Fix compile errors

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/TemplateTool.scala

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.core
 import java.io.{File, PrintWriter}
 
 import nl.lumc.sasc.biopet.utils.summary.Summary
-import nl.lumc.sasc.biopet.utils.{ConfigUtils, Question, ToolCommand}
+import nl.lumc.sasc.biopet.utils.{AbstractOptParser, ConfigUtils, Question, ToolCommand}
 
 import scala.io.Source
 
@@ -30,9 +30,8 @@ trait TemplateTool extends ToolCommand {
                   runScript: Option[File] = None,
                   expert: Boolean = false,
                   template: Option[File] = None)
-      extends AbstractArgs
 
-  class OptParser extends AbstractOptParser {
+  class OptParser extends AbstractOptParser[Args](commandName) {
     opt[File]('o', "outputConfig") required () valueName "<file>" action { (x, c) =>
       c.copy(outputConfig = x)
     } text "Path to output config"

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/pipelinestatus/PipelineStatus.scala

@@ -20,7 +20,7 @@ import akka.actor.ActorSystem
 import akka.stream.ActorMaterializer
 import nl.lumc.sasc.biopet.utils.pim._
 import nl.lumc.sasc.biopet.utils.pim.{Job => PimJob}
-import nl.lumc.sasc.biopet.utils.{ConfigUtils, ToolCommand}
+import nl.lumc.sasc.biopet.utils.{AbstractOptParser, ConfigUtils, ToolCommand}
 import play.api.libs.ws.ahc.AhcWSClient
 
 import scala.concurrent.ExecutionContext.Implicits.global
@@ -41,9 +41,8 @@ object PipelineStatus extends ToolCommand {
                   compressPlots: Boolean = true,
                   pimHost: Option[String] = None,
                   pimRunId: Option[String] = None)
-      extends AbstractArgs
 
-  class OptParser extends AbstractOptParser {
+  class OptParser extends AbstractOptParser[Args](commandName) {
     opt[File]('d', "pipelineDir") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
       c.copy(pipelineDir = x)
     } text "Output directory of the pipeline"

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala

@@ -17,10 +17,10 @@ package nl.lumc.sasc.biopet.core.report
 import java.io._
 
 import nl.lumc.sasc.biopet.core.ToolCommandFunction
-import nl.lumc.sasc.biopet.utils.summary.db.Schema.{Library, Module, Pipeline, Sample, Run}
+import nl.lumc.sasc.biopet.utils.summary.db.Schema.{Library, Module, Pipeline, Run, Sample}
 import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
 import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.{LibraryId, SampleId}
-import nl.lumc.sasc.biopet.utils.{IoUtils, Logging, ToolCommand}
+import nl.lumc.sasc.biopet.utils.{AbstractOptParser, IoUtils, Logging, ToolCommand}
 import org.broadinstitute.gatk.utils.commandline.Input
 import org.fusesource.scalate.TemplateEngine
 
@@ -82,9 +82,8 @@ trait ReportBuilder extends ToolCommand {
                   outputDir: File = null,
                   runId: Int = 0,
                   pageArgs: mutable.Map[String, Any] = mutable.Map())
-      extends AbstractArgs
 
-  class OptParser extends AbstractOptParser {
+  class OptParser extends AbstractOptParser[Args](commandName) {
 
     head(
       s"""

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/VcfStatsOptParser.scala

@@ -2,7 +2,12 @@ package nl.lumc.sasc.biopet.tools.vcfstats
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.tools.vcfstats.VcfStats.{defaultGenotypeFields, defaultInfoFields, generalWiggleOptions, genotypeWiggleOptions}
+import nl.lumc.sasc.biopet.tools.vcfstats.VcfStats.{
+  defaultGenotypeFields,
+  defaultInfoFields,
+  generalWiggleOptions,
+  genotypeWiggleOptions
+}
 import nl.lumc.sasc.biopet.utils.AbstractOptParser
 
 /**