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Commit 91e72434 authored by Peter van 't Hof's avatar Peter van 't Hof
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Switch Gatk pipeline and Basty to new multisample classes

parent 49ba8c53
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protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
View file @ 91e72434
......@@ -12,24 +12,40 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.extensions.{ RunGubbins, Cat, Raxml }
import nl.lumc.sasc.biopet.pipelines.gatk.GatkPipeline
import nl.lumc.sasc.biopet.tools.BastyGenerateFasta
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.queue.QScript
class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
qscript =>
def this() = this(null)
class LibraryOutput extends AbstractLibraryOutput {
}
case class FastaOutput(variants: File, consensus: File, consensusVariants: File)
class SampleOutput extends AbstractSampleOutput {
override def defaults = ConfigUtils.mergeMaps(Map(
"ploidy" -> 1,
"use_haplotypecaller" -> false,
"use_unifiedgenotyper" -> true,
"joint_variantcalling" -> true
), super.defaults)
var gatkPipeline: GatkPipeline = new GatkPipeline(qscript)
def makeSample(id: String) = new Sample(id)
class Sample(sampleId: String) extends AbstractSample(sampleId) {
def makeLibrary(id: String) = new Library(id)
class Library(libraryId: String) extends AbstractLibrary(libraryId) {
def addJobs(): Unit = {}
}
var output: FastaOutput = _
var outputSnps: FastaOutput = _
}
defaults ++= Map("ploidy" -> 1, "use_haplotypecaller" -> false, "use_unifiedgenotyper" -> true, "joint_variantcalling" -> true)
var gatkPipeline: GatkPipeline = new GatkPipeline(this)
gatkPipeline.jointVariantcalling = true
def addJobs(): Unit = {
runLibraryJobs()
output = addGenerateFasta(sampleId, sampleDir)
outputSnps = addGenerateFasta(sampleId, sampleDir, snpsOnly = true)
}
}
def init() {
gatkPipeline.outputDir = outputDir
......@@ -45,19 +61,19 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
runSamplesJobs()
val catVariants = Cat(this, refVariants.variants :: samplesOutput.map(_._2.output.variants).toList, outputDir + "fastas/variant.fasta")
val catVariants = Cat(this, refVariants.variants :: samples.map(_._2.output.variants).toList, outputDir + "fastas/variant.fasta")
add(catVariants)
val catVariantsSnps = Cat(this, refVariantSnps.variants :: samplesOutput.map(_._2.outputSnps.variants).toList, outputDir + "fastas/variant.snps_only.fasta")
val catVariantsSnps = Cat(this, refVariantSnps.variants :: samples.map(_._2.outputSnps.variants).toList, outputDir + "fastas/variant.snps_only.fasta")
add(catVariantsSnps)
val catConsensus = Cat(this, refVariants.consensus :: samplesOutput.map(_._2.output.consensus).toList, outputDir + "fastas/consensus.fasta")
val catConsensus = Cat(this, refVariants.consensus :: samples.map(_._2.output.consensus).toList, outputDir + "fastas/consensus.fasta")
add(catConsensus)
val catConsensusSnps = Cat(this, refVariantSnps.consensus :: samplesOutput.map(_._2.outputSnps.consensus).toList, outputDir + "fastas/consensus.snps_only.fasta")
val catConsensusSnps = Cat(this, refVariantSnps.consensus :: samples.map(_._2.outputSnps.consensus).toList, outputDir + "fastas/consensus.snps_only.fasta")
add(catConsensusSnps)
val catConsensusVariants = Cat(this, refVariants.consensusVariants :: samplesOutput.map(_._2.output.consensusVariants).toList, outputDir + "fastas/consensus.variant.fasta")
val catConsensusVariants = Cat(this, refVariants.consensusVariants :: samples.map(_._2.output.consensusVariants).toList, outputDir + "fastas/consensus.variant.fasta")
add(catConsensusVariants)
val catConsensusVariantsSnps = Cat(this, refVariantSnps.consensusVariants :: samplesOutput.map(_._2.outputSnps.consensusVariants).toList, outputDir + "fastas/consensus.variant.snps_only.fasta")
