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 9beec1e9315da5639ec5b6fa0d2e3c9a67d0c9f2..ca21c3cf64d130bf6e4a66fa1728cbab67f337a7 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
@@ -60,58 +60,63 @@ class Gatk(private var globalConfig: Config) extends QScript {
add(genotypeGVCFs)
//Snp recal
- val snpVariantRecalibrator = new VariantRecalibrator() with gatkArguments
- snpVariantRecalibrator.input +:= genotypeGVCFs.out
- snpVariantRecalibrator.nt = 8
- snpVariantRecalibrator.recal_file = swapExt(genotypeGVCFs.out,".vcf",".snp.recal")
- snpVariantRecalibrator.tranches_file = swapExt(genotypeGVCFs.out,".vcf",".snp.tranches")
- snpVariantRecalibrator.resource :+= new TaggedFile(config.getAsString("hapmap"), "known=false,training=true,truth=true,prior=15.0")
- snpVariantRecalibrator.resource :+= new TaggedFile(config.getAsString("omni"), "known=false,training=true,truth=true,prior=12.0")
- snpVariantRecalibrator.resource :+= new TaggedFile(config.getAsString("1000G"), "known=false,training=true,truth=false,prior=10.0")
- snpVariantRecalibrator.resource :+= new TaggedFile(config.getAsString("dbsnp"), "known=true,training=false,truth=false,prior=2.0")
- snpVariantRecalibrator.an = Seq("QD","MQ","MQRankSum","ReadPosRankSum","FS","DP","InbreedingCoeff")
- snpVariantRecalibrator.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.SNP
+ val snpVariantRecalibrator = new VariantRecalibrator() with gatkArguments {
+ input +:= genotypeGVCFs.out
+ nt = 4; memoryLimit = 2 * nt
+ recal_file = swapExt(genotypeGVCFs.out,".vcf",".snp.recal")
+ tranches_file = swapExt(genotypeGVCFs.out,".vcf",".snp.tranches")
+ resource = Seq(new TaggedFile(config.getAsString("hapmap"), "known=false,training=true,truth=true,prior=15.0"),
+ new TaggedFile(config.getAsString("omni"), "known=false,training=true,truth=true,prior=12.0"),
+ new TaggedFile(config.getAsString("1000G"), "known=false,training=true,truth=false,prior=10.0"),
+ new TaggedFile(config.getAsString("dbsnp"), "known=true,training=false,truth=false,prior=2.0"))
+ an = Seq("QD","MQ","MQRankSum","ReadPosRankSum","FS","DP","InbreedingCoeff")
+ mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.SNP
+ }
add(snpVariantRecalibrator)
- val snpApplyRecalibration = new ApplyRecalibration() with gatkArguments
- snpApplyRecalibration.input +:= genotypeGVCFs.out
- snpApplyRecalibration.recal_file = snpVariantRecalibrator.recal_file
- snpApplyRecalibration.tranches_file = snpVariantRecalibrator.tranches_file
- snpApplyRecalibration.out = swapExt(genotypeGVCFs.out,".vcf",".snp.recal.vcf")
- snpApplyRecalibration.ts_filter_level = 99.5
- snpApplyRecalibration.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.SNP
- snpApplyRecalibration.nt = 3
- snpApplyRecalibration.scatterCount = scatterCount
+ val snpApplyRecalibration = new ApplyRecalibration() with gatkArguments {
+ input +:= genotypeGVCFs.out
+ recal_file = snpVariantRecalibrator.recal_file
+ tranches_file = snpVariantRecalibrator.tranches_file
+ out = swapExt(genotypeGVCFs.out,".vcf",".snp.recal.vcf")
+ ts_filter_level = 99.5
+ mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.SNP
+ nt = 3; memoryLimit = 2 * nt
+ scatterCount = scatterCount
+ }
add(snpApplyRecalibration)
//indel recal
- val indelVariantRecalibrator = new VariantRecalibrator() with gatkArguments
- indelVariantRecalibrator.input +:= genotypeGVCFs.out
- indelVariantRecalibrator.nt = 8
- indelVariantRecalibrator.recal_file = swapExt(genotypeGVCFs.out,".vcf",".indel.recal")
- indelVariantRecalibrator.tranches_file = swapExt(genotypeGVCFs.out,".vcf",".indel.tranches")
- indelVariantRecalibrator.resource :+= new TaggedFile(config.getAsString("mills"), "known=false,training=true,truth=true,prior=12.0")
- indelVariantRecalibrator.resource :+= new TaggedFile(config.getAsString("dbsnp"), "known=true,training=false,truth=false,prior=2.0")
- indelVariantRecalibrator.an = Seq("QD","DP","FS","ReadPosRankSum","MQRankSum","InbreedingCoeff")
- indelVariantRecalibrator.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.INDEL
+ val indelVariantRecalibrator = new VariantRecalibrator() with gatkArguments {
+ input +:= genotypeGVCFs.out
+ nt = 4; memoryLimit = 2 * nt
+ recal_file = swapExt(genotypeGVCFs.out,".vcf",".indel.recal")
+ tranches_file = swapExt(genotypeGVCFs.out,".vcf",".indel.tranches")
+ resource :+= new TaggedFile(config.getAsString("mills"), "known=false,training=true,truth=true,prior=12.0")
+ resource :+= new TaggedFile(config.getAsString("dbsnp"), "known=true,training=false,truth=false,prior=2.0")
+ an = Seq("QD","DP","FS","ReadPosRankSum","MQRankSum","InbreedingCoeff")
+ mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.INDEL
