Commit cd175ab7 authored by Peter van 't Hof's avatar Peter van 't Hof

Added config report

parent 71a74799
package nl.lumc.sasc.biopet.core
//import org.broadinstitute.sting.queue.QScript
import java.io.File
import java.io.PrintWriter
import nl.lumc.sasc.biopet.core.config._
import org.broadinstitute.sting.commandline._
import org.broadinstitute.sting.queue.QSettings
import org.broadinstitute.sting.queue.function.QFunction
trait BiopetQScript extends Configurable {
......@@ -15,13 +16,20 @@ trait BiopetQScript extends Configurable {
var outputFiles:Map[String,File] = Map()
var qSettings: QSettings
def init
def biopetScript
final def script() {
init
biopetScript
// TODO: Config report
val configReport = globalConfig.getReport
val configReportFile = new File(outputDir + qSettings.runName + ".configreport.txt")
val writer = new PrintWriter(configReportFile)
writer.write(configReport)
writer.close()
for (line <- configReport.split("\n")) logger.debug(line)
}
def add(functions: QFunction*) // Gets implemeted at org.broadinstitute.sting.queue.QScript
......
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