Added unit test to do some magic

protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala → protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingGatkTest.scala

@@ -5,25 +5,25 @@ import java.io.File
 import com.google.common.io.Files
 import nl.lumc.sasc.biopet.core.config.Config
 import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
-import nl.lumc.sasc.biopet.extensions.gatk.broad.{UnifiedGenotyper, HaplotypeCaller}
-import nl.lumc.sasc.biopet.tools.{VcfStats, MpileupToVcf, VcfFilter}
+import nl.lumc.sasc.biopet.extensions.gatk.broad.{ UnifiedGenotyper, HaplotypeCaller }
+import nl.lumc.sasc.biopet.tools.{ VcfStats, MpileupToVcf, VcfFilter }
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.apache.commons.io.FileUtils
 import org.broadinstitute.gatk.queue.QSettings
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.{DataProvider, Test, AfterClass}
+import org.testng.annotations.{ DataProvider, Test, AfterClass }
 
 import scala.collection.mutable.ListBuffer
 
 /**
  * Created by pjvan_thof on 3/2/15.
  */
-class ShivaVariantcallingTest extends TestNGSuite with Matchers {
+class ShivaVariantcallingGatkTest extends TestNGSuite with Matchers {
   def initPipeline(map: Map[String, Any]): ShivaVariantcallingGatk = {
     new ShivaVariantcallingGatk() {
       override def configName = "shivavariantcalling"
-      override def globalConfig = new Config(ConfigUtils.mergeMaps(map, ShivaVariantcallingTest.config))
+      override def globalConfig = new Config(ConfigUtils.mergeMaps(map, ShivaVariantcallingGatkTest.config))
       qSettings = new QSettings
       qSettings.runName = "test"
     }
@@ -31,23 +31,17 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
 
   @DataProvider(name = "shivaVariantcallingOptions")
   def shivaVariantcallingOptions = {
-    val raw = Array(true, false)
-    val bcftools = Array(true, false)
-    val haplotypeCallerGvcf = Array(true, false)
-    val haplotypeCallerAllele = Array(true, false)
-    val unifiedGenotyperAllele = Array(true, false)
-    val unifiedGenotyper = Array(true, false)
-    val haplotypeCaller = Array(true, false)
+    val bool = Array(true, false)
 
     (for (
       bams <- 0 to 2;
-      raw <- raw;
-      bcftools <- bcftools;
-      haplotypeCallerGvcf <- haplotypeCallerGvcf;
-      haplotypeCallerAllele <- haplotypeCallerAllele;
-      unifiedGenotyperAllele <- unifiedGenotyperAllele;
-      unifiedGenotyper <- unifiedGenotyper;
-      haplotypeCaller <- haplotypeCaller
+      raw <- bool;
+      bcftools <- bool;
+      haplotypeCallerGvcf <- bool;
+      haplotypeCallerAllele <- bool;
+      unifiedGenotyperAllele <- bool;
+      unifiedGenotyper <- bool;
+      haplotypeCaller <- bool
     ) yield Array[Any](bams, raw, bcftools, unifiedGenotyper, haplotypeCaller, haplotypeCallerGvcf, haplotypeCallerAllele, unifiedGenotyperAllele)
     ).toArray
   }
@@ -69,7 +63,7 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
     if (haplotypeCallerAllele) callers.append("haplotypecaller_allele")
     if (unifiedGenotyperAllele) callers.append("unifiedgenotyper_allele")
     if (haplotypeCaller) callers.append("haplotypecaller")
-    val map = Map("variantcallers"-> callers.toList)
+    val map = Map("variantcallers" -> callers.toList)
     val pipeline = initPipeline(map)
 
     pipeline.inputBams = (for (n <- 1 to bams) yield new File("bam_" + n + ".bam")).toList
@@ -100,11 +94,11 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
   }
 
   @AfterClass def removeTempOutputDir() = {
-    FileUtils.deleteDirectory(ShivaVariantcallingTest.outputDir)
+    FileUtils.deleteDirectory(ShivaVariantcallingGatkTest.outputDir)
   }
 }
 
-object ShivaVariantcallingTest {
+object ShivaVariantcallingGatkTest {
   val outputDir = Files.createTempDir()
 
   val config = Map(

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala

@@ -185,7 +185,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
       addPerLibJobs()
 
       if (preProcessBam.isDefined) {
-        val bamMetrics = new BamMetrics(root)
+        val bamMetrics = new BamMetrics(qscript)
         bamMetrics.sampleId = Some(sampleId)
         bamMetrics.inputBam = preProcessBam.get
         bamMetrics.outputDir = sampleDir

