Commit 11fe02b4 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

change pipeline test, not test on sambambaview, but on samtoolsview

parent 755b864d
......@@ -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
......
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