Adding scala docs

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala

@@ -13,6 +13,7 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
   qscript =>
   def this() = this(null)
 
+  /** Make variantcalling submodule, this with the gatk modes in there */
   override def makeVariantcalling(multisample: Boolean = false): ShivaVariantcallingTrait = {
     if (multisample) new ShivaVariantcalling(qscript) {
       override def namePrefix = "multisample"
@@ -24,10 +25,18 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
     }
   }
 
+  /** Makes a sample */
   override def makeSample(id: String) = new this.Sample(id)
+
+  /** Class will generate sample jobs */
   class Sample(sampleId: String) extends super.Sample(sampleId) {
+    /** Makes a library */
     override def makeLibrary(id: String) = new this.Library(id)
+
+    /** Class will generate library jobs */
     class Library(libId: String) extends super.Library(libId) {
+
+      /** This will adds preprocess steps, gatk indel realignment and base recalibration is included here */
       override def preProcess(input: File): Option[File] = {
         val useIndelRealigner: Boolean = config("use_indel_realign", default = true)
         val useBaseRecalibration: Boolean = config("use_base_recalibration", default = true)
@@ -47,6 +56,7 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
       }
     }
 
+    /** This methods will add double preprocess steps, with GATK indel realignment */
     override protected def addDoublePreProcess(input: List[File], isIntermediate: Boolean = false): Option[File] = {
       if (input.size <= 1) super.addDoublePreProcess(input)
       else super.addDoublePreProcess(input, true).collect {
@@ -60,6 +70,7 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
     }
   }
 
+  /** Adds indel realignment jobs */
   def addIndelRealign(inputBam: File, dir: File, isIntermediate: Boolean): File = {
     val realignerTargetCreator = RealignerTargetCreator(this, inputBam, dir)
     realignerTargetCreator.isIntermediate = true
@@ -72,6 +83,7 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
     return indelRealigner.o
   }
 
+  /** Adds base recalibration jobs */
   def addBaseRecalibrator(inputBam: File, dir: File, isIntermediate: Boolean): File = {
     val baseRecalibrator = BaseRecalibrator(this, inputBam, swapExt(dir, inputBam, ".bam", ".baserecal"))
 
@@ -98,4 +110,5 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
   }
 }
 
+/** This object give a default main methods for this pipeline */
 object Shiva extends PipelineCommand
\ No newline at end of file

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcalling.scala

@@ -13,6 +13,7 @@ class ShivaVariantcalling(val root: Configurable) extends QScript with ShivaVari
   qscript =>
   def this() = this(null)
 
+  /** Will generate all available variantcallers */
   override def callersList = {
     new HaplotypeCallerGvcf ::
       new HaplotypeCallerAllele ::
@@ -22,6 +23,7 @@ class ShivaVariantcalling(val root: Configurable) extends QScript with ShivaVari
       super.callersList
   }
 
+  /** Default mode for the haplotypecaller */
   class HaplotypeCaller extends Variantcaller {
     val name = "haplotypecaller"
     protected val defaultPrio = 1
@@ -36,6 +38,7 @@ class ShivaVariantcalling(val root: Configurable) extends QScript with ShivaVari
     }
   }
 
+  /** Default mode for UnifiedGenotyper */
   class UnifiedGenotyper extends Variantcaller {
     val name = "unifiedgenotyper"
     protected val defaultPrio = 20
@@ -50,6 +53,7 @@ class ShivaVariantcalling(val root: Configurable) extends QScript with ShivaVari
     }
   }
 
+  /** Allele mode for Haplotypecaller */
   class HaplotypeCallerAllele extends Variantcaller {
     val name = "haplotypecaller_allele"
     protected val defaultPrio = 5
@@ -66,6 +70,7 @@ class ShivaVariantcalling(val root: Configurable) extends QScript with ShivaVari
     }
   }
 
+  /** Allele mode for GenotyperAllele */
   class UnifiedGenotyperAllele extends Variantcaller {
     val name = "unifiedgenotyper_allele"
     protected val defaultPrio = 9
@@ -82,6 +87,7 @@ class ShivaVariantcalling(val root: Configurable) extends QScript with ShivaVari
     }
   }
 
