Merge branch 'develop' into feature-gentrap

Conflicts:
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala

protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala

@@ -133,7 +133,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
         raxmlBoot.N = 1
         raxmlBoot.n = outputName + "_boot_" + t
         add(raxmlBoot)
-        raxmlBoot.getBootstrapFile
+        raxmlBoot.getBootstrapFile.get
       }
 
       val cat = Cat(this, bootList.toList, new File(outputDir, "/boot_list"))
@@ -142,7 +142,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
       val raxmlBi = new Raxml(this)
       raxmlBi.input = concensusVariants
       raxmlBi.t = raxmlMl.getBestTreeFile
-      raxmlBi.z = cat.output
+      raxmlBi.z = Some(cat.output)
       raxmlBi.m = config("raxml_ml_model", default = "GTRGAMMAX")
       raxmlBi.p = seed
       raxmlBi.f = "b"
@@ -152,7 +152,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
 
       val gubbins = new RunGubbins(this)
       gubbins.fastafile = concensusVariants
-      gubbins.startingTree = Some(raxmlBi.getBipartitionsFile)
+      gubbins.startingTree = raxmlBi.getBipartitionsFile
       gubbins.outputDirectory = dirSufixGubbins
       add(gubbins)
     }

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

@@ -77,7 +77,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
       }
       List(bamFile)
     } else {
-      val markDup = MarkDuplicates(this, files, new File(outputDir + outputName + ".dedup.bam"))
+      val markDup = MarkDuplicates(this, files, new File(outputDir, outputName + ".dedup.bam"))
       markDup.isIntermediate = useIndelRealigner
       add(markDup)
       if (useIndelRealigner) {

public/biopet-framework/nb-configuration.xml

-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-
-    Biopet is built on top of GATK Queue for building bioinformatic
-    pipelines. It is mainly intended to support LUMC SHARK cluster which is running
-    SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
-    should also be able to execute Biopet tools and pipelines.
-
-    Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
-
-    Contact us at: sasc@lumc.nl
-
-    A dual licensing mode is applied. The source code within this project that are
-    not part of GATK Queue is freely available for non-commercial use under an AGPL
-    license; For commercial users or users who do not want to follow the AGPL
-    license, please contact us to obtain a separate license.
-
--->
-<project-shared-configuration>
-    <!--
-This file contains additional configuration written by modules in the NetBeans IDE.
-The configuration is intended to be shared among all the users of project and
-therefore it is assumed to be part of version control checkout.
-Without this configuration present, some functionality in the IDE may be limited or fail altogether.
--->
-    <config-data xmlns="http://www.netbeans.org/ns/maven-config-data/1">
-        <configurations>
-            <configuration id="yamsvp" profiles=""/>
-        </configurations>
-    </config-data>
-    <properties xmlns="http://www.netbeans.org/ns/maven-properties-data/1">
-        <!--
-Properties that influence various parts of the IDE, especially code formatting and the like. 
-You can copy and paste the single properties, into the pom.xml file and the IDE will pick them up.
-That way multiple projects can share the same settings (useful for formatting rules for example).
-Any value defined here will override the pom.xml file value but is only applicable to the current project.
--->
-        <netbeans.hint.license>apache20</netbeans.hint.license>
-        <com-junichi11-netbeans-changelf.enable>true</com-junichi11-netbeans-changelf.enable>
-        <com-junichi11-netbeans-changelf.use-project>true</com-junichi11-netbeans-changelf.use-project>
-        <com-junichi11-netbeans-changelf.lf-kind>LF</com-junichi11-netbeans-changelf.lf-kind>
-        <com-junichi11-netbeans-changelf.use-global>false</com-junichi11-netbeans-changelf.use-global>
-        <com-junichi11-netbeans-changelf.show-dialog>true</com-junichi11-netbeans-changelf.show-dialog>
-        <org-netbeans-modules-javascript2-requirejs.enabled>true</org-netbeans-modules-javascript2-requirejs.enabled>
-    </properties>
-</project-shared-configuration>

