Commit dcff73d6 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Rename root to parent

parent 463f8002
......@@ -19,7 +19,7 @@ import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class ConiferCall(val root: Configurable) extends Conifer {
class ConiferCall(val parent: Configurable) extends Conifer {
@Input(doc = "Input analysis.hdf5", required = true)
var input: File = _
......
......@@ -19,7 +19,7 @@ import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class ConiferExport(val root: Configurable) extends Conifer {
class ConiferExport(val parent: Configurable) extends Conifer {
@Input(doc = "Input analysis.hdf5", required = true)
var input: File = _
......
......@@ -19,7 +19,7 @@ import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class ConiferRPKM(val root: Configurable) extends Conifer {
class ConiferRPKM(val parent: Configurable) extends Conifer {
@Input(doc = "Bam file", required = true)
var bamFile: File = _
......
......@@ -20,7 +20,7 @@ import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction }
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
class DellyCaller(val root: Configurable) extends BiopetCommandLineFunction with Version {
class DellyCaller(val parent: Configurable) extends BiopetCommandLineFunction with Version {
executable = config("exe", default = "delly")
private lazy val versionexecutable: File = new File(executable)
......
......@@ -20,7 +20,7 @@ import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Reference, Version
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline._
class FreeC(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version {
class FreeC(val parent: Configurable) extends BiopetCommandLineFunction with Reference with Version {
override def defaults = Map("max_walltime_limit" -> 7200)
......
......@@ -20,7 +20,7 @@ import nl.lumc.sasc.biopet.core.extensions.RscriptCommandLineFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class FreeCAssessSignificancePlot(val root: Configurable) extends RscriptCommandLineFunction {
class FreeCAssessSignificancePlot(val parent: Configurable) extends RscriptCommandLineFunction {
protected var script: File = new File("/nl/lumc/sasc/biopet/extensions/freec/freec_assess_significance.R")
@Input(doc = "Output file from FreeC. *_CNV", required = true)
......
......@@ -20,7 +20,7 @@ import nl.lumc.sasc.biopet.core.extensions.RscriptCommandLineFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class FreeCBAFPlot(val root: Configurable) extends RscriptCommandLineFunction {
class FreeCBAFPlot(val parent: Configurable) extends RscriptCommandLineFunction {
protected var script: File = new File("/nl/lumc/sasc/biopet/extensions/freec/freec_BAFPlot.R")
@Input(doc = "Output file from FreeC. *_BAF.txt")
......
......@@ -20,7 +20,7 @@ import nl.lumc.sasc.biopet.core.extensions.{ PythonCommandLineFunction, RscriptC
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class FreeCCNVPlot(val root: Configurable) extends PythonCommandLineFunction {
class FreeCCNVPlot(val parent: Configurable) extends PythonCommandLineFunction {
setPythonScript("freec_CNVPlot.py")
@Input(doc = "Output file from FreeC. *_CNV", required = true)
......
......@@ -20,7 +20,7 @@ import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ }
class AnalyzeCovariates(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
class AnalyzeCovariates(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "AnalyzeCovariates"
scatterClass = classOf[LocusScatterFunction]
setupScatterFunction = { case scatter: GATKScatterFunction => scatter.includeUnmapped = false }
......
......@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Input, Output }
class ApplyRecalibration(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
class ApplyRecalibration(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "ApplyRecalibration"
scatterClass = classOf[LocusScatterFunction]
setupScatterFunction = { case scatter: GATKScatterFunction => scatter.includeUnmapped = false }
......
......@@ -23,7 +23,7 @@ import org.broadinstitute.gatk.queue.function.scattergather.GatherFunction
*/
class BamGatherFunction extends MergeSamFiles(null) with GatherFunction {
override val root = originalFunction match {
override val parent = originalFunction match {
case b: BiopetCommandLineFunction => b
case _ => null
}
......
......@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, Input }
class BaseRecalibrator(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
class BaseRecalibrator(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "BaseRecalibrator"
scatterClass = classOf[ContigScatterFunction]
setupScatterFunction = { case scatter: GATKScatterFunction => scatter.includeUnmapped = false }
......
......@@ -20,7 +20,7 @@ import nl.lumc.sasc.biopet.core.{ BiopetJavaCommandLineFunction, Reference }
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Input, Output }
class CatVariants(val root: Configurable) extends BiopetJavaCommandLineFunction with Reference {
class CatVariants(val parent: Configurable) extends BiopetJavaCommandLineFunction with Reference {
analysisName = "CatVariants"
javaMainClass = "org.broadinstitute.gatk.tools.CatVariants"
......
......@@ -32,7 +32,7 @@ class CatVariantsGatherer extends CatVariants(null) with GatherFunction {
analysisName = "Gather_CatVariants"
override val root = originalFunction match {
override val parent = originalFunction match {
case b: BiopetCommandLineFunction => b
case _ => null
}
......
......@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import org.broadinstitute.gatk.utils.commandline.{ Gather, Input, Output, _ }
class CombineGVCFs(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
class CombineGVCFs(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "CombineGVCFs"
scatterClass = classOf[LocusScatterFunction]
setupScatterFunction = { case scatter: GATKScatterFunction => scatter.includeUnmapped = false }
......
......@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ }
class CombineVariants(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
class CombineVariants(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "CombineVariants"
scatterClass = classOf[LocusScatterFunction]
setupScatterFunction = { case scatter: GATKScatterFunction => scatter.includeUnmapped = false }
......
......@@ -22,7 +22,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/**
* Created by Sander Bollen on 23-11-16.
*/
class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
class DepthOfCoverage(val parent: Configurable) extends CommandLineGATK {
def analysis_type = "DepthOfCoverage"
......
......@@ -24,7 +24,7 @@ import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ }
import org.broadinstitute.gatk.utils.report.{ GATKReport, GATKReportTable }
class GenotypeConcordance(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction with Summarizable {
class GenotypeConcordance(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction with Summarizable {
analysisName = "GenotypeConcordance"
val analysis_type = "GenotypeConcordance"
scatterClass = classOf[LocusScatterFunction]
......
......@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ }
class GenotypeGVCFs(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
class GenotypeGVCFs(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "GenotypeGVCFs"
scatterClass = classOf[LocusScatterFunction]
setupScatterFunction = { case scatter: GATKScatterFunction => scatter.includeUnmapped = false }
......
......@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Input, Output }
class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
class HaplotypeCaller(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "HaplotypeCaller"
scatterClass = classOf[LocusScatterFunction]
setupScatterFunction = { case scatter: GATKScatterFunction => scatter.includeUnmapped = false }
......
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