Fixing null pointer

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

@@ -123,7 +123,11 @@ class QcCommand(val parent: Configurable, val fastqc: Fastqc, val read: String)
           Some(cutadapt)
         } else None
       case (None, _) => None
-      case (c, _)    => c
+      case (Some(c), _)    =>
+        c.fastqInput = seqtk.output
+        c.fastqOutput = new File(output.getParentFile, input.getName + ".cutadapt.fq")
+        c.statsOutput = new File(flexiprep.outputDir, s"${flexiprep.sampleId.getOrElse("x")}-${flexiprep.libId.getOrElse("x")}.$read.clip.stats")
+        Some(c)
     }
 
     trim.foreach { t =>

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

@@ -62,8 +62,11 @@ class FlexiprepTest extends TestNGSuite with Matchers {
   private var dirs: List[File] = Nil
 
   @Test(dataProvider = "flexiprepOptions")
-  def testFlexiprep(f: String, paired: Boolean, skipTrim: Boolean, skipClip: Boolean,
-                    zipped: Boolean, abortOnCorruptFastq: Boolean) = {
+  def testFlexiprep(f: String, paired: Boolean,
+                    skipTrim: Boolean,
+                    skipClip: Boolean,
+                    zipped: Boolean,
+                    abortOnCorruptFastq: Boolean) = {
     val outputDir = FlexiprepTest.outputDir
     dirs :+= outputDir
     val map = ConfigUtils.mergeMaps(Map("output_dir" -> outputDir,