Commit 7f424eb9 authored by Peter van 't Hof's avatar Peter van 't Hof

Fixed bug in loading the mainClass for biopet tools

parent 74f301a6
......@@ -23,7 +23,7 @@ import nl.lumc.sasc.biopet.utils.summary.{ Summary, SummaryValue }
import nl.lumc.sasc.biopet.utils.rscript.{ StackedBarPlot, LinePlot }
class BammetricsReport(val root: Configurable) extends ReportBuilderExtension {
val builder = BammetricsReport
def builder = BammetricsReport
}
/**
......
......@@ -13,8 +13,5 @@ trait ToolCommandFunction extends BiopetJavaCommandLineFunction with Version {
override def getVersion = Some("Biopet " + FullVersion)
override def beforeGraph(): Unit = {
javaMainClass = toolObject.getClass.getName.takeWhile(_ != '$')
super.beforeGraph()
}
javaMainClass = toolObject.getClass.getName.takeWhile(_ != '$')
}
......@@ -33,7 +33,7 @@ import scala.collection.mutable
trait ReportBuilderExtension extends ToolCommandFunction {
/** Report builder object */
val builder: ReportBuilder
def builder: ReportBuilder
def toolObject = builder
......
......@@ -12,8 +12,8 @@ class ToolCommandTest extends TestNGSuite with Matchers {
@Test
def testToolCommand: Unit = {
val tool = new ToolCommandFunction {
val root = null
val toolObject = ToolCommandTest
def root = null
def toolObject = ToolCommandTest
}
tool.versionCommand shouldBe empty
......
......@@ -26,7 +26,7 @@ import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
* Created by pjvanthof on 25/06/15.
*/
class CarpReport(val root: Configurable) extends ReportBuilderExtension {
val builder = CarpReport
def builder = CarpReport
}
object CarpReport extends MultisampleReportBuilder {
......
......@@ -23,7 +23,7 @@ import nl.lumc.sasc.biopet.utils.rscript.StackedBarPlot
import nl.lumc.sasc.biopet.utils.summary.{ Summary, SummaryValue }
class FlexiprepReport(val root: Configurable) extends ReportBuilderExtension {
val builder = FlexiprepReport
def builder = FlexiprepReport
}
/**
......
......@@ -4,7 +4,7 @@ import nl.lumc.sasc.biopet.core.report._
import nl.lumc.sasc.biopet.utils.config.Configurable
class GearsReport(val root: Configurable) extends ReportBuilderExtension {
val builder = GearsReport
def builder = GearsReport
}
object GearsReport extends ReportBuilder {
......
......@@ -26,7 +26,7 @@ import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
* Created by pjvanthof on 25/06/15.
*/
class GentrapReport(val root: Configurable) extends ReportBuilderExtension {
val builder = GentrapReport
def builder = GentrapReport
}
object GentrapReport extends MultisampleReportBuilder {
......
......@@ -21,7 +21,7 @@ import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport
import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
class MappingReport(val root: Configurable) extends ReportBuilderExtension {
val builder = MappingReport
def builder = MappingReport
}
/**
......
......@@ -30,7 +30,7 @@ import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
* Created by pjvan_thof on 3/30/15.
*/
class ShivaReport(val root: Configurable) extends ReportBuilderExtension {
val builder = ShivaReport
def builder = ShivaReport
}
/** Object for report generation for Shiva pipeline */
......
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