Commit 14d93e73 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added place holders for summary

parent 4dd8d4f0
......@@ -40,10 +40,23 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
def makeSample(id: String) = new Sample(id)
class Sample(sampleId: String) extends AbstractSample(sampleId) {
//TODO: Add summary
def summaryFiles: Map[String, File] = Map()
//TODO: Add summary
def summaryStats: Map[String, Any] = Map()
def makeLibrary(id: String) = new Library(id)
class Library(libId: String) extends AbstractLibrary(libId) {
//TODO: Add summary
def summaryFiles: Map[String, File] = Map()
//TODO: Add summary
def summaryStats: Map[String, Any] = Map()
def preProcess(input: File): Option[File] = None
def makeMapping = {
......@@ -168,7 +181,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
md.outputMetrics = new File(sampleDir, sampleId + ".dedup.bam")
md.isIntermediate = isIntermediate
add(md)
addSummarizable(md, "mark_duplicates", Some(sampleId))
addSummarizable(md, "mark_duplicates")
Some(md.output)
}
}
......
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