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Commit ea4f80e1 authored by Peter van 't Hof's avatar Peter van 't Hof
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Changed constructors

parent c7abaef3
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biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Ln.scala
View file @ ea4f80e1
......@@ -7,7 +7,7 @@ import org.broadinstitute.sting.commandline._
import java.io.File
import scala.sys.process._
class Ln(val globalConfig: Config, val configPath: List[String]) extends InProcessFunction with Configurable {
class Ln(val root:Configurable) extends InProcessFunction with Configurable {
this.analysisName = getClass.getSimpleName
@Input(doc="Input file")
......
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Sha1sum.scala
View file @ ea4f80e1
......@@ -5,7 +5,7 @@ import nl.lumc.sasc.biopet.core.config._
import org.broadinstitute.sting.commandline._
import java.io.File
class Sha1sum(val globalConfig: Config, val configPath: List[String]) extends BiopetCommandLineFunction {
class Sha1sum(val root:Configurable) extends BiopetCommandLineFunction {
@Input(doc="Zipped file")
var input: File = _
......
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Zcat.scala
View file @ ea4f80e1
......@@ -6,7 +6,7 @@ import nl.lumc.sasc.biopet.core.config._
import org.broadinstitute.sting.commandline._
import java.io.File
class Zcat(val globalConfig: Config, val configPath: List[String]) extends BiopetCommandLineFunction {
class Zcat(val root:Configurable) extends BiopetCommandLineFunction {
@Input(doc="Zipped file")
var input: File = _
......
flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala
View file @ ea4f80e1
......@@ -7,7 +7,7 @@ import java.io.File
import scala.io.Source._
import scala.sys.process._
class Cutadapt(val globalConfig: Config, val configPath: List[String]) extends BiopetCommandLineFunction {
class Cutadapt(val root:Configurable) extends BiopetCommandLineFunction {
@Input(doc="Input fastq file")
var fastq_input: File = _
......
flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala
View file @ ea4f80e1
......@@ -6,7 +6,8 @@ import org.broadinstitute.sting.commandline._
import java.io.File
import scala.sys.process._
class Fastqc(val globalConfig: Config, val configPath: List[String]) extends BiopetCommandLineFunction {
class Fastqc(val root:Configurable) extends BiopetCommandLineFunction {
@Input(doc="Contaminants", required=false)
var contaminants: File = _
......
flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala
View file @ ea4f80e1
......@@ -7,7 +7,7 @@ import java.io.File
import scala.io.Source._
import scala.sys.process._
class Sickle(val globalConfig: Config, val configPath: List[String]) extends BiopetCommandLineFunction {
class Sickle(val root:Configurable) extends BiopetCommandLineFunction {
@Input(doc="R1 input")
var input_R1: File = null
......
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @ ea4f80e1
......@@ -12,15 +12,20 @@ import scala.util.parsing.json._
import org.broadinstitute.sting.commandline._
import nl.lumc.sasc.biopet.pipelines.flexiprep.scripts._
class Flexiprep(val globalConfig: Config, val configPath: List[String]) extends QScript with BiopetQScript {
def this() = this(new Config(), Nil)
class Flexiprep(val root:Configurable) extends QScript with BiopetQScript {
def this() = this(null)
@Argument(doc="Config Json file",shortName="config", required=false) val configfiles: List[File] = Nil
@Input(doc="R1 fastq file (gzipped allowed)", shortName="R1",required=true) var input_R1: File = _