public/biopet-framework/nbactions-yamsvp.xml

-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-
-    Biopet is built on top of GATK Queue for building bioinformatic
-    pipelines. It is mainly intended to support LUMC SHARK cluster which is running
-    SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
-    should also be able to execute Biopet tools and pipelines.
-
-    Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
-
-    Contact us at: sasc@lumc.nl
-
-    A dual licensing mode is applied. The source code within this project that are
-    not part of GATK Queue is freely available for non-commercial use under an AGPL
-    license; For commercial users or users who do not want to follow the AGPL
-    license, please contact us to obtain a separate license.
-
--->
-<actions>
-        <action>
-            <actionName>run</actionName>
-            <preAction>build-with-dependencies</preAction>
-            <packagings>
-                <packaging>jar</packaging>
-            </packagings>
-            <goals>
-                <goal>process-classes</goal>
-                <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
-            </goals>
-            <properties>
-                <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.yamsvp.Yamsvp -outDir /usr/local/waiyi/ -config ../test/samples.json -run -l debug</exec.args>
-                <exec.executable>java</exec.executable>
-                <exec.workingdir>../test</exec.workingdir>
-            </properties>
-        </action>
-        <action>
-            <actionName>debug</actionName>
-            <packagings>
-                <packaging>jar</packaging>
-            </packagings>
-            <goals>
-                <goal>process-classes</goal>
-                <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
-            </goals>
-            <properties>
-                <exec.args>-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.yamsvp.Yamsvp -outDir /usr/local/waiyi/ -config ../test/samples.json -run -l debug</exec.args>
-                <exec.executable>java</exec.executable>
-                <jpda.listen>true</jpda.listen>
-                <exec.workingdir>../test</exec.workingdir>
-            </properties>
-        </action>
-        <action>
-            <actionName>profile</actionName>
-            <packagings>
-                <packaging>jar</packaging>
-            </packagings>
-            <goals>
-                <goal>process-classes</goal>
-                <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
-            </goals>
-            <properties>
-                <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.yamsvp.Yamsvp -outDir /usr/local/waiyi/ -config ../test/samples.json -run -l debug</exec.args>
-                <exec.executable>java</exec.executable>
-                <exec.workingdir>../test</exec.workingdir>
-            </properties>
-        </action>
-    </actions>

public/biopet-framework/nbactions.xml

-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-
-    Biopet is built on top of GATK Queue for building bioinformatic
-    pipelines. It is mainly intended to support LUMC SHARK cluster which is running
-    SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
-    should also be able to execute Biopet tools and pipelines.
-
-    Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
-
-    Contact us at: sasc@lumc.nl
-
-    A dual licensing mode is applied. The source code within this project that are
-    not part of GATK Queue is freely available for non-commercial use under an AGPL
-    license; For commercial users or users who do not want to follow the AGPL
-    license, please contact us to obtain a separate license.
-
--->
-<actions>
-        <action>
-            <actionName>run</actionName>
-            <packagings>
-                <packaging>jar</packaging>
-            </packagings>
-            <goals>
-                <goal>process-classes</goal>
-                <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
-            </goals>
-            <properties>
-                <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.gatk.GatkPipeline -config /data/DIV5/SASC/project-062-snake/analysis/scripts/biopet/compare_test/samples.json -config /data/DIV5/SASC/project-062-snake/analysis/scripts/biopet/config.json -outDir /home/pjvan_thof/pipelines/test</exec.args>
-                <exec.executable>java</exec.executable>
-                <exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
-            </properties>
-        </action>
-        <action>
-            <actionName>debug</actionName>
-            <packagings>
-                <packaging>jar</packaging>
-            </packagings>
-            <goals>
-                <goal>process-classes</goal>
-                <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
-            </goals>
-            <properties>
-                <exec.args>-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.gatk.GatkPipeline -config /data/DIV5/SASC/project-062-snake/analysis/scripts/biopet/compare_test/samples.json -config /data/DIV5/SASC/project-062-snake/analysis/scripts/biopet/config.json -outDir /home/pjvan_thof/pipelines/test</exec.args>
-                <exec.executable>java</exec.executable>
-                <jpda.listen>true</jpda.listen>
-                <exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
-            </properties>
-        </action>
-        <action>
-            <actionName>profile</actionName>
-            <packagings>
-                <packaging>jar</packaging>
-            </packagings>
-            <goals>
-                <goal>process-classes</goal>
-                <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
-            </goals>
-            <properties>
-                <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.gatk.GatkPipeline -config /data/DIV5/SASC/project-062-snake/analysis/scripts/biopet/compare_test/samples.json -config /data/DIV5/SASC/project-062-snake/analysis/scripts/biopet/config.json -outDir /home/pjvan_thof/pipelines/test</exec.args>
-                <exec.executable>java</exec.executable>
-                <exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
-            </properties>
-        </action>
-    </actions>

