Commit 6ebf4f39 authored by Peter van 't Hof's avatar Peter van 't Hof

Change gvcf input

parent 7bedb39b
......@@ -15,17 +15,15 @@
*/
package nl.lumc.sasc.biopet.pipelines.toucan
import java.io.{ File, PrintWriter }
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.extensions.bcftools.BcftoolsView
import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsMerge, BedtoolsIntersect }
import nl.lumc.sasc.biopet.extensions.manwe.{ ManweSamplesImport, ManweAnnotateVcf, ManweDataSourcesAnnotate }
import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsIntersect, BedtoolsMerge }
import nl.lumc.sasc.biopet.extensions.manwe.{ ManweAnnotateVcf, ManweSamplesImport }
import nl.lumc.sasc.biopet.extensions.tools.{ GvcfToBed, VcfWithVcf, VepNormalizer }
import nl.lumc.sasc.biopet.extensions.{ Bgzip, Ln, VariantEffectPredictor }
import nl.lumc.sasc.biopet.utils.VcfUtils
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.extensions.{ Bgzip, Ln, Gzip, VariantEffectPredictor }
import nl.lumc.sasc.biopet.extensions.tools.{ GvcfToBed, VcfFilter, VcfWithVcf, VepNormalizer }
import nl.lumc.sasc.biopet.utils.{ VcfUtils, ConfigUtils }
import org.broadinstitute.gatk.queue.QScript
/**
......@@ -39,6 +37,9 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
@Input(doc = "Input VCF file", shortName = "Input", required = true)
var inputVCF: File = _
@Input(doc = "Input GVCF file", shortName = "Input", required = false)
var inputGvcf: Option[File] = None
var sampleIds: List[String] = Nil
def init(): Unit = {
inputFiles :+= new InputFile(inputVCF)
......@@ -53,17 +54,14 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
override def defaults = Map(
"varianteffectpredictor" -> Map("everything" -> true, "failed" -> 1, "allow_non_variant" -> true)
)
//defaults ++= Map("varianteffectpredictor" -> Map("everything" -> true))
def biopetScript(): Unit = {
val doVarda: Boolean = config("use_varda", default = false)
val useVcf: File = if (doVarda) {
val gVcfRoot: Option[File] = config("varda_gvcf")
val gVcf = gVcfRoot match {
case Some(s) => s
inputGvcf match {
case Some(s) => varda(inputVCF, s)
case _ => throw new IllegalArgumentException("You have not specified a GVCF file")
}
varda(inputVCF, gVcf)
} else inputVCF
val vep = new VariantEffectPredictor(this)
vep.input = useVcf
......
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