Commit 8df9dd6a authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

More efficient code

parent abb2a682
......@@ -5,12 +5,8 @@ import nl.lumc.sasc.biopet.core.config.Configurable
trait MultiSampleQScript extends BiopetQScript {
var samples: Map[String, Any] = Map()
var globalSampleDir: String = _
def globalSampleDir: String = outputDir + "samples/"
def init {
globalSampleDir = outputDir + "samples/"
}
final def runSamplesJobs: Map[String, Map[String, File]] = {
var output: Map[String, Map[String, File]] = Map()
samples = config("samples")
......
......@@ -26,8 +26,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
var gvcfFiles: List[File] = Nil
var finalBamFiles: List[File] = Nil
override def init() {
super.init
def init() {
reference = config("reference", required = true)
dbsnp = config("dbsnp")
if (config.contains("gvcfFiles"))
......
......@@ -35,8 +35,7 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
)
)
override def init() {
super.init
def init() {
if (!outputDir.endsWith("/")) outputDir += "/"
if (countBed == null) countBed = config("count_bed")
if (squishedCountBed == null) squishedCountBed = config("squished_count_bed")
......
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