@Input(doc="R2 fastq file (gzipped allowed)", shortName="R2", required=false) var input_R2: File = _
@Argument(doc="Output directory", shortName="outputDir", required=true) var outputDir: String = _
@Argument(doc="Skip Trim fastq files", shortName="skiptrim", required=false) var skipTrim: Boolean = false
@Argument(doc="Skip Clip fastq files", shortName="skipclip", required=false) var skipClip: Boolean = false
@Input(doc="R1 fastq file (gzipped allowed)", shortName="R1",required=true)
var input_R1: File = _
@Input(doc="R2 fastq file (gzipped allowed)", shortName="R2", required=false)
var input_R2: File = _
@Argument(doc="Skip Trim fastq files", shortName="skiptrim", required=false)
var skipTrim: Boolean = false
@Argument(doc="Skip Clip fastq files", shortName="skipclip", required=false)
var skipClip: Boolean = false
var paired: Boolean = (input_R2 != null)
var R1_ext: String = _
......@@ -30,7 +35,6 @@ class Flexiprep(val globalConfig: Config, val configPath: List[String]) extends
def init() {
for (file <- configfiles) globalConfig.loadConfigFile(file)
//config = Config.mergeConfigs(globalConfig.getAsConfig("flexiprep"), globalConfig)
if (!skipTrim) skipTrim = config("skiptrim", false)
if (!skipClip) skipClip = config("skipclip", false)
if (input_R1 == null) throw new IllegalStateException("Missing R1 on flexiprep module")
......@@ -53,8 +57,7 @@ class Flexiprep(val globalConfig: Config, val configPath: List[String]) extends
}
}
def script() {
init()
def biopetScript() {
runInitialFastqc()
outputFiles += ("fastq_input_R1" -> zcatIfNeeded(input_R1,outputDir))
......@@ -87,7 +90,7 @@ class Flexiprep(val globalConfig: Config, val configPath: List[String]) extends
}
def getQualtype(fastqc:Fastqc, pairname:String): File = {
val fastqcToQualtype = new FastqcToQualtype(globalConfig, configFullPath)
val fastqcToQualtype = new FastqcToQualtype(this)
fastqcToQualtype.fastqc_output = fastqc.output
fastqcToQualtype.out = new File(outputDir + pairname + ".qualtype.txt")
add(fastqcToQualtype)
......@@ -95,7 +98,7 @@ class Flexiprep(val globalConfig: Config, val configPath: List[String]) extends
}
def getContams(fastqc:Fastqc, pairname:String): File = {
val fastqcToContams = new FastqcToContams(globalConfig, configFullPath)
val fastqcToContams = new FastqcToContams(this)
fastqcToContams.fastqc_output = fastqc.output
fastqcToContams.out = new File(outputDir + pairname + ".contams.txt")
fastqcToContams.contams_file = fastqc.contaminants
......@@ -119,7 +122,7 @@ class Flexiprep(val globalConfig: Config, val configPath: List[String]) extends
var R2: File = new File(R2_in)
if (!skipClip) { // Adapter clipping
val cutadapt_R1 = new Cutadapt(globalConfig, configFullPath)
val cutadapt_R1 = new Cutadapt(this)
if (!skipTrim || paired) cutadapt_R1.isIntermediate = true
cutadapt_R1.fastq_input = R1
cutadapt_R1.fastq_output = swapExt(outDir, R1, R1_ext, ".clip"+R1_ext)
......@@ -127,14 +130,14 @@ class Flexiprep(val globalConfig: Config, val configPath: List[String]) extends
add(cutadapt_R1)
R1 = cutadapt_R1.fastq_output
if (paired) {
val cutadapt_R2 = new Cutadapt(globalConfig, configFullPath)
val cutadapt_R2 = new Cutadapt(this)
if (!skipTrim || paired) cutadapt_R2.isIntermediate = true
cutadapt_R2.fastq_input = R2
cutadapt_R2.fastq_output = swapExt(outDir, R2, R2_ext, ".clip"+R2_ext)
if (outputFiles.contains("contams_R2")) cutadapt_R2.contams_file = outputFiles("contams_R2")
add(cutadapt_R2)
R2 = cutadapt_R2.fastq_output
val fastqSync = new FastqSync(globalConfig, configFullPath)
val fastqSync = new FastqSync(this)
if (!skipTrim) fastqSync.isIntermediate = true
fastqSync.input_start_fastq = cutadapt_R1.fastq_input
