
+   *
    * @param that Function that will read from stdin
    * @return BiopetPipe function
    */
@@ -141,6 +143,7 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
 
   /**
    * This operator can be used to give a program a file as stdin
+   *
    * @param file File that will become stdin for this program
    * @return It's own class
    */
@@ -152,6 +155,7 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
 
   /**
    * This operator can be used to give a program a file write it's atdout
+   *
    * @param file File that will become stdout for this program
    * @return It's own class
    */
@@ -169,6 +173,7 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
 
   /**
    * This function needs to be implemented to define the command that is executed
+   *
    * @return Command to run
    */
   protected[core] def cmdLine: String
@@ -176,6 +181,7 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
   /**
    * implementing a final version of the commandLine from org.broadinstitute.gatk.queue.function.CommandLineFunction
    * User needs to implement cmdLine instead
+   *
    * @return Command to run
    */
   override final def commandLine: String = {
@@ -187,10 +193,11 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
     cmd
   }
 
-  private[core] var pipesJobs: List[BiopetCommandLineFunction] = Nil
+  private[core] var _pipesJobs: List[BiopetCommandLineFunction] = Nil
+  def pipesJobs = _pipesJobs
   def addPipeJob(job: BiopetCommandLineFunction) {
-    pipesJobs :+= job
-    pipesJobs = pipesJobs.distinct
+    _pipesJobs :+= job
+    _pipesJobs = _pipesJobs.distinct
   }
 }
 

public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetFifoPipe.scala

@@ -67,8 +67,8 @@ class BiopetFifoPipe(val root: Configurable,
     deps :::= inputs.values.toList.flatten.filter(!fifoFiles.contains(_))
     deps = deps.distinct
 
-    pipesJobs :::= commands
-    pipesJobs = pipesJobs.distinct
+    _pipesJobs :::= commands
+    _pipesJobs = _pipesJobs.distinct
   }
 
   override def beforeCmd(): Unit = {

public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala

@@ -41,7 +41,7 @@ class BiopetPipe(val commands: List[BiopetCommandLineFunction]) extends BiopetCo
     case e: Exception => Nil
   }
 
-  pipesJobs :::= commands
+  _pipesJobs :::= commands
 
   override def beforeGraph() {
     super.beforeGraph()
@@ -61,7 +61,7 @@ class BiopetPipe(val commands: List[BiopetCommandLineFunction]) extends BiopetCo
   }
 
   override def setResources(): Unit = {
-    combineResources(pipesJobs)
+    combineResources(_pipesJobs)
   }
 
   override def setupRetry(): Unit = {

public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala

@@ -18,16 +18,17 @@ package nl.lumc.sasc.biopet.pipelines.shiva
 import java.io.{ File, FileOutputStream }
 
 import com.google.common.io.Files
-import nl.lumc.sasc.biopet.utils.config.Config
+import nl.lumc.sasc.biopet.core.BiopetPipe
 import nl.lumc.sasc.biopet.extensions.Freebayes
+import nl.lumc.sasc.biopet.extensions.bcftools.{ BcftoolsCall, BcftoolsMerge }
 import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
-import nl.lumc.sasc.biopet.extensions.tools.VcfFilter
+import nl.lumc.sasc.biopet.extensions.tools.{ MpileupToVcf, VcfFilter }
 import nl.lumc.sasc.biopet.utils.ConfigUtils
-import org.apache.commons.io.FileUtils
+import nl.lumc.sasc.biopet.utils.config.Config
 import org.broadinstitute.gatk.queue.QSettings
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.{ AfterClass, DataProvider, Test }
+import org.testng.annotations.{ DataProvider, Test }
 
 import scala.collection.mutable.ListBuffer
 
@@ -88,11 +89,13 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
       pipeline.init()
       pipeline.script()
 
+      val pipesJobs = pipeline.functions.filter(_.isInstanceOf[BiopetPipe]).flatMap(_.asInstanceOf[BiopetPipe].pipesJobs)
+
       pipeline.functions.count(_.isInstanceOf[CombineVariants]) shouldBe (1 + (if (raw) 1 else 0) + (if (varscanCnsSinglesample) 1 else 0))
-      //pipeline.functions.count(_.isInstanceOf[Bcftools]) shouldBe (if (bcftools) 1 else 0)
-      //FIXME: Can not check for bcftools because of piping
-      pipeline.functions.count(_.isInstanceOf[Freebayes]) shouldBe (if (freebayes) 1 else 0)
-      //pipeline.functions.count(_.isInstanceOf[MpileupToVcf]) shouldBe (if (raw) bams else 0)
+      pipesJobs.count(_.isInstanceOf[BcftoolsCall]) shouldBe (if (bcftools) 1 else 0) + (if (bcftoolsSinglesample) bams else 0)
+      pipeline.functions.count(_.isInstanceOf[BcftoolsMerge]) shouldBe (if (bcftoolsSinglesample && bams > 1) 1 else 0)
+      pipesJobs.count(_.isInstanceOf[Freebayes]) shouldBe (if (freebayes) 1 else 0)
+      pipesJobs.count(_.isInstanceOf[MpileupToVcf]) shouldBe (if (raw) bams else 0)
       pipeline.functions.count(_.isInstanceOf[VcfFilter]) shouldBe (if (raw) bams else 0)
     }
   }