Set defaults

biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/WipeReads.scala

@@ -42,10 +42,10 @@ class WipeReads(val root: Configurable) extends ToolCommandFunction {
   var readgroup: Set[String] = config("read_group", default = Nil)
 
   @Argument(doc = "Whether to remove multiple-mapped reads outside the target regions (default: yes)")
-  var limitRemoval: Boolean = config("limit_removal")
+  var limitRemoval: Boolean = config("limit_removal", default=true)
 
-  @Argument(doc = "Whether to index output BAM file or not (default: yes)")
-  var noMakeIndex: Boolean = config("no_make_index")
+  @Argument(doc = "Whether to index output BAM file or not")
+  var noMakeIndex: Boolean = config("no_make_index", default=false)
 
   @Argument(doc = "GTF feature containing intervals (default: exon)")
   var featureType: Option[String] = config("feature_type")

gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala

@@ -119,6 +119,10 @@ class Gentrap(val root: Configurable) extends QScript
     "mapping" -> Map(
       "aligner" -> "gsnap",
       "skip_markduplicates" -> true
+    ),
+    "wipereads" -> Map(
+      "limit_removal" -> true,
+      "no_make_index" -> false
     )
   )
 

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

@@ -14,20 +14,20 @@
  */
 package nl.lumc.sasc.biopet.pipelines.gentrap
 
-import java.io.{File, FileOutputStream}
+import java.io.{ File, FileOutputStream }
 
 import com.google.common.io.Files
-import nl.lumc.sasc.biopet.core.{BiopetFifoPipe, BiopetPipe}
+import nl.lumc.sasc.biopet.core.{ BiopetFifoPipe, BiopetPipe }
 import nl.lumc.sasc.biopet.extensions._
 import nl.lumc.sasc.biopet.extensions.gmap.Gsnap
 import nl.lumc.sasc.biopet.extensions.hisat.Hisat2
-import nl.lumc.sasc.biopet.extensions.tools.{BaseCounter, WipeReads}
+import nl.lumc.sasc.biopet.extensions.tools.{ BaseCounter, WipeReads }
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import nl.lumc.sasc.biopet.utils.config.Config
 import org.broadinstitute.gatk.queue.QSettings
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.{DataProvider, Test}
+import org.testng.annotations.{ DataProvider, Test }
 
 abstract class GentrapTestAbstract(val expressionMeasure: String, val aligner: Option[String]) extends TestNGSuite with Matchers {
 
@@ -192,6 +192,7 @@ object GentrapTest {
     "annotation_gtf" -> (outputDir + File.separator + "ref.fa"),
     "annotation_bed" -> (outputDir + File.separator + "ref.fa"),
     "annotation_refflat" -> (outputDir + File.separator + "ref.fa"),
+    "ribosome_refflat" -> (outputDir + File.separator + "ref.fa"),
     "varscan_jar" -> "test",
     "rscript" -> Map("exe" -> "test")
   ) ++ Seq(