Added scala docs

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala

@@ -25,6 +25,10 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import scala.collection.mutable
 import scala.io.Source
 
+/**
+ * Extension for sickle
+ * Based on version 1.33
+ */
 class Sickle(val root: Configurable) extends BiopetCommandLineFunction with Summarizable {
   @Input(doc = "R1 input")
   var input_R1: File = _
@@ -57,10 +61,12 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction with Summ
   override val versionRegex = """sickle version (.*)""".r
   override def versionCommand = executable + " --version"
 
+  /** Sets qualityType is still empty */
   override def beforeGraph {
     if (qualityType.isEmpty) qualityType = Some(defaultQualityType)
   }
 
+  /** Return command to execute */
   def cmdLine = {
     var cmd: String = required(executable)
     if (input_R2 != null) {
@@ -81,6 +87,7 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction with Summ
       " > " + required(output_stats)
   }
 
+  /** returns stats map for summary */
   def summaryStats: Map[String, Any] = {
     val pairKept = """FastQ paired records kept: (\d*) \((\d*) pairs\)""".r
     val singleKept = """FastQ single records kept: (\d*) \(from PE1: (\d*), from PE2: (\d*)\)""".r
@@ -108,6 +115,7 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction with Summ
     stats.toMap
   }
 
+  /** Merge stats incase of chunking */
   override def resolveSummaryConflict(v1: Any, v2: Any, key: String): Any = {
     (v1, v2) match {
       case (v1: Int, v2: Int) => v1 + v2

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala

@@ -21,6 +21,7 @@ import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
+/** Extension for stampy */
 class Stampy(val root: Configurable) extends BiopetCommandLineFunction {
   @Input(doc = "FastQ file R1", shortName = "R1")
   var R1: File = _
@@ -68,12 +69,14 @@ class Stampy(val root: Configurable) extends BiopetCommandLineFunction {
 
   override def versionCommand = executable + " --help"
 
+  /** Sets readgroup when not set yet */
   override def beforeGraph: Unit = {
     super.beforeGraph
     require(readgroup != null)
   }
 
-  def cmdLine: String = {
+  /** Returns command to execute */
+  def cmdLine = {
     var cmd: String = required(executable) +
       optional("-t", nCoresRequest) +
       conditional(solexa, "--solexa") +
@@ -99,6 +102,6 @@ class Stampy(val root: Configurable) extends BiopetCommandLineFunction {
       " -h " + required(hash) +
       " -o " + required(output) +
       " -M " + required(R1) + optional(R2)
-    return cmd
+    cmd
   }
 }

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala

@@ -21,6 +21,9 @@ import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
 
+/**
+ * Extension for STAR
+ */
 class Star(val root: Configurable) extends BiopetCommandLineFunction {
   @Input(doc = "The reference file for the bam files.", required = false)
   var reference: File = new File(config("reference"))
@@ -62,6 +65,7 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction {
   override val defaultVmem = "6G"
   override val defaultThreads = 8
 
+  /** Sets output files for the graph */
   override def beforeGraph() {
     if (outFileNamePrefix != null && !outFileNamePrefix.endsWith(".")) outFileNamePrefix += "."
     val prefix = if (outFileNamePrefix != null) outputDir + outFileNamePrefix else outputDir
@@ -77,7 +81,8 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction {
     }
   }
 
-  def cmdLine: String = {
+  /** Returns command to execute */
+  def cmdLine = {
     var cmd: String = required("cd", outputDir) + "&&" + required(executable)
     if (runmode != null && runmode == "genomeGenerate") { // Create index
       cmd += required("--runMode", runmode) +
@@ -91,11 +96,22 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction {
       optional("--outFileNamePrefix", outFileNamePrefix)
     if (sjdbOverhang > 0) cmd += optional("--sjdbOverhang", sjdbOverhang)
 
-    return cmd
+    cmd
   }
 }
 
 object Star {
+  /**
+   * Create default star
+   * @param configurable root object
+   * @param R1 R1 fastq file
+   * @param R2 R2 fastq file
+   * @param outputDir Outputdir for Star
+   * @param isIntermediate
+   * @param deps Deps to add to wait on run
+   * @return Return Star
+   *
+   */
   def apply(configurable: Configurable, R1: File, R2: File, outputDir: File, isIntermediate: Boolean = false, deps: List[File] = Nil): Star = {
     val star = new Star(configurable)
     star.R1 = R1
@@ -107,7 +123,22 @@ object Star {
     return star
   }
 
-  def _2pass(configurable: Configurable, R1: File, R2: File, outputDir: File, isIntermediate: Boolean = false, deps: List[File] = Nil): (File, List[Star]) = {
+  /**
+   * returns Star with 2pass star method
+   * @param configurable root object
+   * @param R1 R1 fastq file
+   * @param R2 R2 fastq file
+   * @param outputDir Outputdir for Star
+   * @param isIntermediate
+   * @param deps Deps to add to wait on run
+   * @return Return Star
+   */
+  def _2pass(configurable: Configurable,
+             R1: File,
+             R2: File,
+             outputDir: File,
+             isIntermediate: Boolean = false,
+             deps: List[File] = Nil): (File, List[Star]) = {
     val starCommand_pass1 = Star(configurable, R1, if (R2 != null) R2 else null, new File(outputDir, "aln-pass1"))
     starCommand_pass1.isIntermediate = isIntermediate
     starCommand_pass1.deps = deps

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala

@@ -21,6 +21,9 @@ import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
 
+/**
+ * Extension for TopHad
+ */
 class TopHat(val root: Configurable) extends BiopetCommandLineFunction {
   @Input(doc = "FastQ file R1", shortName = "R1")
   var R1: File = _
@@ -70,11 +73,10 @@ class TopHat(val root: Configurable) extends BiopetCommandLineFunction {
   }
 
   def cmdLine: String = {
-    var cmd: String = required(executable) +
+    required(executable) +
       optional("-p", nCoresRequest) +
       "--no-convert-bam" +
       required(bowtie_index) +
       required(R1) + optional(R2)
-    return cmd
   }
 }

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala

@@ -7,6 +7,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
 
 /**
+ * Extension for VariantEffectPredictor
  * Created by ahbbollen on 15-1-15.
  */
 class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFunction {
@@ -134,6 +135,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
     }
   }
 
+  /** Returns command to execute */
   def cmdLine = required(executable) +
     required(vep_script) +
     required("-i", input) +

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala

@@ -27,6 +27,7 @@ class WigToBigWig(val root: Configurable) extends BiopetCommandLineFunction {
   var clip: Boolean = config("clip", default = false)
   var unc: Boolean = config("unc", default = false)
 
+  /** Returns command to execute */
   def cmdLine = required(executable) +
     optional("-blockSize=", blockSize, spaceSeparated = false) +
     optional("-itemsPerSlot=", itemsPerSlot, spaceSeparated = false) +

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala

@@ -20,6 +20,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import java.io.File
 
+/** Extension for zcat */
 class Zcat(val root: Configurable) extends BiopetCommandLineFunction {
   @Input(doc = "Zipped file")
   var input: File = _
@@ -29,10 +30,12 @@ class Zcat(val root: Configurable) extends BiopetCommandLineFunction {
 
   executable = config("exe", default = "zcat")
 
+  /** Returns command to execute */
   def cmdLine = required(executable) + required(input) + " > " + required(output)
 }
 
 object Zcat {
+  /** Returns a default zcat */
   def apply(root: Configurable, input: File, output: File): Zcat = {
     val zcat = new Zcat(root)
     zcat.input = input