+  /** Gvcf mode for haplotypecaller */
   class HaplotypeCallerGvcf extends Variantcaller {
     val name = "haplotypecaller_gvcf"
     protected val defaultPrio = 5
@@ -104,4 +110,5 @@ class ShivaVariantcalling(val root: Configurable) extends QScript with ShivaVari
   }
 }
 
+/** object to add default main method to pipeline */
 object ShivaVariantcalling extends PipelineCommand
\ No newline at end of file

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala

@@ -11,4 +11,5 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
   def this() = this(null)
 }
 
+/** This object give a default main method to the pipelines */
 object Shiva extends PipelineCommand
\ No newline at end of file

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala

@@ -12,21 +12,25 @@ import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
 import scala.collection.JavaConversions._
 
 /**
+ * This is a trait for the Shiva pipeline
+ *
  * Created by pjvan_thof on 2/26/15.
  */
 trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
   qscript =>
 
+  /** Executed before running the script */
   def init: Unit = {
-
   }
 
+  /** Method to add jobs */
   def biopetScript: Unit = {
     addSamplesJobs()
 
     addSummaryJobs
   }
 
+  /** Method to make the variantcalling submodule of shiva */
   def makeVariantcalling(multisample: Boolean = false): ShivaVariantcallingTrait = {
     if (multisample) new ShivaVariantcalling(qscript) {
       override def namePrefix = "multisample"
@@ -38,27 +42,43 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
     }
   }
 
+  /** Method to make a sample */
   def makeSample(id: String) = new Sample(id)
-  class Sample(sampleId: String) extends AbstractSample(sampleId) {
 
-    //TODO: Add summary
-    def summaryFiles: Map[String, File] = Map()
+  /** Class that will generate jobs for a sample */
+  class Sample(sampleId: String) extends AbstractSample(sampleId) {
+    /** Sample specific files to add to summary */
+    def summaryFiles: Map[String, File] = {
+      preProcessBam match {
+        case Some(preProcessBam) => Map("bamFile" -> preProcessBam)
+        case _                   => Map()
+      }
+    }
 
-    //TODO: Add summary
+    /** Sample specific stats to add to summary */
     def summaryStats: Map[String, Any] = Map()
 
+    /** Method to make a library */
     def makeLibrary(id: String) = new Library(id)
 
+    /** Class to generate jobs for a library */
     class Library(libId: String) extends AbstractLibrary(libId) {
+      /** Library specific files to add to the summary */
+      def summaryFiles: Map[String, File] = {
+        (bamFile, preProcessBam) match {
+          case (Some(bamFile), Some(preProcessBam)) => Map("bamFile" -> bamFile, "preProcessBam" -> preProcessBam)
+          case (Some(bamFile), _)                   => Map("bamFile" -> bamFile)
+          case _                                    => Map()
+        }
+      }
 
-      //TODO: Add summary
-      def summaryFiles: Map[String, File] = Map()
-
-      //TODO: Add summary
+      /** Library specific stats to add to summary */
       def summaryStats: Map[String, Any] = Map()
 
+      /** Method to execute library preprocess */
       def preProcess(input: File): Option[File] = None
 
+      /** Method to make the mapping submodule */
       def makeMapping = {
         val mapping = new Mapping(qscript)
         mapping.sampleId = Some(sampleId)
@@ -87,6 +107,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
         Some(makeVariantcalling(multisample = false))
       } else None
 
+      /** This will add jobs for this library */
       def addJobs(): Unit = {
         (config.contains("R1"), config.contains("bam")) match {
           case (true, _) => mapping.foreach(mapping => {
@@ -165,6 +186,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
       }
     }
 
+    /** This will add jobs for the double preprocessing */
     protected def addDoublePreProcess(input: List[File], isIntermediate: Boolean = false): Option[File] = {
       if (input == Nil) None
       else if (input.tail == Nil) {
@@ -202,6 +224,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
       Some(makeVariantcalling(multisample = true))
     } else None
 
+    /** This will add sample jobs */
     def addJobs(): Unit = {
       addPerLibJobs()
 
@@ -232,6 +255,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
     Some(makeVariantcalling(multisample = true))
   } else None
 
+  /** This will add the mutisample variantcalling */
   def addMultiSampleJobs(): Unit = {
     variantcalling.foreach(vc => {
       vc.outputDir = new File(outputDir, "variantcalling")
@@ -243,9 +267,12 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
     })
   }
 