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

@@ -25,9 +25,7 @@ import scala.util.matching.Regex
 import java.io.FileInputStream
 import java.security.MessageDigest
 
-/**
- * Biopet command line trait to auto check executable and cluster values
- */
+/** Biopet command line trait to auto check executable and cluster values */
 trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurable {
   analysisName = configName
 
@@ -47,14 +45,10 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
    */
   protected[core] def beforeCmd {}
 
-  /**
-   * Can override this method. This is executed after the script is done en queue starts to generate the graph
-   */
+  /** Can override this method. This is executed after the script is done en queue starts to generate the graph */
   protected[core] def beforeGraph {}
 
-  /**
-   * Set default output file, threads and vmem for current job
-   */
+  /** Set default output file, threads and vmem for current job */
   override def freezeFieldValues() {
     preProcesExecutable
     beforeGraph
@@ -118,9 +112,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
     addJobReportBinding("md5sum_exe", md5.getOrElse("None"))
   }
 
-  /**
-   * executes checkExecutable method and fill job report
-   */
+  /** executes checkExecutable method and fill job report */
   final protected def preCmdInternal {
     preProcesExecutable
 
@@ -133,10 +125,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
     addJobReportBinding("version", getVersion)
   }
 
-  /**
-   * Command to get version of executable
-   * @return
-   */
+  /** Command to get version of executable */
   protected def versionCommand: String = null
 
   /** Regex to get version from version command output */
@@ -146,10 +135,10 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
   protected val versionExitcode = List(0)
 
   /** Executes the version command */
-  private def getVersionInternal: String = {
-    if (versionCommand == null || versionRegex == null) return "N/A"
+  private def getVersionInternal: Option[String] = {
+    if (versionCommand == null || versionRegex == null) return None
     val exe = new File(versionCommand.trim.split(" ")(0))
-    if (!exe.exists()) return "N/A"
+    if (!exe.exists()) return None
     val stdout = new StringBuffer()
     val stderr = new StringBuffer()
     def outputLog = "Version command: \n" + versionCommand +
@@ -158,25 +147,28 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
     val process = Process(versionCommand).run(ProcessLogger(stdout append _ + "\n", stderr append _ + "\n"))
     if (!versionExitcode.contains(process.exitValue)) {
       logger.warn("getVersion give exit code " + process.exitValue + ", version not found \n" + outputLog)
-      return "N/A"
+      return None
     }
     for (line <- stdout.toString.split("\n") ++ stderr.toString.split("\n")) {
       line match {
-        case versionRegex(m) => return m
+        case versionRegex(m) => return Some(m)
         case _               =>
       }
     }
     logger.warn("getVersion give a exit code " + process.exitValue + " but no version was found, executable correct? \n" + outputLog)
-    return "N/A"
+    return None
   }
 
   /** Get version from cache otherwise execute the version command  */
-  def getVersion: String = {
+  def getVersion: Option[String] = {
     if (!BiopetCommandLineFunctionTrait.executableCache.contains(executable))
       preProcesExecutable
-    if (!BiopetCommandLineFunctionTrait.versionCache.contains(executable))
-      BiopetCommandLineFunctionTrait.versionCache += executable -> getVersionInternal
-    return BiopetCommandLineFunctionTrait.versionCache(executable)
+    if (!BiopetCommandLineFunctionTrait.versionCache.contains(versionCommand))
+      getVersionInternal match {
+        case Some(version) => BiopetCommandLineFunctionTrait.versionCache += versionCommand -> version
+        case _             =>
+      }
+    BiopetCommandLineFunctionTrait.versionCache.get(versionCommand)
   }
 
