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package core
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import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.sting.queue.function.ListWriterFunction
import net.sf.samtools. { SAMFileReader , SAMReadGroupRecord }
import scala.io.Source._
import collection.JavaConversions._
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import org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner.ConsensusDeterminationModel
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import org.broadinstitute.sting.queue.extensions.picard._
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class DataProcessingPipeline extends QScript {
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qscript =>
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Required Parameters ( if default values are not good for you )
****************************************************************************/
@Input ( doc = "input BAM file - or list of BAM files" , fullName = "input" , shortName = "i" , required = true )
var input : File = _
@Input ( doc = "path to R resources folder inside the Sting repository" , fullName = "path_to_r" , shortName = "r" , required = true )
var R : String = _
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@Input ( doc = "Reference fasta file" , fullName = "reference" , shortName = "R" , required = true )
var reference : File = _
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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Optional Parameters
****************************************************************************/
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// @Input(doc="path to Picard's SortSam.jar (if re-aligning a previously processed BAM file)", fullName="path_to_sort_jar", shortName="sort", required=false)
// var sortSamJar: File = _
//
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@Input ( doc = "The path to the binary of bwa (usually BAM files have already been mapped - but if you want to remap this is the option)" , fullName = "path_to_bwa" , shortName = "bwa" , required = false )
var bwaPath : File = _
@Input ( doc = "dbsnp ROD to use (must be in VCF format)" , fullName = "dbsnp" , shortName = "D" , required = false )
var dbSNP : File = new File ( "/humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf" )
@Input ( doc = "extra VCF files to use as reference indels for Indel Realignment" , fullName = "extra_indels" , shortName = "indels" , required = false )
var indels : File = new File ( "/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/AFR+EUR+ASN+1KG.dindel_august_release_merged_pilot1.20110126.sites.vcf" )
@Input ( doc = "the project name determines the final output (BAM file) base name. Example NA12878 yields NA12878.processed.bam" , fullName = "project" , shortName = "p" , required = false )
var projectName : String = "project"
@Input ( doc = "Output path for the processed BAM files." , fullName = "output_directory" , shortName = "outputDir" , required = false )
var outputDir : String = ""
@Input ( doc = "the -L interval string to be used by GATK - output bams at interval only" , fullName = "gatk_interval_string" , shortName = "L" , required = false )
var intervalString : String = ""
@Input ( doc = "an intervals file to be used by GATK - output bams at intervals only" , fullName = "gatk_interval_file" , shortName = "intervals" , required = false )
var intervals : File = _
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@Input ( doc = "Cleaning model: KNOWNS_ONLY, USE_READS or USE_SW" , fullName = "clean_model" , shortName = "cm" , required = false )
var cleaningModel : String = "USE_READS"
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@Input ( doc = "Decompose input BAM file and fully realign it using BWA and assume Single Ended reads" , fullName = "use_bwa_single_ended" , shortName = "bwase" , required = false )
var useBWAse : Boolean = false
@Input ( doc = "Decompose input BAM file and fully realign it using BWA and assume Pair Ended reads" , fullName = "use_bwa_pair_ended" , shortName = "bwape" , required = false )
var useBWApe : Boolean = false
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Global Variables
****************************************************************************/
val queueLogDir : String = ".qlog/" // Gracefully hide Queue's output
var nContigs : Int = 0 // Use the number of contigs for scatter gathering jobs
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var cleanModelEnum : ConsensusDeterminationModel = ConsensusDeterminationModel . USE_READS
if ( cleaningModel == "KNOWNS_ONLY" ) {
cleanModelEnum = ConsensusDeterminationModel . KNOWNS_ONLY
}
else if ( cleaningModel == "USE_SW" ) {
cleanModelEnum = ConsensusDeterminationModel . USE_SW
}
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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Helper classes and methods
****************************************************************************/
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class ReadGroup ( val id : String ,
val lb : String ,
val pl : String ,
val pu : String ,
val sm : String ,
val cn : String ,
val ds : String )
{ }
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// Utility function to check if there are multiple samples in a BAM file (currently we can't deal with that)
def hasMultipleSamples ( readGroups : java.util.List [ SAMReadGroupRecord ] ) : Boolean = {
var sample : String = ""
for ( r <- readGroups ) {
if ( sample . isEmpty )
sample = r . getSample
else if ( sample != r . getSample )
return true ;
}
return false
}
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// Utility function to merge all bam files of similar samples. Generates one BAM file per sample.
