Commit 9ca827e9 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix add method

parent 5d834e35
......@@ -18,11 +18,14 @@ package nl.lumc.sasc.biopet.pipelines.shiva
import java.io.File
import htsjdk.samtools.SamReaderFactory
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.{ PipelineCommand, BiopetQScript, Reference, SampleLibraryTag }
import nl.lumc.sasc.biopet.extensions.breakdancer.Breakdancer
import nl.lumc.sasc.biopet.extensions.clever.CleverCaller
import nl.lumc.sasc.biopet.extensions.delly.Delly
import nl.lumc.sasc.biopet.tools.VcfStats
import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.utils.commandline.Input
import scala.collection.JavaConversions._
......@@ -31,9 +34,11 @@ import scala.collection.JavaConversions._
*
* Created by pjvan_thof on 2/26/15.
*/
class ShivaSvCalling extends SummaryQScript with SampleLibraryTag with Reference {
class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag with Reference {
qscript =>
def this() = this(null)
@Input(doc = "Bam files (should be deduped bams)", shortName = "BAM", required = true)
protected var inputBamsArg: List[File] = Nil
......@@ -73,6 +78,8 @@ class ShivaSvCalling extends SummaryQScript with SampleLibraryTag with Reference
require(inputBams.nonEmpty, "No input bams found")
require(callers.nonEmpty, "must select at least 1 SV caller, choices are: " + callersList.map(_.name).mkString(", "))
callers.foreach(_.addJobs())
addSummaryJobs()
}
......@@ -113,7 +120,7 @@ class ShivaSvCalling extends SummaryQScript with SampleLibraryTag with Reference
//TODO: check double directories
for ((sample, bamFile) <- inputBams) {
val cleverDir = new File(outputDir, sample)
val clever = CleverCaller(qscript, bamFile, qscript.reference, cleverDir, cleverDir)
val clever = CleverCaller(qscript, bamFile, cleverDir, cleverDir)
add(clever)
}
}
......
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