From 4459b837a64cbe1b60fc86fb092f88e2149e8690 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sat, 1 Aug 2015 14:50:15 +0200
Subject: [PATCH] Adding gonl annotation step
---
.../sasc/biopet/pipelines/toucan/Toucan.scala | 17 +++++++++++++++--
1 file changed, 15 insertions(+), 2 deletions(-)
diff --git a/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala b/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
index 315b61cef..f7fe32091 100644
--- a/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
+++ b/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
@@ -19,7 +19,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand, Reference }
import nl.lumc.sasc.biopet.extensions.VariantEffectPredictor
-import nl.lumc.sasc.biopet.tools.VepNormalizer
+import nl.lumc.sasc.biopet.tools.{ VcfWithVcf, VepNormalizer }
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.queue.QScript
@@ -53,8 +53,21 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
val normalizer = new VepNormalizer(this)
normalizer.inputVCF = vep.output
- normalizer.outputVCF = swapExt(vep.output, ".vcf", ".normalized.vcf.gz")
+ normalizer.outputVcf = swapExt(outputDir, vep.output, ".vcf", ".normalized.vcf.gz")
add(normalizer)
+
+ val gonlVcfFile: Option[File] = config("gonl_vcf")
+ gonlVcfFile match {
+ case Some(gonlVcfFile) => {
+ val vcfWithVcf = new VcfWithVcf(this)
+ vcfWithVcf.input = normalizer.outputVcf
+ vcfWithVcf.secondaryVcf = gonlVcfFile
+ vcfWithVcf.output = swapExt(outputDir, normalizer.outputVcf, ".vcf.gz", ".gonl.vcf.gz")
+ vcfWithVcf.fields ::= ("AF", "AF_gonl", None)
+ add(vcfWithVcf)
+ }
+ case _ => normalizer.outputVcf
+ }
}
def summaryFile = new File(outputDir, "Toucan.summary.json")
--
GitLab