convert AddOrReplaceReadGroups to biopet function

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala

+package nl.lumc.sasc.biopet.extensions.picard
+
+import java.io.File
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
+
+class AddOrReplaceReadGroups(val root: Configurable) extends Picard {
+  javaMainClass = "picard.sam.AddOrReplaceReadGroups"
+
+  @Input(doc = "The input SAM or BAM files to analyze.", required = true)
+  var input: File = _
+
+  @Output(doc = "The output file to bam file to", required = true)
+  var output: File = _
+
+  @Argument(doc = "Sort order of output file Required. Possible values: {unsorted, queryname, coordinate} ", required = true)
+  var sortOrder: String = _
+  
+  @Argument(doc = "RGID", required = true)
+  var RGID: String = _
+  
+  @Argument(doc = "RGLB", required = true)
+  var RGLB: String = _
+  
+  @Argument(doc = "RGPL", required = true)
+  var RGPL: String = _
+  
+  @Argument(doc = "RGPU", required = true)
+  var RGPU: String = _
+  
+  @Argument(doc = "RGSM", required = true)
+  var RGSM: String = _
+  
+  @Argument(doc = "RGCN", required = false)
+  var RGCN: String = _
+  
+  @Argument(doc = "RGDS", required = false)
+  var RGDS: String = _
+  
+  @Argument(doc = "RGDT", required = false)
+  var RGDT: String = _
+  
+  @Argument(doc = "RGPI", required = false)
+  var RGPI: Option[Int] = _
+
+  override def commandLine = super.commandLine +
+    required("INPUT=", input, spaceSeparated = false) +
+    required("OUTPUT=", output, spaceSeparated = false) +
+    required("SORT_ORDER=", sortOrder, spaceSeparated = false) +
+    required("RGID=", RGID, spaceSeparated = false) +
+    required("RGLB=", RGLB, spaceSeparated = false) +
+    required("RGPL=", RGPL, spaceSeparated = false) +
+    required("RGPU=", RGPU, spaceSeparated = false) +
+    required("RGSM=", RGSM, spaceSeparated = false) +
+    optional("RGCN=", RGCN, spaceSeparated = false) +
+    optional("RGDS=", RGDS, spaceSeparated = false) +
+    optional("RGDT=", RGDT, spaceSeparated = false) +
+    optional("RGPI=", RGPI, spaceSeparated = false)
+}
+
+object AddOrReplaceReadGroups {
+  def apply(root: Configurable, input: File, outputDir: String, sortOrder: String = null): AddOrReplaceReadGroups = {
+    val addOrReplaceReadGroups = new AddOrReplaceReadGroups(root)
+    addOrReplaceReadGroups.input = input
+    addOrReplaceReadGroups.output = new File(outputDir, input.getName.stripSuffix(".bam").stripSuffix(".sam") + ".sorted.bam")
+    if (sortOrder == null) addOrReplaceReadGroups.sortOrder = "coordinate"
+    else addOrReplaceReadGroups.sortOrder = sortOrder
+    return addOrReplaceReadGroups
+  }
+}
\ No newline at end of file

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

@@ -6,12 +6,11 @@ import java.util.Date
 import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
 import nl.lumc.sasc.biopet.core.apps.FastqSplitter
 import nl.lumc.sasc.biopet.extensions.aligners.{ Bwa, Star }
-import nl.lumc.sasc.biopet.extensions.picard.{MarkDuplicates, SortSam, MergeSamFiles}
+import nl.lumc.sasc.biopet.extensions.picard.{MarkDuplicates, SortSam, MergeSamFiles, AddOrReplaceReadGroups}
 import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
 import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
 import org.broadinstitute.gatk.queue.QScript
 import org.broadinstitute.gatk.utils.commandline.{ Input, Argument, ClassType }
-import org.broadinstitute.gatk.queue.extensions.picard.{ AddOrReplaceReadGroups }
 import scala.math._
 
 class Mapping(val root: Configurable) extends QScript with BiopetQScript {
@@ -202,11 +201,11 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
       } else if (aligner == "star") {
         val starCommand = Star(this, R1, if (paired) R2 else null, outputDir, isIntermediate = true, deps = deps)
         add(starCommand)
-        bamFiles :+= addAddOrReplaceReadGroups(List(starCommand.outputSam), new File(chunkDir + outputName + ".bam"), chunkDir)
+        bamFiles :+= addAddOrReplaceReadGroups(starCommand.outputSam, chunkDir)
       } else if (aligner == "star-2pass") {
         val star2pass = Star._2pass(this, R1, if (paired) R2 else null, chunkDir, isIntermediate = true, deps = deps)
         addAll(star2pass._2)
-        bamFiles :+= addAddOrReplaceReadGroups(List(star2pass._1), new File(chunkDir + outputName + ".bam"), chunkDir)
+        bamFiles :+= addAddOrReplaceReadGroups(star2pass._1, chunkDir)
       } else throw new IllegalStateException("Option Alginer: '" + aligner + "' is not valid")
     }
     if (!skipFlexiprep) {
@@ -259,14 +258,9 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
 //    return mergeSam.output
 //  }
 
-  def addAddOrReplaceReadGroups(inputSam: List[File], outputFile: File, dir: String): File = {
-    val addOrReplaceReadGroups = new AddOrReplaceReadGroups
-    addOrReplaceReadGroups.input = inputSam
-    addOrReplaceReadGroups.output = outputFile
+  def addAddOrReplaceReadGroups(inputSam: File, outputDir: String): File = {
+    val addOrReplaceReadGroups = AddOrReplaceReadGroups(this, inputSam, outputDir)
     addOrReplaceReadGroups.createIndex = true
-    addOrReplaceReadGroups.memoryLimit = 2
-    addOrReplaceReadGroups.nCoresRequest = 2
-    addOrReplaceReadGroups.jobResourceRequests :+= "h_vmem=4G"
 
     addOrReplaceReadGroups.RGID = RGID
     addOrReplaceReadGroups.RGLB = RGLB