Commit a9f86490 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Switch to new multisample part

parent 944b9af0
...@@ -25,31 +25,29 @@ class Kopisu(val root: Configurable) extends QScript with MultiSampleQScript { ...@@ -25,31 +25,29 @@ class Kopisu(val root: Configurable) extends QScript with MultiSampleQScript {
@Input(doc = "Input bamfile", required = true) @Input(doc = "Input bamfile", required = true)
var bamFile: File = config("bam") var bamFile: File = config("bam")
class LibraryOutput extends AbstractLibraryOutput {
}
class SampleOutput extends AbstractSampleOutput {
}
def init() { def init() {
if (!outputDir.endsWith("/")) outputDir += "/" if (!outputDir.endsWith("/")) outputDir += "/"
} }
def biopetScript() { def biopetScript() {
runSamplesJobs this.addPerSampleJobs()
} }
// Called for each sample def makeSample(id: String) = new Sample(id)
def runSingleSampleJobs(sampleConfig: Map[String, Any]): SampleOutput = { class Sample(sampleId: String) extends AbstractSample(sampleId) {
val sampleOutput = new SampleOutput def makeLibrary(id: String) = new Library(id)
class Library(libraryId: String) extends AbstractLibrary(libraryId) {
def addJobs(): Unit = {
}
}
def addJobs(): Unit = {
return sampleOutput }
} }
// Called for each run from a sample def addMultiSampleJobs(): Unit = {
def runSingleLibraryJobs(runConfig: Map[String, Any], sampleConfig: Map[String, Any]): LibraryOutput = {
val libraryOutput = new LibraryOutput
return libraryOutput
} }
} }
......
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