Added flexiprep testing

public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala

+package nl.lumc.sasc.biopet.pipelines.flexiprep
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.config.Config
+import nl.lumc.sasc.biopet.extensions.{ Gzip, Zcat }
+import nl.lumc.sasc.biopet.tools.FastqSync
+import nl.lumc.sasc.biopet.utils.ConfigUtils
+import org.broadinstitute.gatk.queue.QSettings
+import org.broadinstitute.gatk.queue.function.QFunction
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+/**
+ * Created by pjvan_thof on 2/11/15.
+ */
+class FlexiprepTest extends TestNGSuite with Matchers {
+
+  def initPipeline(map: Map[String, Any]): Flexiprep = {
+    new Flexiprep() {
+      override def configName = "flexiprep"
+      override def globalConfig = new Config(map)
+      qSettings = new QSettings
+      qSettings.runName = "test." + System.currentTimeMillis
+    }
+  }
+
+  @Test def TestDefault = {
+    val map = ConfigUtils.mergeMaps(Map("output_dir" -> FlexiprepTest.outputDir), Map(FlexiprepTest.excutables.toSeq: _*))
+    val flexiprep: Flexiprep = initPipeline(map)
+
+    flexiprep.input_R1 = new File(flexiprep.outputDir, "bla.fq")
+    flexiprep.sampleId = "1"
+    flexiprep.libId = "1"
+    flexiprep.script()
+
+    flexiprep.functions.count(_.isInstanceOf[Fastqc]) shouldBe 2
+    flexiprep.functions.count(_.isInstanceOf[Zcat]) shouldBe 0
+    flexiprep.functions.count(_.isInstanceOf[SeqtkSeq]) shouldBe 1
+    flexiprep.functions.count(_.isInstanceOf[Cutadapt]) shouldBe 1
+    flexiprep.functions.count(_.isInstanceOf[FastqSync]) shouldBe 0
+    flexiprep.functions.count(_.isInstanceOf[Sickle]) shouldBe 1
+    flexiprep.functions.count(_.isInstanceOf[Gzip]) shouldBe 1
+  }
+
+  @Test def TestDefaultPaired = {
+    val map = ConfigUtils.mergeMaps(Map("output_dir" -> FlexiprepTest.outputDir), Map(FlexiprepTest.excutables.toSeq: _*))
+    val flexiprep: Flexiprep = initPipeline(map)
+
+    flexiprep.input_R1 = new File(flexiprep.outputDir, "bla_R1.fq.gz")
+    flexiprep.input_R2 = Some(new File(flexiprep.outputDir, "bla_R2.fq.gz"))
+    flexiprep.sampleId = "1"
+    flexiprep.libId = "1"
+    flexiprep.script()
+
+    flexiprep.functions.count(_.isInstanceOf[Fastqc]) shouldBe 4
+    flexiprep.functions.count(_.isInstanceOf[Zcat]) shouldBe 2
+    flexiprep.functions.count(_.isInstanceOf[SeqtkSeq]) shouldBe 2
+    flexiprep.functions.count(_.isInstanceOf[Cutadapt]) shouldBe 2
+    flexiprep.functions.count(_.isInstanceOf[FastqSync]) shouldBe 1
+    flexiprep.functions.count(_.isInstanceOf[Sickle]) shouldBe 1
+    flexiprep.functions.count(_.isInstanceOf[Gzip]) shouldBe 2
+  }
+
+  @Test def TestClipTrimPaired = {
+    val map = ConfigUtils.mergeMaps(Map("output_dir" -> FlexiprepTest.outputDir, "skip_trim" -> false, "skip_clip" -> false),
+      Map(FlexiprepTest.excutables.toSeq: _*))
+    val flexiprep: Flexiprep = initPipeline(map)
+
+    flexiprep.input_R1 = new File(flexiprep.outputDir, "bla_R1.fq.gz")
+    flexiprep.input_R2 = Some(new File(flexiprep.outputDir, "bla_R2.fq.gz"))
+    flexiprep.sampleId = "1"
+    flexiprep.libId = "1"
+    flexiprep.script()
+
+    flexiprep.functions.count(_.isInstanceOf[Fastqc]) shouldBe 4
+    flexiprep.functions.count(_.isInstanceOf[Zcat]) shouldBe 2
+    flexiprep.functions.count(_.isInstanceOf[SeqtkSeq]) shouldBe 2
+    flexiprep.functions.count(_.isInstanceOf[Cutadapt]) shouldBe 2
