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