diff --git a/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala b/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala
index c1294eb773b86d42048d268986c826f4c5fcc1f4..247b650bdb6ff49f60aa03ec33f1d7497b42fa1d 100644
--- a/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala
+++ b/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala
@@ -17,7 +17,6 @@ class Gatk(private var globalConfig: Config) extends QScript {
@Argument(doc="Output directory", shortName="outputDir", required=true) var outputDir: String = _
def this() = this(new Config())
var config: Config = _
- var scatterCount: Int = _
var referenceFile: File = _
var dbsnp: File = _
var gvcfFiles: List[File] = Nil
@@ -34,7 +33,6 @@ class Gatk(private var globalConfig: Config) extends QScript {
referenceFile = config.getAsString("referenceFile")
dbsnp = config.getAsString("dbsnp")
gvcfFiles = config.getAsListOfStrings("gvcfFiles", Nil)
- scatterCount = config.getAsInt("scatterCount", 1)
if (outputDir == null) throw new IllegalStateException("Missing Output directory on flexiprep module")
else if (!outputDir.endsWith("/")) outputDir += "/"
}
@@ -55,14 +53,16 @@ class Gatk(private var globalConfig: Config) extends QScript {
//SampleWide jobs
if (gvcfFiles.size > 0) {
val genotypeGVCFs = new GenotypeGVCFs() with gatkArguments {
+ val config: Config = Config.mergeConfigs(qscript.config.getAsConfig("genotypegvcfs"), qscript.config)
this.variant = gvcfFiles
- this.scatterCount = scatterCount
+ if (config.contains("scattercount")) this.scatterCount = config.getAsInt("scattercount")
this.out = new File(outputDir,"final.vcf")
}
add(genotypeGVCFs)
//Snp recal
val snpVariantRecalibrator = new VariantRecalibrator() with gatkArguments {
+ val config: Config = Config.mergeConfigs(qscript.config.getAsConfig("variantrecalibrator"), qscript.config)
this.input +:= genotypeGVCFs.out
this.nt = 4
this.memoryLimit = 2 * nt
@@ -78,6 +78,7 @@ class Gatk(private var globalConfig: Config) extends QScript {
add(snpVariantRecalibrator)
val snpApplyRecalibration = new ApplyRecalibration() with gatkArguments {
+ val config: Config = Config.mergeConfigs(qscript.config.getAsConfig("applyrecalibration"), qscript.config)
this.input +:= genotypeGVCFs.out
this.recal_file = snpVariantRecalibrator.recal_file
this.tranches_file = snpVariantRecalibrator.tranches_file
@@ -86,12 +87,13 @@ class Gatk(private var globalConfig: Config) extends QScript {
this.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.SNP
this.nt = 3
this.memoryLimit = 2 * nt
- if (scatterCount > 1) this.scatterCount = qscript.scatterCount
+ if (config.contains("scattercount")) this.scatterCount = config.getAsInt("scattercount")
}
add(snpApplyRecalibration)
//indel recal
val indelVariantRecalibrator = new VariantRecalibrator() with gatkArguments {
+ val config: Config = Config.mergeConfigs(qscript.config.getAsConfig("variantrecalibrator"), qscript.config)
this.input +:= genotypeGVCFs.out
this.nt = 4
this.memoryLimit = 2 * nt
@@ -105,6 +107,7 @@ class Gatk(private var globalConfig: Config) extends QScript {
add(indelVariantRecalibrator)
val indelApplyRecalibration = new ApplyRecalibration() with gatkArguments {
+ val config: Config = Config.mergeConfigs(qscript.config.getAsConfig("applyrecalibration"), qscript.config)
this.input +:= genotypeGVCFs.out
this.recal_file = indelVariantRecalibrator.recal_file
this.tranches_file = indelVariantRecalibrator.tranches_file
@@ -113,7 +116,7 @@ class Gatk(private var globalConfig: Config) extends QScript {
this.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.INDEL
this.nt = 3
this.memoryLimit = 2 * nt
- if (scatterCount > 1) this.scatterCount = qscript.scatterCount
+ if (config.contains("scattercount")) this.scatterCount = config.getAsInt("scattercount")
}
add(indelApplyRecalibration)
} else logger.warn("No gVCFs to genotype")
@@ -141,19 +144,20 @@ class Gatk(private var globalConfig: Config) extends QScript {
}
// Variant calling
- val haplotypeCaller = new HaplotypeCaller with gatkArguments
- if (scatterCount > 1) haplotypeCaller.scatterCount = scatterCount * 15
- haplotypeCaller.input_file = outputFiles("FinalBams")
- haplotypeCaller.out = new File(outputDir,sampleID + "/" + sampleID + ".gvcf.vcf")
- if (dbsnp != null) haplotypeCaller.dbsnp = qscript.dbsnp
- haplotypeCaller.nct = 3
- haplotypeCaller.memoryLimit = haplotypeCaller.nct * 2
-
- // GVCF options
- haplotypeCaller.emitRefConfidence = org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.ReferenceConfidenceMode.GVCF
