Remove some test from shiva-gatk

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",

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>