   /**
@@ -205,9 +197,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
   }
 }
 
-/**
- * stores global caches
- */
+/** 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/extensions/Bowtie.scala

@@ -21,6 +21,11 @@ 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 bowtie 1
+ *
+ * Based on version 1.1.1
+ */
 class Bowtie(val root: Configurable) extends BiopetCommandLineFunction {
   @Input(doc = "Fastq file R1", shortName = "R1")
   var R1: File = null
@@ -53,6 +58,7 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction {
   var strata: Boolean = config("strata", default = false)
   var maqerr: Option[Int] = config("maqerr")
 
+  /** return commandline to execute */
   def cmdLine = {
     required(executable) +
       optional("--threads", nCoresRequest) +

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

@@ -20,6 +20,9 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import java.io.File
 
+/**
+ * Extension for GNU cat
+ */
 class Cat(val root: Configurable) extends BiopetCommandLineFunction {
   @Input(doc = "Input file", required = true)
   var input: List[File] = Nil
@@ -29,10 +32,21 @@ class Cat(val root: Configurable) extends BiopetCommandLineFunction {
 
   executable = config("exe", default = "cat")
 
+  /** return commandline to execute */
   def cmdLine = required(executable) + repeat(input) + " > " + required(output)
 }
 
+/**
+ * Object for constructors for cat
+ */
 object Cat {
+  /**
+   * Basis constructor
+   * @param root root object for config
+   * @param input list of files to use
+   * @param output output File
+   * @return
+   */
   def apply(root: Configurable, input: List[File], output: File): Cat = {
     val cat = new Cat(root)
     cat.input = input

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

@@ -24,6 +24,10 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 import scala.collection.mutable
 import scala.io.Source
 
+/**
+ * Extension for cutadept
+ * Based on version 1.5
+ */
 class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Summarizable {
   @Input(doc = "Input fastq file")
   var fastq_input: File = _
@@ -39,17 +43,15 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
   override val versionRegex = """(.*)""".r
 
   var default_clip_mode: String = config("default_clip_mode", default = "3")
-  var opt_adapter: Set[String] = Set()
-  if (config.contains("adapter")) for (adapter <- config("adapter").asList) opt_adapter += adapter.toString
-  var opt_anywhere: Set[String] = Set()
-  if (config.contains("anywhere")) for (adapter <- config("anywhere").asList) opt_anywhere += adapter.toString
-  var opt_front: Set[String] = Set()
-  if (config.contains("front")) for (adapter <- config("front").asList) opt_front += adapter.toString
+  var opt_adapter: Set[String] = config("adapter", default = Nil)
+  var opt_anywhere: Set[String] = config("anywhere", default = Nil)
+  var opt_front: Set[String] = config("front", default = Nil)
 
   var opt_discard: Boolean = config("discard", default = false)
   var opt_minimum_length: Int = config("minimum_length", 1)
   var opt_maximum_length: Option[Int] = config("maximum_length")
 
+  /** return commandline to execute */
   def cmdLine = required(executable) +
     // options
     repeat("-a", opt_adapter) +
@@ -63,6 +65,7 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
     required("--output", fastq_output) +
     " > " + required(stats_output)
 
+  /** Output summary stats */
   def summaryStats: Map[String, Any] = {
     val trimR = """.*Trimmed reads: *(\d*) .*""".r
     val tooShortR = """.*Too short reads: *(\d*) .*""".r
@@ -89,6 +92,7 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
     )
   }
 
+  /** Merges values that can be merged for the summary */
   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/Fastqc.scala

@@ -22,6 +22,10 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 import nl.lumc.sasc.biopet.core.config.Configurable
 
+/**
+ * Extension for fastqc
+ * Based on version 0.10.1 and 0.11.2
+ */
 class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
 
   @Input(doc = "Contaminants", required = false)
@@ -48,6 +52,7 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
   override def versionCommand = executable + " --version"
   override val defaultThreads = 4
 
+  /** Sets contaminants and adapters when not yet set */
   override def beforeGraph {
     this.preProcesExecutable
 
