Commit 8506c344 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Config name change

parent fea40cc0
...@@ -38,7 +38,7 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait { ...@@ -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 */ /** This will adds preprocess steps, gatk indel realignment and base recalibration is included here */
override def preProcess(input: File): Option[File] = { 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) val useBaseRecalibration: Boolean = config("use_base_recalibration", default = true)
if (!useIndelRealigner && !useBaseRecalibration) None if (!useIndelRealigner && !useBaseRecalibration) None
...@@ -61,7 +61,7 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait { ...@@ -61,7 +61,7 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
if (input.size <= 1) super.addDoublePreProcess(input) if (input.size <= 1) super.addDoublePreProcess(input)
else super.addDoublePreProcess(input, true).collect { else super.addDoublePreProcess(input, true).collect {
case file => { 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 true => addIndelRealign(file, sampleDir, false)
case false => file case false => file
} }
......
...@@ -48,7 +48,9 @@ class ShivaTest extends TestNGSuite with Matchers { ...@@ -48,7 +48,9 @@ class ShivaTest extends TestNGSuite with Matchers {
ConfigUtils.mergeMaps(Map("multisample_sample_variantcalling" -> multi, ConfigUtils.mergeMaps(Map("multisample_sample_variantcalling" -> multi,
"single_sample_variantcalling" -> single, "single_sample_variantcalling" -> single,
"library_variantcalling" -> library, "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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