val catConsensusVariantsSnps = Cat(this, refVariantSnps.consensusVariants :: samples.map(_._2.outputSnps.consensusVariants).toList, outputDir + "fastas/consensus.variant.snps_only.fasta")
add(catConsensusVariantsSnps)
val seed: Int = config("seed", default = 12345)
......@@ -115,42 +131,20 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
addTreeJobs(catVariants.output, catConsensusVariants.output, outputDir + "trees" + File.separator + "snps_indels", "snps_indels")
}
// Called for each sample
def runSingleSampleJobs(sampleID: String): SampleOutput = {
val sampleOutput = new SampleOutput
val sampleDir = globalSampleDir + sampleID + "/"
sampleOutput.libraries = runLibraryJobs(sampleID)
sampleOutput.output = addGenerateFasta(sampleID, sampleDir)
sampleOutput.outputSnps = addGenerateFasta(sampleID, sampleDir, snpsOnly = true)
return sampleOutput
}
// Called for each run from a sample
def runSingleLibraryJobs(libraryID: String, sampleID: String): LibraryOutput = {
val libraryOutput = new LibraryOutput
val runDir: String = globalSampleDir + sampleID + "/run_" + libraryID + "/"
return libraryOutput
}
def addGenerateFasta(sampleName: String, outputDir: String, outputName: String = null,
snpsOnly: Boolean = false): FastaOutput = {
val bastyGenerateFasta = new BastyGenerateFasta(this)
bastyGenerateFasta.outputName = if (outputName != null) outputName else sampleName
bastyGenerateFasta.inputVcf = gatkPipeline.multisampleVariantcalling.scriptOutput.finalVcfFile
if (gatkPipeline.samplesOutput.contains(sampleName)) {
bastyGenerateFasta.bamFile = gatkPipeline.samplesOutput(sampleName).variantcalling.bamFiles.head
if (gatkPipeline.samples.contains(sampleName)) {
bastyGenerateFasta.bamFile = gatkPipeline.samples(sampleName).gatkVariantcalling.scriptOutput.bamFiles.head
}
bastyGenerateFasta.outputVariants = outputDir + bastyGenerateFasta.outputName + ".variants" + (if (snpsOnly) ".snps_only" else "") + ".fasta"
bastyGenerateFasta.outputConsensus = outputDir + bastyGenerateFasta.outputName + ".consensus" + (if (snpsOnly) ".snps_only" else "") + ".fasta"
bastyGenerateFasta.outputConsensusVariants = outputDir + bastyGenerateFasta.outputName + ".consensus_variants" + (if (snpsOnly) ".snps_only" else "") + ".fasta"
bastyGenerateFasta.sampleName = sampleName
bastyGenerateFasta.snpsOnly = snpsOnly
add(bastyGenerateFasta)
qscript.add(bastyGenerateFasta)
return FastaOutput(bastyGenerateFasta.outputVariants, bastyGenerateFasta.outputConsensus, bastyGenerateFasta.outputConsensusVariants)
}
}
......
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/ApplyRecalibration.scala
View file @ 91e72434
......@@ -9,13 +9,17 @@ import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
class ApplyRecalibration(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.ApplyRecalibration with GatkGeneral {
scatterCount = config("scattercount", default = 0)
override def afterGraph {
super.afterGraph
if (config.contains("scattercount")) scatterCount = config("scattercount")
nt = Option(getThreads(3))
memoryLimit = Option(nt.getOrElse(1) * 2)
import org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode
if (mode == Mode.INDEL) ts_filter_level = config("ts_filter_level", default = 99.0)
else if (mode == Mode.SNP) ts_filter_level = config("ts_filter_level", default = 99.5)
ts_filter_level = config("ts_filter_level")
}
}
......@@ -24,11 +28,9 @@ object ApplyRecalibration {
def apply(root: Configurable, input: File, output: File, recal_file: File, tranches_file: File, indel: Boolean = false): ApplyRecalibration = {
val ar = if (indel) new ApplyRecalibration(root) {
mode = org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.INDEL
defaults ++= Map("ts_filter_level" -> 99.0)
}
else new ApplyRecalibration(root) {
mode = org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.SNP
defaults ++= Map("ts_filter_level" -> 99.5)
}
ar.input :+= input
ar.recal_file = recal_file
......
