Commit 2c5d1151 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Automatic class name conversion

parent 16182a89
......@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.core
trait PipelineCommand extends MainCommand {
val pipeline = ""
def pipeline = "/" + getClass.getName.stripSuffix("$").replaceAll("\\.", "/") + ".class"
def main(args: Array[String]): Unit = {
var argv: Array[String] = Array()
......
......@@ -73,8 +73,6 @@ class BamMetrics(val root: Configurable) extends QScript with BiopetQScript {
}
object BamMetrics extends PipelineCommand {
override val pipeline = "/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.class"
def apply(root: Configurable, bamFile: File, outputDir: String): BamMetrics = {
val bamMetrics = new BamMetrics(root)
bamMetrics.inputBam = bamFile
......
......@@ -55,6 +55,4 @@ class Basty (val root: Configurable) extends QScript with MultiSampleQScript {
}
}
object Basty extends PipelineCommand {
override val pipeline = "/nl/lumc/sasc/biopet/pipelines/basty/Basty.class"
}
object Basty extends PipelineCommand
......@@ -272,6 +272,4 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
}
}
object Flexiprep extends PipelineCommand {
override val pipeline = "/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.class"
}
object Flexiprep extends PipelineCommand
......@@ -58,6 +58,4 @@ class GatkBenchmarkGenotyping(val root: Configurable) extends QScript with Biope
}
}
object GatkBenchmarkGenotyping extends PipelineCommand {
override val pipeline = "/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.class"
}
object GatkBenchmarkGenotyping extends PipelineCommand
......@@ -57,6 +57,4 @@ class GatkGenotyping(val root: Configurable) extends QScript with BiopetQScript
}
}
object GatkGenotyping extends PipelineCommand {
override val pipeline = "/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.class"
}
object GatkGenotyping extends PipelineCommand
......@@ -214,6 +214,4 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
}
}
object GatkPipeline extends PipelineCommand {
override val pipeline = "/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.class"
}
object GatkPipeline extends PipelineCommand
......@@ -73,6 +73,4 @@ class GatkVariantRecalibration(val root: Configurable) extends QScript with Biop
}
}
object GatkVariantRecalibration extends PipelineCommand {
override val pipeline = "/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantRecalibration.class"
}
object GatkVariantRecalibration extends PipelineCommand
......@@ -221,8 +221,6 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
}
object GatkVariantcalling extends PipelineCommand {
override val pipeline = "/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.class"
class ScriptOutput {
var bamFiles: List[File] = _
var gvcfFile: File = _
......
......@@ -87,6 +87,4 @@ class GatkVcfSampleCompare(val root: Configurable) extends QScript with BiopetQS
}
}
object GatkVcfSampleCompare extends PipelineCommand {
override val pipeline = "/nl/lumc/sasc/biopet/pipelines/gatk/GatkVcfSampleCompare.class"
}
object GatkVcfSampleCompare extends PipelineCommand
......@@ -76,6 +76,4 @@ class Gentrap(val root: Configurable) extends QScript with BiopetQScript {
}
}
object Gentrap extends PipelineCommand {
override val pipeline = "/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.class"
}
object Gentrap extends PipelineCommand
......@@ -278,8 +278,6 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
}
object Mapping extends PipelineCommand {
override val pipeline = "/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.class"
def loadFromLibraryConfig(root: Configurable, runConfig: Map[String, Any], sampleConfig: Map[String, Any], runDir: String): Mapping = {
val mapping = new Mapping(root)
......
......@@ -197,6 +197,4 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
}
}
object Sage extends PipelineCommand {
override val pipeline = "/nl/lumc/sasc/biopet/pipelines/sage/Sage.class"
}
object Sage extends PipelineCommand
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