From 8506c3445b508dbf5ebee7d4b55c0d6b944b0fe7 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 9 Mar 2015 09:06:24 +0100
Subject: [PATCH] Config name change
---
.../main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala | 4 ++--
.../scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala | 4 +++-
2 files changed, 5 insertions(+), 3 deletions(-)
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala
index dede78c02..f52d77465 100644
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala
+++ b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala
@@ -38,7 +38,7 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
/** This will adds preprocess steps, gatk indel realignment and base recalibration is included here */
override def preProcess(input: File): Option[File] = {
- val useIndelRealigner: Boolean = config("use_indel_realign", default = true)
+ val useIndelRealigner: Boolean = config("use_indel_realigner", default = true)
val useBaseRecalibration: Boolean = config("use_base_recalibration", default = true)
if (!useIndelRealigner && !useBaseRecalibration) None
@@ -61,7 +61,7 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
if (input.size <= 1) super.addDoublePreProcess(input)
else super.addDoublePreProcess(input, true).collect {
case file => {
- config("use_indel_realign", default = true).asBoolean match {
+ config("use_indel_realigner", default = true).asBoolean match {
case true => addIndelRealign(file, sampleDir, false)
case false => file
}
diff --git a/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala b/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
index 79f3ac9bd..76ac82d34 100644
--- a/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
+++ b/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
@@ -48,7 +48,9 @@ class ShivaTest extends TestNGSuite with Matchers {
ConfigUtils.mergeMaps(Map("multisample_sample_variantcalling" -> multi,
"single_sample_variantcalling" -> single,
"library_variantcalling" -> library,
- "use_analyze_covariates" -> covariates, "use_indel_realign" -> realign, "use_base_recalibration" -> baseRecalibration), m.toMap)
+ "use_analyze_covariates" -> covariates,
+ "use_indel_realigner" -> realign,
+ "use_base_recalibration" -> baseRecalibration), m.toMap)
}
--
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