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantRecalibrator.scala
View file @ 91e72434
......@@ -27,11 +27,9 @@ object VariantRecalibrator {
override def configPath: List[String] = (if (indel) "indel" else "snp") :: super.configPath
if (indel) {
mode = org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.INDEL
defaults ++= Map("ts_filter_level" -> 99.0)
if (config.contains("mills")) resource :+= new TaggedFile(config("mills").asString, "known=false,training=true,truth=true,prior=12.0")
} else {
mode = org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.SNP
defaults ++= Map("ts_filter_level" -> 99.5)
if (config.contains("hapmap")) resource +:= new TaggedFile(config("hapmap").asString, "known=false,training=true,truth=true,prior=15.0")
if (config.contains("omni")) resource +:= new TaggedFile(config("omni").asString, "known=false,training=true,truth=true,prior=12.0")
if (config.contains("1000G")) resource +:= new TaggedFile(config("1000G").asString, "known=false,training=true,truth=false,prior=10.0")
......
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
View file @ 91e72434
......@@ -9,9 +9,7 @@ import nl.lumc.sasc.biopet.core.MultiSampleQScript
import nl.lumc.sasc.biopet.core.PipelineCommand
import nl.lumc.sasc.biopet.core.config.Configurable
import htsjdk.samtools.SamReaderFactory
import nl.lumc.sasc.biopet.pipelines.mapping.Mapping._
import scala.collection.JavaConversions._
import java.io.File
import nl.lumc.sasc.biopet.extensions.gatk.{ CombineVariants, CombineGVCFs }
import nl.lumc.sasc.biopet.extensions.picard.AddOrReplaceReadGroups
import nl.lumc.sasc.biopet.extensions.picard.SamToFastq
......@@ -21,40 +19,139 @@ import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.utils.commandline.{ Argument }
class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScript {
qscript =>
def this() = this(null)
@Argument(doc = "Skip Genotyping step", shortName = "skipgenotyping", required = false)
var skipGenotyping: Boolean = false
var skipGenotyping: Boolean = config("skip_genotyping", default = false)
@Argument(doc = "Merge gvcfs", shortName = "mergegvcfs", required = false)
var mergeGvcfs: Boolean = false
/** Merge gvcfs */
var mergeGvcfs: Boolean = config("merge_gvcfs", default = false)
@Argument(doc = "Joint variantcalling", shortName = "jointVariantCalling", required = false)
/** Joint variantcalling */
var jointVariantcalling: Boolean = config("joint_variantcalling", default = false)
@Argument(doc = "Joint genotyping", shortName = "jointGenotyping", required = false)
/** Joint genotyping */
var jointGenotyping: Boolean = config("joint_genotyping", default = false)
var singleSampleCalling = config("single_sample_calling", default = true)
var reference: File = config("reference", required = true)
var dbsnp: File = config("dbsnp")
var gvcfFiles: List[File] = Nil
var finalBamFiles: List[File] = Nil
var useAllelesOption: Boolean = config("use_alleles_option", default = false)
val externalGvcfs = config("external_gvcfs_files", default = Nil).asFileList
/**
* class LibraryOutput extends AbstractLibraryOutput {
* var mappedBamFile: File = _
* var variantcalling: GatkVariantcalling.ScriptOutput = _
* }
*
* class SampleOutput extends AbstractSampleOutput {
* var variantcalling: GatkVariantcalling.ScriptOutput = _
* }
*/
def makeSample(id: String) = new Sample(id)
class Sample(sampleId: String) extends AbstractSample(sampleId) {
def makeLibrary(id: String) = new Library(id)
class Library(libraryId: String) extends AbstractLibrary(libraryId) {
val mapping = new Mapping(qscript)
mapping.sampleId = sampleId
mapping.libraryId = libraryId
mapping.outputDir = libDir + "/variantcalling/"
/** Library variantcalling */
val gatkVariantcalling = new GatkVariantcalling(qscript)
gatkVariantcalling.sampleID = sampleId
gatkVariantcalling.outputDir = libDir
