Clean up the possible run modes

gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala

@@ -71,10 +71,6 @@ abstract class GentrapTestAbstract(val expressionMeasure: String, val aligner: O
       .toMap
     )
 
-  val validExpressionMeasures = Set(
-    "fragments_per_gene", "fragments_per_exon", "base_counts",
-    "cufflinks_strict", "cufflinks_guided", "cufflinks_blind")
-
   @DataProvider(name = "expMeasuresstrandProtocol")
   def expMeasuresStrandProtocolProvider = {
 
@@ -89,27 +85,23 @@ abstract class GentrapTestAbstract(val expressionMeasure: String, val aligner: O
     } yield makeSamplesConfig(sampleNum, libNum, libType)
 
     val strandProtocols = Array("non_specific", "dutp")
-    // get all possible combinations of expression measures
-    val expressionMeasures = validExpressionMeasures
-      //.subsets
-      //.map(_.toList)
-      .toArray
 
     for {
       sampleConfig <- sampleConfigs.toArray
-      //expressionMeasure <- expressionMeasures
       strandProtocol <- strandProtocols
-    } yield Array(sampleConfig, List(expressionMeasure), strandProtocol)
+      removeRiboReads <- Array(true, false)
+    } yield Array(sampleConfig, List(expressionMeasure), strandProtocol, removeRiboReads)
   }
 
   @Test(dataProvider = "expMeasuresstrandProtocol")
-  def testGentrap(sampleConfig: SamplesConfig, expMeasures: List[String], strandProtocol: String) = {
+  def testGentrap(sampleConfig: SamplesConfig, expMeasures: List[String], strandProtocol: String, removeRiboReads: Boolean) = {
 
     val settings = Map(
       "output_dir" -> GentrapTest.outputDir,
       "gsnap" -> Map("db" -> "test", "dir" -> "test"),
       "expression_measures" -> expMeasures,
-      "strand_protocol" -> strandProtocol
+      "strand_protocol" -> strandProtocol,
+      "remove_ribosomal_reads" -> removeRiboReads
     ) ++ aligner.map("aligner" -> _)
     val config = ConfigUtils.mergeMaps(settings ++ sampleConfig, Map(GentrapTest.executables.toSeq: _*))
     val gentrap: Gentrap = initPipeline(config)