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Commit 27813378 authored by Peter van 't Hof's avatar Peter van 't Hof
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Added intermediate

parent 38402a6c
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public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
View file @ 27813378
...@@ -98,6 +98,7 @@ trait ShivaVariantcallingTrait extends SummaryQScript ...@@ -98,6 +98,7 @@ trait ShivaVariantcallingTrait extends SummaryQScript
if (normalize && decompose) { if (normalize && decompose) {
vtNormalize.outputVcf = swapExt(caller.outputDir, caller.outputFile, ".vcf.gz", ".normaize.vcf.gz") vtNormalize.outputVcf = swapExt(caller.outputDir, caller.outputFile, ".vcf.gz", ".normaize.vcf.gz")
vtNormalize.isIntermediate = true
add(vtNormalize) add(vtNormalize)
vtDecompose.inputVcf = vtNormalize.outputVcf vtDecompose.inputVcf = vtNormalize.outputVcf
vtDecompose.outputVcf = swapExt(caller.outputDir, vtNormalize.outputVcf, ".vcf.gz", ".decompose.vcf.gz") vtDecompose.outputVcf = swapExt(caller.outputDir, vtNormalize.outputVcf, ".vcf.gz", ".decompose.vcf.gz")
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