Added some scala docs

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala

@@ -15,8 +15,21 @@
  */
 package nl.lumc.sasc.biopet.core
 
+/**
+ * This class is for commandline programs where the executable is a non JVM based program
+ */
 abstract class BiopetCommandLineFunction extends BiopetCommandLineFunctionTrait {
+  /**
+   * This function needs to be implemented to define the command that is executed
+   * @return Command to run
+   */
   protected def cmdLine: String
+
+  /**
+   * implementing a final version of the commandLine from org.broadinstitute.gatk.queue.function.CommandLineFunction
+   * User needs to implement cmdLine instead
+   * @return Command to run
+   */
   final def commandLine: String = {
     preCmdInternal
     val cmd = cmdLine

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala

@@ -27,29 +27,38 @@ import scala.util.matching.Regex
 import java.io.FileInputStream
 import java.security.MessageDigest
 
+/**
+ * Biopet command line trait to auto check executable and cluster values
+ */
 trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurable {
   analysisName = configName
 
   @Input(doc = "deps", required = false)
   var deps: List[File] = Nil
 
-  @Argument(doc = "Threads", required = false)
+
   var threads = 0
   val defaultThreads = 1
 
-  @Argument(doc = "Vmem", required = false)
   var vmem: Option[String] = None
   val defaultVmem: String = ""
-
-  @Argument(doc = "Executable", required = false)
   var executable: String = _
 
-  protected[core] def beforeCmd {
-  }
-
-  protected[core] def afterGraph {
-  }
-
+  /**
+   * Can override this method. This is executed just before the job is ready to run.
+   * Can check on run time files from pipeline here
+   */
+  protected[core] def beforeCmd { }
+
+  /**
+   * Can override this method. This is executed after the script is done en queue starts to generate the graph
+   */
+  protected[core] def afterGraph { }
+  //TODO: function need rename to beforeGraph
+
+  /**
+   * Set default output file, threads and vmem for current job
+   */
   override def freezeFieldValues() {
     checkExecutable
     afterGraph
@@ -68,6 +77,9 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
     super.freezeFieldValues()
   }
 
+  /**
+   * Checks executable. Follow full CanonicalPath, checks if it is existing and do a md5sum on it to store in job report
+   */
   protected def checkExecutable {
     if (!BiopetCommandLineFunctionTrait.executableMd5Cache.contains(executable)) {
       try if (executable != null) {
@@ -108,6 +120,9 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
     else addJobReportBinding("md5sum_exe", "None")
   }
 
+  /**
+   * executes checkExecutable method and fill job report
+   */
   final protected def preCmdInternal {
     checkExecutable
 
@@ -117,9 +132,19 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
     addJobReportBinding("version", getVersion)
   }
 
+  /**
+   * Command to get version of executable
+   * @return
+   */
   protected def versionCommand: String = null
+
+  /** Regex to get version from version command output */
   protected val versionRegex: Regex = null
-  protected val versionExitcode = List(0) // Can select multiple
+
+  /** Allowed exit codes for the version command */
+  protected val versionExitcode = List(0)
+
+  /** Executes the version command */
   private def getVersionInternal: String = {
     if (versionCommand == null || versionRegex == null) return "N/A"
     val stdout = new StringBuffer()
@@ -142,12 +167,18 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
     return "N/A"
   }
 
+  /** Get version from cache otherwise execute the version command  */
   def getVersion: String = {
     if (!BiopetCommandLineFunctionTrait.versionCache.contains(executable))
       BiopetCommandLineFunctionTrait.versionCache += executable -> getVersionInternal
     return BiopetCommandLineFunctionTrait.versionCache(executable)
   }
 
+  /**
+   * Get threads from config
+   * @param default default when not found in config
+   * @return number of threads
+   */
   def getThreads(default: Int): Int = {
     val maxThreads: Int = config("maxthreads", default = 8)
     val threads: Int = config("threads", default = default)
@@ -155,6 +186,12 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
     else return maxThreads
   }
 
+  /**
+   * Get threads from config
+   * @param default default when not found in config
+   * @param module Module when this is difrent from default
+   * @return number of threads
+   */
   def getThreads(default: Int, module: String): Int = {
     val maxThreads: Int = config("maxthreads", default = 8, submodule = module)
     val threads: Int = config("threads", default = default, submodule = module)
@@ -163,6 +200,9 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
   }
 }
 
+/**
+ * stores global caches
+ */
 object BiopetCommandLineFunctionTrait {
   import scala.collection.mutable.Map
   private val versionCache: Map[String, String] = Map()

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Logging.scala

@@ -17,10 +17,20 @@ package nl.lumc.sasc.biopet.core
 
 import org.apache.log4j.Logger
 
+/**
+ * Trait to implement logger function on local class/object
+ */
 trait Logging {
+  /**
+   *
+   * @return Global biopet logger
+   */
   def logger = Logging.logger
 }
 
+/**
+ * Logger object, has a global logger
+ */
 object Logging {
   val logger = Logger.getRootLogger
 }
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