Commit 6598b281 authored by Peter van 't Hof's avatar Peter van 't Hof

Added gears as optional step into mapping

parent bbc185f4
......@@ -43,6 +43,11 @@
<artifactId>Flexiprep</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Gears</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BamMetrics</artifactId>
......
......@@ -19,6 +19,7 @@ import java.io.File
import java.util.Date
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.pipelines.gears.Gears
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.extensions.bwa.{ BwaAln, BwaMem, BwaSampe, BwaSamse }
......@@ -273,6 +274,15 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
add(Ln(this, bamFile, finalBamFile))
outputFiles += ("finalBamFile" -> finalBamFile.getAbsoluteFile)
if (config("unmapped_to_gears", default = false).asBoolean) {
val gears = new Gears(this)
gears.bamFile = Some(finalBamFile)
gears.outputDir = new File(outputDir, "gears")
gears.init()
gears.biopetScript()
addAll(gears.functions)
}
if (config("generate_wig", default = false).asBoolean)
addAll(Bam2Wig(this, finalBamFile).functions)
......
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