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

Rename root to parent

parent 463f8002
......@@ -24,7 +24,7 @@ import org.broadinstitute.gatk.utils.commandline._
/**
* Created by wyleung on 8-1-16.
*/
class Pysvtools(val root: Configurable) extends BiopetCommandLineFunction {
class Pysvtools(val parent: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "Input file", required = true)
var input: List[File] = Nil
......
......@@ -26,7 +26,7 @@ import scalaz.std.boolean.option
* extension for raxml
* based on version 8.1.3
*/
class Raxml(val root: Configurable) extends BiopetCommandLineFunction with Version {
class Raxml(val parent: Configurable) extends BiopetCommandLineFunction with Version {
override def defaultThreads = 1
def versionCommand = executable + " -v"
......
......@@ -25,7 +25,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
* See; https://github.com/sanger-pathogens/gubbins
* No version known
*/
class RunGubbins(val root: Configurable) extends BiopetCommandLineFunction {
class RunGubbins(val parent: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "Contaminants", required = false)
var startingTree: Option[File] = config("starting_tree")
......
......@@ -25,7 +25,7 @@ import scala.util.matching.Regex
/**
* Created by pjvanthof on 18/05/16.
*/
class Sed(val root: Configurable) extends BiopetCommandLineFunction with Version {
class Sed(val parent: Configurable) extends BiopetCommandLineFunction with Version {
executable = config("exe", default = "sed", freeVar = false)
/** Command to get version of executable */
......
......@@ -21,7 +21,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/** Extension for sha1sum */
class Sha1sum(val root: Configurable) extends BiopetCommandLineFunction {
class Sha1sum(val parent: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "Input file")
var input: File = _
......
......@@ -28,7 +28,7 @@ import scala.io.Source
* Extension for sickle
* Based on version 1.33
*/
class Sickle(val root: Configurable) extends BiopetCommandLineFunction with Summarizable with Version {
class Sickle(val parent: Configurable) extends BiopetCommandLineFunction with Summarizable with Version {
@Input(doc = "R1 input")
var inputR1: File = _
......
......@@ -25,7 +25,7 @@ import scala.util.matching.Regex
/**
* Created by pjvan_thof on 3/25/16.
*/
class Snptest(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version {
class Snptest(val parent: Configurable) extends BiopetCommandLineFunction with Reference with Version {
@Input(required = true)
var inputGenotypes: List[File] = Nil
......
......@@ -21,7 +21,7 @@ import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction, Reference
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/** Extension for stampy */
class Stampy(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version {
class Stampy(val parent: Configurable) extends BiopetCommandLineFunction with Reference with Version {
@Input(doc = "FastQ file R1", shortName = "R1")
var R1: File = _
......
......@@ -23,7 +23,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/**
* Extension for STAR
*/
class Star(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version {
class Star(val parent: Configurable) extends BiopetCommandLineFunction with Reference with Version {
@Input(doc = "The reference file for the bam files.", required = false)
var reference: File = null
......
......@@ -26,7 +26,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
* Note that tabix can either index a file (no stdout stream) or retrieve regions from an indexed file (stdout stream)
*
*/
class Tabix(val root: Configurable) extends BiopetCommandLineFunction with Version {
class Tabix(val parent: Configurable) extends BiopetCommandLineFunction with Version {
@Input(doc = "Input bgzipped file", required = true)
var input: File = null
......
......@@ -23,7 +23,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input }
/**
* Created by pjvan_thof on 8/11/15.
*/
class TarExtract(val root: Configurable) extends BiopetCommandLineFunction with Version {
class TarExtract(val parent: Configurable) extends BiopetCommandLineFunction with Version {
@Input(required = true)
var inputTar: File = _
......
......@@ -23,7 +23,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/**
* Extension for Tophat
*/
class Tophat(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version {
class Tophat(val parent: Configurable) extends BiopetCommandLineFunction with Reference with Version {
executable = config("exe", default = "tophat", freeVar = false)
......
......@@ -28,7 +28,7 @@ import scala.io.Source
* Extension for VariantEffectPredictor
* Created by ahbbollen on 15-1-15.
*/
class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version with Summarizable {
class VariantEffectPredictor(val parent: Configurable) extends BiopetCommandLineFunction with Reference with Version with Summarizable {
lazy val vepVersion = new LazyCheck({
val s: Option[String] = config("vep_version")
......
......@@ -24,7 +24,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
* Created by pjvan_thof on 1/29/15.
* Versions from the executable are not reliable, this extension is based on md5 '3d033ff8a1f4ea9cb3ede12939561141' from the executable
*/
class WigToBigWig(val root: Configurable) extends BiopetCommandLineFunction {
class WigToBigWig(val parent: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "Input wig file")
var inputWigFile: File = _
......
......@@ -21,7 +21,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/** Extension for zcat */
class Zcat(val root: Configurable) extends BiopetCommandLineFunction with Version {
class Zcat(val parent: Configurable) extends BiopetCommandLineFunction with Version {
@Input(doc = "Zipped file", required = true)
var input: List[File] = Nil
......
......@@ -20,7 +20,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/** This extension is based on bcftools 1.1-134 */
class BcftoolsCall(val root: Configurable) extends Bcftools {
class BcftoolsCall(val parent: Configurable) extends Bcftools {
@Input(doc = "Input File", required = false)
var input: File = _
......
......@@ -22,7 +22,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
/**
* Created by sajvanderzeeuw on 16-10-15.
*/
class BcftoolsMerge(val root: Configurable) extends Bcftools {
class BcftoolsMerge(val parent: Configurable) extends Bcftools {
@Input(doc = "Input File", required = true)
var input: List[File] = Nil
......
......@@ -22,7 +22,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/**
* Created by ahbbollen on 12-10-15.
*/
class BcftoolsView(val root: Configurable) extends Bcftools {
class BcftoolsView(val parent: Configurable) extends Bcftools {
@Input(doc = "Input VCF file")
var input: File = _
......
......@@ -23,7 +23,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
import scala.io.Source
/** Extension for bedtools coverage */
class BedtoolsCoverage(val root: Configurable) extends Bedtools with Reference {
class BedtoolsCoverage(val parent: Configurable) extends Bedtools with Reference {
@Input(doc = "Input file (bed/gff/vcf/bam)")
var input: File = null
......
......@@ -23,9 +23,9 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
* Wrapper for the bedtools groupby tool
* Written based on bedtools v2.21.0 (md5: b5a9a64bad721d96f6cbf2b3805b0fbe)
*
* @param root [[Configurable]] object
* @param parent [[Configurable]] object
*/
class BedtoolsGroupby(val root: Configurable) extends Bedtools {
class BedtoolsGroupby(val parent: Configurable) extends Bedtools {
// input can be from stdin or a file
@Input(doc = "Input file", required = false)
......
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