From 046d7d2b00b98d93cdb8639072593aa0adb2ab08 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sat, 1 Aug 2015 15:04:46 +0200
Subject: [PATCH] Adding exac annotation step
---
.../sasc/biopet/pipelines/toucan/Toucan.scala | 23 +++++++++++++++++--
1 file changed, 21 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 f7fe32091..8774bdc98 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
@@ -56,17 +56,36 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
normalizer.outputVcf = swapExt(outputDir, vep.output, ".vcf", ".normalized.vcf.gz")
add(normalizer)
+ // Optional annotation steps, depend is some files existing in the config
val gonlVcfFile: Option[File] = config("gonl_vcf")
+ val exacVcfFile: Option[File] = config("exac_vcf")
+
+ var outputFile = normalizer.outputVcf
+
gonlVcfFile match {
case Some(gonlVcfFile) => {
val vcfWithVcf = new VcfWithVcf(this)
- vcfWithVcf.input = normalizer.outputVcf
+ vcfWithVcf.input = outputFile
vcfWithVcf.secondaryVcf = gonlVcfFile
vcfWithVcf.output = swapExt(outputDir, normalizer.outputVcf, ".vcf.gz", ".gonl.vcf.gz")
vcfWithVcf.fields ::= ("AF", "AF_gonl", None)
add(vcfWithVcf)
+ outputFile = vcfWithVcf.output
+ }
+ case _ =>
+ }
+
+ exacVcfFile match {
+ case Some(exacVcfFile) => {
+ val vcfWithVcf = new VcfWithVcf(this)
+ vcfWithVcf.input = outputFile
+ vcfWithVcf.secondaryVcf = exacVcfFile
+ vcfWithVcf.output = swapExt(outputDir, outputFile, ".vcf.gz", ".exac.vcf.gz")
+ vcfWithVcf.fields ::= ("MAF", "MAF_exac", None)
+ add(vcfWithVcf)
+ outputFile = vcfWithVcf.output
}
- case _ => normalizer.outputVcf
+ case _ =>
}
}
--
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