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Commit ea14a2ad authored by Peter van 't Hof's avatar Peter van 't Hof
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Fix test

parent df5b8d8c
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shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
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...@@ -122,7 +122,7 @@ trait ShivaVariantcallingTestTrait extends TestNGSuite with Matchers { ...@@ -122,7 +122,7 @@ trait ShivaVariantcallingTestTrait extends TestNGSuite with Matchers {
pipeline.functions.count(_.isInstanceOf[VtDecompose]) shouldBe (if (decompose) callers.size else 0) pipeline.functions.count(_.isInstanceOf[VtDecompose]) shouldBe (if (decompose) callers.size else 0)
pipeline.functions.count(_.isInstanceOf[GenotypeConcordance]) shouldBe (if (referenceVcf.isDefined) 1 + callers.size else 0) pipeline.functions.count(_.isInstanceOf[GenotypeConcordance]) shouldBe (if (referenceVcf.isDefined) 1 + callers.size else 0)
pipeline.summarySettings.get("variantcallers") shouldBe Some(callers.toList) pipeline.summarySettings.get("variantcallers").map(_.asInstanceOf[List[String]].toSet) shouldBe Some(callers.toSet)
pipeline.summarySettings.get("amplicon_bed") shouldBe Some(ampliconBedFile.map(_.getAbsolutePath)) pipeline.summarySettings.get("amplicon_bed") shouldBe Some(ampliconBedFile.map(_.getAbsolutePath))
pipeline.summarySettings.get("regions_of_interest") shouldBe Some(roiBedFiles.map(_.getAbsolutePath)) pipeline.summarySettings.get("regions_of_interest") shouldBe Some(roiBedFiles.map(_.getAbsolutePath))
} }
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