+ }
add(indelVariantRecalibrator)
- val indelApplyRecalibration = new ApplyRecalibration() with gatkArguments
- indelApplyRecalibration.input +:= genotypeGVCFs.out
- indelApplyRecalibration.recal_file = indelVariantRecalibrator.recal_file
- indelApplyRecalibration.tranches_file = indelVariantRecalibrator.tranches_file
- indelApplyRecalibration.out = swapExt(genotypeGVCFs.out,".vcf",".indel.recal.vcf")
- indelApplyRecalibration.ts_filter_level = 99.0
- indelApplyRecalibration.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.INDEL
- indelApplyRecalibration.nt = 3
- indelApplyRecalibration.scatterCount = scatterCount
+ val indelApplyRecalibration = new ApplyRecalibration() with gatkArguments {
+ input +:= genotypeGVCFs.out
+ recal_file = indelVariantRecalibrator.recal_file
+ tranches_file = indelVariantRecalibrator.tranches_file
+ out = swapExt(genotypeGVCFs.out,".vcf",".indel.recal.vcf")
+ ts_filter_level = 99.0
+ mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.INDEL
+ nt = 3; memoryLimit = 2 * nt
+ scatterCount = scatterCount
+ }
add(indelApplyRecalibration)
// merge snp and indels
- val catVariants = new CatVariants()
- catVariants.variant = Seq(snpApplyRecalibration.out,indelApplyRecalibration.out)
- catVariants.outputFile = swapExt(genotypeGVCFs.out,".vcf",".recal.vcf")
- catVariants.reference = referenceFile
+ val catVariants = new CatVariants() {
+ variant = Seq(snpApplyRecalibration.out,indelApplyRecalibration.out)
+ outputFile = swapExt(genotypeGVCFs.out,".vcf",".recal.vcf")
+ reference = referenceFile
+ }
add(catVariants)
} else logger.warn("No gVCFs to genotype")
diff --git a/mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
index 74573e2a18d8c083eacfb9ad2f149b1058fd9351..7f680b3a617681bba2c5270e740b238a59cb5eb0 100644
--- a/mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -80,7 +80,6 @@ class Mapping(private var globalConfig: Config) extends QScript {
if (paired) fastq_R2 = flexiprep.outputFiles("output_R2")
}
var bamFile:File = ""
- //var samFile:File = ""
if (aligner == "bwa") {
val bwaCommand = new Bwa(config) { R1 = fastq_R1; if (paired) R2 = fastq_R2;
RG = getReadGroup; output = new File(outputDir + outputName + ".sam") }
@@ -96,46 +95,48 @@ class Mapping(private var globalConfig: Config) extends QScript {
}
def addSortSam(inputSam:List[File], outputFile:File, dir:String) : File = {
- val sortSam = new SortSam
- sortSam.input = inputSam
- sortSam.createIndex = true
- sortSam.output = outputFile
- sortSam.memoryLimit = 2
- sortSam.nCoresRequest = 2
- sortSam.jobResourceRequests :+= "h_vmem=4G"
+ val sortSam = new SortSam {
+ input = inputSam
+ createIndex = true
+ output = outputFile
+ memoryLimit = 2
+ nCoresRequest = 2
+ jobResourceRequests :+= "h_vmem=4G"
+ }
add(sortSam)
return sortSam.output
}
def addAddOrReplaceReadGroups(inputSam:List[File], outputFile:File, dir:String) : File = {
- val addOrReplaceReadGroups = new AddOrReplaceReadGroups
- addOrReplaceReadGroups.input = inputSam
- addOrReplaceReadGroups.createIndex = true
- addOrReplaceReadGroups.output = outputFile
- addOrReplaceReadGroups.memoryLimit = 2
- addOrReplaceReadGroups.nCoresRequest = 2
- addOrReplaceReadGroups.jobResourceRequests :+= "h_vmem=4G"
-
- addOrReplaceReadGroups.RGLB = RGLB
- addOrReplaceReadGroups.RGPL = RGPL
- addOrReplaceReadGroups.RGPU = RGPU
- addOrReplaceReadGroups.RGSM = RGSM
- if (RGCN != null) addOrReplaceReadGroups.RGCN = RGCN
- if (RGDS != null) addOrReplaceReadGroups.RGDS = RGDS
-
+ val addOrReplaceReadGroups = new AddOrReplaceReadGroups {
+ input = inputSam
+ output = outputFile
+ createIndex = true
+ memoryLimit = 2
+ nCoresRequest = 2
+ jobResourceRequests :+= "h_vmem=4G"
+
+ this.RGLB = RGLB
+ this.RGPL = RGPL
+ this.RGPU = RGPU
+ this.RGSM = RGSM
+ if (RGCN != null) this.RGCN = RGCN
+ if (RGDS != null) this.RGDS = RGDS
+ }
return addOrReplaceReadGroups.output
}
def addMarkDuplicates(inputBams:List[File], outputFile:File, dir:String) : File = {
- val markDuplicates = new MarkDuplicates
- markDuplicates.input = inputBams
- markDuplicates.output = outputFile
- markDuplicates.REMOVE_DUPLICATES = false
- markDuplicates.metrics = swapExt(dir,outputFile,".bam",".metrics")
- markDuplicates.outputIndex = swapExt(dir,markDuplicates.output,".bam",".bai")
- markDuplicates.memoryLimit = 2
- markDuplicates.jobResourceRequests :+= "h_vmem=4G"
+ val markDuplicates = new MarkDuplicates {
+ input = inputBams
+ output = outputFile
+ REMOVE_DUPLICATES = false
+ metrics = swapExt(dir,outputFile,".bam",".metrics")
+ outputIndex = swapExt(dir,this.output,".bam",".bai")
+ memoryLimit = 2
+ jobResourceRequests :+= "h_vmem=4G"
+ }
add(markDuplicates)
return markDuplicates.output