From c02fcacd9ca231b61838082ee08ad1fab5593379 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 24 Sep 2015 17:10:36 +0200
Subject: [PATCH] Remove some test from shiva-gatk
---
.../biopet/pipelines/gatk/ShivaTest.scala | 43 ++++++-------------
public/pom.xml | 7 ++-
2 files changed, 20 insertions(+), 30 deletions(-)
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 9395daa1d..767b655e4 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
@@ -39,31 +39,27 @@ class ShivaTest extends TestNGSuite with Matchers {
val bool = Array(true, false)
for (
- s1 <- bool; s2 <- bool; s3 <- bool; multi <- bool; single <- bool;
- library <- bool; dbsnp <- bool; covariates <- bool; realign <- bool; baseRecalibration <- bool
- ) yield Array("", s1, s2, s3, multi, single, library, dbsnp, covariates, realign, baseRecalibration)
+ s1 <- bool; s2 <- bool; multi <- bool;
+ dbsnp <- bool; realign <- bool; baseRecalibration <- bool
+ ) yield Array("", s1, s2, multi, dbsnp, realign, baseRecalibration)
}
@Test(dataProvider = "shivaOptions")
- def testShiva(f: String, sample1: Boolean, sample2: Boolean, sample3: Boolean,
- multi: Boolean, single: Boolean, library: Boolean, dbsnp: Boolean,
- covariates: Boolean, realign: Boolean, baseRecalibration: Boolean): Unit = {
+ def testShiva(f: String, sample1: Boolean, sample2: Boolean,
+ multi: Boolean, dbsnp: Boolean,
+ realign: Boolean, baseRecalibration: Boolean): Unit = {
val map = {
var m: Map[String, Any] = ShivaTest.config
if (sample1) m = ConfigUtils.mergeMaps(ShivaTest.sample1, m)
if (sample2) m = ConfigUtils.mergeMaps(ShivaTest.sample2, m)
- if (sample3) m = ConfigUtils.mergeMaps(ShivaTest.sample3, m)
if (dbsnp) m = ConfigUtils.mergeMaps(Map("dbsnp" -> "test"), m)
ConfigUtils.mergeMaps(Map("multisample_variantcalling" -> multi,
- "single_sample_variantcalling" -> single,
- "library_variantcalling" -> library,
- "use_analyze_covariates" -> covariates,
"use_indel_realigner" -> realign,
"use_base_recalibration" -> baseRecalibration), m)
}
- if (!sample1 && !sample2 && !sample3) { // When no samples
+ if (!sample1 && !sample2) { // When no samples
intercept[IllegalArgumentException] {
initPipeline(map).script()
}
@@ -71,22 +67,20 @@ class ShivaTest extends TestNGSuite with Matchers {
val pipeline = initPipeline(map)
pipeline.script()
- val numberLibs = (if (sample1) 1 else 0) + (if (sample2) 1 else 0) + (if (sample3) 2 else 0)
- val numberSamples = (if (sample1) 1 else 0) + (if (sample2) 1 else 0) + (if (sample3) 1 else 0)
+ val numberLibs = (if (sample1) 1 else 0) + (if (sample2) 2 else 0)
+ val numberSamples = (if (sample1) 1 else 0) + (if (sample2) 1 else 0)
pipeline.functions.count(_.isInstanceOf[BwaMem]) shouldBe numberLibs
pipeline.functions.count(_.isInstanceOf[SortSam]) shouldBe numberLibs
- pipeline.functions.count(_.isInstanceOf[MarkDuplicates]) shouldBe (numberLibs + (if (sample3) 1 else 0))
+ pipeline.functions.count(_.isInstanceOf[MarkDuplicates]) shouldBe (numberLibs + (if (sample2) 1 else 0))
// Gatk preprocess
- pipeline.functions.count(_.isInstanceOf[IndelRealigner]) shouldBe (numberLibs + (if (sample3) 1 else 0)) * (if (realign) 1 else 0)
- pipeline.functions.count(_.isInstanceOf[RealignerTargetCreator]) shouldBe (numberLibs + (if (sample3) 1 else 0)) * (if (realign) 1 else 0)
- pipeline.functions.count(_.isInstanceOf[BaseRecalibrator]) shouldBe (if (dbsnp && baseRecalibration) numberLibs else 0) * (if (covariates) 2 else 1)
- pipeline.functions.count(_.isInstanceOf[AnalyzeCovariates]) shouldBe (if (dbsnp && covariates && baseRecalibration) numberLibs else 0)
+ pipeline.functions.count(_.isInstanceOf[IndelRealigner]) shouldBe (numberLibs * (if (realign) 1 else 0) + (if (sample2 && realign) 1 else 0))
+ pipeline.functions.count(_.isInstanceOf[RealignerTargetCreator]) shouldBe (numberLibs * (if (realign) 1 else 0) + (if (sample2 && realign) 1 else 0))
+ pipeline.functions.count(_.isInstanceOf[BaseRecalibrator]) shouldBe (if (dbsnp && baseRecalibration) numberLibs else 0)
pipeline.functions.count(_.isInstanceOf[PrintReads]) shouldBe (if (dbsnp && baseRecalibration) numberLibs else 0)
- pipeline.functions.count(_.isInstanceOf[VcfStats]) shouldBe (if (multi) 2 else 0) +
- (if (single) numberSamples * 2 else 0) + (if (library) numberLibs * 2 else 0)
+ pipeline.functions.count(_.isInstanceOf[VcfStats]) shouldBe (if (multi) 2 else 0)
}
}
}
@@ -143,15 +137,6 @@ object ShivaTest {
)))
val sample2 = Map(
- "samples" -> Map("sample2" -> Map("libraries" -> Map(
- "lib1" -> Map(
- "R1" -> "2_1_R1.fq",
- "R2" -> "2_1_R2.fq"
- )
- )
- )))
-
- val sample3 = Map(
"samples" -> Map("sample3" -> Map("libraries" -> Map(
"lib1" -> Map(
"R1" -> "3_1_R1.fq",
diff --git a/public/pom.xml b/public/pom.xml
index cf2ea52f0..3c49b66c1 100644
--- a/public/pom.xml
+++ b/public/pom.xml
@@ -50,7 +50,7 @@
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
- <scoverage.plugin.version>1.0.4</scoverage.plugin.version>
+ <scoverage.plugin.version>1.1.1</scoverage.plugin.version>
</properties>
<build>
@@ -246,6 +246,11 @@
<scalaVersion>2.10.2</scalaVersion>
<!-- other parameters -->
</configuration>
+ <executions>
+ <execution>
+ <phase>test</phase>
+ </execution>
+ </executions>
</plugin>
</plugins>
</build>
--
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