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// It uses the sample information on the header of the input BAM files.
//
// Because the realignment only happens after these scripts are executed, in case you are using
// bwa realignment, this function will operate over the original bam files and output over the
// (to be realigned) bam files.
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def createSampleFiles ( bamFiles : List [ File ] , realignedBamFiles : List [ File ] ) : Map [ String , File ] = {
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// Creating a table with SAMPLE information from each input BAM file
val sampleTable = scala . collection . mutable . Map . empty [ String , List [ File ] ]
val realignedIterator = realignedBamFiles . iterator
for ( bam <- bamFiles ) {
val rBam = realignedIterator . next // advance to next element in the realignedBam list so they're in sync.
val samReader = new SAMFileReader ( bam )
val header = samReader . getFileHeader
val readGroups = header . getReadGroups
// only allow one sample per file. Bam files with multiple samples would require pre-processing of the file
// with PrintReads to separate the samples. Tell user to do it himself!
assert ( ! hasMultipleSamples ( readGroups ) , "The pipeline requires that only one sample is present in a BAM file. Please separate the samples in " + bam )
// Fill out the sample table with the readgroups in this file
for ( rg <- readGroups ) {
val sample = rg . getSample
if ( ! sampleTable . contains ( sample ) )
sampleTable ( sample ) = List ( rBam )
else if ( ! sampleTable ( sample ) . contains ( rBam ) )
sampleTable ( sample ) : += rBam
}
}
// Creating one file for each sample in the dataset
val sampleBamFiles = scala . collection . mutable . Map . empty [ String , File ]
for ( ( sample , flist ) <- sampleTable ) {
val sampleFileName = new File ( qscript . outputDir + qscript . projectName + "." + sample + ".bam" )
sampleBamFiles ( sample ) = sampleFileName
add ( joinBams ( flist , sampleFileName ) )
}
return sampleBamFiles . toMap
}
// Checks how many contigs are in the dataset. Uses the BAM file header information.
def getNumberOfContigs ( bamFile : File ) : Int = {
val samReader = new SAMFileReader ( new File ( bamFile ) )
return samReader . getFileHeader . getSequenceDictionary . getSequences . size ( )
}
// Rebuilds the Read Group string to give BWA
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def addReadGroups ( inBam : File , outBam : File , samReader : SAMFileReader ) {
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val readGroups = samReader . getFileHeader . getReadGroups
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var index : Int = readGroups . length
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for ( rg <- readGroups ) {
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val intermediateInBam : File = if ( index == readGroups . length ) { inBam } else { swapExt ( outBam , ".bam" , index + 1 + "-rg.bam" ) }
val intermediateOutBam : File = if ( index > 1 ) { swapExt ( outBam , ".bam" , index + "-rg.bam" ) } else { outBam }
val readGroup = new ReadGroup ( rg . getReadGroupId , rg . getPlatform , rg . getLibrary , rg . getPlatformUnit , rg . getSample , rg . getSequencingCenter , rg . getDescription )
add ( addReadGroup ( intermediateInBam , intermediateOutBam , readGroup ) )
index = index - 1
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}
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}
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// Takes a list of processed BAM files and realign them using the BWA option requested (bwase or bwape).