fastqSync.input_R1 = cutadapt_R1.fastq_output
......@@ -150,7 +153,7 @@ class Flexiprep(val globalConfig: Config, val configPath: List[String]) extends
}
if (!skipTrim) { // Quality trimming
val sickle = new Sickle(globalConfig, configFullPath)
val sickle = new Sickle(this)
sickle.input_R1 = R1
sickle.output_R1 = swapExt(outDir, R1, R1_ext, ".trim"+R1_ext)
if (outputFiles.contains("qualtype_R1")) sickle.qualityTypeFile = outputFiles("qualtype_R1")
......@@ -183,13 +186,13 @@ class Flexiprep(val globalConfig: Config, val configPath: List[String]) extends
}
if (!config("skip_native_link", false)) {
val lnR1 = new Ln(globalConfig, configFullPath)
val lnR1 = new Ln(this)
lnR1.in = R1
R1 = new File(outputDir + R1_name + ".qc" + R1_ext)
lnR1.out = R1
add(lnR1)
if (paired) {
val lnR2 = new Ln(globalConfig, configFullPath)
val lnR2 = new Ln(this)
lnR2.in = R2
R2 = new File(outputDir + R2_name + ".qc" + R2_ext)
lnR2.out = R2
......@@ -208,7 +211,7 @@ class Flexiprep(val globalConfig: Config, val configPath: List[String]) extends
if (paired) outputFiles += ("fastqc_R2_final" -> runFastqc(outputFiles("output_R2"),outputDir + "/" + R2_name + ".qc.fastqc/").output)
}
val summarize = new Summarize(globalConfig, configFullPath)
val summarize = new Summarize(this)
summarize.runDir = outputDir
summarize.samplea = R1_name
if (paired) summarize.sampleb = R2_name
......@@ -221,7 +224,7 @@ class Flexiprep(val globalConfig: Config, val configPath: List[String]) extends
}
def runFastqc(fastqfile:File, outDir:String) : Fastqc = {
val fastqcCommand = new Fastqc(globalConfig, configFullPath)
val fastqcCommand = new Fastqc(this)
fastqcCommand.fastqfile = fastqfile
var filename: String = fastqfile.getName()
if (filename.endsWith(".gz")) filename = filename.substring(0,filename.size - 3)
......@@ -238,7 +241,7 @@ class Flexiprep(val globalConfig: Config, val configPath: List[String]) extends
if (file.getName().endsWith(".gz") || file.getName().endsWith(".gzip")) {
var newFile: File = swapExt(file,".gz","")
if (file.getName().endsWith(".gzip")) newFile = swapExt(file,".gzip","")
val zcatCommand = new Zcat(globalConfig, configFullPath)
val zcatCommand = new Zcat(this)
zcatCommand.input = file
zcatCommand.output = new File(runDir + newFile)
//zcatCommand.jobOutputFile = outputDir + "." + file.getName + ".out"
......@@ -250,7 +253,7 @@ class Flexiprep(val globalConfig: Config, val configPath: List[String]) extends
def addSeqstat(fastq:File, key:String) {
val ext = fastq.getName.substring(fastq.getName.lastIndexOf("."))
val seqstat = new Seqstat(globalConfig, configFullPath)
val seqstat = new Seqstat(this)
seqstat.input_fastq = fastq
seqstat.out = swapExt(outputDir, fastq, ext, ".seqstats.json")
add(seqstat)
......@@ -259,7 +262,7 @@ class Flexiprep(val globalConfig: Config, val configPath: List[String]) extends
def addSha1sum(fastq:File, key:String) {
val ext = fastq.getName.substring(fastq.getName.lastIndexOf("."))
val sha1sum = new Sha1sum(globalConfig, configFullPath)
val sha1sum = new Sha1sum(this)
sha1sum.input = fastq
sha1sum.output = swapExt(outputDir, fastq, ext, ".sha1")
add(sha1sum)
......
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala
View file @ ea4f80e1
......@@ -7,7 +7,7 @@ import nl.lumc.sasc.biopet.function.PythonCommandLineFunction
import org.broadinstitute.sting.commandline._
import java.io.File
class FastqSync(val globalConfig: Config, val configPath: List[String]) extends PythonCommandLineFunction {
class FastqSync(val root:Configurable) extends PythonCommandLineFunction {
setPythonScript("__init__.py", "pyfastqc/")
setPythonScript("sync_paired_end_reads.py")
......
