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Commit 43a4bc76 authored by Peter van 't Hof's avatar Peter van 't Hof
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Fix sample and library flag

parent 0d010c88
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public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
+ 2
− 2
View file @ 43a4bc76
...@@ -198,8 +198,8 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference { ...@@ -198,8 +198,8 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
}) })
variantcalling.foreach(vc => { variantcalling.foreach(vc => {
vc.sampleId = Some(libId) vc.sampleId = Some(sampleId)
vc.libId = Some(sampleId) vc.libId = Some(libId)
vc.outputDir = new File(libDir, "variantcalling") vc.outputDir = new File(libDir, "variantcalling")
if (preProcessBam.isDefined) vc.inputBams = preProcessBam.get :: Nil if (preProcessBam.isDefined) vc.inputBams = preProcessBam.get :: Nil
else vc.inputBams = bamFile.get :: Nil else vc.inputBams = bamFile.get :: Nil
......
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