Commit df5b8d8c authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed tests

parent 53c59c03
......@@ -179,8 +179,8 @@ class ShivaVariantcalling(val root: Configurable) extends QScript
/** Settings for the summary */
def summarySettings = Map(
"variantcallers" -> configCallers.toList,
"regions_of_interest" -> roiBedFiles.map(_.getName.stripSuffix(".bed")),
"amplicon_bed" -> ampliconBedFile.map(_.getName.stripSuffix(".bed"))
"regions_of_interest" -> roiBedFiles.map(_.getName),
"amplicon_bed" -> ampliconBedFile.map(_.getAbsolutePath)
)
/** Files for the summary */
......
......@@ -117,13 +117,13 @@ trait ShivaVariantcallingTestTrait extends TestNGSuite with Matchers {
(if (haplotypeCallerAllele) 1 else 0) + (if (haplotypeCallerGvcf) bams else 0)
pipeline.functions.count(_.isInstanceOf[UnifiedGenotyper]) shouldBe (if (unifiedGenotyper) 1 else 0) +
(if (unifiedGenotyperAllele) 1 else 0)
pipeline.functions.count(_.isInstanceOf[VcfStats]) shouldBe (1 + callers.size + (roiBedFiles ++ ampliconBedFile).length)
pipeline.functions.count(_.isInstanceOf[VcfStats]) shouldBe (1 + callers.size + (roiBedFiles ++ ampliconBedFile).length * (1+ callers.size))
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.functions.count(_.isInstanceOf[GenotypeConcordance]) shouldBe (if (referenceVcf.isDefined) 1 + callers.size else 0)
pipeline.summarySettings.get("variantcallers") shouldBe Some(callers.toList)
pipeline.summarySettings.get("amplicon_bed") shouldBe ampliconBedFile.map(_.getAbsolutePath)
pipeline.summarySettings.get("amplicon_bed") shouldBe Some(ampliconBedFile.map(_.getAbsolutePath))
pipeline.summarySettings.get("regions_of_interest") shouldBe Some(roiBedFiles.map(_.getAbsolutePath))
}
}
......
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