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToContams.scala
View file @ ea4f80e1
......@@ -6,7 +6,7 @@ import nl.lumc.sasc.biopet.function.PythonCommandLineFunction
import org.broadinstitute.sting.commandline._
import java.io.File
class FastqcToContams(val globalConfig: Config, val configPath: List[String]) extends PythonCommandLineFunction {
class FastqcToContams(val root:Configurable) extends PythonCommandLineFunction {
setPythonScript("__init__.py", "pyfastqc/")
setPythonScript("fastqc_contam.py")
......
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToQualtype.scala
View file @ ea4f80e1
......@@ -6,7 +6,7 @@ import nl.lumc.sasc.biopet.function.PythonCommandLineFunction
import org.broadinstitute.sting.commandline._
import java.io.File
class FastqcToQualtype(val globalConfig: Config, val configPath: List[String]) extends PythonCommandLineFunction {
class FastqcToQualtype(val root:Configurable) extends PythonCommandLineFunction {
setPythonScript("__init__.py", "pyfastqc/")
setPythonScript("qual_type_sickle.py")
......
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala
View file @ ea4f80e1
......@@ -6,7 +6,7 @@ import nl.lumc.sasc.biopet.function.PythonCommandLineFunction
import org.broadinstitute.sting.commandline._
import java.io.File
class Seqstat(val globalConfig: Config, val configPath: List[String]) extends PythonCommandLineFunction {
class Seqstat(val root:Configurable) extends PythonCommandLineFunction {
setPythonScript("__init__.py", "pyfastqc/")
setPythonScript("seq_stat.py")
......
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala
View file @ ea4f80e1
......@@ -6,7 +6,7 @@ import nl.lumc.sasc.biopet.function.PythonCommandLineFunction
import org.broadinstitute.sting.commandline._
import java.io.File
class Summarize(val globalConfig: Config, val configPath: List[String]) extends PythonCommandLineFunction {
class Summarize(val root:Configurable) extends PythonCommandLineFunction {
setPythonScript("__init__.py", "pyfastqc/")
setPythonScript("summarize_flexiprep.py")
......
gatk/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala
View file @ ea4f80e1
......@@ -13,14 +13,13 @@ import org.broadinstitute.sting.queue.function._
import scala.util.parsing.json._
import org.broadinstitute.sting.utils.variant._
class Gatk(val globalConfig: Config, val configPath: List[String]) extends QScript with BiopetQScript {
class Gatk(val root:Configurable) extends QScript with MultiSampleQScript {
qscript =>
def this() = this(new Config(), Nil)
@Argument(doc="Config Json file",shortName="config") var configfiles: List[File] = Nil
@Argument(doc="Only Sample",shortName="sample", required=false) var onlySample: String = ""
@Argument(doc="Output directory", shortName="outputDir", required=true) var outputDir: String = _
def this() = this(null)
@Argument(doc="Only Sample",shortName="sample", required=false)
val onlySample: String = ""
var referenceFile: File = _
var dbsnp: File = _
var gvcfFiles: List[File] = Nil
......@@ -28,7 +27,6 @@ class Gatk(val globalConfig: Config, val configPath: List[String]) extends QScri
def init() {
for (file <- configfiles) globalConfig.loadConfigFile(file)
//config = Config.mergeConfigs(globalConfig.getAsConfig("gatk"), globalConfig)
referenceFile = config("referenceFile")
if (configContains("dbsnp")) dbsnp = config("dbsnp")
gvcfFiles = config("gvcfFiles", Nil) :: Nil
......@@ -36,8 +34,7 @@ class Gatk(val globalConfig: Config, val configPath: List[String]) extends QScri
else if (!outputDir.endsWith("/")) outputDir += "/"
}
def script() {
init()
def biopetScript() {
if (onlySample.isEmpty) {
runSamplesJobs
......@@ -54,7 +51,7 @@ class Gatk(val globalConfig: Config, val configPath: List[String]) extends QScri
