- Fixed output of star

biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Star.scala

@@ -9,39 +9,31 @@ import scala.sys.process._
 class Star(private var globalConfig: Config) extends CommandLineFunction {
   def this() = this(new Config(Map()))
   this.analysisName = "STAR"
-  var config: Config = _
+  var config: Config = Config.mergeConfigs(globalConfig.getAsConfig("star"), globalConfig)
 
-  @Argument(doc="STAR executeble", shortName="star_exe", required=false) var star_exe: String = _
-  @Input(doc="The reference file for the bam files.", shortName="R") var referenceFile: File = _
+  @Argument(doc="STAR executeble", shortName="star_exe", required=false)
+  var star_exe: String = config.getAsString("exe", "/usr/local/bin/STAR")
+  @Input(doc="The reference file for the bam files.", shortName="R") var referenceFile: File = new File(config.getAsString("referenceFile"))
   @Input(doc="Fastq file R1", shortName="R1") var R1: File = _
   @Input(doc="Fastq file R2", shortName="R2", required=false) var R2: File = _
   @Argument(doc="Output Directory", shortName="outputDir") var outputDir: String = _
   @Argument(doc="GenomeDir", required=false) var genomeDir: String = _
+  if (genomeDir == null) genomeDir = config.getAsString("genomeDir", referenceFile.getParent + "/star")
   
   @Argument(doc="STAR runmode", shortName="runmode", required=false) var runmode: String = _
   
-  @Output
-  var outputSam: File = _
-  
-  def init() {
-    config = Config.mergeConfigs(globalConfig.getAsConfig("star"), globalConfig)
-    star_exe = config.getAsString("exe", "/usr/local/bin/STAR")
-    if (genomeDir == null) genomeDir = config.getAsString("genomeDir", referenceFile.getParent + "/star")
-    this.addJobReportBinding("version", "NA")
-    
-    jobResourceRequests :+= "h_vmem=" + config.getAsString("vmem", "6G")
-    var threads: Int = config.getAsInt("threads", 8)
-    var maxThreads: Int = config.getAsInt("maxthreads", 24)
-    if (threads > maxThreads) threads = maxThreads
-    nCoresRequest = Option(threads)
-    
-    referenceFile = new File(config.getAsString("referenceFile"))
-    
-    outputSam = new File(outputDir + "/star_output.sam")
-  }
+  this.addJobReportBinding("version", "NA")
+
+  jobResourceRequests :+= "h_vmem=" + config.getAsString("vmem", "6G")
+  var threads: Int = config.getAsInt("threads", 8)
+  var maxThreads: Int = config.getAsInt("maxthreads", 24)
+  if (threads > maxThreads) threads = maxThreads
+  nCoresRequest = Option(threads)
+
+  @Output var outputSam: File = new File(outputDir + "/star_output.sam")
   
   def commandLine : String= {
-    init()
+    //init()
     var cmd: String = required("cd",outputDir) + "&&" + required(star_exe)
     if (runmode != null && runmode == "genomeGenerate") { // Create index
       cmd += required("--runmode", runmode) +

mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

@@ -14,6 +14,7 @@ import scala.util.parsing.json._
 import org.broadinstitute.sting.utils.variant._
 
 class Mapping(private var globalConfig: Config) extends QScript {
+  qscript =>
   @Argument(doc="Config Json file",shortName="config", required=false) var configfiles: List[File] = Nil
   @Input(doc="R1 fastq file", shortName="R1",required=true) var input_R1: File = _
   @Input(doc="R2 fastq file", shortName="R2", required=false) var input_R2: File = _
@@ -79,21 +80,22 @@ class Mapping(private var globalConfig: Config) extends QScript {
       fastq_R1 = flexiprep.outputFiles("output_R1")
       if (paired) fastq_R2 = flexiprep.outputFiles("output_R2")
     }
-    var bamFile:File = ""
+    var bamFile:File = null
     if (aligner == "bwa") {
       val bwaCommand = new Bwa(config) { R1 = fastq_R1; if (paired) R2 = fastq_R2; 
                                         RG = getReadGroup; output = new File(outputDir + outputName + ".sam") }
       add(bwaCommand)
       bamFile = addSortSam(List(bwaCommand.output), swapExt(outputDir,bwaCommand.output,".sam",".bam"), outputDir)
     } else if (aligner == "star") {
-      val starCommand = new Star(config) { R1 = fastq_R1; if (paired) R2 = fastq_R2; this.outputDir = outputDir }
+      val starCommand = new Star(config) { R1 = fastq_R1; if (paired) R2 = fastq_R2; this.outputDir = qscript.outputDir + "star/" ;
+                                          outputSam = new File(this.outputDir + "/star_output.sam") }
       add(starCommand)
       bamFile = addAddOrReplaceReadGroups(List(starCommand.outputSam), swapExt(outputDir,starCommand.outputSam,".sam",".bam"), outputDir)
     }
     
     if (!skipMarkduplicates) bamFile = addMarkDuplicates(List(bamFile), swapExt(outputDir,bamFile,".bam",".dedup.bam"), outputDir)
   }
-    
+  
   def addSortSam(inputSam:List[File], outputFile:File, dir:String) : File = {
     val sortSam = new SortSam {
       input = inputSam
@@ -124,6 +126,8 @@ class Mapping(private var globalConfig: Config) extends QScript {
       if (RGCN != null) this.RGCN = RGCN
       if (RGDS != null) this.RGDS = RGDS
     }
+    add(addOrReplaceReadGroups)
+    
     return addOrReplaceReadGroups.output
   }