Commit ca0d9e93 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added a apply function

parent dde4c848
package nl.lumc.sasc.biopet.pipelines.bamtobigwig
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import nl.lumc.sasc.biopet.extensions.WigToBigWig
......@@ -41,4 +43,13 @@ class Bam2Wig(val root: Configurable) extends QScript with BiopetQScript {
}
}
object Bam2Wig extends PipelineCommand
\ No newline at end of file
object Bam2Wig extends PipelineCommand {
def apply(root: Configurable, bamFile: File): Bam2Wig = {
val bamToBigWig = new Bam2Wig(root)
bamToBigWig.outputDir = bamFile.getParent
bamToBigWig.bamFile = bamFile
bamToBigWig.init()
bamToBigWig.biopetScript()
bamToBigWig
}
}
\ No newline at end of file
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