Commit 31a835a1 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added files to summary

parent 7501f792
......@@ -35,7 +35,7 @@ class MultisampleMapping(val root: Configurable) extends QScript
}
def biopetScript: Unit = {
addSamplesJobs() // This executes jobs for all samples
addSamplesJobs()
addSummaryJobs()
}
......@@ -47,14 +47,16 @@ class MultisampleMapping(val root: Configurable) extends QScript
def summaryFiles: Map[String, File] = Map()
def summarySettings: Map[String, Any] = Map()
def summarySettings: Map[String, Any] = Map("merge_strategy" -> mergeStrategy.toString)
def makeSample(id: String) = new Sample(id)
class Sample(sampleId: String) extends AbstractSample(sampleId) {
def makeLibrary(id: String) = new Library(id)
class Library(libId: String) extends AbstractLibrary(libId) {
def summaryFiles: Map[String, File] = Map()
def summaryFiles: Map[String, File] = (inputR1.map("input_R1" -> _) :: inputR2.map("input_R2" -> _) ::
inputBam.map("input_bam" -> _) :: bamFile.map("output_bam" -> _) ::
preProcessBam.map("output_preProcessBam" -> _) :: Nil).flatten.toMap
def summaryStats: Map[String, Any] = Map()
......@@ -145,7 +147,8 @@ class MultisampleMapping(val root: Configurable) extends QScript
}
}
def summaryFiles: Map[String, File] = Map()
def summaryFiles: Map[String, File] = (bamFile.map("output_bam" -> _) ::
preProcessBam.map("output_preProcessBam" -> _) :: Nil).flatten.toMap
def summaryStats: Map[String, Any] = Map()
......
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