From cfcb552701d0de9a844e18a05862fd2cf23d2da2 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 8 Apr 2016 08:20:11 +0200
Subject: [PATCH] Adding snptestToVcf to pipeline
---
.../biopet/pipelines/gwastest/GwasTest.scala | 19 +++++++++++++++----
1 file changed, 15 insertions(+), 4 deletions(-)
diff --git a/public/gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTest.scala b/public/gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTest.scala
index 9035928e8..15669af9b 100644
--- a/public/gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTest.scala
+++ b/public/gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTest.scala
@@ -4,10 +4,10 @@ import java.io.File
import java.util
import htsjdk.samtools.reference.FastaSequenceFile
-import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand, Reference }
+import nl.lumc.sasc.biopet.core.{BiopetQScript, PipelineCommand, Reference}
import nl.lumc.sasc.biopet.extensions.Snptest
-import nl.lumc.sasc.biopet.extensions.gatk.{ CatVariants, SelectVariants }
-import nl.lumc.sasc.biopet.extensions.tools.GensToVcf
+import nl.lumc.sasc.biopet.extensions.gatk.{CatVariants, SelectVariants}
+import nl.lumc.sasc.biopet.extensions.tools.{GensToVcf, SnptestToVcf}
import nl.lumc.sasc.biopet.pipelines.gwastest.impute.ImputeOutput
import nl.lumc.sasc.biopet.utils.Logging
import nl.lumc.sasc.biopet.utils.config.Configurable
@@ -114,8 +114,19 @@ class GwasTest(val root: Configurable) extends QScript with BiopetQScript with R
snptest.inputSampleFiles :+= phenotypeFile
snptest.outputFile = Some(new File(regionDir, s"${region.chr}-${region.start + 1}-${region.end}.snptest"))
add(snptest)
- region -> snptest
+
+ val snptestToVcf = new SnptestToVcf(this)
+ snptestToVcf.inputInfo = snptest.outputFile.get
+ snptestToVcf.outputVcf = new File(regionDir, s"${region.chr}-${region.start + 1}-${region.end}.snptest.vcf.gz")
+ add(snptestToVcf)
+
+ region -> snptestToVcf.outputVcf
}
+
+ val cv = new CatVariants(this)
+ cv.inputFiles = snpTests.map(_._2).toList
+ cv.outputFile = new File(outputDir, "snptest" + File.separator + "snptest.vcf.gz")
+ add(cv)
}
}
--
GitLab