+  /** Location of summary file */
   def summaryFile = new File(outputDir, "Shiva.summary.json")
 
+  /** Settings of pipeline for summary */
   def summarySettings = Map()
 
+  /** Files for the summary */
   def summaryFiles = Map()
 }

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala

@@ -24,6 +24,7 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
   @Input(doc = "Bam files (should be deduped bams)", shortName = "BAM", required = true)
   var inputBams: List[File] = Nil
 
+  /** Name prefix, can override this methods if neeeded */
   def namePrefix: String = {
     (sampleId, libId) match {
       case (Some(sampleId), Some(libId)) => sampleId + "-" + libId
@@ -32,14 +33,18 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
     }
   }
 
+  /** Executed before script */
   def init: Unit = {
   }
 
+  /** Final merged output files of all variantcaller modes */
   def finalFile = new File(outputDir, namePrefix + ".final.vcf.gz")
 
-  def biopetScript: Unit = {
-    val configCallers: Set[String] = config("variantcallers")
+  /** Variantcallers requested by the config */
+  protected val configCallers: Set[String] = config("variantcallers")
 
+  /** This will add jobs for this pipeline */
+  def biopetScript: Unit = {
     for (cal <- configCallers) {
       if (!callersList.exists(_.name == cal))
         BiopetQScript.addError("variantcaller '" + cal + "' does not exist, possible to use: " + callersList.map(_.name).mkString(", "))
@@ -77,21 +82,36 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
     addSummaryJobs
   }
 
+  /** Will generate all available variantcallers */
   protected def callersList: List[Variantcaller] = List(new Freebayes, new RawVcf, new Bcftools)
 
+  /** General trait for a variantcaller mode */
   trait Variantcaller {
+    /** Name of mode, this should also be used in the config */
     val name: String
+
+    /** Output dir for this mode */
     def outputDir = new File(qscript.outputDir, name)
+
+    /** Prio in merging  in the final file */
     protected val defaultPrio: Int
+
+    /** Prio from the config */
     lazy val prio: Int = config("prio_" + name, default = defaultPrio)
+
+    /** This should add the variantcaller jobs */
     def addJobs()
+
+    /** Final output file of this mode */
     def outputFile: File
   }
 
+  /** default mode of freebayes */
   class Freebayes extends Variantcaller {
     val name = "freebayes"
     protected val defaultPrio = 7
 
+    /** Final output file of this mode */
     def outputFile = new File(outputDir, namePrefix + ".freebayes.vcf.gz")
 
     def addJobs() {
@@ -101,7 +121,7 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
       fb.isIntermediate = true
       add(fb)
 
-      //TODO: need piping for this
+      //TODO: need piping for this, see also issue #114
       val bz = new Bgzip(qscript)
       bz.input = List(fb.outputVcf)
       bz.output = outputFile
@@ -114,10 +134,12 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
     }
   }
 
+  /** default mode of bcftools */
   class Bcftools extends Variantcaller {
     val name = "bcftools"
     protected val defaultPrio = 8
 
+    /** Final output file of this mode */
     def outputFile = new File(outputDir, namePrefix + ".bcftools.vcf.gz")
 
     def addJobs() {
@@ -143,10 +165,12 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
     }
   }
 
+  /** Makes a vcf file from a mpileup without statistics */
   class RawVcf extends Variantcaller {
     val name = "raw"
     protected val defaultPrio = 999
 
+    /** Final output file of this mode */
     def outputFile = new File(outputDir, namePrefix + ".raw.vcf.gz")
 
     def addJobs() {
@@ -179,10 +203,13 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
     }
   }
 
+  /** Location of summary file */
   def summaryFile = new File(outputDir, "ShivaVariantcalling.summary.json")
 
-  def summarySettings = Map()
+  /** Settings for the summary */
+  def summarySettings = Map("variantcallers" -> configCallers.toList)
 
+  /** Files for the summary */
   def summaryFiles: Map[String, File] = {
     val callers: Set[String] = config("variantcallers")
     callersList.filter(x => callers.contains(x.name)).map(x => (x.name -> x.outputFile)).toMap + ("final" -> finalFile)