Commit 4143a145 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Moved summaryFile

parent 6e4327e7
......@@ -52,7 +52,7 @@ class Carp(val root: Configurable) extends QScript with MultisampleMappingTrait
)
)
override def summaryFile = new File(outputDir, "Carp.summary.json")
def summaryFile = new File(outputDir, "Carp.summary.json")
override def makeSample(id: String) = new Sample(id)
class Sample(sampleId: String) extends super.Sample(sampleId) {
......
......@@ -41,8 +41,6 @@ trait MultisampleMappingTrait extends MultiSampleQScript
// this code will be executed after all code of all samples is executed
}
def summaryFile: File = new File(outputDir, "MultisamplePipeline.summary.json")
def summaryFiles: Map[String, File] = Map("referenceFasta" -> referenceFasta())
def summarySettings: Map[String, Any] = Map(
......@@ -199,6 +197,8 @@ trait MultisampleMappingTrait extends MultiSampleQScript
class MultisampleMapping(val root: Configurable) extends QScript with MultisampleMappingTrait {
def this() = this(null)
def summaryFile: File = new File(outputDir, "MultisamplePipeline.summary.json")
}
object MultisampleMapping extends PipelineCommand {
......
......@@ -154,7 +154,7 @@ trait ShivaTrait extends MultisampleMappingTrait with Reference with TargetRegio
}
/** Location of summary file */
override def summaryFile = new File(outputDir, "Shiva.summary.json")
def summaryFile = new File(outputDir, "Shiva.summary.json")
/** Settings of pipeline for summary */
override def summarySettings = super.summarySettings ++ Map(
......
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