Commit 53c59c03 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added amplicon test

parent fc3c33c0
......@@ -121,6 +121,10 @@ trait ShivaVariantcallingTestTrait extends TestNGSuite with Matchers {
pipeline.functions.count(_.isInstanceOf[VtNormalize]) shouldBe (if (normalize) 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 else 0)
pipeline.summarySettings.get("variantcallers") shouldBe Some(callers.toList)
pipeline.summarySettings.get("amplicon_bed") shouldBe ampliconBedFile.map(_.getAbsolutePath)
pipeline.summarySettings.get("regions_of_interest") shouldBe Some(roiBedFiles.map(_.getAbsolutePath))
}
}
}
......
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