Commit 4a9966de authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixing code warnings

parent 793b521d
...@@ -16,9 +16,11 @@ package nl.lumc.sasc.biopet.extensions ...@@ -16,9 +16,11 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File import java.io.File
import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction } import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Version}
import nl.lumc.sasc.biopet.utils.config.Configurable import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output } import org.broadinstitute.gatk.utils.commandline.{Input, Output}
import scala.util.matching.Regex
/** /**
* Wrapper for the cuffquant command line tool. * Wrapper for the cuffquant command line tool.
...@@ -116,11 +118,11 @@ class Cuffquant(val root: Configurable) extends BiopetCommandLineFunction with V ...@@ -116,11 +118,11 @@ class Cuffquant(val root: Configurable) extends BiopetCommandLineFunction with V
/** Disable SCV correction */ /** Disable SCV correction */
var noScvCorrection: Boolean = config("no_scv_correction", default = false) var noScvCorrection: Boolean = config("no_scv_correction", default = false)
def versionRegex = """cuffquant v(.*)""".r def versionRegex: Regex = """cuffquant v(.*)""".r
def versionCommand = executable def versionCommand: String = executable
override def versionExitcode = List(0, 1) override def versionExitcode = List(0, 1)
def cmdLine = def cmdLine: String =
required(executable) + required(executable) +
required("--output-dir", outputDir) + required("--output-dir", outputDir) +
optional("--mask-file", maskFile) + optional("--mask-file", maskFile) +
......
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