Start on yamsvp Scala version

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala

+/*
+ * Structural variation calling
+ */
+
+package nl.lumc.sasc.biopet.pipelines.yamsvp
+
+import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.core.BiopetQScript
+import nl.lumc.sasc.biopet.core.MultiSampleQScript
+import nl.lumc.sasc.biopet.core.PipelineCommand
+
+import nl.lumc.sasc.biopet.extensions.Cat
+import nl.lumc.sasc.biopet.extensions.picard.MergeSamFiles
+
+import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
+import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
+
+import nl.lumc.sasc.biopet.scripts.PrefixFastq
+
+import org.broadinstitute.gatk.queue.QScript
+import org.broadinstitute.gatk.queue.function._
+import org.broadinstitute.gatk.utils.commandline.{ Argument }
+
+
+
+
+class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
+  def this() = this(null)
+
+  var reference: File = _
+  var finalBamFiles: List[File] = Nil
+  
+  @Input(doc = "countBed", required = false)
+  var countBed : File = _
+  
+  def init() {
+    for (file <- configfiles) globalConfig.loadConfigFile(file)
+    reference = config("reference", required = true)
+    if (outputDir == null)
+      throw new IllegalStateException("Output directory is not specified in the config / argument")
+    else if (!outputDir.endsWith("/"))
+      outputDir += "/"
+  }
+
+  def biopetScript() {
+    // write the pipeline here
+    // start with QC, alignment, call sambamba, call sv callers, reporting
+
+    // read config and set all parameters for the pipeline
+    logger.warn("runSamplesJobs")
+    runSamplesJobs
+
+  }
+  
+  def runSingleSampleJobs(sampleConfig: Map[String, Any]): Map[String, List[File]] = {
+    var outputFiles: Map[String, List[File]] = Map()
+    var libraryBamfiles: List[File] = List()
+    var libraryFastqFiles: List[File] = List()
+    val sampleID: String = sampleConfig("ID").toString
+    val sampleDir: String = outputDir + sampleID + "/" 
+    for ((library, libraryFiles) <- runLibraryJobs(sampleConfig)) {
+      libraryFastqFiles +:= libraryFiles("prefix_fastq")
+      libraryBamfiles +:= libraryFiles("FinalBam")
+    }
+    
+    val bamFile: File = if (libraryBamfiles.size == 1) libraryBamfiles.head
+                  else if (libraryBamfiles.size > 1) {
+                    val mergeSamFiles = MergeSamFiles(this, libraryBamfiles, sampleDir)
+                    add(mergeSamFiles)
+                    mergeSamFiles.output
+                  } else null
+    val fastqFile: File = if (libraryFastqFiles.size == 1) libraryFastqFiles.head
+                  else if (libraryFastqFiles.size > 1) {
+                    val cat = Cat.apply(this, libraryFastqFiles, sampleDir + sampleID + ".fastq")
+                    add(cat)
+                    cat.output
+                  } else null
+    
+    return outputFiles
+  }
+  
+  // Called for each run from a sample
+  def runSingleLibraryJobs(runConfig: Map[String, Any], sampleConfig: Map[String, Any]): Map[String, File] = {
+    var outputFiles: Map[String, File] = Map()
+    val runID: String = runConfig("ID").toString
+    val sampleID: String = sampleConfig("ID").toString
+    val runDir: String = outputDir + sampleID + "/run_" + runID + "/"
+    if (runConfig.contains("R1")) {
+      val flexiprep = new Flexiprep(this)
+      flexiprep.outputDir = runDir + "flexiprep/"
+      flexiprep.input_R1 = new File(runConfig("R1").toString)
+      flexiprep.skipClip = true
+      flexiprep.skipTrim = true
+      flexiprep.sampleName = sampleID
+      flexiprep.libraryName = runID
+      flexiprep.init
+      flexiprep.biopetScript
+      addAll(flexiprep.functions)
+      
+      val flexiprepOutput = for ((key,file) <- flexiprep.outputFiles if key.endsWith("output_R1")) yield file
+      val prefixFastq = PrefixFastq.apply(this, flexiprepOutput.head, runDir)
+      prefixFastq.prefix = config("sage_tag", default = "CATG")
+      prefixFastq.deps +:= flexiprep.outputFiles("fastq_input_R1")
+      add(prefixFastq)
+      outputFiles += ("prefix_fastq" -> prefixFastq.output)
+      
+      val mapping = new Mapping(this)
+      mapping.skipFlexiprep = true
+      mapping.skipMarkduplicates = true
+      mapping.defaultAligner = "bwa"
+      mapping.input_R1 = prefixFastq.output
+      mapping.RGLB = runConfig("ID").toString
+      mapping.RGSM = sampleConfig("ID").toString
+      if (runConfig.contains("PL")) mapping.RGPL = runConfig("PL").toString
+      if (runConfig.contains("PU")) mapping.RGPU = runConfig("PU").toString
+      if (runConfig.contains("CN")) mapping.RGCN = runConfig("CN").toString
+      mapping.outputDir = runDir
+      mapping.init
+      mapping.biopetScript
+      addAll(mapping.functions)
+      
+      outputFiles += ("FinalBam" -> mapping.outputFiles("finalBamFile"))
+    } else this.logger.error("Sample: " + sampleID + ": No R1 found for run: " + runConfig)
+    return outputFiles
+  }
+  
+}
+
+object Yamsvp extends PipelineCommand {
+  override val pipeline = "/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.class"
+}