From ffa834681aff5535ec03215158a0ea7336693bf9 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 25 Mar 2016 17:32:22 +0100
Subject: [PATCH] Added output file to snptest
---
.../nl/lumc/sasc/biopet/extensions/Snptest.scala | 8 ++++----
.../sasc/biopet/pipelines/gwastest/GwasTest.scala | 3 ++-
.../pipelines/gwastest/impute/ImputeOutput.scala | 12 ++++--------
3 files changed, 10 insertions(+), 13 deletions(-)
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Snptest.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Snptest.scala
index 24ff7f029..9d43e04e7 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Snptest.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Snptest.scala
@@ -2,15 +2,15 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
-import nl.lumc.sasc.biopet.core.{Version, Reference, BiopetCommandLineFunction}
+import nl.lumc.sasc.biopet.core.{ Version, Reference, BiopetCommandLineFunction }
import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Output, Input}
+import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
import scala.util.matching.Regex
/**
- * Created by pjvan_thof on 3/25/16.
- */
+ * Created by pjvan_thof on 3/25/16.
+ */
class Snptest(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version {
@Input(required = true)
var inputGenotypes: List[File] = Nil
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 b18c3f6e2..ea8bc0b22 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
@@ -5,7 +5,7 @@ import java.util
import htsjdk.samtools.reference.FastaSequenceFile
import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference, BiopetQScript }
-import nl.lumc.sasc.biopet.extensions.{Snptest, Cat}
+import nl.lumc.sasc.biopet.extensions.{ Snptest, Cat }
import nl.lumc.sasc.biopet.extensions.gatk.{ SelectVariants, CombineVariants }
import nl.lumc.sasc.biopet.extensions.tools.GensToVcf
import nl.lumc.sasc.biopet.utils.Logging
@@ -104,6 +104,7 @@ class GwasTest(val root: Configurable) extends QScript with BiopetQScript with R
val snptest = new Snptest(this)
snptest.inputGenotypes :+= sv.outputFile
snptest.inputSampleFiles :+= phenotypeFile
+ snptest.outputFile = Some(new File(regionDir, s"${region.chr}-${region.start + 1}-${region.end}.snptest"))
add(snptest)
region -> snptest
}
diff --git a/public/gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/impute/ImputeOutput.scala b/public/gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/impute/ImputeOutput.scala
index 5beda972d..41574f0cd 100644
--- a/public/gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/impute/ImputeOutput.scala
+++ b/public/gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/impute/ImputeOutput.scala
@@ -58,21 +58,17 @@ object ImputeOutput {
else if (summaryLines.contains(NO_TYPE_2)) {
Logging.logger.warn(s"No Type 2 SNPs found, skipping this chunk: '${chunk.summary}'")
None
- }
- else if (summaryLines.exists(ASSESSMENT_HEADER.findFirstIn(_).isDefined)) None
+ } else if (summaryLines.exists(ASSESSMENT_HEADER.findFirstIn(_).isDefined)) None
else if (!chunk.gens.exists()) {
addError(s"Gens file '${chunk.gens}' does not exist, please check Impute output")
None
- }
- else if (!chunk.gensInfo.exists()) {
+ } else if (!chunk.gensInfo.exists()) {
addError(s"GensInfo file '${chunk.gensInfo}' does not exist, please check Impute output")
None
- }
- else if (!chunk.gensInfoBySample.exists()) {
+ } else if (!chunk.gensInfoBySample.exists()) {
addError(s"GensInfoBySample file '${chunk.gensInfoBySample}' does not exist, please check Impute output")
None
- }
- else {
+ } else {
if (!summaryLines.contains(CORRECT_LOG)) {
Logging.logger.warn(s"Impute says it did not run but the gens files are there, pipeline will still continue")
Logging.logger.warn(s" Please check: ${chunk.summary}")
--
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