Move generate index to separated pipeline

generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexes.scala

+package nl.lumc.sasc.biopet.pipelines.generateindexes
+
+import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
+import nl.lumc.sasc.biopet.extensions.bowtie.{Bowtie2Build, BowtieBuild}
+import nl.lumc.sasc.biopet.extensions.{Ln, Star}
+import nl.lumc.sasc.biopet.extensions.bwa.BwaIndex
+import nl.lumc.sasc.biopet.extensions.gmap.GmapBuild
+import nl.lumc.sasc.biopet.extensions.hisat.Hisat2Build
+import nl.lumc.sasc.biopet.extensions.picard.CreateSequenceDictionary
+import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFaidx
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.queue.QScript
+
+import scala.collection.mutable.ListBuffer
+
+/**
+  * Created by pjvan_thof on 21-9-16.
+  */
+class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript {
+  def this() = this(null)
+
+  @Input(doc = "Input fasta file", shortName = "R")
+  var fastaFile: File = _
+
+  @Argument(required = true)
+  var speciesName: String = _
+
+  @Argument(required = true)
+  var genomeName: String = _
+
+  @Input(required = false)
+  var gtfFile: Option[File] = None
+
+  var fastaUris: Array[String] = Array()
+
+  /** Init for pipeline */
+  def init(): Unit = {
+    if (outputDir == null) outputDir = fastaFile.getParentFile
+  }
+
+  /** Pipeline itself */
+  def biopetScript(): Unit = {
+
+    var outputConfig: Map[String, Any] = Map("reference_fasta" -> fastaFile)
+    val configDeps = new ListBuffer[File]()
+
+    val faidx = SamtoolsFaidx(this, fastaFile)
+    add(faidx)
+    configDeps += faidx.output
+
+    val createDict = new CreateSequenceDictionary(this)
+    createDict.reference = fastaFile
+    createDict.output = new File(outputDir, fastaFile.getName.stripSuffix(".fa") + ".dict")
+    createDict.species = Some(speciesName)
+    createDict.genomeAssembly = Some(genomeName)
+    if (fastaUris.nonEmpty) createDict.uri = Some(fastaUris.mkString(","))
+    add(createDict)
+    configDeps += createDict.output
+
+    def createLinks(dir: File): File = {
+      val newFastaFile = new File(dir, fastaFile.getName)
+      val newFai = new File(dir, faidx.output.getName)
+      val newDict = new File(dir, createDict.output.getName)
+
+      add(Ln(this, faidx.output, newFai))
+      add(Ln(this, createDict.output, newDict))
+      val lnFasta = Ln(this, fastaFile, newFastaFile)
+      lnFasta.deps ++= List(newFai, newDict)
+      add(lnFasta)
+      newFastaFile
+    }
+
+    // Bwa index
+    val bwaIndex = new BwaIndex(this)
+    bwaIndex.reference = createLinks(new File(outputDir, "bwa"))
+    add(bwaIndex)
+    configDeps += bwaIndex.jobOutputFile
+    outputConfig += "bwa" -> Map("reference_fasta" -> bwaIndex.reference.getAbsolutePath)
+
+    // Gmap index
+    val gmapDir = new File(outputDir, "gmap")
+    val gmapBuild = new GmapBuild(this)
+    gmapBuild.dir = gmapDir
+    gmapBuild.db = genomeName
+    gmapBuild.fastaFiles ::= createLinks(gmapDir)
+    add(gmapBuild)
+    configDeps += gmapBuild.jobOutputFile
+    outputConfig += "gsnap" -> Map("dir" -> gmapBuild.dir.getAbsolutePath, "db" -> genomeName)
+    outputConfig += "gmap" -> Map("dir" -> gmapBuild.dir.getAbsolutePath, "db" -> genomeName)
+
+    // STAR index
+    val starDir = new File(outputDir, "star")
+    val starIndex = new Star(this)
+    starIndex.outputDir = starDir
+    starIndex.reference = createLinks(starDir)
+    starIndex.runmode = "genomeGenerate"
+    starIndex.sjdbGTFfile = gtfFile
+    add(starIndex)
+    configDeps += starIndex.jobOutputFile
+    outputConfig += "star" -> Map(
+      "reference_fasta" -> starIndex.reference.getAbsolutePath,
+      "genomeDir" -> starDir.getAbsolutePath
+    )
+
+    // Bowtie index
+    val bowtieIndex = new BowtieBuild(this)
+    bowtieIndex.reference = createLinks(new File(outputDir, "bowtie"))
+    bowtieIndex.baseName = "reference"
+    add(bowtieIndex)
+    configDeps += bowtieIndex.jobOutputFile
+    outputConfig += "bowtie" -> Map("reference_fasta" -> bowtieIndex.reference.getAbsolutePath)
+
+    // Bowtie2 index
+    val bowtie2Index = new Bowtie2Build(this)
+    bowtie2Index.reference = createLinks(new File(outputDir, "bowtie2"))
+    bowtie2Index.baseName = "reference"
+    add(bowtie2Index)
+    configDeps += bowtie2Index.jobOutputFile
+    outputConfig += "bowtie2" -> Map("reference_fasta" -> bowtie2Index.reference.getAbsolutePath)
+    outputConfig += "tophat" -> Map(
+      "bowtie_index" -> bowtie2Index.reference.getAbsolutePath.stripSuffix(".fa").stripSuffix(".fasta")
+    )
+
+    // Hisat2 index
+    val hisat2Index = new Hisat2Build(this)
+    hisat2Index.inputFasta = createLinks(new File(outputDir, "hisat2"))
+    hisat2Index.hisat2IndexBase = new File(new File(outputDir, "hisat2"), "reference").getAbsolutePath
+    add(hisat2Index)
+    configDeps += hisat2Index.jobOutputFile
+    outputConfig += "hisat2" -> Map(
+      "reference_fasta" -> hisat2Index.inputFasta.getAbsolutePath,
+      "hisat_index" -> hisat2Index.inputFasta.getAbsolutePath.stripSuffix(".fa").stripSuffix(".fasta")
+    )
+
+    val writeConfig = new WriteConfig
+    writeConfig.deps = configDeps.toList
+    writeConfig.out = configFile
+    writeConfig.config = Map("references" -> Map(speciesName -> Map(genomeName -> outputConfig)))
+    add(writeConfig)
+
+  }
+
+  def configFile = new File(outputDir, s"$speciesName-$genomeName.json")
+}
+
+object GenerateIndexes extends PipelineCommand
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