diff --git a/public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala b/public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala index f417bfadd6047fb51a40b323283caf0619acc105..9091635548b5a9124409ce61b80868ba5a5c2a08 100644 --- a/public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala +++ b/public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala @@ -18,10 +18,10 @@ 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.sambamba.SambambaView -import nl.lumc.sasc.biopet.extensions.tools.{ FastqSync, KrakenReportToJson } +import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView +import nl.lumc.sasc.biopet.extensions.tools.{FastqSync, KrakenReportToJson} import nl.lumc.sasc.biopet.utils.ConfigUtils import nl.lumc.sasc.biopet.utils.config.Config import org.apache.commons.io.FileUtils @@ -97,7 +97,8 @@ class GearsPipelineTest(val testset: String) extends TestNGSuite with Matchers { // SamToFastq should have started if it was started from bam gears.functions.count(_.isInstanceOf[SamToFastq]) shouldBe (if (fromBam) 1 else 0) - gears.functions.count(_.isInstanceOf[SambambaView]) shouldBe (if (fromBam) 1 else 0) + // gears.functions.count(_.isInstanceOf[SambambaView]) shouldBe (if (fromBam) 1 else 0) + gears.functions.count(_.isInstanceOf[SamtoolsView]) shouldBe (if (fromBam) 1 else 0) gears.functions.count(_.isInstanceOf[FastqSync]) shouldBe (if (fromBam) 1 else 0) gears.functions.count(_.isInstanceOf[Kraken]) shouldBe 1