Commit 73d6d6d7 authored by Peter van 't Hof's avatar Peter van 't Hof

Adding final files for sample and library variantcaling to summary

(cherry picked from commit 7b205dd)
parent a278b762
......@@ -77,6 +77,8 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
/** Class to generate jobs for a library */
class Library(libId: String) extends super.Library(libId) {
override def summaryFiles = super.summaryFiles ++ variantcalling.map("final" -> _.finalFile)
lazy val useIndelRealigner: Boolean = config("use_indel_realigner", default = true)
lazy val useBaseRecalibration: Boolean = {
val c: Boolean = config("use_base_recalibration", default = true)
......@@ -141,6 +143,8 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
bamFile.map(swapExt(sampleDir, _, ".bam", ".realign.bam"))
} else bamFile
override def summaryFiles = super.summaryFiles ++ variantcalling.map("final" -> _.finalFile)
/** This will add sample jobs */
override def addJobs(): Unit = {
super.addJobs()
......
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