- haplotypeCaller.variant_index_type = GATKVCFIndexType.LINEAR
- haplotypeCaller.variant_index_parameter = 128000
-
+ val haplotypeCaller = new HaplotypeCaller with gatkArguments {
+ val config: Config = Config.mergeConfigs(qscript.config.getAsConfig("haplotypecaller"), qscript.config)
+ if (config.contains("scattercount")) this.scatterCount = config.getAsInt("scattercount")
+ this.input_file = outputFiles("FinalBams")
+ this.out = new File(outputDir,sampleID + "/" + sampleID + ".gvcf.vcf")
+ if (dbsnp != null) this.dbsnp = qscript.dbsnp
+ this.nct = 3
+ this.memoryLimit = this.nct * 2
+
+ // GVCF options
+ this.emitRefConfidence = org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.ReferenceConfidenceMode.GVCF
+ this.variant_index_type = GATKVCFIndexType.LINEAR
+ this.variant_index_parameter = 128000
+ }
if (haplotypeCaller.input_file.size > 0) {
add(haplotypeCaller)
outputFiles += ("gvcf" -> List(haplotypeCaller.out))
@@ -165,22 +169,15 @@ class Gatk(private var globalConfig: Config) extends QScript {
}
// Called for each run from a sample
- def runJobs(runConfig:Config,sampleConfig:Config) : Map[String,File] = {
+ def runJobs(runConfig:Config, sampleConfig:Config) : Map[String,File] = {
var outputFiles:Map[String,File] = Map()
- var paired: Boolean = false
- var runID: String = ""
- var fastq_R1: String = ""
- var fastq_R2: String = ""
- var sampleID: String = sampleConfig.get("ID").toString
- if (runConfig.contains("R1")) {
- fastq_R1 = runConfig.get("R1").toString
- if (runConfig.contains("R2")) {
- fastq_R2 = runConfig.get("R2").toString
- paired = true
- }
- if (runConfig.contains("ID")) runID = runConfig.get("ID").toString
- else throw new IllegalStateException("Missing ID on run for sample: " + sampleID)
- var runDir: String = outputDir + sampleID + "/run_" + runID + "/"
+ val runID: String = runConfig.getAsString("ID")
+ val fastq_R1: String = runConfig.getAsString("R1", null)
+ val fastq_R2: String = runConfig.getAsString("R2", null)
+ val paired: Boolean = (fastq_R2 != null)
+ val sampleID: String = sampleConfig.get("ID").toString
+ if (fastq_R1 != null) {
+ val runDir: String = outputDir + sampleID + "/run_" + runID + "/"
val flexiprep = new Flexiprep(config)
flexiprep.input_R1 = fastq_R1
@@ -246,18 +243,20 @@ class Gatk(private var globalConfig: Config) extends QScript {
def addIndelRealign(inputBam:File, dir:String): File = {
val realignerTargetCreator = new RealignerTargetCreator with gatkArguments {
+ val config: Config = Config.mergeConfigs(qscript.config.getAsConfig("realignertargetcreator"), qscript.config)
this.I :+= inputBam
this.o = swapExt(dir,inputBam,".bam",".realign.intervals")
this.jobResourceRequests :+= "h_vmem=5G"
- if (scatterCount > 1) this.scatterCount = qscript.scatterCount
+ if (config.contains("scattercount")) this.scatterCount = config.getAsInt("scattercount")
}
add(realignerTargetCreator)
val indelRealigner = new IndelRealigner with gatkArguments {
+ val config: Config = Config.mergeConfigs(qscript.config.getAsConfig("indelrealigner"), qscript.config)
this.I :+= inputBam
this.targetIntervals = realignerTargetCreator.o
this.o = swapExt(dir,inputBam,".bam",".realign.bam")
- if (scatterCount > 1) this.scatterCount = qscript.scatterCount
+ if (config.contains("scattercount")) this.scatterCount = config.getAsInt("scattercount")
}
add(indelRealigner)
@@ -266,19 +265,21 @@ class Gatk(private var globalConfig: Config) extends QScript {
def addBaseRecalibrator(inputBam:File, dir:String): File = {
val baseRecalibrator = new BaseRecalibrator with gatkArguments {
+ val config: Config = Config.mergeConfigs(qscript.config.getAsConfig("baserecalibrator"), qscript.config)
this.I :+= inputBam
this.o = swapExt(dir,inputBam,".bam",".baserecal")
this.knownSites :+= dbsnp
- if (scatterCount > 1) this.scatterCount = qscript.scatterCount
+ if (config.contains("scattercount")) this.scatterCount = config.getAsInt("scattercount")
this.nct = 2
}
add(baseRecalibrator)
val printReads = new PrintReads with gatkArguments {
+ val config: Config = Config.mergeConfigs(qscript.config.getAsConfig("printreads"), qscript.config)
this.I :+= inputBam
this.o = swapExt(dir,inputBam,".bam",".baserecal.bam")
this.BQSR = baseRecalibrator.o
- if (scatterCount > 1) this.scatterCount = qscript.scatterCount
+ if (config.contains("scattercount")) this.scatterCount = config.getAsInt("scattercount")
}
return printReads.o