Commit c3da88c0 authored by Sander Bollen's avatar Sander Bollen
Browse files

add to kopisu

parent bfa23873
......@@ -15,9 +15,9 @@
package nl.lumc.sasc.biopet.pipelines.kopisu
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference }
import nl.lumc.sasc.biopet.pipelines.kopisu.methods.{ CnmopsMethod, ConiferMethod, FreecMethod }
import nl.lumc.sasc.biopet.utils.{ BamUtils, Logging }
import nl.lumc.sasc.biopet.core.{PipelineCommand, Reference}
import nl.lumc.sasc.biopet.pipelines.kopisu.methods.{CnmopsMethod, ConiferMethod, FreecMethod, XhmmMethod}
import nl.lumc.sasc.biopet.utils.{BamUtils, Logging}
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
......@@ -49,9 +49,13 @@ class Kopisu(val root: Configurable) extends QScript with SummaryQScript with Re
Some(new CnmopsMethod(this))
} else None
lazy val xhmmMethod = if (config("use_xhmm_method", default = false)) {
Some(new XhmmMethod(this))
} else None
// This script is in fact FreeC only.
def biopetScript() {
if (freecMethod.isEmpty && coniferMethod.isEmpty && cnMopsMethod.isEmpty) Logging.addError("No CNV method selected")
if (freecMethod.isEmpty && coniferMethod.isEmpty && cnMopsMethod.isEmpty && xhmmMethod.isEmpty) Logging.addError("No CNV method selected")
freecMethod.foreach { method =>
method.inputBams = inputBams
......@@ -71,6 +75,11 @@ class Kopisu(val root: Configurable) extends QScript with SummaryQScript with Re
add(method)
}
xhmmMethod.foreach{ method =>
method.inputBams = inputBams
method.outputDir = new File(outputDir, "xhmm_methid")
}
addSummaryJobs()
}
......@@ -79,7 +88,8 @@ class Kopisu(val root: Configurable) extends QScript with SummaryQScript with Re
"reference" -> referenceSummary,
"freec_method" -> freecMethod.isDefined,
"conifer_method" -> coniferMethod.isDefined,
"cnmops_method" -> cnMopsMethod.isDefined
"cnmops_method" -> cnMopsMethod.isDefined,
"xhmm_method" -> xhmmMethod.isDefined
)
/** File to put in the summary for thie pipeline */
......
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