+    flexiprep.functions.count(_.isInstanceOf[FastqSync]) shouldBe 1
+    flexiprep.functions.count(_.isInstanceOf[Sickle]) shouldBe 1
+    flexiprep.functions.count(_.isInstanceOf[Gzip]) shouldBe 2
+  }
+
+  @Test def TestTrimPaired = {
+    val map = ConfigUtils.mergeMaps(Map("output_dir" -> FlexiprepTest.outputDir, "skip_trim" -> false, "skip_clip" -> true),
+      Map(FlexiprepTest.excutables.toSeq: _*))
+    val flexiprep: Flexiprep = initPipeline(map)
+
+    flexiprep.input_R1 = new File(flexiprep.outputDir, "bla_R1.fq.gz")
+    flexiprep.input_R2 = Some(new File(flexiprep.outputDir, "bla_R2.fq.gz"))
+    flexiprep.sampleId = "1"
+    flexiprep.libId = "1"
+    flexiprep.script()
+
+    flexiprep.functions.count(_.isInstanceOf[Fastqc]) shouldBe 4
+    flexiprep.functions.count(_.isInstanceOf[Zcat]) shouldBe 2
+    flexiprep.functions.count(_.isInstanceOf[SeqtkSeq]) shouldBe 2
+    flexiprep.functions.count(_.isInstanceOf[Cutadapt]) shouldBe 0
+    flexiprep.functions.count(_.isInstanceOf[FastqSync]) shouldBe 0
+    flexiprep.functions.count(_.isInstanceOf[Sickle]) shouldBe 1
+    flexiprep.functions.count(_.isInstanceOf[Gzip]) shouldBe 2
+  }
+
+  @Test def TestClipPaired = {
+    val map = ConfigUtils.mergeMaps(Map("output_dir" -> FlexiprepTest.outputDir, "skip_trim" -> true, "skip_clip" -> false),
+      Map(FlexiprepTest.excutables.toSeq: _*))
+    val flexiprep: Flexiprep = initPipeline(map)
+
+    flexiprep.input_R1 = new File(flexiprep.outputDir, "bla_R1.fq.gz")
+    flexiprep.input_R2 = Some(new File(flexiprep.outputDir, "bla_R2.fq.gz"))
+    flexiprep.sampleId = "1"
+    flexiprep.libId = "1"
+    flexiprep.script()
+
+    flexiprep.functions.count(_.isInstanceOf[Fastqc]) shouldBe 4
+    flexiprep.functions.count(_.isInstanceOf[Zcat]) shouldBe 2
+    flexiprep.functions.count(_.isInstanceOf[SeqtkSeq]) shouldBe 2
+    flexiprep.functions.count(_.isInstanceOf[Cutadapt]) shouldBe 2
+    flexiprep.functions.count(_.isInstanceOf[FastqSync]) shouldBe 1
+    flexiprep.functions.count(_.isInstanceOf[Sickle]) shouldBe 0
+    flexiprep.functions.count(_.isInstanceOf[Gzip]) shouldBe 2
+  }
+
+  @Test def TestPaired = {
+    val map = ConfigUtils.mergeMaps(Map("output_dir" -> FlexiprepTest.outputDir, "skip_trim" -> true, "skip_clip" -> true),
+      Map(FlexiprepTest.excutables.toSeq: _*))
+    val flexiprep: Flexiprep = initPipeline(map)
+
+    flexiprep.input_R1 = new File(flexiprep.outputDir, "bla_R1.fq.gz")
+    flexiprep.input_R2 = Some(new File(flexiprep.outputDir, "bla_R2.fq.gz"))
+    flexiprep.sampleId = "1"
+    flexiprep.libId = "1"
+    flexiprep.script()
+
+    flexiprep.functions.count(_.isInstanceOf[Fastqc]) shouldBe 2
+    flexiprep.functions.count(_.isInstanceOf[Zcat]) shouldBe 2
+    flexiprep.functions.count(_.isInstanceOf[SeqtkSeq]) shouldBe 2
+    flexiprep.functions.count(_.isInstanceOf[Cutadapt]) shouldBe 0
+    flexiprep.functions.count(_.isInstanceOf[FastqSync]) shouldBe 0
+    flexiprep.functions.count(_.isInstanceOf[Sickle]) shouldBe 0
+    flexiprep.functions.count(_.isInstanceOf[Gzip]) shouldBe 2
+  }
+}
+object FlexiprepTest {
+  val outputDir = System.getProperty("java.io.tmpdir") + File.separator + "flexiprep"
+
+  val excutables = Map(
+    "seqstat" -> Map("exe" -> "test"),
+    "fastqc" -> Map("exe" -> "test"),
+    "seqtk" -> Map("exe" -> "test"),
+    "sickle" -> Map("exe" -> "test")
+  )
+}
\ No newline at end of file