// Returns a list of realigned BAM files.
def performAlignment ( bams : List [ File ] ) : List [ File ] = {
var realignedBams : List [ File ] = List ( )
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var index = 1
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for ( bam <- bams ) {
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val saiFile1 = swapExt ( bam , ".bam" , "." + index + ".1.sai" )
val saiFile2 = swapExt ( bam , ".bam" , "." + index + ".2.sai" )
val realignedSamFile = swapExt ( bam , ".bam" , "." + index + ".realigned.sam" )
val realignedBamFile = swapExt ( bam , ".bam" , "." + index + ".realigned.bam" )
val rgRealignedBamFile = swapExt ( bam , ".bam" , "." + index + ".realigned.rg.bam" )
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if ( useBWAse ) {
add ( bwa_aln_se ( bam , saiFile1 ) ,
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bwa_sam_se ( bam , saiFile1 , realignedSamFile ) )
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}
else {
add ( bwa_aln_pe ( bam , saiFile1 , 1 ) ,
bwa_aln_pe ( bam , saiFile2 , 2 ) ,
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bwa_sam_pe ( bam , saiFile1 , saiFile2 , realignedSamFile ) )
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}
add ( sortSam ( realignedSamFile , realignedBamFile ) )
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addReadGroups ( realignedBamFile , rgRealignedBamFile , new SAMFileReader ( bam ) )
realignedBams : += rgRealignedBamFile
index = index + 1
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}
return realignedBams
}
// Reads a BAM LIST file and creates a scala list with all the files
def createListFromFile ( in : File ) : List [ File ] = {
if ( in . toString . endsWith ( "bam" ) )
return List ( in )
var l : List [ File ] = List ( )
for ( bam <- fromFile ( in ) . getLines )
l : += new File ( bam )
return l
}
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Main script
****************************************************************************/
def script = {
// keep a record of the number of contigs in the first bam file in the list
val bams = createListFromFile ( input )
nContigs = getNumberOfContigs ( bams ( 0 ) )
val realignedBams = if ( useBWApe || useBWAse ) { performAlignment ( bams ) } else { bams }
// Generate a BAM file per sample joining all per lane files if necessary
val sampleBamFiles : Map [ String , File ] = createSampleFiles ( bams , realignedBams )
println ( "nContigs: " + nContigs )
// Final output list of processed bam files
var cohortList : List [ File ] = List ( )
// Simple progress report
println ( "\nFound the following samples: " )
for ( ( sample , file ) <- sampleBamFiles )
println ( "\t" + sample + " -> " + file )
// If this is a 'knowns only' indel realignment run, do it only once for all samples.
val globalIntervals = new File ( outputDir + projectName + ".intervals" )
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if ( cleaningModel == ConsensusDeterminationModel . KNOWNS_ONLY )
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add ( target ( null , globalIntervals ) )
// Put each sample through the pipeline
for ( ( sample , bam ) <- sampleBamFiles ) {
// BAM files generated by the pipeline
val cleanedBam = swapExt ( bam , ".bam" , ".clean.bam" )
val dedupedBam = swapExt ( bam , ".bam" , ".clean.dedup.bam" )
val recalBam = swapExt ( bam , ".bam" , ".clean.dedup.recal.bam" )
// Accessory files
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val targetIntervals = if ( cleaningModel == ConsensusDeterminationModel . KNOWNS_ONLY ) { globalIntervals } else { swapExt ( bam , ".bam" , ".intervals" ) }
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val metricsFile = swapExt ( bam , ".bam" , ".metrics" )
val preRecalFile = swapExt ( bam , ".bam" , ".pre_recal.csv" )
val postRecalFile = swapExt ( bam , ".bam" , ".post_recal.csv" )
val preOutPath = swapExt ( bam , ".bam" , ".pre" )
val postOutPath = swapExt ( bam , ".bam" , ".post" )
val preValidateLog = swapExt ( bam , ".bam" , ".pre.validation" )
val postValidateLog = swapExt ( bam , ".bam" , ".post.validation" )
add ( validate ( bam , preValidateLog ) )
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if ( cleaningModel != ConsensusDeterminationModel . KNOWNS_ONLY )
