Commit 449889d4 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixing code warnings

parent d793f5dd
......@@ -2,9 +2,7 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.extensions.gatk.CommandLineGATK.isFileWithTag
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import org.broadinstitute.gatk.utils.commandline.{Argument, Input, Output}
class ContEst(val parent: Configurable) extends CommandLineGATK {
......@@ -59,7 +57,7 @@ class ContEst(val parent: Configurable) extends CommandLineGATK {
@Argument(fullName = "trim_fraction", required = false)
var trimFraction: Option[Double] = config("trim_fraction")
override def cmdLine = super.cmdLine +
override def cmdLine: String = super.cmdLine +
required("--popfile", popFile) +
required("--out", output) +
optional("--base_report", baseReportFile) +
......
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