Commit c2ff92e7 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed executable in test

parent ab10d3b9
......@@ -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()
......
......@@ -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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