ShivaTest.scala

/**
 * Biopet is built on top of GATK Queue for building bioinformatic
 * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
 * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
 * should also be able to execute Biopet tools and pipelines.
 *
 * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
 *
 * Contact us at: sasc@lumc.nl
 *
 * A dual licensing mode is applied. The source code within this project that are
 * not part of GATK Queue is freely available for non-commercial use under an AGPL
 * license; For commercial users or users who do not want to follow the AGPL
 * license, please contact us to obtain a separate license.
 */
package nl.lumc.sasc.biopet.pipelines.shiva

import java.io.{ File, FileOutputStream }

import com.google.common.io.Files
import nl.lumc.sasc.biopet.utils.config.Config
import nl.lumc.sasc.biopet.extensions.bwa.BwaMem
import nl.lumc.sasc.biopet.extensions.picard.{ MarkDuplicates, SortSam }
import nl.lumc.sasc.biopet.extensions.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.{ DataProvider, Test }

/**
 * Test class for [[Shiva]]
 *
 * 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, ShivaTest.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)
      if (sample2) m = ConfigUtils.mergeMaps(ShivaTest.sample2, m)
      if (sample3) m = ConfigUtils.mergeMaps(ShivaTest.sample3, m)
      ConfigUtils.mergeMaps(Map("multisample_variantcalling" -> multi,
        "single_sample_variantcalling" -> single,
        "library_variantcalling" -> library), m)
    }

    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[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()
  new File(outputDir, "input").mkdirs()
  def inputTouch(name: String): String = {
    val file = new File(outputDir, "input" + File.separator + name)
    Files.touch(file)
    file.getAbsolutePath
  }

  private def copyFile(name: String): Unit = {
    val is = getClass.getResourceAsStream("/" + name)
    val os = new FileOutputStream(new File(outputDir, name))
    org.apache.commons.io.IOUtils.copy(is, os)
    os.close()
  }

  copyFile("ref.fa")
  copyFile("ref.dict")
  copyFile("ref.fa.fai")

  val config = Map(
    "name_prefix" -> "test",
    "output_dir" -> outputDir,
    "cache" -> true,
    "dir" -> "test",
    "vep_script" -> "test",
    "reference_fasta" -> (outputDir + File.separator + "ref.fa"),
    "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"),
    "md5sum" -> Map("exe" -> "test"),
    "bgzip" -> Map("exe" -> "test"),
    "tabix" -> Map("exe" -> "test")
  )

  val sample1 = Map(
    "samples" -> Map("sample1" -> Map("libraries" -> Map(
      "lib1" -> Map(
        "R1" -> inputTouch("1_1_R1.fq"),
        "R2" -> inputTouch("1_1_R2.fq")
      )
    )
    )))

  val sample2 = Map(
    "samples" -> Map("sample2" -> Map("libraries" -> Map(
      "lib1" -> Map(
        "R1" -> inputTouch("2_1_R1.fq"),
        "R2" -> inputTouch("2_1_R2.fq")
      )
    )
    )))

  val sample3 = Map(
    "samples" -> Map("sample3" -> Map("libraries" -> Map(
      "lib1" -> Map(
        "R1" -> inputTouch("3_1_R1.fq"),
        "R2" -> inputTouch("3_1_R2.fq")
      ),
      "lib2" -> Map(
        "R1" -> inputTouch("3_2_R1.fq"),
        "R2" -> inputTouch("3_2_R2.fq")
      )
    )
    )))
}