Commit 1b56691e authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Changed default options

parent a91e1f83
......@@ -2,31 +2,30 @@ package nl.lumc.sasc.biopet.extensions.delly
import java.io.File
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import nl.lumc.sasc.biopet.core.{ Reference, BiopetQScript, PipelineCommand }
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.extensions.Ln
import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.queue.extensions.gatk.CatVariants
class Delly(val root: Configurable) extends QScript with BiopetQScript {
class Delly(val root: Configurable) extends QScript with BiopetQScript with Reference {
def this() = this(null)
@Input(doc = "Input file (bam)")
var input: File = _
@Argument(doc = "Work directory")
var workdir: String = _
var workdir: File = _
@Output(doc = "Delly result VCF")
var outputvcf: File = _
var outputBaseName: String = _
var outputBaseName: File = _
// select the analysis types DEL,DUP,INV,TRA
var del: Boolean = config("DEL", default = false)
var dup: Boolean = config("DUP", default = false)
var inv: Boolean = config("INV", default = false)
var tra: Boolean = config("TRA", default = false)
var del: Boolean = config("DEL", default = true)
var dup: Boolean = config("DUP", default = true)
var inv: Boolean = config("INV", default = true)
var tra: Boolean = config("TRA", default = true)
override def init() {
}
......@@ -77,13 +76,11 @@ class Delly(val root: Configurable) extends QScript with BiopetQScript {
var finalVCF = if (vcfFiles.size > 1) {
// do merging
// CatVariants is a $org.broadinstitute.gatk.utils.commandline.CommandLineProgram$;
//TODO: convert to biopet extension
val variants = new CatVariants()
variants.jobResourceRequests :+= "h_vmem=4G"
variants.nCoresRequest = 1
variants.memoryLimit = Option(2.0)
variants.variant = vcfFiles.values.toList
variants.reference = config("reference")
variants.outputFile = this.outputvcf
variants.reference = referenceFasta()
// add the job
add(variants)
this.outputvcf
......@@ -103,7 +100,7 @@ class Delly(val root: Configurable) extends QScript with BiopetQScript {
object Delly extends PipelineCommand {
override val pipeline = "/nl/lumc/sasc/biopet/extensions/svcallers/Delly/Delly.class"
def apply(root: Configurable, input: File, runDir: String): Delly = {
def apply(root: Configurable, input: File, runDir: File): Delly = {
val dellypipeline = new Delly(root)
dellypipeline.input = input
dellypipeline.workdir = runDir
......
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