Commit 3835e14b authored by pjvan_thof's avatar pjvan_thof
Browse files

Fix compile errors

parent 8f9236a6
......@@ -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"
......
......@@ -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"
......
......@@ -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"""
......
......@@ -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
/**
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment