Commit 96c33eab authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

fix bug on single sample calling

parent 5e7634c1
...@@ -82,7 +82,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript { ...@@ -82,7 +82,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
case _ => (None, None, None) case _ => (None, None, None)
} }
val variantcalling = if (config("library_variantcalling", default = false).asBoolean && lazy val variantcalling = if (config("library_variantcalling", default = false).asBoolean &&
(bamFile.isDefined || preProcessBam.isDefined)) { (bamFile.isDefined || preProcessBam.isDefined)) {
Some(makeVariantcalling(multisample = false)) Some(makeVariantcalling(multisample = false))
} else None } else None
...@@ -198,7 +198,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript { ...@@ -198,7 +198,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
} }
}).flatten.toList) }).flatten.toList)
val variantcalling = if (config("multisample_sample_variantcalling", default = true).asBoolean) { lazy val variantcalling = if (config("single_sample_variantcalling", default = true).asBoolean) {
Some(makeVariantcalling(multisample = true)) Some(makeVariantcalling(multisample = true))
} else None } else None
...@@ -228,7 +228,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript { ...@@ -228,7 +228,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
} }
} }
val variantcalling = if (config("multisample_sample_variantcalling", default = true).asBoolean) { lazy val variantcalling = if (config("multisample_sample_variantcalling", default = true).asBoolean) {
Some(makeVariantcalling(multisample = true)) Some(makeVariantcalling(multisample = true))
} else None } else None
......
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