Commit dd732af4 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added init functions

parent 715d7f82
......@@ -54,8 +54,9 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
)
)
def initSample(id: String) = new Sample(id)
class Sample(sampleId: String) extends AbstractSample(sampleId) {
def initLibrary(id: String) = new Library(id)
class Library(libraryId: String) extends AbstractLibrary(libraryId) {
val inputFastq: File = config("R1", required = true)
val prefixFastq: File = new File(getLibraryDir, sampleId + "-" + libraryId + ".prefix.fastq")
......@@ -105,6 +106,7 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
}
def runJobs(): Unit = {
runLibraryJobs()
val libraryBamfiles = libraries.map(_._2.mapping.outputFiles("finalBamFile")).toList
val libraryFastqFiles = libraries.map(_._2.prefixFastq).toList
......@@ -194,11 +196,4 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
}
}
object Sage extends PipelineCommand
object SageTest {
def main(args: Array[String]): Unit = {
val sage = new Sage()
println("done")
}
}
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object Sage extends PipelineCommand
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