Commit 768f5596 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed tests

parent 2bfef3ed
......@@ -74,9 +74,9 @@ class GearsSingleTest extends TestNGSuite with Matchers {
seqCount: Boolean) = {
val map = ConfigUtils.mergeMaps(Map(
"gears_use_kraken" -> kraken,
"gear_use_qiime_rtax" -> qiimeRtax,
"gear_use_qiime_closed" -> qiimeClosed,
"gear_use_seq_count" -> seqCount,
"gears_use_qiime_rtax" -> qiimeRtax,
"gears_use_qiime_closed" -> qiimeClosed,
"gears_use_seq_count" -> seqCount,
"output_dir" -> GearsSingleTest.outputDir
), Map(GearsSingleTest.executables.toSeq: _*))
......@@ -100,6 +100,11 @@ class GearsSingleTest extends TestNGSuite with Matchers {
gears.outputName shouldBe (if (fromBam) "bamfile" else "R1")
}
gears.krakenScript.isDefined shouldBe kraken
gears.qiimeClosed.isDefined shouldBe qiimeClosed
gears.qiimeRatx.isDefined shouldBe qiimeRtax
gears.seqCount.isDefined shouldBe seqCount
// SamToFastq should have started if it was started from bam
gears.functions.count(_.isInstanceOf[SamtoolsView]) shouldBe (if (fromBam) 1 else 0)
gears.functions.count(_.isInstanceOf[SamToFastq]) shouldBe (if (fromBam) 1 else 0)
......
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