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Commit b3553528 authored by Peter van 't Hof's avatar Peter van 't Hof
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Gatk now uses the mapping module

parent 8d195010
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gatk/examples/test.json 0 → 100644
View file @ b3553528
{
"fastqc": { "exe": "/home/pjvan_thof/Downloads/FastQC/fastqc" },
"bwa" : {"exe":"/home/pjvan_thof/pipelines/test/test"},
"flexiprep": {
"fastqc": {"exe":"/home/pjvan_thof/pipelines/test/test"},
"cutadapt": {"exe":"/home/pjvan_thof/pipelines/test/test"},
"sickle": {"exe":"/home/pjvan_thof/pipelines/test/test"}
},
"gatk": {
"referenceFile" : "/home/pjvan_thof/pipelines/test/test",
"dbsnp": "/home/pjvan_thof/pipelines/test/test",
"hapmap": "/home/pjvan_thof/pipelines/test/test",
"omni": "/home/pjvan_thof/pipelines/test/test",
"1000G": "/home/pjvan_thof/pipelines/test/test",
"mills": "/home/pjvan_thof/pipelines/test/test"
},
"Samples": {
"test": {
"ID": "test",
"Runs": {
"1" : {
"ID": "1",
"R1" : "/home/pjvan_thof/pipelines/test/test.fastq"
}
}
}
}
}
gatk/nbactions.xml
View file @ b3553528
......@@ -10,7 +10,7 @@
<goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
</goals>
<properties>
<exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.gatk.Gatk</exec.args>
<exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.gatk.Gatk -config /home/pjvan_thof/pipelines/biopet/gatk/examples/test.json -outputDir /home/pjvan_thof/pipelines/test -l debug</exec.args>
<exec.executable>java</exec.executable>
<exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
</properties>
......@@ -25,7 +25,7 @@
<goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
</goals>
<properties>
<exec.args>-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.gatk.Gatk</exec.args>
<exec.args>-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.gatk.Gatk -config /home/pjvan_thof/pipelines/biopet/gatk/examples/test.json -outputDir /home/pjvan_thof/pipelines/test -l debug</exec.args>
<exec.executable>java</exec.executable>
<jpda.listen>true</jpda.listen>
<exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
......@@ -41,7 +41,7 @@
<goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
</goals>
<properties>
<exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.gatk.Gatk</exec.args>
<exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.gatk.Gatk -config /home/pjvan_thof/pipelines/biopet/gatk/examples/test.json -outputDir /home/pjvan_thof/pipelines/test -l debug</exec.args>
<exec.executable>java</exec.executable>
<exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
</properties>
......
gatk/pom.xml
View file @ b3553528
......@@ -49,7 +49,7 @@
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Flexiprep</artifactId>
<artifactId>Mapping</artifactId>
<version>0.1.0</version>
</dependency>
<dependency>
......
gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala
View file @ b3553528
package nl.lumc.sasc.biopet.pipelines.gatk
import nl.lumc.sasc.biopet.wrappers._
import nl.lumc.sasc.biopet.wrappers.aligners._
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.pipelines.mapping._
import nl.lumc.sasc.biopet.pipelines.flexiprep._
import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.sting.queue.extensions.gatk._
......@@ -120,8 +122,6 @@ class Gatk(private var globalConfig: Config) extends QScript {
}
add(indelApplyRecalibration)
} else logger.warn("No gVCFs to genotype")
}
}
......@@ -179,67 +179,40 @@ class Gatk(private var globalConfig: Config) extends QScript {
if (fastq_R1 != null) {
val runDir: String = outputDir + sampleID + "/run_" + runID + "/"
val flexiprep = new Flexiprep(config)
flexiprep.input_R1 = fastq_R1
if (paired) flexiprep.input_R2 = fastq_R2
flexiprep.outputDir = runDir + "flexiprep/"
flexiprep.script
addAll(flexiprep.functions) // Add functions of flexiprep to curent function pool
val bwaCommand = new Bwa(config)
bwaCommand.R1 = flexiprep.outputFiles("output_R1")
if (paired) bwaCommand.R2 = flexiprep.outputFiles("output_R2")
//bwaCommand.referenceFile = qscript.referenceFile
//bwaCommand.nCoresRequest = 8
bwaCommand.jobResourceRequests :+= "h_vmem=6G"
bwaCommand.RG = "@RG\\t" +