}
// Called for each sample
override def runSingleSampleJobs(sampleConfig:Map[String,Any]) : Map[String,List[File]] = {
def runSingleSampleJobs(sampleConfig:Map[String,Any]) : Map[String,List[File]] = {
var outputFiles:Map[String,List[File]] = Map()
var runBamfiles: List[File] = List()
var sampleID: String = sampleConfig("ID").toString
......@@ -73,7 +70,7 @@ class Gatk(val globalConfig: Config, val configPath: List[String]) extends QScri
}
// Called for each run from a sample
override def runSingleRunJobs(runConfig:Map[String,Any], sampleConfig:Map[String,Any]) : Map[String,File] = {
def runSingleRunJobs(runConfig:Map[String,Any], sampleConfig:Map[String,Any]) : Map[String,File] = {
var outputFiles:Map[String,File] = Map()
val runID: String = runConfig("ID").toString
val sampleID: String = sampleConfig("ID").toString
......@@ -82,7 +79,7 @@ class Gatk(val globalConfig: Config, val configPath: List[String]) extends QScri
if (runConfig.contains("inputtype")) inputType = runConfig("inputtype").toString
else inputType = config("inputtype", "dna").toString
if (runConfig.contains("R1")) {
val mapping = new Mapping(globalConfig, configFullPath)
val mapping = new Mapping(this)
mapping.loadRunConfig(runConfig, sampleConfig, runDir)
mapping.script
addAll(mapping.functions) // Add functions of mapping to curent function pool
......@@ -114,7 +111,6 @@ class Gatk(val globalConfig: Config, val configPath: List[String]) extends QScri
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"
......@@ -123,7 +119,6 @@ class Gatk(val globalConfig: Config, val configPath: List[String]) extends QScri
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")
......@@ -136,7 +131,6 @@ class Gatk(val globalConfig: Config, val configPath: List[String]) extends QScri
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")
if (dbsnp != null) this.knownSites :+= dbsnp
......@@ -146,7 +140,6 @@ class Gatk(val globalConfig: Config, val configPath: List[String]) extends QScri
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
......@@ -159,7 +152,6 @@ class Gatk(val globalConfig: Config, val configPath: List[String]) extends QScri
def addSplitNCigarReads(inputBam:File, dir:String) : File = {
val splitNCigarReads = new SplitNCigarReads with gatkArguments {
//val config: Config = Config.mergeConfigs(qscript.config.getAsConfig("splitncigarreads"), qscript.config)
if (configContains("scattercount", "splitncigarreads")) this.scatterCount = config("scattercount", "splitncigarreads")
this.input_file = Seq(inputBam)
this.out = swapExt(dir,inputBam,".bam",".split.bam")
......@@ -174,7 +166,6 @@ class Gatk(val globalConfig: Config, val configPath: List[String]) extends QScri
def addHaplotypeCaller(bamfiles:List[File], outputfile:File): File = {
val haplotypeCaller = new HaplotypeCaller with gatkArguments {
//val config: Config = Config.mergeConfigs(qscript.config.getAsConfig("haplotypecaller"), qscript.config)
if (configContains("scattercount", "haplotypecaller")) this.scatterCount = config("scattercount", "haplotypecaller")
this.input_file = bamfiles
this.out = outputfile
......@@ -236,19 +227,15 @@ class Gatk(val globalConfig: Config, val configPath: List[String]) extends QScri
def getVariantRecalibrator(mode_arg:String) : VariantRecalibrator = {
val variantRecalibrator = new VariantRecalibrator() with gatkArguments {
//var config = Config.mergeConfigs(qscript.config.getAsConfig("variantrecalibrator"), qscript.config)
if (mode_arg == "indel") {
this.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.INDEL
//this.config = Config.mergeConfigs(this.config.getAsConfig("indel"),this.config)
if (configContains("mills", "variantrecalibrator")) this.resource :+= new TaggedFile(config("mills", "variantrecalibrator").getString, "known=false,training=true,truth=true,prior=12.0")