def addJobs(): Unit = {
val bamFile: Option[File] = if (config.contains("R1")) {
mapping.input_R1 = config("R1")
mapping.input_R2 = config("R2")
mapping.init
mapping.biopetScript
addAll(mapping.functions) // Add functions of mapping to curent function pool
Some(mapping.finalBamFile)
} else if (config.contains("bam")) {
var bamFile: File = config("bam")
if (!bamFile.exists) throw new IllegalStateException("Bam in config does not exist, file: " + bamFile)
if (config("bam_to_fastq", default = false).asBoolean) {
val samToFastq = SamToFastq(qscript, bamFile, libDir + sampleId + "-" + libraryId + ".R1.fastq",
libDir + sampleId + "-" + libraryId + ".R2.fastq")
samToFastq.isIntermediate = true
qscript.add(samToFastq)
mapping.input_R1 = samToFastq.fastqR1
mapping.input_R2 = samToFastq.fastqR2
mapping.init
mapping.biopetScript
addAll(mapping.functions) // Add functions of mapping to curent function pool
Some(mapping.finalBamFile)
} else {
var readGroupOke = true
val inputSam = SamReaderFactory.makeDefault.open(bamFile)
val header = inputSam.getFileHeader.getReadGroups
for (readGroup <- inputSam.getFileHeader.getReadGroups) {
if (readGroup.getSample != sampleId) logger.warn("Sample ID readgroup in bam file is not the same")
if (readGroup.getLibrary != libraryId) logger.warn("Library ID readgroup in bam file is not the same")
if (readGroup.getSample != sampleId || readGroup.getLibrary != libraryId) readGroupOke = false
}
inputSam.close
if (!readGroupOke) {
if (config("correct_readgroups", default = false)) {
logger.info("Correcting readgroups, file:" + bamFile)
val aorrg = AddOrReplaceReadGroups(qscript, bamFile, new File(libDir + sampleId + "-" + libraryId + ".bam"))
aorrg.RGID = sampleId + "-" + libraryId
aorrg.RGLB = libraryId
aorrg.RGSM = sampleId
aorrg.isIntermediate = true
qscript.add(aorrg)
bamFile = aorrg.output
} else throw new IllegalStateException("Sample readgroup and/or library of input bamfile is not correct, file: " + bamFile +
"\nPlease note that it is possible to set 'correct_readgroups' to true in the config to automatic fix this")
}
addAll(BamMetrics(qscript, bamFile, libDir + "metrics/").functions)
Some(bamFile)
}
} else {
logger.error("Sample: " + sampleId + ": No R1 found for run: " + libraryId)
None
}
class LibraryOutput extends AbstractLibraryOutput {
var mappedBamFile: File = _
var variantcalling: GatkVariantcalling.ScriptOutput = _
}
if (bamFile.isDefined) {
gatkVariantcalling.inputBams = List(bamFile.get)
gatkVariantcalling.variantcalling = config("library_variantcalling", default = false)
gatkVariantcalling.preProcesBams = true
gatkVariantcalling.init
gatkVariantcalling.biopetScript
addAll(gatkVariantcalling.functions)
}
}
}
/** sample variantcalling */
val gatkVariantcalling = new GatkVariantcalling(qscript)
gatkVariantcalling.sampleID = sampleId
gatkVariantcalling.outputDir = sampleDir + "/variantcalling/"
class SampleOutput extends AbstractSampleOutput {
var variantcalling: GatkVariantcalling.ScriptOutput = _
def addJobs(): Unit = {
runLibraryJobs()
gatkVariantcalling.inputBams = libraries.map(_._2.mapping.finalBamFile).toList
gatkVariantcalling.preProcesBams = false
if (!singleSampleCalling) {
gatkVariantcalling.useHaplotypecaller = false
gatkVariantcalling.useUnifiedGenotyper = false
}
gatkVariantcalling.init
gatkVariantcalling.biopetScript
addAll(gatkVariantcalling.functions)
}
}
def init() {
if (config.contains("gvcfFiles"))
for (file <- config("gvcfFiles").asList)
gvcfFiles :+= file.toString
if (outputDir == null) throw new IllegalStateException("Missing Output directory on gatk module")
else if (!outputDir.endsWith("/")) outputDir += "/"
}
......@@ -68,11 +165,11 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
runSamplesJobs
//SampleWide jobs
if (mergeGvcfs && gvcfFiles.size > 0) {
