Commit 19f7d266 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Style fixes

parent f88088e3
......@@ -19,7 +19,7 @@ import java.io.File
import nl.lumc.sasc.biopet.core.extensions.RscriptCommandLineFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Output}
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* Wrapper for the Cnmops command line tool.
......
......@@ -15,9 +15,9 @@
*/
package nl.lumc.sasc.biopet.extensions.freec
import java.io.{File, PrintWriter}
import java.io.{ File, PrintWriter }
import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Reference, Version}
import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Reference, Version }
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline._
......
......@@ -4,7 +4,7 @@ import java.io.File
import nl.lumc.sasc.biopet.core.extensions.RscriptCommandLineFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Output}
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class FreeCAssessSignificancePlot(val root: Configurable) extends RscriptCommandLineFunction {
protected var script: File = new File("/nl/lumc/sasc/biopet/extensions/freec/freec_assess_significance.R")
......
......@@ -4,7 +4,7 @@ import java.io.File
import nl.lumc.sasc.biopet.core.extensions.RscriptCommandLineFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Output}
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class FreeCBAFPlot(val root: Configurable) extends RscriptCommandLineFunction {
protected var script: File = new File("/nl/lumc/sasc/biopet/extensions/freec/freec_BAFPlot.R")
......
......@@ -4,7 +4,7 @@ import java.io.File
import nl.lumc.sasc.biopet.core.extensions.RscriptCommandLineFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Output}
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class FreeCCNVPlot(val root: Configurable) extends RscriptCommandLineFunction {
protected var script: File = new File("/nl/lumc/sasc/biopet/extensions/freec/freec_CNVPlot.R")
......
......@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.sambamba
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Output}
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class SambambaMpileup(val root: Configurable) extends Sambamba {
override val defaultThreads = 4
......
......@@ -5,8 +5,8 @@ import nl.lumc.sasc.biopet.core.Reference
import org.broadinstitute.gatk.queue.QScript
/**
* Created by pjvanthof on 10/05/16.
*/
* Created by pjvanthof on 10/05/16.
*/
trait CnvMethod extends QScript with SummaryQScript with Reference {
/** Name of mode, this should also be used in the config */
......
......@@ -2,51 +2,52 @@ package nl.lumc.sasc.biopet.pipelines.kopisu.methods
import java.io.File
import nl.lumc.sasc.biopet.extensions.freec.{FreeC, FreeCAssessSignificancePlot, FreeCBAFPlot, FreeCCNVPlot}
import nl.lumc.sasc.biopet.extensions.freec.{ FreeC, FreeCAssessSignificancePlot, FreeCBAFPlot, FreeCCNVPlot }
import nl.lumc.sasc.biopet.utils.config.Configurable
/**
* Created by pjvanthof on 10/05/16.
*/
* Created by pjvanthof on 10/05/16.
*/
class FreecMethod(val root: Configurable) extends CnvMethod {
def name = "freec"
var snpFile: Option[File] = config("snp_file", freeVar = false)
def biopetScript: Unit = {
inputBams.foreach { case (sampleName, bamFile) =>
inputBams.foreach {
case (sampleName, bamFile) =>
val sampleOutput = new File(outputDir, sampleName)
val sampleOutput = new File(outputDir, sampleName)
val freec = new FreeC(this)
freec.input = bamFile
freec.inputFormat = Some("BAM")
freec.outputPath = sampleOutput
freec.snpFile = snpFile
add(freec)
val freec = new FreeC(this)
freec.input = bamFile
freec.inputFormat = Some("BAM")
freec.outputPath = sampleOutput
freec.snpFile = snpFile
add(freec)
/*
/*
* These scripts will wait for FreeC to Finish
*
* R-scripts to plot FreeC results
* */
val fcAssessSignificancePlot = new FreeCAssessSignificancePlot(this)
fcAssessSignificancePlot.cnv = freec.cnvOutput
fcAssessSignificancePlot.ratios = freec.ratioOutput
fcAssessSignificancePlot.output = new File(sampleOutput, sampleName + ".freec_significant_calls.txt")
add(fcAssessSignificancePlot)
val fcCnvPlot = new FreeCCNVPlot(this)
fcCnvPlot.input = freec.ratioOutput
fcCnvPlot.output = new File(sampleOutput, sampleName + ".freec_cnv")
add(fcCnvPlot)
snpFile.foreach { _ =>
val fcBAFPlot = new FreeCBAFPlot(this)
fcBAFPlot.input = freec.bafOutput
fcBAFPlot.output = new File(sampleOutput, sampleName + ".freec_baf")
add(fcBAFPlot)
}
val fcAssessSignificancePlot = new FreeCAssessSignificancePlot(this)
fcAssessSignificancePlot.cnv = freec.cnvOutput
fcAssessSignificancePlot.ratios = freec.ratioOutput
fcAssessSignificancePlot.output = new File(sampleOutput, sampleName + ".freec_significant_calls.txt")
add(fcAssessSignificancePlot)
val fcCnvPlot = new FreeCCNVPlot(this)
fcCnvPlot.input = freec.ratioOutput
fcCnvPlot.output = new File(sampleOutput, sampleName + ".freec_cnv")
add(fcCnvPlot)
snpFile.foreach { _ =>
val fcBAFPlot = new FreeCBAFPlot(this)
fcBAFPlot.input = freec.bafOutput
fcBAFPlot.output = new File(sampleOutput, sampleName + ".freec_baf")
add(fcBAFPlot)
}
}
}
......
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