added initial carp setup

public/carp/.gitignore

+/target/
\ No newline at end of file

public/carp/pom.xml

+<!--
+
+    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 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>Carp</artifactId>
+    <packaging>jar</packaging>
+    
+    <parent>
+        <groupId>nl.lumc.sasc</groupId>
+        <artifactId>Biopet</artifactId>
+        <version>0.3.0-DEV</version>
+        <relativePath>../</relativePath>
+    </parent>
+    
+    <inceptionYear>2014</inceptionYear>
+    <name>Carp</name>
+
+    <dependencies>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>BiopetFramework</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>Mapping</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+    </dependencies>
+</project>

public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala

+/**
+ * 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.
+ */
+package nl.lumc.sasc.biopet.pipelines.carp
+
+import nl.lumc.sasc.biopet.extensions.sambamba.SambambaMerge
+import org.broadinstitute.gatk.queue.QScript
+import org.broadinstitute.gatk.queue.extensions.gatk._
+import org.broadinstitute.gatk.queue.extensions.picard._
+import org.broadinstitute.gatk.queue.function._
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Input }
+import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
+import nl.lumc.sasc.biopet.extensions.aligners.{ Bwa, Star, Bowtie, Stampy }
+import nl.lumc.sasc.biopet.core._
+import nl.lumc.sasc.biopet.core.config._
+import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
+import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
+import nl.lumc.sasc.biopet.extensions.picard.{ MarkDuplicates, SortSam, MergeSamFiles, AddOrReplaceReadGroups }
+import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
+import nl.lumc.sasc.biopet.extensions.macs2.Macs2
+
+/**
+ * Carp pipeline
+ * Chip-Seq analysis pipeline
+ * This pipeline performs QC,mapping and peak calling
+ */
+class Carp(val root: Configurable) extends QScript with MultiSampleQScript {
+  def this() = this(null)
+
+  class LibraryOutput extends AbstractLibraryOutput {
+    var mappedBamFile: File = _
+  }
+
+  class SampleOutput extends AbstractSampleOutput {
+  }
+
+  def init() {
+
+  }
+
+  def biopetScript() {
+    // Define what the pipeline should do
+    // First step is QC, this will be done with Flexiprep
+    // Second step is mapping, this will be done with the Mapping pipeline
+    // Third step is calling peaks on the bam files produced with the mapping pipeline, this will be done with MACS2
+    logger.info("Starting CArP pipeline")
+
+    runSamplesJobs
+
+    //val macs2 = new Macs2CallPeak(this)
+    //macs2.treatment = new File("patient.bam")
+    //macs2.control = new File("control.bam")
+  }
+
+  def runSingleSampleJobs(sampleConfig: Map[String, Any]): SampleOutput = {
+    val sampleOutput = new SampleOutput
+    val sampleID: String = sampleConfig("ID").toString
+
+    sampleOutput.libraries = runLibraryJobs(sampleConfig)
+
+    return sampleOutput
+  }
+
+  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 runDir: String = globalSampleDir + sampleID + "/run_" + runID + "/"
+
+    if (runConfig.contains("R1")) {
+      val mapping = new Mapping(this)
+
+      mapping.skipMarkduplicates = config("skip_markduplicates", default = true) // we do the dedup marking using Sambamba
+
+      mapping.input_R1 = new File(runConfig("R1").toString)
+      if (runConfig.contains("R2")) mapping.input_R2 = new File(runConfig("R2").toString)
+      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)
+
+      libraryOutput.mappedBamFile = mapping.outputFiles("finalBamFile")
+    } else this.logger.error("Sample: " + sampleID + ": No R1 found for run: " + runConfig)
+    return libraryOutput
+  }
+
+}
+
+object Carp extends PipelineCommand