val gvcfFiles: List[File] = if (mergeGvcfs && externalGvcfs.size + samples.size > 1) {
val newFile = outputDir + "merged.gvcf.vcf.gz"
add(CombineGVCFs(this, gvcfFiles, newFile))
gvcfFiles = List(newFile)
}
add(CombineGVCFs(this, externalGvcfs ++ samples.map(_._2.gatkVariantcalling.scriptOutput.gvcfFile), newFile))
List(newFile)
} else externalGvcfs ++ samples.map(_._2.gatkVariantcalling.scriptOutput.gvcfFile)
if (!skipGenotyping && gvcfFiles.size > 0) {
if (jointGenotyping) {
......@@ -87,11 +184,8 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
} else logger.warn("No gVCFs to genotype")
if (jointVariantcalling) {
val allBamfiles = for (
(sampleID, sampleOutput) <- samplesOutput;
file <- sampleOutput.variantcalling.bamFiles
) yield file
val allRawVcfFiles = for ((sampleID, sampleOutput) <- samplesOutput) yield sampleOutput.variantcalling.rawFilterVcfFile
val allBamfiles = samples.map(_._2.gatkVariantcalling.scriptOutput.bamFiles).toList.fold(Nil)(_ ++ _)
val allRawVcfFiles = samples.map(_._2.gatkVariantcalling.scriptOutput.rawVcfFile).filter(_ != null).toList
val gatkVariantcalling = new GatkVariantcalling(this) {
override def configName = "gatkvariantcalling"
......@@ -116,7 +210,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
if (config("inputtype", default = "dna").asString != "rna" && config("recalibration", default = false).asBoolean) {
val recalibration = new GatkVariantRecalibration(this)
recalibration.inputVcf = multisampleVariantcalling.scriptOutput.finalVcfFile
recalibration.bamFiles = finalBamFiles
recalibration.bamFiles = allBamfiles
recalibration.outputDir = outputDir + "recalibration/"
recalibration.init
recalibration.biopetScript
......@@ -124,6 +218,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
}
}
/*
// Called for each sample
def runSingleSampleJobs(sampleID: String): SampleOutput = {
val sampleOutput = new SampleOutput
......@@ -246,6 +341,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
return libraryOutput
}
*/
}
object GatkPipeline extends PipelineCommand
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
View file @ 91e72434
......@@ -11,6 +11,7 @@ import nl.lumc.sasc.biopet.tools.{ MpileupToVcf, VcfFilter, MergeAlleles }
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.extensions.gatk.{ AnalyzeCovariates, BaseRecalibrator, GenotypeGVCFs, HaplotypeCaller, IndelRealigner, PrintReads, RealignerTargetCreator, SelectVariants, CombineVariants, UnifiedGenotyper }
import nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
......@@ -68,7 +69,8 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
if (files.isEmpty) throw new IllegalStateException("Files can't be empty")
if (!doublePreProces.get) return files
val markDup = MarkDuplicates(this, files, new File(outputDir + outputName + ".dedup.bam"))
add(markDup, isIntermediate = useIndelRealigner)
markDup.isIntermediate = useIndelRealigner
add(markDup)
if (useIndelRealigner) {
List(addIndelRealign(markDup.output, outputDir, isIntermediate = false))
} else {
......@@ -141,11 +143,13 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
add(m2v)
scriptOutput.rawVcfFile = m2v.output
val vcfFilter = new VcfFilter(this)
vcfFilter.defaults ++= Map("min_sample_depth" -> 8,
"min_alternate_depth" -> 2,
"min_samples_pass" -> 1,
"filter_ref_calls" -> true)
val vcfFilter = new VcfFilter(this) {
override def defaults = ConfigUtils.mergeMaps(Map("min_sample_depth" -> 8,
"min_alternate_depth" -> 2,
"min_samples_pass" -> 1,
"filter_ref_calls" -> true
), super.defaults)
}
vcfFilter.inputVcf = m2v.output
vcfFilter.outputVcf = this.swapExt(outputDir, m2v.output, ".vcf", ".filter.vcf.gz")
add(vcfFilter)
......@@ -157,7 +161,8 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
// Allele mode
if (useAllelesOption.get) {
val mergeAlleles = MergeAlleles(this, mergeList.toList, outputDir + "raw.allele__temp_only.vcf.gz")
