Commit afe2bbcb authored by Wai Yi Leung's avatar Wai Yi Leung

Set defaults

parent d475e1dc
......@@ -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")
......
......@@ -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
)
)
......
......@@ -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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