Commit e2b5ad1d authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added cnv to summary settings

parent ef10b38d
...@@ -209,6 +209,7 @@ class Shiva(val root: Configurable) extends QScript with MultisampleMappingTrait ...@@ -209,6 +209,7 @@ class Shiva(val root: Configurable) extends QScript with MultisampleMappingTrait
"annotation" -> annotation.isDefined, "annotation" -> annotation.isDefined,
"multisample_variantcalling" -> multisampleVariantCalling.isDefined, "multisample_variantcalling" -> multisampleVariantCalling.isDefined,
"sv_calling" -> svCalling.isDefined, "sv_calling" -> svCalling.isDefined,
"cnv_calling" -> cnvCalling.isDefined,
"regions_of_interest" -> roiBedFiles.map(_.getName.stripSuffix(".bed")), "regions_of_interest" -> roiBedFiles.map(_.getName.stripSuffix(".bed")),
"amplicon_bed" -> ampliconBedFile.map(_.getName.stripSuffix(".bed")) "amplicon_bed" -> ampliconBedFile.map(_.getName.stripSuffix(".bed"))
) )
......
...@@ -104,6 +104,7 @@ trait ShivaTestTrait extends TestNGSuite with Matchers { ...@@ -104,6 +104,7 @@ trait ShivaTestTrait extends TestNGSuite with Matchers {
pipeline.summarySettings.get("annotation") shouldBe Some(annotation) pipeline.summarySettings.get("annotation") shouldBe Some(annotation)
pipeline.summarySettings.get("sv_calling") shouldBe Some(svCalling) pipeline.summarySettings.get("sv_calling") shouldBe Some(svCalling)
pipeline.summarySettings.get("cnv_calling") shouldBe Some(cnvCalling)
pipeline.samples foreach { pipeline.samples foreach {
case (sampleId, sample) => case (sampleId, sample) =>
......
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