@@ -59,8 +64,8 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
       // otherwise, use default contaminants file (depending on FastQC version)
       case None =>
         val defaultContams = getVersion match {
-          case "v0.11.2" => new File(fastqcDir + "/Configuration/contaminant_list.txt")
-          case _         => new File(fastqcDir + "/Contaminants/contaminant_list.txt")
+          case Some("v0.11.2") => new File(fastqcDir + "/Configuration/contaminant_list.txt")
+          case _               => new File(fastqcDir + "/Contaminants/contaminant_list.txt")
         }
         config("contaminants", default = defaultContams)
     }
@@ -71,13 +76,14 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
       // otherwise, check if adapters are already present (depending on FastQC version)
       case None =>
         val defaultAdapters = getVersion match {
-          case "v0.11.2" => Option(new File(fastqcDir + "/Configuration/adapter_list.txt"))
-          case _         => None
+          case Some("v0.11.2") => Option(new File(fastqcDir + "/Configuration/adapter_list.txt"))
+          case _               => None
         }
         defaultAdapters.collect { case adp => config("adapters", default = adp) }
     }
   }
 
+  /** return commandline to execute */
   def cmdLine = required(executable) +
     optional("--java", java_exe) +
     optional("--threads", threads) +

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

@@ -21,6 +21,9 @@ import org.broadinstitute.gatk.queue.function.InProcessFunction
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import nl.lumc.sasc.biopet.core.config.Configurable
 
+/**
+ * This class can execute ln as InProcessFunction or used to only generate the ln command
+ */
 class Ln(val root: Configurable) extends InProcessFunction with Configurable {
   this.analysisName = getClass.getSimpleName
 
@@ -35,12 +38,14 @@ class Ln(val root: Configurable) extends InProcessFunction with Configurable {
 
   var relative: Boolean = true
 
+  /** Generate out file for job */
   override def freezeFieldValues(): Unit = {
     val outLog: String = ".%s.%s.out".format(output.getName, analysisName)
     jobOutputFile = new File(output.getAbsoluteFile.getParentFile, outLog)
     super.freezeFieldValues()
   }
 
+  /** return commandline to execute */
   lazy val cmd: String = {
     lazy val inCanonical: String = {
       // need to remove "/~" to correctly expand path with tilde
@@ -113,7 +118,17 @@ class Ln(val root: Configurable) extends InProcessFunction with Configurable {
   }
 }
 
+/** Object for constructors for ln */
 object Ln {
+  /**
+   * Basis constructor
+   * @param root root object for config
+   * @param input list of files to use
+   * @param output output File
+   * @param relative make reletive links (default true)
+   * @return
+   */
+
   def apply(root: Configurable, input: File, output: File, relative: Boolean = true): Ln = {
     val ln = new Ln(root)
     ln.input = input

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala

@@ -23,6 +23,7 @@ import argonaut._, Argonaut._
 import scalaz._, Scalaz._
 import scala.io.Source
 
+/** Extension for md5sum */
 class Md5sum(val root: Configurable) extends BiopetCommandLineFunction {
   @Input(doc = "Input")
   var input: File = _
@@ -32,17 +33,13 @@ class Md5sum(val root: Configurable) extends BiopetCommandLineFunction {
 
   executable = config("exe", default = "md5sum")
 
+  /** return commandline to execute */
   def cmdLine = required(executable) + required(input) + " > " + required(output)
-
-  def getSummary: Json = {
-    val data = Source.fromFile(output).mkString.split(" ")
-    return ("path" := output.getAbsolutePath) ->:
-      ("md5sum" := data(0)) ->:
-      jEmptyObject
-  }
 }
 
+/** Object for constructors for md5sum */
 object Md5sum {
+  /** Makes md5sum with md5 file in given dir */
   def apply(root: Configurable, fastqfile: File, outDir: File): Md5sum = {
     val md5sum = new Md5sum(root)
     md5sum.input = fastqfile
@@ -50,6 +47,7 @@ object Md5sum {
     return md5sum
   }
 
+  /** Makes md5sum with md5 file in same dir as input file */
   def apply(root: Configurable, file: File): Md5sum = {
     val md5sum = new Md5sum(root)
     md5sum.input = file

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.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 pbzip2 */
 class Pbzip2(val root: Configurable) extends BiopetCommandLineFunction {
   @Input(doc = "Zipped file")
   var input: File = _
@@ -39,6 +40,7 @@ class Pbzip2(val root: Configurable) extends BiopetCommandLineFunction {
     if (!memory.isEmpty) memory = Option(memory.get * threads)
   }
 
+  /** return commandline to execute */
   def cmdLine = required(executable) +
     conditional(decomrpess, "-d") +
     conditional(!decomrpess, "-z") +
@@ -48,7 +50,9 @@ class Pbzip2(val root: Configurable) extends BiopetCommandLineFunction {
     required(input)
 }
 
+/** Object for constructors for Pbzip2 */
 object Pbzip2 {
+  /** Default constructor */
   def apply(root: Configurable, input: File, output: File): Pbzip2 = {
     val pbzip2 = new Pbzip2(root)
     pbzip2.input = input

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

@@ -28,6 +28,11 @@ trait PythonCommandLineFunction extends BiopetCommandLineFunction {
   executable = config("exe", default = "python", submodule = "python")
 
   protected var python_script_name: String = _
+
+  /**
+   * checks if script already exist in jar otherwise try to fetch from the jar
+   * @param script name / location of script
+   */
   def setPythonScript(script: String) {
     python_script = new File(script)
     if (!python_script.exists()) {
@@ -36,6 +41,12 @@ trait PythonCommandLineFunction extends BiopetCommandLineFunction {
       python_script_name = script
     }
   }
+
+  /**
+   * Set and extract python script from jar file
+   * @param script name of script in jar
+   * @param subpackage location of script in jar
+   */
   def setPythonScript(script: String, subpackage: String) {
     python_script_name = script
     python_script = new File(".queue/tmp/" + subpackage + python_script_name)
@@ -46,6 +57,7 @@ trait PythonCommandLineFunction extends BiopetCommandLineFunction {
     os.close()
   }
 
+  /** return basic command to prefix the complete command with */
   def getPythonCommand(): String = {
     required(executable) + required(python_script)
   }

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

@@ -19,7 +19,12 @@ import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
 import java.io.File
+import scalaz.std.boolean.option
 
+/**
+ * extension for raxml
+ * based on version 8.1.3
+ */
 class Raxml(val root: Configurable) extends BiopetCommandLineFunction {
 
   override val defaultThreads = 1
@@ -50,49 +55,51 @@ class Raxml(val root: Configurable) extends BiopetCommandLineFunction {
   @Argument(doc = "Output directory", required = true)
   var w: File = null
 
-  var noBfgs: Boolean = config("no_bfgs", default = false)
-
   @Input(required = false)
-  var t: File = _
+  var t: Option[File] = _
 
   @Input(required = false)
-  var z: File = _
+  var z: Option[File] = _
 
   @Output(doc = "Output files", required = false)
   private var out: List[File] = Nil
 
+  var noBfgs: Boolean = config("no_bfgs", default = false)
+
   var executableNonThreads: String = config("exe", default = "raxmlHPC")
   var executableThreads: Option[String] = config("exe_pthreads")
 
+  /** Sets correct output files to job */
   override def beforeGraph {
     require(w != null)
     if (threads == 0) threads = getThreads(defaultThreads)
     executable = if (threads > 1 && executableThreads.isDefined) executableThreads.get else executableNonThreads
     super.beforeGraph
-    out +:= getInfoFile
+    out :::= List(Some(getInfoFile), getBestTreeFile, getBootstrapFile, getBipartitionsFile).flatten
     f match {
-      case "d" if b.isEmpty => {
-        out +:= getBestTreeFile
-        for (t <- 0 until N.getOrElse(1)) {
-          out +:= new File(w, "RAxML_log." + n + ".RUN." + t)
-          out +:= new File(w, "RAxML_parsimonyTree." + n + ".RUN." + t)
-          out +:= new File(w, "RAxML_result." + n + ".RUN." + t)
-        }
-      }
-      case "d" if b.isDefined => out +:= getBootstrapFile
-      case "b" => {
-        out +:= new File(w, "RAxML_bipartitionsBranchLabels." + n)
-        out +:= new File(w, "RAxML_bipartitions." + n)
+      case "d" if b.isEmpty => for (t <- 0 until N.getOrElse(1)) {
+        out +:= new File(w, "RAxML_log." + n + ".RUN." + t)
+        out +:= new File(w, "RAxML_parsimonyTree." + n + ".RUN." + t)
+        out +:= new File(w, "RAxML_result." + n + ".RUN." + t)
       }
-      case _ =>
+      case "b" => out +:= new File(w, "RAxML_bipartitionsBranchLabels." + n)
+      case _   =>
     }
   }
 
-  def getBestTreeFile: File = new File(w, "RAxML_bestTree." + n)
-  def getBootstrapFile: File = new File(w, "RAxML_bootstrap." + n)
-  def getBipartitionsFile: File = new File(w, "RAxML_bipartitions." + n)
-  def getInfoFile: File = new File(w, "RAxML_info." + n)
+  /** Returns bestTree file */
+  def getBestTreeFile = option(f == "d" && b.isEmpty, new File(w, "RAxML_bestTree." + n))
+
+  /** Returns bootstrap file */
+  def getBootstrapFile = option(f == "d" && b.isDefined, new File(w, "RAxML_bootstrap." + n))
+
+  /** Returns bipartitions file */
+  def getBipartitionsFile = option(f == "b", new File(w, "RAxML_bipartitions." + n))
+
+  /** Returns info file */
+  def getInfoFile = new File(w, "RAxML_info." + n)
 
+  /** return commandline to execute */
   def cmdLine = required(executable) +
     required("-m", m) +
     required("-s", input) +

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

@@ -21,6 +21,11 @@ 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 gubbins
+ * See; https://github.com/sanger-pathogens/gubbins
+ * No version known
+ */
 class RunGubbins(val root: Configurable) extends BiopetCommandLineFunction {
 
   @Input(doc = "Contaminants", required = false)
@@ -47,6 +52,7 @@ class RunGubbins(val root: Configurable) extends BiopetCommandLineFunction {
   var verbose: Boolean = config("verbose", default = false)
   var noCleanup: Boolean = config("no_cleanup", default = false)
 
+  /** Set correct output files */
   override def beforeGraph: Unit = {
     super.beforeGraph
     require(outputDirectory != null)
@@ -63,6 +69,7 @@ class RunGubbins(val root: Configurable) extends BiopetCommandLineFunction {
     for (t <- out) outputFiles ::= new File(outputDirectory + File.separator + prefix.getOrElse("gubbins") + t)
   }
 
+  /** Return command to execute */
   def cmdLine = required("cd", outputDirectory) + " && " + required(executable) +
     optional("--outgroup", outgroup) +
     optional("--starting_tree", startingTree) +

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala

@@ -23,6 +23,7 @@ import argonaut._, Argonaut._
 import scalaz._, Scalaz._
 import scala.io.Source
 
+/** Extension for sha1sum */
 class Sha1sum(val root: Configurable) extends BiopetCommandLineFunction {
   @Input(doc = "Input file")
   var input: File = _
@@ -32,21 +33,16 @@ class Sha1sum(val root: Configurable) extends BiopetCommandLineFunction {
 
   executable = config("exe", default = "sha1sum")
 
+  /** Set correct output files */
   def cmdLine = required(executable) + required(input) + " > " + required(output)
-
-  def getSummary: Json = {
-    val data = Source.fromFile(output).mkString.split(" ")
-    return ("path" := output.getAbsolutePath) ->:
-      ("sha1sum" := data(0)) ->:
-      jEmptyObject
-  }
 }
 
 object Sha1sum {
-  def apply(root: Configurable, fastqfile: File, outDir: String): Sha1sum = {
+  /** Create default sha1sum */
+  def apply(root: Configurable, input: File, outDir: File): Sha1sum = {
     val sha1sum = new Sha1sum(root)
-    sha1sum.input = fastqfile
-    sha1sum.output = new File(outDir + fastqfile.getName + ".sha1")
+    sha1sum.input = input
+    sha1sum.output = new File(outDir, input.getName + ".sha1")
     return sha1sum
   }
 }

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] = {
     // regex for single run
     val sKept = """FastQ records kept: (\d+)""".r
@@ -123,6 +130,7 @@ 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