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

Rename root to parent

parent 463f8002
......@@ -20,7 +20,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/** Extension for bedtools intersect */
class BedtoolsIntersect(val root: Configurable) extends Bedtools {
class BedtoolsIntersect(val parent: Configurable) extends Bedtools {
@Input(doc = "Input file (bed/gff/vcf/bam)")
var input: File = null
......
......@@ -22,7 +22,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Output, Input }
/**
* Created by ahbbollen on 5-1-16.
*/
class BedtoolsMerge(val root: Configurable) extends Bedtools {
class BedtoolsMerge(val parent: Configurable) extends Bedtools {
@Input(doc = "Input bed file")
var input: File = _
......
......@@ -23,7 +23,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/**
* Created by Sander Bollen on 26-5-16.
*/
class BedtoolsSort(val root: Configurable) extends Bedtools with Reference {
class BedtoolsSort(val parent: Configurable) extends Bedtools with Reference {
@Input
var input: File = null
......
......@@ -26,7 +26,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
*
* Based on version 1.1.1
*/
class Bowtie(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version {
class Bowtie(val parent: Configurable) extends BiopetCommandLineFunction with Reference with Version {
@Input(doc = "Fastq file R1", shortName = "R1")
var R1: File = null
......
......@@ -26,7 +26,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
*
* Based on version 2.2.6
*/
class Bowtie2(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version {
class Bowtie2(val parent: Configurable) extends BiopetCommandLineFunction with Reference with Version {
@Input(doc = "Fastq file R1", shortName = "R1")
var R1: File = null
......
......@@ -23,7 +23,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/**
* Created by pjvan_thof on 8/15/15.
*/
class Bowtie2Build(val root: Configurable) extends BiopetCommandLineFunction with Version {
class Bowtie2Build(val parent: Configurable) extends BiopetCommandLineFunction with Version {
@Input(required = true)
var reference: File = _
......
......@@ -23,7 +23,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/**
* Created by pjvan_thof on 8/15/15.
*/
class BowtieBuild(val root: Configurable) extends BiopetCommandLineFunction with Version {
class BowtieBuild(val parent: Configurable) extends BiopetCommandLineFunction with Version {
@Input(required = true)
var reference: 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.{ Input, Output }
class BreakdancerCaller(val root: Configurable) extends BiopetCommandLineFunction with Version {
class BreakdancerCaller(val parent: Configurable) extends BiopetCommandLineFunction with Version {
executable = config("exe", default = "breakdancer-max", freeVar = false)
override def defaultThreads = 1 // breakdancer can only work on 1 single thread
......
......@@ -20,7 +20,7 @@ import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class BreakdancerConfig(val root: Configurable) extends BiopetCommandLineFunction {
class BreakdancerConfig(val parent: Configurable) extends BiopetCommandLineFunction {
executable = config("exe", default = "bam2cfg.pl", freeVar = false)
@Input(doc = "Bam File")
......
......@@ -20,7 +20,7 @@ import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline._
class BreakdancerVCF(val root: Configurable) extends PythonCommandLineFunction {
class BreakdancerVCF(val parent: Configurable) extends PythonCommandLineFunction {
setPythonScript("breakdancer2vcf.py")
@Input(doc = "Breakdancer TSV")
......
......@@ -27,7 +27,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
*
* Created by pjvan_thof on 1/16/15.
*/
class BwaAln(val root: Configurable) extends Bwa with Reference {
class BwaAln(val parent: Configurable) extends Bwa with Reference {
@Input(doc = "Fastq file", required = true)
var fastq: File = _
......
......@@ -26,7 +26,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
*
* Created by pjvan_thof on 1/16/15.
*/
class BwaIndex(val root: Configurable) extends Bwa {
class BwaIndex(val parent: Configurable) extends Bwa {
@Input(doc = "Fastq file", required = true)
var reference: File = _
......
......@@ -25,7 +25,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
*
* Based on version 0.7.12-r1039
*/
class BwaMem(val root: Configurable) extends Bwa with Reference {
class BwaMem(val parent: Configurable) extends Bwa with Reference {
@Input(doc = "Fastq file R1", shortName = "R1")
var R1: File = _
......
......@@ -26,7 +26,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
* based on executable version 0.7.10-r789
*
*/
class BwaSampe(val root: Configurable) extends Bwa with Reference {
class BwaSampe(val parent: Configurable) extends Bwa with Reference {
@Input(doc = "Fastq file R1", required = true)
var fastqR1: File = _
......
......@@ -26,7 +26,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
* based on executable version 0.7.10-r789
*
*/
class BwaSamse(val root: Configurable) extends Bwa with Reference {
class BwaSamse(val parent: Configurable) extends Bwa with Reference {
@Input(doc = "Fastq file", required = true)
var fastq: File = _
......
......@@ -28,7 +28,7 @@ import scala.util.matching.Regex
/**
* Created by pjvanthof on 19/09/16.
*/
class Centrifuge(val root: Configurable) extends BiopetCommandLineFunction with Version with Summarizable {
class Centrifuge(val parent: Configurable) extends BiopetCommandLineFunction with Version with Summarizable {
@Input(doc = "Input: FastQ or FastA", required = true)
var inputR1: File = _
......
......@@ -23,7 +23,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* Created by pjvanthof on 19/09/16.
*/
class CentrifugeKreport(val root: Configurable) extends BiopetCommandLineFunction {
class CentrifugeKreport(val parent: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "Output files centrifuge", required = true)
var centrifugeOutputFiles: List[File] = Nil
......
......@@ -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.{ Input, Output }
class CleverCaller(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version {
class CleverCaller(val parent: Configurable) extends BiopetCommandLineFunction with Reference with Version {
executable = config("exe", default = "clever")
private lazy val versionExecutable: File = config("version_exe", default = new File(executable).getParent + "/ctk-version")
......
......@@ -27,7 +27,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
import scala.io.Source
class CleverFixVCF(val root: Configurable) extends BiopetJavaCommandLineFunction {
class CleverFixVCF(val parent: Configurable) extends BiopetJavaCommandLineFunction {
javaMainClass = getClass.getName
@Input(doc = "Input Clever VCF")
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.{ Argument, Input, Output }
class ConiferAnalyze(val root: Configurable) extends Conifer {
class ConiferAnalyze(val parent: Configurable) extends Conifer {
@Input(doc = "Probes / capture kit definition as bed file: chr,start,stop,gene-annot", required = true)
var probes: File = _
......
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