...
 
Commits (7)
......@@ -6,14 +6,14 @@ node('local') {
tool 'Apache Maven 3.3.9'
}
timeout(45) {
timeout(120) {
stage('Checkout') {
checkout scm
sh 'git submodule update --init --recursive'
}
}
timeout(45) {
timeout(120) {
stage('Build and Test') {
withMaven(maven: 'Apache Maven 3.3.9', jdk: 'JDK 8u102') {
sh 'mvn -B -T 2 -Dmaven.test.failure.ignore clean package'
......
......@@ -118,10 +118,10 @@ samples:
sample1:
tags:
type: tumor
normal: sample2
control: sample2
sample2:
tags:
type: normal
type: control
```
## Config options
......
......@@ -87,12 +87,12 @@ class ShivaVariantcalling(val parent: Configurable)
if (Option(tumorSamples).isEmpty)
tumorSamples = inputBams.keys
.filter(name =>
config("type", path = "samples" :: name :: "tags" :: Nil, default = "normal").asString.toLowerCase == "tumor")
config("type", path = "samples" :: name :: "tags" :: Nil, default = "control").asString.toLowerCase == "tumor")
.map { tumorSample =>
val normal: String = config("normal", path = "samples" :: tumorSample :: "tags" :: Nil)
if (!inputBams.keySet.contains(normal))
Logging.addError(s"Normal sample '$normal' does not exist")
TumorNormalPair(tumorSample, normal)
val control: String = config("control", path = "samples" :: tumorSample :: "tags" :: Nil)
if (!inputBams.keySet.contains(control))
Logging.addError(s"Control sample '$control' does not exist")
TumorNormalPair(tumorSample, control)
}
.toList
}
......
......@@ -133,7 +133,7 @@ trait ShivaVariantcallingTestTrait extends TestNGSuite with Matchers {
case (m, pair) =>
val tag = Map(
"samples" -> Map(pair.tumorSample -> Map(
"tags" -> Map("type" -> "tumor", "normal" -> pair.normalSample))))
"tags" -> Map("type" -> "tumor", "control" -> pair.normalSample))))
ConfigUtils.mergeMaps(m, tag)
}
val map = sampleTags ++ Map(
......