Added test for bam arg

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala

@@ -33,7 +33,7 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
   def this() = this(null)
 
   @Input(doc = "Bam files (should be deduped bams)", shortName = "BAM", required = true)
-  protected var inputBamsArg: List[File] = Nil
+  protected[shiva] var inputBamsArg: List[File] = Nil
 
   var inputBams: Map[String, File] = Map()
 

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

@@ -16,6 +16,7 @@
 package nl.lumc.sasc.biopet.pipelines.shiva
 
 import java.io.{ File, FileOutputStream }
+import java.nio.file.Paths
 
 import com.google.common.io.Files
 import nl.lumc.sasc.biopet.extensions.breakdancer.{ BreakdancerVCF, BreakdancerConfig, BreakdancerCaller }
@@ -149,6 +150,25 @@ class ShivaSvCallingTest extends TestNGSuite with Matchers {
     }
   }
 
+  private def resourcePath(p: String): String = {
+    Paths.get(getClass.getResource(p).toURI).toString
+  }
+
+  @Test
+  def testInputBamsArg(): Unit = {
+    val pipeline = initPipeline(Map())
+
+    pipeline.inputBamsArg :+= new File(resourcePath("/paired01.bam"))
+
+    pipeline.init()
+    pipeline.script()
+
+    val summaryCallers = pipeline.summarySettings("sv_callers")
+    assert(summaryCallers.contains("delly"))
+    assert(summaryCallers.contains("clever"))
+    assert(summaryCallers.contains("breakdancer"))
+  }
+
   @AfterClass def removeTempOutputDir() = {
     FileUtils.deleteDirectory(ShivaSvCallingTest.outputDir)
   }