Fixed testing

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

@@ -45,8 +45,11 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
 
   /** Returns files to store in summary */
   def summaryFiles: Map[String, File] = {
-    Map("input_R1" -> input_R1, "output_R1" -> outputFiles("output_R1_gzip")) ++
-      (if (paired) Map("input_R2" -> input_R2.get, "output_R2" -> outputFiles("output_R2_gzip")) else Map())
+    if (!skipTrim || !skipClip)
+      Map("input_R1" -> input_R1, "output_R1" -> outputFiles("output_R1_gzip")) ++
+        (if (paired) Map("input_R2" -> input_R2.get, "output_R2" -> outputFiles("output_R2_gzip")) else Map())
+    else Map("input_R1" -> input_R1) ++
+      (if (paired) Map("input_R2" -> input_R2.get) else Map())
   }
 
   /** returns settings to store in summary */

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

@@ -84,7 +84,7 @@ class FlexiprepTest extends TestNGSuite with Matchers {
     flexiprep.functions.count(_.isInstanceOf[Cutadapt]) shouldBe (if (skipClip) 0 else if (paired) 2 else 1)
     flexiprep.functions.count(_.isInstanceOf[FastqSync]) shouldBe (if (skipClip) 0 else if (paired) 1 else 0)
     flexiprep.functions.count(_.isInstanceOf[Sickle]) shouldBe (if (skipTrim) 0 else 1)
-    flexiprep.functions.count(_.isInstanceOf[Gzip]) shouldBe (if (paired) 2 else 1)
+    flexiprep.functions.count(_.isInstanceOf[Gzip]) shouldBe (if (skipClip && skipTrim) 0 else if (paired) 2 else 1)
   }
 
   // remove temporary run directory all tests in the class have been run