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 {
/** 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
}
......
......@@ -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)
}
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment