Added mapping as separated artifact

public/mapping/.gitignore

+/target/
\ No newline at end of file

public/mapping/pom.xml

+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+
+    <groupId>nl.lumc.sasc</groupId>
+    <artifactId>Mapping</artifactId>
+    <version>0.2.0-DEV</version>
+    <packaging>jar</packaging>
+    
+    <inceptionYear>2014</inceptionYear>
+    <name>Mapping</name>
+    <url>http://maven.apache.org</url>
+
+    <properties>
+        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+        <sting.unpack.phase>prepare-package</sting.unpack.phase>
+        <sting.shade.phase>package</sting.shade.phase>
+        <app.main.class>nl.lumc.sasc.biopet.core.BiopetExecutable</app.main.class>
+    </properties>
+
+    <dependencies>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>BiopetFramework</artifactId>
+            <version>0.2.0-DEV</version>
+        </dependency>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>Flexiprep</artifactId>
+            <version>0.2.0-DEV</version>
+        </dependency>
+    </dependencies>
+    <build>
+        <resources>
+            <resource>
+                <directory>src/main/resources</directory>
+                <includes>
+                    <include>**/*</include>
+                </includes>
+            </resource>
+        </resources>
+        <plugins>
+            <plugin>
+                <groupId>org.scala-tools</groupId>
+                <artifactId>maven-scala-plugin</artifactId>
+                <version>2.15.2</version>
+                <executions>
+                    <execution>
+                        <id>scala-compile</id>
+                        <goals>
+                            <goal>compile</goal>
+                            <goal>testCompile</goal>
+                        </goals>
+                        <configuration>
+                            <args>
+                                <arg>-dependencyfile</arg>
+                                <arg>${project.build.directory}/.scala_dependencies</arg>
+                                <arg>-deprecation</arg>
+                                <arg>-feature</arg>
+                            </args>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-jar-plugin</artifactId>
+                <version>2.5</version>
+                <configuration>
+                    <archive>
+                        <manifest>
+                            <addDefaultImplementationEntries>true</addDefaultImplementationEntries>
+                            <addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
+                        </manifest>
+                    </archive>
+                </configuration>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-compiler-plugin</artifactId>
+                <version>2.3.2</version>
+                <configuration>
+                    <showDeprecation>true</showDeprecation>
+                </configuration>
+            </plugin>
+        </plugins>
+    </build>
+</project>

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

+package nl.lumc.sasc.biopet.pipelines.mapping
+
+import nl.lumc.sasc.biopet.core.config.Configurable
+import java.io.File
+import java.util.Date
+import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
+import nl.lumc.sasc.biopet.tools.FastqSplitter
+import nl.lumc.sasc.biopet.extensions.aligners.{ Bwa, Star, Bowtie, Stampy }
+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 scala.math._
+
+class Mapping(val root: Configurable) extends QScript with BiopetQScript {
+  qscript =>
+  def this() = this(null)
+
+  @Input(doc = "R1 fastq file", shortName = "R1", required = true)
+  var input_R1: File = _
+
+  @Input(doc = "R2 fastq file", shortName = "R2", required = false)
+  var input_R2: File = _
+
+  @Argument(doc = "Output name", shortName = "outputName", required = false)
+  var outputName: String = _
+