} else { // SNP
this.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.SNP
//this.config = Config.mergeConfigs(this.config.getAsConfig("snp"),this.config)
if (configContains("hapmap", "variantrecalibrator")) this.resource +:= new TaggedFile(config("hapmap", "variantrecalibrator").getString, "known=false,training=true,truth=true,prior=15.0")
if (configContains("omni", "variantrecalibrator")) this.resource +:= new TaggedFile(config("omni", "variantrecalibrator").getString, "known=false,training=true,truth=true,prior=12.0")
if (configContains("1000G", "variantrecalibrator")) this.resource +:= new TaggedFile(config("1000G", "variantrecalibrator").getString, "known=false,training=true,truth=false,prior=10.0")
}
//logger.debug("VariantRecalibrator-" + mode_arg + ": " + this.config)
if (configContains("dbsnp", "variantrecalibrator")) this.resource :+= new TaggedFile(config("dbsnp", "variantrecalibrator").getString, "known=true,training=false,truth=false,prior=2.0")
this.nt = getThreads(4, "variantrecalibrator")
this.memoryLimit = nt * 2
......@@ -261,14 +248,11 @@ class Gatk(val globalConfig: Config, val configPath: List[String]) extends QScri
def getApplyRecalibration(mode_arg:String) : ApplyRecalibration = {
val applyRecalibration = new ApplyRecalibration() with gatkArguments {
//var config = Config.mergeConfigs(qscript.config.getAsConfig("applyrecalibration"), qscript.config)
if (mode_arg == "indel") {
this.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.INDEL
//this.config = Config.mergeConfigs(this.config.getAsConfig("indel"),this.config)
this.ts_filter_level = config("ts_filter_level", 99.0, "applyrecalibration")
} else { // SNP
this.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.SNP
//this.config = Config.mergeConfigs(this.config.getAsConfig("snp"),this.config)
this.ts_filter_level = config("ts_filter_level", 99.5, "applyrecalibration")
}
this.nt = getThreads(3, "applyrecalibration")
......@@ -280,7 +264,6 @@ class Gatk(val globalConfig: Config, val configPath: List[String]) extends QScri
def addGenotypeGVCFs(gvcfFiles: List[File], dir:String): File = {
val genotypeGVCFs = new GenotypeGVCFs() with gatkArguments {
//val config: Config = Config.mergeConfigs(qscript.config.getAsConfig("genotypegvcfs"), qscript.config)
this.variant = gvcfFiles
this.annotation ++= Seq("FisherStrand", "QualByDepth", "ChromosomeCounts")
if (configContains("scattercount", "genotypegvcfs")) this.scatterCount = config("scattercount", "genotypegvcfs")
......@@ -292,13 +275,10 @@ class Gatk(val globalConfig: Config, val configPath: List[String]) extends QScri
def addVariantAnnotator(inputvcf:File, bamfiles:List[File], dir:String): File = {
val variantAnnotator = new VariantAnnotator with gatkArguments {
//val config: Config = Config.mergeConfigs(qscript.config.getAsConfig("variantannotator"), qscript.config)
this.variant = inputvcf
this.input_file = bamfiles
this.dbsnp = config("dbsnp", "variantannotator")
this.out = swapExt(dir, inputvcf,".vcf",".anotated.vcf")
//this.all = true
//this.excludeAnnotation +:= "SnpEff"
if (configContains("scattercount", "variantannotator")) this.scatterCount = config("scattercount", "variantannotator")
}
add(variantAnnotator)
......
mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Bwa.scala
View file @ ea4f80e1
......@@ -6,7 +6,7 @@ import org.broadinstitute.sting.commandline._
import java.io.File
import scala.sys.process._
class Bwa(val globalConfig: Config, val configPath: List[String]) extends BiopetCommandLineFunction {
class Bwa(val root:Configurable) extends BiopetCommandLineFunction {
@Input(doc="Fastq file R1", shortName="R1")
var R1: File = _
......
