DownloadGenomesTest.scala 4.4 KB
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/**
 * 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 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.
 */
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package nl.lumc.sasc.biopet.pipelines.generateindexes

import com.google.common.io.Files
import nl.lumc.sasc.biopet.utils.ConfigUtils
import nl.lumc.sasc.biopet.utils.config.Config
import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.Test

/**
 * Created by pjvan_thof on 13-5-16.
 */
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class DownloadGenomesTest extends TestNGSuite with Matchers {
  def initPipeline(map: Map[String, Any]): DownloadGenomes = {
    new DownloadGenomes() {
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      override def configNamespace = "generateindexes"
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      override def globalConfig = new Config(ConfigUtils.mergeMaps(map, DownloadGenomesTest.config))
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      qSettings = new QSettings
      qSettings.runName = "test"
    }
  }

  @Test
  def testNoFastaUri: Unit = {
    val pipeline = initPipeline(Map())
    pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("" -> "")))
    intercept[IllegalArgumentException] {
      pipeline.script()
    }
  }

  @Test
  def testSingleFasta: Unit = {
    val pipeline = initPipeline(Map())
    pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri")))
    pipeline.script()
  }

  @Test
  def testMultiFasta: Unit = {
    val pipeline = initPipeline(Map())
    pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> List("uri", "uri2", "uri3.gz"))))
    pipeline.script()
  }

  @Test
  def testSingleDbsnp: Unit = {
    val pipeline = initPipeline(Map())
    pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri", "dbsnp_vcf_uri" -> "uri.vcf.gz")))
    pipeline.script()
  }

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  @Test
  def testContigMapDbsnp: Unit = {
    val pipeline = initPipeline(Map())
    pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri", "dbsnp_vcf_uri" -> "uri.vcf.gz", "dbsnp_contig_map" -> Map("1" -> "chr1"))))
    pipeline.script()
  }

  @Test
  def testUnzippedContigMapDbsnp: Unit = {
    val pipeline = initPipeline(Map())
    pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri", "dbsnp_vcf_uri" -> "uri.vcf", "dbsnp_contig_map" -> Map("1" -> "chr1"))))
    pipeline.script()
  }

  @Test
  def testSingleUnzippedDbsnp: Unit = {
    val pipeline = initPipeline(Map())
    pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri", "dbsnp_vcf_uri" -> "uri.vcf")))
    pipeline.script()
  }

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  @Test
  def testMultiDbsnp: Unit = {
    val pipeline = initPipeline(Map())
    pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri", "dbsnp_vcf_uri" -> List("uri.vcf.gz", "uri2.vcf.gz"))))
    pipeline.script()
  }

  @Test
  def testVep: Unit = {
    val pipeline = initPipeline(Map())
    pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri", "vep_cache_uri" -> "something/human_vep_80_hg19.tar.gz")))
    pipeline.script()
  }

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  @Test
  def testGtfZipped: Unit = {
    val pipeline = initPipeline(Map())
    pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri", "gtf_uri" -> "bla.gf.gz")))
    pipeline.script()
  }

  @Test
  def testGtf: Unit = {
    val pipeline = initPipeline(Map())
    pipeline.referenceConfig = Map("s1" -> Map("g1" -> Map("fasta_uri" -> "uri", "gtf_uri" -> "bla.gf")))
    pipeline.script()
  }

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}

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object DownloadGenomesTest {
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  val outputDir = Files.createTempDir()
  outputDir.deleteOnExit()

  val config = Map("output_dir" -> outputDir,
    "bwa" -> Map("exe" -> "test"),
    "star" -> Map("exe" -> "test"),
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    "hisat2build" -> Map("exe" -> "test"),
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    "bowtiebuild" -> Map("exe" -> "test"),
    "bowtie2build" -> Map("exe" -> "test"),
    "gmapbuild" -> Map("exe" -> "test"),
    "samtools" -> Map("exe" -> "test"),
    "md5sum" -> Map("exe" -> "test"),
    "gatk_jar" -> "test",
    "tabix" -> Map("exe" -> "test")
  )
}