From c2ff92e787ad1388d9ca75be1bb4d825d6b193a7 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 27 Jun 2016 13:10:26 +0200
Subject: [PATCH] Fixed executable in test
---
.../lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala | 5 +++--
.../nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala | 3 ++-
2 files changed, 5 insertions(+), 3 deletions(-)
diff --git a/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala b/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala
index 40a2611e3..da6d7637d 100644
--- a/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala
+++ b/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala
@@ -17,11 +17,11 @@ package nl.lumc.sasc.biopet.pipelines.gears
import java.io.File
import com.google.common.io.Files
-import nl.lumc.sasc.biopet.extensions.kraken.{ Kraken, KrakenReport }
+import nl.lumc.sasc.biopet.extensions.kraken.{Kraken, KrakenReport}
import nl.lumc.sasc.biopet.extensions.picard.SamToFastq
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
import nl.lumc.sasc.biopet.extensions.tools.KrakenReportToJson
-import nl.lumc.sasc.biopet.utils.ConfigUtils
+import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
import nl.lumc.sasc.biopet.utils.config.Config
import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers
@@ -90,6 +90,7 @@ abstract class TestGearsSingle extends TestNGSuite with Matchers {
intercept[IllegalArgumentException] {
gears.script()
}
+ Logging.errors.clear()
} else {
gears.script()
diff --git a/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala b/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala
index 33b90bd8e..835d514be 100644
--- a/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala
+++ b/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala
@@ -128,7 +128,8 @@ object GearsTest {
"fastqc" -> Map("exe" -> "test"),
"seqtk" -> Map("exe" -> "test"),
"sickle" -> Map("exe" -> "test"),
- "cutadapt" -> Map("exe" -> "test")
+ "cutadapt" -> Map("exe" -> "test"),
+ "pickopenreferenceotus" -> Map("exe" -> "test")
)
val sample1 = Map(
--
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