Commit 8f6b31f2 authored by Sander van der Zeeuw's avatar Sander van der Zeeuw
Browse files

added initial carp setup

parent f193f599
/target/
\ No newline at end of file
<!--
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>
/**
* 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
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment