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

Rename root to parent

parent 463f8002
......@@ -130,7 +130,7 @@ object SummaryQScriptTest {
def summaryFile: File = tempFile
def init(): Unit = ???
def biopetScript(): Unit = ???
def root: Configurable = null
def parent: Configurable = null
}
def makeSummarizable(files: Map[String, File] = Map(), stats: Map[String, Any] = Map()) = new Summarizable {
......
......@@ -238,7 +238,7 @@ object WriteSummaryTest {
def summaryFile: File = tempFile
def init(): Unit = {}
def biopetScript(): Unit = {}
def root: Configurable = null
def parent: Configurable = null
}
def makeSampleLibraryQscript(name: String,
......@@ -260,7 +260,7 @@ object WriteSummaryTest {
def summaryFile: File = tempFile
def init(): Unit = {}
def biopetScript(): Unit = {}
def root: Configurable = null
def parent: Configurable = null
}
def makeMultisampleQscript(name: String,
......@@ -278,7 +278,7 @@ object WriteSummaryTest {
def summaryFile: File = tempFile
def init(): Unit = {}
def biopetScript(): Unit = {}
def root: Configurable = null
def parent: Configurable = null
class Sample(id: String) extends AbstractSample(id) {
class Library(id: String) extends AbstractLibrary(id) {
......@@ -310,7 +310,7 @@ object WriteSummaryTest {
c: Map[String, Any] = Map()) = new BiopetJavaCommandLineFunction with Summarizable with Version {
override def globalConfig = new Config(c)
override def configNamespace = "java_command"
def root: Configurable = null
def parent: Configurable = null
def summaryStats: Map[String, Any] = stats
def summaryFiles: Map[String, File] = files
......@@ -335,7 +335,7 @@ object WriteSummaryTest {
new CommandLineFunction with Configurable with Summarizable with Version {
override def globalConfig = new Config(c)
override def configNamespace = "version_command"
def root: Configurable = null
def parent: Configurable = null
def summaryFiles: Map[String, File] = files
def summaryStats: Any = stats
......
......@@ -25,7 +25,7 @@ import scala.util.matching.Regex
/**
* Created by pjvan_thof on 17-5-16.
*/
class Awk(val root: Configurable) extends BiopetCommandLineFunction with Version {
class Awk(val parent: Configurable) extends BiopetCommandLineFunction with Version {
executable = config("exe", default = "awk", freeVar = false)
def versionCommand: String = executable + " --version"
......
......@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/** Wrapper for the bgzip command */
class Bgzip(val root: Configurable) extends BiopetCommandLineFunction {
class Bgzip(val parent: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "Input files", required = false)
var input: List[File] = Nil
......
......@@ -23,7 +23,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* Extension for GNU cat
*/
class Cat(val root: Configurable) extends BiopetCommandLineFunction {
class Cat(val parent: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "Input file", required = true)
var input: List[File] = Nil
......
......@@ -27,7 +27,7 @@ import nl.lumc.sasc.biopet.utils.getSemanticVersion
* Wrapper for the Cnmops command line tool.
* Written based on Cnmops version v2.2.1.
*/
class Cnmops(val root: Configurable) extends RscriptCommandLineFunction with Version {
class Cnmops(val parent: Configurable) extends RscriptCommandLineFunction with Version {
override def defaultThreads = 4
override def defaultCoreMemory: Double = 4.0
......
......@@ -24,7 +24,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
* Wrapper for the cufflinks command line tool.
* Written based on cufflinks version v2.2.1 (md5: 07c831c4f8b4e161882731ea5694ff80)
*/
class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction with Version {
class Cufflinks(val parent: Configurable) extends BiopetCommandLineFunction with Version {
/** default executable */
executable = config("exe", default = "cufflinks")
......
......@@ -24,7 +24,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
* Wrapper for the cuffquant command line tool.
* Written based on cuffquant version v2.2.1 (md5: 0765b82b11db9256f5be341a7da884d6)
*/
class Cuffquant(val root: Configurable) extends BiopetCommandLineFunction with Version {
class Cuffquant(val parent: Configurable) extends BiopetCommandLineFunction with Version {
/** default executable */
executable = config("exe", default = "cuffquant")
......
