Commit 54d818a2 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Changed Queue wrapper

parent 48cfa704
......@@ -9,7 +9,7 @@ import java.io.PrintWriter
import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import nl.lumc.sasc.biopet.core.ToolCommand
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import scala.collection.JavaConversions._
import nl.lumc.sasc.biopet.util.VcfUtils._
......@@ -22,30 +22,39 @@ class BastyGenerateFasta(val root: Configurable) extends BiopetJavaCommandLineFu
@Input(doc = "Bam File", required = false)
var bamFile: File = _
@Input(doc = "reference", required = false)
var reference: File = config("reference")
@Output(doc = "Output fasta, variants only", required = false)
var outputVariants: File = _
@Argument(doc = "Output interval list", required = false)
var snpsOnly: Boolean = config("snps_only", default = false)
@Output(doc = "Output fasta, variants only", required = false)
var outputConsensus: File = _
@Argument(doc = "Sample name", required = false)
var sampleName: String = _
@Output(doc = "Output fasta, variants only", required = false)
var outputConsensusVariants: File = _
@Argument(doc = "minAD", required = false)
var snpsOnly: Boolean = config("snps_only", default = false)
var sampleName: String = _
var minAD: Int = config("min_ad", default = 8)
var minDepth: Int = config("min_depth", default = 8)
var outputName: String = _
override val defaultVmem = "8G"
memoryLimit = Option(4.0)
var reference = false
override def commandLine = super.commandLine +
optional("--inputVcf", inputVcf) +
optional("--bamFile", bamFile) +
optional("--outputVariants", outputVariants) +
optional("--outputVariants", outputConsensus) +
optional("--outputVariants", outputConsensusVariants) +
conditional(snpsOnly, "--snpsOnly") +
optional("--sampleName", sampleName) +
required("--outputName", outputName) +
optional("--minAD", minAD) +
conditional(reference, "--reference")
optional("--minDepth", minDepth) +
optional("--reference", reference)
}
object BastyGenerateFasta extends ToolCommand {
......
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