Added test for no sample to flexiprep

flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

@@ -78,28 +78,33 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
     if (sampleId == null || sampleId == None) Logging.addError("Missing sample ID on flexiprep module")
     if (libId == null || libId == None) Logging.addError("Missing library ID on flexiprep module")
 
-    paired = inputR2.isDefined
+    if (inputR1 == null) Logging.addError("Missing input R1 on flexiprep module")
+    else {
+      paired = inputR2.isDefined
 
-    inputFiles :+= new InputFile(inputR1)
-    inputR2.foreach(inputFiles :+= new InputFile(_))
+      inputFiles :+= new InputFile(inputR1)
+      inputR2.foreach(inputFiles :+= new InputFile(_))
 
-    R1Name = getUncompressedFileName(inputR1)
-    inputR2.foreach { fileR2 =>
-      paired = true
-      R2Name = getUncompressedFileName(fileR2)
+      R1Name = getUncompressedFileName(inputR1)
+      inputR2.foreach { fileR2 =>
+        paired = true
+        R2Name = getUncompressedFileName(fileR2)
+      }
     }
   }
 
   /** Script to add jobs */
   def biopetScript() {
-    runInitialJobs()
+    if (inputR1 != null) {
+      runInitialJobs()
 
-    if (paired) runTrimClip(inputR1, inputR2, outputDir)
-    else runTrimClip(inputR1, outputDir)
+      if (paired) runTrimClip(inputR1, inputR2, outputDir)
+      else runTrimClip(inputR1, outputDir)
 
-    val R1Files = for ((k, v) <- outputFiles if k.endsWith("output_R1")) yield v
-    val R2Files = for ((k, v) <- outputFiles if k.endsWith("output_R2")) yield v
-    runFinalize(R1Files.toList, R2Files.toList)
+      val R1Files = for ((k, v) <- outputFiles if k.endsWith("output_R1")) yield v
+      val R2Files = for ((k, v) <- outputFiles if k.endsWith("output_R2")) yield v
+      runFinalize(R1Files.toList, R2Files.toList)
+    }
   }
 
   /** Add init non chunkable jobs */

flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala

@@ -17,14 +17,14 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
 import java.io.File
 
 import com.google.common.io.Files
-import nl.lumc.sasc.biopet.extensions.tools.{ ValidateFastq, SeqStat }
+import nl.lumc.sasc.biopet.extensions.tools.{SeqStat, ValidateFastq}
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import nl.lumc.sasc.biopet.utils.config.Config
 import org.apache.commons.io.FileUtils
 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.{AfterClass, DataProvider, Test}
 
 /**
  * Test class for [[Flexiprep]]
@@ -83,6 +83,18 @@ class FlexiprepTest extends TestNGSuite with Matchers {
 
   }
 
+  @Test
+  def testNoSample: Unit = {
+    val map = ConfigUtils.mergeMaps(Map(
+      "output_dir" -> FlexiprepTest.outputDir
+    ), Map(FlexiprepTest.executables.toSeq: _*))
+    val flexiprep: Flexiprep = initPipeline(map)
+
+    intercept[IllegalStateException] {
+      flexiprep.script()
+    }
+  }
+
   // remove temporary run directory all tests in the class have been run
   @AfterClass def removeTempOutputDir() = {
     FileUtils.deleteDirectory(FlexiprepTest.outputDir)