mapping/src/main/scala/nl/lumc/sasc/biopet/function/aligners/Star.scala
View file @ ea4f80e1
......@@ -6,7 +6,7 @@ import org.broadinstitute.sting.commandline._
import java.io.File
import scala.sys.process._
class Star(val globalConfig: Config, val configPath: List[String]) extends BiopetCommandLineFunction {
class Star(val root:Configurable) extends BiopetCommandLineFunction {
@Input(doc="The reference file for the bam files.", required=false)
var referenceFile: File = new File(config("referenceFile"))
......@@ -59,6 +59,7 @@ class Star(val globalConfig: Config, val configPath: List[String]) extends Biope
outputGenome = new File(prefix + "Genome")
outputSA = new File(prefix + "SA")
outputSAindex = new File(prefix + "SAindex")
sjdbOverhang = config("sjdboverhang", 75)
}
}
......@@ -81,11 +82,30 @@ class Star(val globalConfig: Config, val configPath: List[String]) extends Biope
}
object Star {
def apply(globalConfig: Config, configPath: List[String], R1:File, R2:File, outputDir:String): Star = {
val star = new Star(globalConfig, configPath)
def apply(configurable:Configurable, R1:File, R2:File, outputDir:String): Star = {
val star = new Star(configurable)
star.R1 = R1
if (R2 != null) star.R2 = R2
star.outputDir = outputDir
star.afterGraph
return star
}
def _2pass(configurable:Configurable, R1:File, R2:File, outputDir:String) : (File, List[Star]) = {
val outDir = if (outputDir.endsWith("/")) outputDir else outputDir + "/"
val starCommand_pass1 = Star(configurable, R1, if (R2 != null) R2 else null, outDir + "aln-pass1/")
starCommand_pass1.afterGraph
val starCommand_reindex = new Star(configurable)
starCommand_reindex.sjdbFileChrStartEnd = starCommand_pass1.outputTab
starCommand_reindex.outputDir = outDir + "re-index/"
starCommand_reindex.runmode = "genomeGenerate"
starCommand_reindex.afterGraph
val starCommand_pass2 = Star(configurable, R1, if (R2 != null) R2 else null, outDir + "aln-pass2/")
starCommand_pass2.genomeDir = starCommand_reindex.outputDir
starCommand_pass2.afterGraph
return (starCommand_pass2.outputSam, List(starCommand_pass1, starCommand_reindex, starCommand_pass2))
}
}
\ No newline at end of file
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @ ea4f80e1
......@@ -15,36 +15,65 @@ import org.broadinstitute.sting.queue.function._
import scala.util.parsing.json._
import org.broadinstitute.sting.utils.variant._
class Mapping(val globalConfig: Config, val configPath: List[String]) extends QScript with BiopetQScript {
class Mapping(val root:Configurable) extends QScript with BiopetQScript {
qscript =>
@Argument(doc="Config Json file",shortName="config", required=false) var configfiles: List[File] = Nil
@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=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 = _
@Argument(doc="Reference", shortName="R", required=false) var referenceFile: File = _
def this() = this(null)
@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 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 = _
@Argument(doc="Reference", shortName="R", required=false)
var referenceFile: File = _
// Readgroup items
@Argument(doc="Readgroup ID", shortName="RGID", required=false) var RGID: String = _
@Argument(doc="Readgroup Library", shortName="RGLB", required=false) var RGLB: String = _
@Argument(doc="Readgroup Platform", shortName="RGPL", required=false) var RGPL: String = _
@Argument(doc="Readgroup platform unit", shortName="RGPU", required=false) var RGPU: String = _
@Argument(doc="Readgroup sample", shortName="RGSM", required=false) var RGSM: String = _
@Argument(doc="Readgroup sequencing center", shortName="RGCN", required=false) var RGCN: String = _
@Argument(doc="Readgroup description", shortName="RGDS", required=false) var RGDS: String = _
@Argument(doc="Readgroup sequencing date", shortName="RGDT", required=false) var RGDT: Date = _
@Argument(doc="Readgroup predicted insert size", shortName="RGPI", required=false) var RGPI: Int = _
def this() = this(new Config(), Nil)
@Argument(doc="Readgroup ID", shortName="RGID", required=false)
var RGID: String = _
@Argument(doc="Readgroup Library", shortName="RGLB", required=false)
var RGLB: String = _
@Argument(doc="Readgroup Platform", shortName="RGPL", required=false)
var RGPL: String = _
@Argument(doc="Readgroup platform unit", shortName="RGPU", required=false)
var RGPU: String = _