+  @Argument(doc = "Skip flexiprep", shortName = "skipflexiprep", required = false)
+  var skipFlexiprep: Boolean = false
+
+  @Argument(doc = "Skip mark duplicates", shortName = "skipmarkduplicates", required = false)
+  var skipMarkduplicates: Boolean = false
+
+  @Argument(doc = "Skip metrics", shortName = "skipmetrics", required = false)
+  var skipMetrics: Boolean = false
+
+  @Argument(doc = "Aligner", shortName = "ALN", required = false)
+  var aligner: String = config("aligner", default = "bwa")
+
+  @Argument(doc = "Reference", shortName = "R", required = false)
+  var reference: File = config("reference")
+
+  @Argument(doc = "Chunking", shortName = "chunking", required = false)
+  var chunking: Boolean = config("chunking", false)
+
+  @ClassType(classOf[Int])
+  @Argument(doc = "Number of chunks, when not defined pipeline will automatic calculate number of chunks", shortName = "numberChunks", required = false)
+  var numberChunks: Option[Int] = None
+
+  // Readgroup items
+  @Argument(doc = "Readgroup ID", shortName = "RGID", required = false)
+  var RGID: String = config("RGID")
+
+  @Argument(doc = "Readgroup Library", shortName = "RGLB", required = false)
+  var RGLB: String = config("RGLB")
+
+  @Argument(doc = "Readgroup Platform", shortName = "RGPL", required = false)
+  var RGPL: String = config("RGPL", default = "illumina")
+
+  @Argument(doc = "Readgroup platform unit", shortName = "RGPU", required = false)
+  var RGPU: String = config("RGPU", default = "na")
+
+  @Argument(doc = "Readgroup sample", shortName = "RGSM", required = false)
+  var RGSM: String = config("RGSM")
+
+  @Argument(doc = "Readgroup sequencing center", shortName = "RGCN", required = false)
+  var RGCN: String = config("RGCN")
+
+  @Argument(doc = "Readgroup description", shortName = "RGDS", required = false)
+  var RGDS: String = config("RGDS")
+
+  @Argument(doc = "Readgroup sequencing date", shortName = "RGDT", required = false)
+  var RGDT: Date = _
+
+  @Argument(doc = "Readgroup predicted insert size", shortName = "RGPI", required = false)
+  var RGPI: Int = config("RGPI")
+
+  var paired: Boolean = false
+  val flexiprep = new Flexiprep(this)
+
+  def init() {
+    if (outputDir == null) throw new IllegalStateException("Missing Output directory on mapping module")
+    else if (!outputDir.endsWith("/")) outputDir += "/"
+    if (input_R1 == null) throw new IllegalStateException("Missing FastQ R1 on mapping module")
+    paired = (input_R2 != null)
+
+    if (RGLB == null) throw new IllegalStateException("Missing Readgroup library on mapping module")
+    if (RGLB == null) throw new IllegalStateException("Missing Readgroup sample on mapping module")
+    if (RGID == null && RGSM != null && RGLB != null) RGID = RGSM + "-" + RGLB
+    else if (RGID == null) throw new IllegalStateException("Missing Readgroup ID on mapping module")
+
+    if (outputName == null) outputName = RGID
+
+    if (chunking) {
+      if (numberChunks.isEmpty) {
+        if (config.contains("numberchunks")) numberChunks = config("numberchunks", default = None)
+        else {
+          val chunkSize: Int = config("chunksize", (1 << 30))
+          val filesize = if (input_R1.getName.endsWith(".gz") || input_R1.getName.endsWith(".gzip")) input_R1.length * 3
+          else input_R1.length
+          numberChunks = Option(ceil(filesize.toDouble / chunkSize).toInt)
+        }
+      }
+      logger.debug("Chunks: " + numberChunks.getOrElse(1))
+    }
+  }
+
+  def biopetScript() {
+    var fastq_R1: File = input_R1
+    var fastq_R2: File = if (paired) input_R2 else ""
+    if (!skipFlexiprep) {
+      flexiprep.outputDir = outputDir + "flexiprep/"
+      flexiprep.input_R1 = fastq_R1
+      if (paired) flexiprep.input_R2 = fastq_R2
+      flexiprep.sampleName = this.RGSM
+      flexiprep.libraryName = this.RGLB
+      flexiprep.init
+      flexiprep.runInitialJobs
+    }
