Added yamsvp as artifact

public/yamsvp/.gitignore

+/target/
\ No newline at end of file

public/yamsvp/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>Yamsvp</artifactId>
+    <version>0.2.0-DEV</version>
+    <packaging>jar</packaging>
+    
+    <inceptionYear>2014</inceptionYear>
+    <name>Yamsvp</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>Mapping</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/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala

+/*
+ * Structural variation calling
+ */
+
+package nl.lumc.sasc.biopet.pipelines.yamsvp
+
+import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.core.MultiSampleQScript
+import nl.lumc.sasc.biopet.core.PipelineCommand
+
+import nl.lumc.sasc.biopet.extensions.sambamba.{ SambambaIndex, SambambaMerge }
+import nl.lumc.sasc.biopet.extensions.svcallers.pindel.Pindel
+import nl.lumc.sasc.biopet.extensions.svcallers.{ Breakdancer, Clever }
+
+import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
+
+import org.broadinstitute.gatk.queue.QScript
+import org.broadinstitute.gatk.queue.function._
+import org.broadinstitute.gatk.queue.engine.JobRunInfo
+
+class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
+  def this() = this(null)
+
+  var reference: File = config("reference", required = true)
+  var finalBamFiles: List[File] = Nil
+
+  class LibraryOutput extends AbstractLibraryOutput {
+    var mappedBamFile: File = _
+  }
+
+  class SampleOutput extends AbstractSampleOutput {
+    var vcf: Map[String, List[File]] = Map()
+    var mappedBamFile: File = _
+  }
+
+  override def init() {
+    if (outputDir == null)
+      throw new IllegalStateException("Output directory is not specified in the config / argument")
+    else if (!outputDir.endsWith("/"))
+      outputDir += "/"
+  }
+
+  def biopetScript() {
+    // write the pipeline here
+    // start with QC, alignment, call sambamba, call sv callers, reporting
+
+    // read config and set all parameters for the pipeline
+    logger.info("Starting YAM SV Pipeline")
+    runSamplesJobs
+    //
+
+  }
+
+  override def onExecutionDone(jobs: Map[QFunction, JobRunInfo], success: Boolean) {
+    logger.info("YAM SV Pipeline has run .......................")
+  }
+
+  def runSingleSampleJobs(sampleConfig: Map[String, Any]): SampleOutput = {
+    val sampleOutput = new SampleOutput
+    var libraryBamfiles: List[File] = List()
+    var outputFiles: Map[String, List[File]] = Map()
+    var libraryFastqFiles: List[File] = List()
+    val sampleID: String = sampleConfig("ID").toString
+    val sampleDir: String = outputDir + sampleID + "/"
+    val alignmentDir: String = sampleDir + "alignment/"
+
+    val svcallingDir: String = sampleDir + "svcalls/"
+
+    sampleOutput.libraries = runLibraryJobs(sampleConfig)
+    for ((libraryID, libraryOutput) <- sampleOutput.libraries) {
+      // this is extending the libraryBamfiles list like '~=' in D or .append in Python or .push_back in C++
+      libraryBamfiles ++= List(libraryOutput.mappedBamFile)
+    }
+
+    val bamFile: File =
+      if (libraryBamfiles.size == 1) libraryBamfiles.head
+      else if (libraryBamfiles.size > 1) {
+        val mergeSamFiles = new SambambaMerge(root)
+        mergeSamFiles.input = libraryBamfiles
+        mergeSamFiles.output = alignmentDir + sampleID + ".merged.bam"
+        add(mergeSamFiles)
+        mergeSamFiles.output
+      } else null
+
+    val bamIndex = SambambaIndex(root, bamFile)
+    add(bamIndex)
+
+    /// bamfile will be used as input for the SV callers. First run Clever
+    //    val cleverVCF : File = sampleDir + "/" + sampleID + ".clever.vcf"
+
+    val cleverDir = svcallingDir + sampleID + ".clever/"
+    val clever = Clever(this, bamFile, this.reference, svcallingDir, cleverDir)
+    clever.deps = List(bamIndex.output)
+    sampleOutput.vcf += ("clever" -> List(clever.outputvcf))
+    add(clever)
+
+    val breakdancerDir = svcallingDir + sampleID + ".breakdancer/"
+    val breakdancer = Breakdancer(this, bamFile, this.reference, breakdancerDir)
+    sampleOutput.vcf += ("breakdancer" -> List(breakdancer.outputvcf))
+    addAll(breakdancer.functions)
+
+    // for pindel we should use per library config collected into one config file
+    //    val pindelDir = svcallingDir + sampleID + ".pindel/"
+    //    val pindel = Pindel(this, bamFile, this.reference, pindelDir)
+    //    sampleOutput.vcf += ("pindel" -> List(pindel.outputvcf))
+    //    addAll(pindel.functions)
+    //
+    //    
+    return sampleOutput
+  }
+
+  // Called for each run from a sample
+
+  def runSingleLibraryJobs(runConfig: Map[String, Any], sampleConfig: Map[String, Any]): LibraryOutput = {
+    val libraryOutput = new LibraryOutput
+
+    val runID: String = runConfig("ID").toString
+    val sampleID: String = sampleConfig("ID").toString
+    val alignmentDir: String = outputDir + sampleID + "/alignment/"
+    val runDir: String = alignmentDir + "run_" + runID + "/"
+
+    if (runConfig.contains("R1")) {
+      val mapping = new Mapping(this)
+
+      mapping.aligner = config("aligner", default = "stampy")
+      mapping.skipFlexiprep = false
+      mapping.skipMarkduplicates = true // we do the dedup marking using Sambamba
+
+      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
+
+      mapping.init
+      mapping.biopetScript
+      addAll(mapping.functions)
+
+      // start sambamba dedup
+
+      libraryOutput.mappedBamFile = mapping.outputFiles("finalBamFile")
+    } else this.logger.error("Sample: " + sampleID + ": No R1 found for run: " + runConfig)
+    return libraryOutput
+    //    logger.debug(outputFiles)
+    //    return outputFiles
+  }
+}
+
+object Yamsvp extends PipelineCommand
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