add(mergeAlleles, isIntermediate = true)
mergeAlleles.isIntermediate = true
add(mergeAlleles)
if (useHaplotypecaller.get) {
val hcAlleles = new HaplotypeCaller(this)
......@@ -187,7 +192,8 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
val sv = SelectVariants(this, input, output)
sv.excludeFiltered = true
sv.excludeNonVariants = true
add(sv, isIntermediate = true)
sv.isIntermediate = true
add(sv)
sv.out
}
......@@ -200,10 +206,12 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
def addIndelRealign(inputBam: File, dir: String, isIntermediate: Boolean = true): File = {
val realignerTargetCreator = RealignerTargetCreator(this, inputBam, dir)
add(realignerTargetCreator, isIntermediate = true)
realignerTargetCreator.isIntermediate = true
add(realignerTargetCreator)
val indelRealigner = IndelRealigner.apply(this, inputBam, realignerTargetCreator.out, dir)
add(indelRealigner, isIntermediate = isIntermediate)
indelRealigner.isIntermediate = isIntermediate
add(indelRealigner)
return indelRealigner.o
}
......@@ -227,7 +235,8 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
val printReads = PrintReads(this, inputBam, swapExt(dir, inputBam, ".bam", ".baserecal.bam"))
printReads.BQSR = baseRecalibrator.o
add(printReads, isIntermediate = isIntermediate)
printReads.isIntermediate = isIntermediate
add(printReads)
return printReads.o
}
......
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
View file @ 91e72434
......@@ -45,7 +45,7 @@ trait MultiSampleQScript extends BiopetQScript {
abstract class AbstractLibrary(val libraryId: String) {
/** Overrules config of qscript with default sample and default library */
val config = new ConfigFunctions(defaultSample = sampleId, defaultLibrary = libraryId)
/** Adds the library jobs */
final def add(): Unit = {
currentSample = Some(sampleId)
......@@ -116,10 +116,10 @@ trait MultiSampleQScript extends BiopetQScript {
/**
* Factory method for Sample class
* @param id SampleId
* @param id SampleId
* @return Sample class
*/
def makeSample(id: String): Sample
def makeSample(id: String): Sample
/** Stores all samples */
val samples: Map[String, Sample] = sampleIds.map(id => id -> makeSample(id)).toMap
......
public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
View file @ 91e72434
......@@ -79,7 +79,7 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
flexiprep.input_R1 = inputFastq
flexiprep.init
flexiprep.biopetScript
addAll(flexiprep.functions)
qscript.addAll(flexiprep.functions)
val flexiprepOutput = for ((key, file) <- flexiprep.outputFiles if key.endsWith("output_R1")) yield file
val pf = new PrefixFastq(qscript)
......@@ -87,13 +87,13 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
pf.outputFastq = prefixFastq
pf.prefixSeq = config("sage_tag", default = "CATG")
pf.deps +:= flexiprep.outputFiles("fastq_input_R1")
add(pf)
qscript.add(pf)
mapping.input_R1 = pf.outputFastq
mapping.outputDir = libDir
mapping.init
mapping.biopetScript
addAll(mapping.functions)
qscript.addAll(mapping.functions)
if (config("library_counts", default = false).asBoolean) {
addBedtoolsCounts(mapping.finalBamFile, sampleId + "-" + libraryId, libDir)
......@@ -110,13 +110,13 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
val bamFile: File = if (libraryBamfiles.size == 1) libraryBamfiles.head
else if (libraryBamfiles.size > 1) {
val mergeSamFiles = MergeSamFiles(qscript, libraryBamfiles, sampleDir)
add(mergeSamFiles)
qscript.add(mergeSamFiles)
mergeSamFiles.output
} else null
val fastqFile: File = if (libraryFastqFiles.size == 1) libraryFastqFiles.head
else if (libraryFastqFiles.size > 1) {
val cat = Cat(qscript, libraryFastqFiles, sampleDir + sampleId + ".fastq")
add(cat)
qscript.add(cat)
cat.output
} else null
......
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