+    var bamFiles: List[File] = Nil
+    var fastq_R1_output: List[File] = Nil
+    var fastq_R2_output: List[File] = Nil
+
+    def removeGz(file: String): String = {
+      if (file.endsWith(".gz")) return file.substring(0, file.lastIndexOf(".gz"))
+      else if (file.endsWith(".gzip")) return file.substring(0, file.lastIndexOf(".gzip"))
+      else return file
+    }
+    var chunks: Map[String, (String, String)] = Map()
+    if (chunking) for (t <- 1 to numberChunks.getOrElse(1)) {
+      val chunkDir = outputDir + "chunks/" + t + "/"
+      chunks += (chunkDir -> (removeGz(chunkDir + fastq_R1.getName),
+        if (paired) removeGz(chunkDir + fastq_R2.getName) else ""))
+    }
+    else chunks += (outputDir -> (flexiprep.extractIfNeeded(fastq_R1, flexiprep.outputDir),
+      flexiprep.extractIfNeeded(fastq_R2, flexiprep.outputDir)))
+
+    if (chunking) {
+      val fastSplitter_R1 = new FastqSplitter(this)
+      fastSplitter_R1.input = fastq_R1
+      for ((chunkDir, fastqfile) <- chunks) fastSplitter_R1.output :+= fastqfile._1
+      add(fastSplitter_R1, isIntermediate = true)
+
+      if (paired) {
+        val fastSplitter_R2 = new FastqSplitter(this)
+        fastSplitter_R2.input = fastq_R2
+        for ((chunkDir, fastqfile) <- chunks) fastSplitter_R2.output :+= fastqfile._2
+        add(fastSplitter_R2, isIntermediate = true)
+      }
+    }
+
+    for ((chunkDir, fastqfile) <- chunks) {
+      var R1 = fastqfile._1
+      var R2 = fastqfile._2
+      var deps: List[File] = Nil
+      if (!skipFlexiprep) {
+        val flexiout = flexiprep.runTrimClip(R1, R2, chunkDir + "flexiprep/", chunkDir)
+        logger.debug(chunkDir + " - " + flexiout)
+        R1 = flexiout._1
+        if (paired) R2 = flexiout._2
+        deps = flexiout._3
+        fastq_R1_output :+= R1
+        fastq_R2_output :+= R2
+      }
+
+      val outputBam = new File(chunkDir + outputName + ".bam")
+      bamFiles :+= outputBam
+      aligner match {
+        case "bwa"        => addBwa(R1, R2, outputBam, deps)
+        case "bowtie"     => addBowtie(R1, R2, outputBam, deps)
+        case "stampy"     => addStampy(R1, R2, outputBam, deps)
+        case "star"       => addStar(R1, R2, outputBam, deps)
+        case "star-2pass" => addStar2pass(R1, R2, outputBam, deps)
+        case _            => throw new IllegalStateException("Option Aligner: '" + aligner + "' is not valid")
+      }
+      if (config("chunk_metrics", default = false))
+        addAll(BamMetrics(this, outputBam, chunkDir + "metrics/").functions)
+    }
+    if (!skipFlexiprep) {
+      flexiprep.runFinalize(fastq_R1_output, fastq_R2_output)
+      addAll(flexiprep.functions) // Add function of flexiprep to curent function pool
+    }
+
+    var bamFile = bamFiles.head
+    if (!skipMarkduplicates) {
+      bamFile = new File(outputDir + outputName + ".dedup.bam")
+      add(MarkDuplicates(this, bamFiles, bamFile))
+    } else if (skipMarkduplicates && chunking) {
+      val mergeSamFile = MergeSamFiles(this, bamFiles, outputDir)
+      add(mergeSamFile)
+      bamFile = mergeSamFile.output
+    }
+
+    if (!skipMetrics) addAll(BamMetrics(this, bamFile, outputDir + "metrics/").functions)
+
+    outputFiles += ("finalBamFile" -> bamFile)
+  }
+
+  def addBwa(R1: File, R2: File, output: File, deps: List[File]): File = {
+    val bwaCommand = new Bwa(this)
+    bwaCommand.R1 = R1
+    if (paired) bwaCommand.R2 = R2
+    bwaCommand.deps = deps
+    bwaCommand.R = getReadGroup
+    bwaCommand.output = this.swapExt(output.getParent, output, ".bam", ".sam")
+    add(bwaCommand, isIntermediate = true)
+    val sortSam = SortSam(this, bwaCommand.output, output)
+    if (chunking || !skipMarkduplicates) sortSam.isIntermediate = true
+    add(sortSam)
+    return sortSam.output
+  }
+
+  def addStampy(R1: File, R2: File, output: File, deps: List[File]): File = {
+
+    var RG: String = "ID:" + RGID + ","