public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala

+package nl.lumc.sasc.biopet.pipelines.shiva
+
+import com.google.common.io.Files
+import nl.lumc.sasc.biopet.core.config.Config
+import nl.lumc.sasc.biopet.extensions.bwa.BwaMem
+import nl.lumc.sasc.biopet.extensions.picard.{ MarkDuplicates, MergeSamFiles, SortSam }
+import nl.lumc.sasc.biopet.tools.VcfStats
+import nl.lumc.sasc.biopet.utils.ConfigUtils
+import org.broadinstitute.gatk.queue.QSettings
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.{ Test, DataProvider }
+
+/**
+ * Created by pjvan_thof on 3/2/15.
+ */
+class ShivaTest extends TestNGSuite with Matchers {
+  def initPipeline(map: Map[String, Any]): Shiva = {
+    new Shiva() {
+      override def configName = "shiva"
+      override def globalConfig = new Config(ConfigUtils.mergeMaps(map, ShivaVariantcallingTest.config))
+      qSettings = new QSettings
+      qSettings.runName = "test"
+    }
+  }
+
+  @DataProvider(name = "shivaOptions")
+  def shivaOptions = {
+    val bool = Array(true, false)
+
+    for (s1 <- bool; s2 <- bool; s3 <- bool; multi <- bool; single <- bool; library <- bool)
+      yield Array("", s1, s2, s3, multi, single, library)
+  }
+
+  @Test(dataProvider = "shivaOptions")
+  def testShiva(f: String, sample1: Boolean, sample2: Boolean, sample3: Boolean,
+                multi: Boolean, single: Boolean, library: Boolean): Unit = {
+    val map = {
+      var m: Map[String, Any] = ShivaTest.config
+      if (sample1) m = ConfigUtils.mergeMaps(ShivaTest.sample1, m.toMap)
+      if (sample2) m = ConfigUtils.mergeMaps(ShivaTest.sample2, m.toMap)
+      if (sample3) m = ConfigUtils.mergeMaps(ShivaTest.sample3, m.toMap)
+      ConfigUtils.mergeMaps(Map("multisample_sample_variantcalling" -> multi,
+        "single_sample_variantcalling" -> single,
+        "library_variantcalling" -> library), m.toMap)
+
+    }
+
+    if (!sample1 && !sample2 && !sample3) { // When no samples
+      intercept[IllegalArgumentException] {
+        initPipeline(map).script()
+      }
+    } else {
+      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)
+
+      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[VcfStats]) shouldBe (if (multi) 2 else 0) +
+        (if (single) numberSamples * 2 else 0) + (if (library) numberLibs * 2 else 0)
+    }
+  }
+}
+
+object ShivaTest {
+  val outputDir = Files.createTempDir()
+
+  val config = Map(
+    "name_prefix" -> "test",
+    "output_dir" -> outputDir,
+    "reference" -> "test",
+    "gatk_jar" -> "test",
+    "samtools" -> Map("exe" -> "test"),
+    "bcftools" -> Map("exe" -> "test"),
+    "fastqc" -> Map("exe" -> "test"),
+    "input_alleles" -> "test",
+    "variantcallers" -> "raw",
+    "fastqc" -> Map("exe" -> "test"),
+    "seqtk" -> Map("exe" -> "test"),
+    "sickle" -> Map("exe" -> "test"),
+    "cutadapt" -> Map("exe" -> "test"),
+    "bwa" -> Map("exe" -> "test"),
+    "samtools" -> Map("exe" -> "test"),
+    "macs2" -> Map("exe" -> "test"),
+    "igvtools" -> Map("exe" -> "test"),
+    "wigtobigwig" -> Map("exe" -> "test")
+  )
+
+  val sample1 = Map(
+    "samples" -> Map("sample1" -> Map("libraries" -> Map(
+      "lib1" -> Map(
+        "R1" -> "1_1_R1.fq",
+        "R2" -> "1_1_R2.fq"
+      )
+    )
+    )))
+
+  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",
+        "R2" -> "3_1_R2.fq"
+      ),
+      "lib2" -> Map(
+        "R1" -> "3_2_R1.fq",
+        "R2" -> "3_2_R2.fq"
+      )
+    )
+    )))
+}
\ No newline at end of file

public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala

@@ -5,7 +5,7 @@ import java.io.File
 import com.google.common.io.Files
 import nl.lumc.sasc.biopet.core.config.Config
 import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
-import nl.lumc.sasc.biopet.tools.{VcfFilter, MpileupToVcf}
+import nl.lumc.sasc.biopet.tools.{ VcfFilter, MpileupToVcf }
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.apache.commons.io.FileUtils
 import org.broadinstitute.gatk.queue.QSettings
@@ -30,15 +30,8 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
 
   @DataProvider(name = "shivaVariantcallingOptions")
   def shivaVariantcallingOptions = {
-    val raw = Array(true, false)
-    val bcftools = Array(true, false)
-
-    (for (
-      bams <- 0 to 3;
-      raw <- raw;
-      bcftools <- bcftools
-    ) yield Array[Any](bams, raw, bcftools)
-      ).toArray
+    val bool = Array(true, false)
+    (for (bams <- 0 to 3; raw <- bool; bcftools <- bool) yield Array(bams, raw, bcftools)).toArray
   }
 
   @Test(dataProvider = "shivaVariantcallingOptions")
@@ -46,7 +39,7 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
     val callers: ListBuffer[String] = ListBuffer()
     if (raw) callers.append("raw")
     if (bcftools) callers.append("bcftools")
-    val map = Map("variantcallers"-> callers.toList)
+    val map = Map("variantcallers" -> callers.toList)
     val pipeline = initPipeline(map)
 
     pipeline.inputBams = (for (n <- 1 to bams) yield new File("bam_" + n + ".bam")).toList