Commit bbaaa914 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed intermediate files

parent 09fe4d50
......@@ -43,8 +43,12 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
/** Class will generate library jobs */
class Library(libId: String) extends super.Library(libId) {
val useIndelRealigner: Boolean = config("use_indel_realigner", default = true)
val useBaseRecalibration: Boolean = config("use_base_recalibration", default = true)
lazy val useIndelRealigner: Boolean = config("use_indel_realigner", default = true)
lazy val useBaseRecalibration: Boolean = config("use_base_recalibration", default = true)
override def summarySettings = super.summarySettings +
("use_indel_realigner" -> useIndelRealigner) +
("use_base_recalibration" ->useBaseRecalibration)
/** Return true when baserecalibration is executed */
protected def doneBaseRecalibrator: Boolean = {
......@@ -69,12 +73,16 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
}
}
override def summarySettings = super.summarySettings + ("use_indel_realigner" -> useIndelRealigner)
lazy val useIndelRealigner: Boolean = config("use_indel_realigner", default = true)
/** This methods will add double preprocess steps, with GATK indel realignment */
override protected def addDoublePreProcess(input: List[File], isIntermediate: Boolean = false): Option[File] = {
if (input.size <= 1) super.addDoublePreProcess(input)
else super.addDoublePreProcess(input, isIntermediate = true).collect {
else super.addDoublePreProcess(input, isIntermediate = useIndelRealigner).collect {
case file =>
config("use_indel_realigner", default = true).asBoolean match {
useIndelRealigner match {
case true => addIndelRealign(file, sampleDir, isIntermediate = false)
case false => file
}
......
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