......@@ -23,7 +23,7 @@ import org.broadinstitute.gatk.utils.commandline.Output
/**
* Created by pjvan_thof on 8/11/15.
*/
class Curl(val root: Configurable) extends BiopetCommandLineFunction with Version {
class Curl(val parent: Configurable) extends BiopetCommandLineFunction with Version {
@Output
var output: File = _
......
......@@ -30,7 +30,7 @@ import scala.util.matching.Regex
* Started with version 1.5
* Updated to version 1.9 (18-01-2016 by wyleung)
*/
class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Summarizable with Version {
class Cutadapt(val parent: Configurable) extends BiopetCommandLineFunction with Summarizable with Version {
@Input(doc = "Input fastq file")
var fastqInput: File = _
......
......@@ -24,7 +24,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
* Extension for fastqc
* Based on version 0.10.1 and 0.11.2
*/
class Fastqc(val root: Configurable) extends BiopetCommandLineFunction with Version {
class Fastqc(val parent: Configurable) extends BiopetCommandLineFunction with Version {
@Input(doc = "Contaminants", required = false)
var contaminants: Option[File] = None
......
......@@ -25,7 +25,7 @@ import scala.util.matching.Regex
/**
* Created by pjvanthof on 16/12/15.
*/
class Flash(val root: Configurable) extends BiopetCommandLineFunction with Version {
class Flash(val parent: Configurable) extends BiopetCommandLineFunction with Version {
executable = config("exe", default = "flash", freeVar = false)
/** Command to get version of executable */
......
......@@ -25,7 +25,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
*
* Created by pjvan_thof on 3/3/15.
*/
class Freebayes(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version {
class Freebayes(val parent: Configurable) extends BiopetCommandLineFunction with Reference with Version {
@Input(required = true)
var bamfiles: List[File] = Nil
......
......@@ -23,7 +23,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* Created by pjvanthof on 20/06/16.
*/
class GffRead(val root: Configurable) extends BiopetCommandLineFunction {
class GffRead(val parent: Configurable) extends BiopetCommandLineFunction {
executable = config("exe", default = "gffread", freeVar = false)
......
......@@ -23,7 +23,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* Created by pjvanthof on 30/03/16.
*/
class Grep(val root: Configurable) extends BiopetCommandLineFunction {
class Grep(val parent: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "Input file", required = true)
var input: File = _
......
......@@ -23,7 +23,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* Created by pjvan_thof on 17-5-16.
*/
class GtfToGenePred(val root: Configurable) extends BiopetCommandLineFunction {
class GtfToGenePred(val parent: Configurable) extends BiopetCommandLineFunction {
executable = config("exe", default = "gtfToGenePred", freeVar = false)
@Input
......
......@@ -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 Gzip(val root: Configurable) extends BiopetCommandLineFunction with Version {
class Gzip(val parent: Configurable) extends BiopetCommandLineFunction with Version {
@Input(doc = "Input file", required = true)
var input: List[File] = Nil
......
......@@ -24,7 +24,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
* Wrapper for the htseq-count command line tool
* Written based on htseq-count version 0.6.1p1
*/
class HtseqCount(val root: Configurable) extends BiopetCommandLineFunction with Version {
class HtseqCount(val parent: Configurable) extends BiopetCommandLineFunction with Version {
/** default executable */
executable = config("exe", default = "htseq-count")
......
......@@ -25,7 +25,7 @@ import scala.sys.process.{ Process, ProcessLogger }
/**
* This class can execute ln as InProcessFunction or used to only generate the ln command
*/
class Ln(val root: Configurable) extends InProcessFunction with Configurable {
class Ln(val parent: Configurable) extends InProcessFunction with Configurable {
this.analysisName = getClass.getSimpleName
@Input(doc = "Input file")
......
......@@ -21,7 +21,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/** Extension for pbzip2 */
class Pbzip2(val root: Configurable) extends BiopetCommandLineFunction {
class Pbzip2(val parent: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "Zipped file")
var input: File = _
......
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