+    RG += "SM:" + RGSM + ","
+    RG += "LB:" + RGLB + ","
+    if (RGDS != null) RG += "DS" + RGDS + ","
+    RG += "PU:" + RGPU + ","
+    if (RGPI > 0) RG += "PI:" + RGPI + ","
+    if (RGCN != null) RG += "CN:" + RGCN + ","
+    if (RGDT != null) RG += "DT:" + RGDT + ","
+    RG += "PL:" + RGPL
+
+    val stampyCmd = new Stampy(this)
+    stampyCmd.R1 = R1
+    if (paired) stampyCmd.R2 = R2
+    stampyCmd.deps = deps
+    stampyCmd.readgroup = RG
+    stampyCmd.sanger = true
+    stampyCmd.output = this.swapExt(output.getParent, output, ".bam", ".sam")
+    add(stampyCmd, isIntermediate = true)
+    val sortSam = SortSam(this, stampyCmd.output, output)
+    if (chunking || !skipMarkduplicates) sortSam.isIntermediate = true
+    add(sortSam)
+    return sortSam.output
+  }
+
+  def addBowtie(R1: File, R2: File, output: File, deps: List[File]): File = {
+    val bowtie = new Bowtie(this)
+    bowtie.R1 = R1
+    if (paired) bowtie.R2 = R2
+    bowtie.deps = deps
+    bowtie.output = this.swapExt(output.getParent, output, ".bam", ".sam")
+    add(bowtie, isIntermediate = true)
+    return addAddOrReplaceReadGroups(bowtie.output, output)
+  }
+
+  def addStar(R1: File, R2: File, output: File, deps: List[File]): File = {
+    val starCommand = Star(this, R1, if (paired) R2 else null, outputDir, isIntermediate = true, deps = deps)
+    add(starCommand)
+    return addAddOrReplaceReadGroups(starCommand.outputSam, output)
+  }
+
+  def addStar2pass(R1: File, R2: File, output: File, deps: List[File]): File = {
+    val starCommand = Star._2pass(this, R1, if (paired) R2 else null, outputDir, isIntermediate = true, deps = deps)
+    addAll(starCommand._2)
+    return addAddOrReplaceReadGroups(starCommand._1, output)
+  }
+
+  def addAddOrReplaceReadGroups(input: File, output: File): File = {
+    val addOrReplaceReadGroups = AddOrReplaceReadGroups(this, input, output)
+    addOrReplaceReadGroups.createIndex = true
+
+    addOrReplaceReadGroups.RGID = RGID
+    addOrReplaceReadGroups.RGLB = RGLB
+    addOrReplaceReadGroups.RGPL = RGPL
+    addOrReplaceReadGroups.RGPU = RGPU
+    addOrReplaceReadGroups.RGSM = RGSM
+    if (RGCN != null) addOrReplaceReadGroups.RGCN = RGCN
+    if (RGDS != null) addOrReplaceReadGroups.RGDS = RGDS
+    if (!skipMarkduplicates) addOrReplaceReadGroups.isIntermediate = true
+    add(addOrReplaceReadGroups)
+
+    return addOrReplaceReadGroups.output
+  }
+
+  def getReadGroup(): String = {
+    var RG: String = "@RG\\t" + "ID:" + RGID + "\\t"
+    RG += "LB:" + RGLB + "\\t"
+    RG += "PL:" + RGPL + "\\t"
+    RG += "PU:" + RGPU + "\\t"
+    RG += "SM:" + RGSM + "\\t"
+    if (RGCN != null) RG += "CN:" + RGCN + "\\t"
+    if (RGDS != null) RG += "DS" + RGDS + "\\t"
+    if (RGDT != null) RG += "DT" + RGDT + "\\t"
+    if (RGPI > 0) RG += "PI" + RGPI + "\\t"
+
+    return RG.substring(0, RG.lastIndexOf("\\t"))
+  }
+}
+
+object Mapping extends PipelineCommand {
+  def loadFromLibraryConfig(root: Configurable, runConfig: Map[String, Any], sampleConfig: Map[String, Any],
+                            runDir: String, startJobs: Boolean = true): Mapping = {
+    val mapping = new Mapping(root)
+
+    logger.debug("Mapping runconfig: " + runConfig)
+    if (runConfig.contains("R1")) mapping.input_R1 = new File(runConfig("R1").toString)
+    if (runConfig.contains("R2")) mapping.input_R2 = new File(runConfig("R2").toString)
+    mapping.paired = (mapping.input_R2 != null)
+    mapping.RGLB = runConfig("ID").toString
+    mapping.RGSM = sampleConfig("ID").toString
+    if (runConfig.contains("PL")) mapping.RGPL = runConfig("PL").toString
+    if (runConfig.contains("PU")) mapping.RGPU = runConfig("PU").toString
+    if (runConfig.contains("CN")) mapping.RGCN = runConfig("CN").toString
+    mapping.outputDir = runDir
+
+    if (startJobs) {
+      mapping.init
+      mapping.biopetScript
+    }
+    return mapping
+  }
+}