"ID:" + sampleID + "_" + runID + "\\t" +
"LB:" + sampleID + "_" + runID + "\\t" +
"PL:illumina\\t" +
"CN:SASC\\t" +
"SM:" + sampleID + "\\t" +
"PU:na"
bwaCommand.output = new File(runDir + sampleID + "-run_" + runID + ".sam")
add(bwaCommand)
val mapping = new Mapping(config)
mapping.input_R1 = fastq_R1
if (paired) mapping.input_R2 = fastq_R2
mapping.outputDir = runDir + "mapping/"
mapping.RGSM = sampleID
mapping.RGLB = runID
if (runConfig.contains("PL")) mapping.RGPL = runConfig.getAsString("PL")
if (runConfig.contains("PU")) mapping.RGPU = runConfig.getAsString("PU")
if (runConfig.contains("CN")) mapping.RGCN = runConfig.getAsString("CN")
mapping.script
addAll(mapping.functions) // Add functions of mapping to curent function pool
var bamFile:File = addSortSam(List(bwaCommand.output), swapExt(runDir,bwaCommand.output,".sam",".bam"), runDir)
bamFile = addMarkDuplicates(List(bamFile), swapExt(runDir,bamFile,".bam",".dedup.bam"), runDir)
bamFile = addIndelRealign(bamFile,runDir) // Indel realigner
var bamFile:File = addIndelRealign(mapping.outputFiles("finalBamFile"),runDir) // Indel realigner
bamFile = addBaseRecalibrator(bamFile,runDir) // Base recalibrator
outputFiles += ("FinalBam" -> bamFile)
} else this.logger.error("Sample: " + sampleID + ": No R1 found for runs: " + runConfig)
return outputFiles
}
def addSortSam(inputSam:List[File], outputFile:File, dir:String) : File = {
val sortSam = new SortSam {
this.input = inputSam
this.createIndex = true
this.output = outputFile
this.memoryLimit = 2
this.nCoresRequest = 2
this.jobResourceRequests :+= "h_vmem=4G"
}
add(sortSam)
return sortSam.output
}
def addMarkDuplicates(inputBams:List[File], outputFile:File, dir:String) : File = {
val markDuplicates = new MarkDuplicates {
this.input = inputBams
this.output = outputFile
this.REMOVE_DUPLICATES = false
this.metrics = swapExt(dir,outputFile,".bam",".metrics")
this.outputIndex = swapExt(dir,this.output,".bam",".bai")
this.memoryLimit = 2
this.jobResourceRequests :+= "h_vmem=4G"
}
add(markDuplicates)
return markDuplicates.output
}
// def addMarkDuplicates(inputBams:List[File], outputFile:File, dir:String) : File = {
// val markDuplicates = new MarkDuplicates {
// this.input = inputBams
// this.output = outputFile
// this.REMOVE_DUPLICATES = false
// this.metrics = swapExt(dir,outputFile,".bam",".metrics")
// this.outputIndex = swapExt(dir,this.output,".bam",".bai")
// this.memoryLimit = 2
// this.jobResourceRequests :+= "h_vmem=4G"
// }
// add(markDuplicates)
//
// return markDuplicates.output
// }
def addIndelRealign(inputBam:File, dir:String): File = {
val realignerTargetCreator = new RealignerTargetCreator with gatkArguments {
......
mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @ b3553528
package nl.lumc.sasc.biopet.pipelines.mapping
import nl.lumc.sasc.biopet.wrappers._
import nl.lumc.sasc.biopet.wrappers.aligners._
import java.util.Date
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.pipelines.flexiprep._
......@@ -19,7 +20,7 @@ class Mapping(private var globalConfig: Config) extends QScript {
@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 directory", shortName="outputDir", required=true) var outputDir: String = _
@Argument(doc="Output name", shortName="outputName", required=true) var outputName: String = _
@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="Alginer", shortName="ALN", required=false) var aligner: String = _
......@@ -64,6 +65,8 @@ class Mapping(private var globalConfig: Config) extends QScript {
if (RGPU == null) RGPU = config.getAsString("RGPU", "na")
if (RGCN == null && config.contains("RGCN")) RGCN = config.getAsString("RGCN")
if (RGDS == null && config.contains("RGDS")) RGDS = config.getAsString("RGDS")
if (outputName == null) outputName = RGID
}
def script() {
......@@ -94,6 +97,7 @@ class Mapping(private var globalConfig: Config) extends QScript {
}
if (!skipMarkduplicates) bamFile = addMarkDuplicates(List(bamFile), swapExt(outputDir,bamFile,".bam",".dedup.bam"), outputDir)
outputFiles += ("finalBamFile" -> bamFile)
}
def addSortSam(inputSam:List[File], outputFile:File, dir:String) : File = {
......
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