From afe2bbcb91a01eff25a46c1801320d1c11e24c7c Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Fri, 24 Jun 2016 15:46:43 +0200
Subject: [PATCH] Set defaults
---
.../nl/lumc/sasc/biopet/extensions/tools/WipeReads.scala | 6 +++---
.../nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala | 4 ++++
.../lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala | 9 +++++----
3 files changed, 12 insertions(+), 7 deletions(-)
diff --git a/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/WipeReads.scala b/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/WipeReads.scala
index cc6cd023b..81012df74 100644
--- a/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/WipeReads.scala
+++ b/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")
diff --git a/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala b/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
index 349b56df9..ed2eb5aff 100644
--- a/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
+++ b/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
)
)
diff --git a/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala b/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
index fd6ad7736..9b834708d 100644
--- a/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
+++ b/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(
--
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