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add ( target ( bam , targetIntervals ) )
add ( clean ( bam , targetIntervals , cleanedBam ) ,
dedup ( cleanedBam , dedupedBam , metricsFile ) ,
cov ( dedupedBam , preRecalFile ) ,
recal ( dedupedBam , preRecalFile , recalBam ) ,
cov ( recalBam , postRecalFile ) ,
analyzeCovariates ( preRecalFile , preOutPath ) ,
analyzeCovariates ( postRecalFile , postOutPath ) ,
validate ( recalBam , postValidateLog ) )
cohortList : += recalBam
}
// output a BAM list with all the processed per sample files
val cohortFile = new File ( qscript . outputDir + qscript . projectName + ".cohort.list" )
add ( writeList ( cohortList , cohortFile ) )
}
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
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* Classes ( GATK Walkers )
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****************************************************************************/
// General arguments to GATK walkers
trait CommandLineGATKArgs extends CommandLineGATK {
this . reference_sequence = qscript . reference
this . memoryLimit = 4
this . isIntermediate = true
}
case class target ( inBams : File , outIntervals : File ) extends RealignerTargetCreator with CommandLineGATKArgs {
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if ( cleaningModel != ConsensusDeterminationModel . KNOWNS_ONLY )
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this . input_file : += inBams
this . out = outIntervals
this . mismatchFraction = 0.0
this . rodBind : += RodBind ( " dbsnp " , " VCF " , dbSNP )
this . rodBind : += RodBind ( " indels " , " VCF " , indels )
this . scatterCount = nContigs
this . analysisName = queueLogDir + outIntervals + ".target"
this . jobName = queueLogDir + outIntervals + ".target"
}
case class clean ( inBams : File , tIntervals : File , outBam : File ) extends IndelRealigner with CommandLineGATKArgs {
this . input_file : += inBams
this . targetIntervals = tIntervals
this . out = outBam
this . rodBind : += RodBind ( " dbsnp " , " VCF " , dbSNP )
this . rodBind : += RodBind ( " indels " , " VCF " , qscript . indels )
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this . consensusDeterminationModel = consensusDeterminationModel
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this . compress = 0
this . scatterCount = nContigs
this . analysisName = queueLogDir + outBam + ".clean"
this . jobName = queueLogDir + outBam + ".clean"
}
case class cov ( inBam : File , outRecalFile : File ) extends CountCovariates with CommandLineGATKArgs {
this . rodBind : += RodBind ( " dbsnp " , " VCF " , dbSNP )
this . covariate ++= List ( "ReadGroupCovariate" , "QualityScoreCovariate" , "CycleCovariate" , "DinucCovariate" )
this . input_file : += inBam
this . recal_file = outRecalFile
if ( ! qscript . intervalString . isEmpty ( ) ) this . intervalsString ++= List ( qscript . intervalString )
else if ( qscript . intervals != null ) this . intervals : += qscript.intervals
this . scatterCount = nContigs
this . analysisName = queueLogDir + outRecalFile + ".covariates"
this . jobName = queueLogDir + outRecalFile + ".covariates"
}
case class recal ( inBam : File , inRecalFile : File , outBam : File ) extends TableRecalibration with CommandLineGATKArgs {
this . input_file : += inBam
this . recal_file = inRecalFile
this . baq = org . broadinstitute . sting . utils . baq . BAQ . CalculationMode . CALCULATE_AS_NECESSARY
this . out = outBam
if ( ! qscript . intervalString . isEmpty ( ) ) this . intervalsString ++= List ( qscript . intervalString )
else if ( qscript . intervals != null ) this . intervals : += qscript.intervals
this . scatterCount = nContigs
this . isIntermediate = false
this . analysisName = queueLogDir + outBam + ".recalibration"
this . jobName = queueLogDir + outBam + ".recalibration"
}
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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Classes ( non - GATK programs )
****************************************************************************/
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case class analyzeCovariates ( inRecalFile : File , outPath : File ) extends AnalyzeCovariates {
this . resources = qscript . R
this . recal_file = inRecalFile
this . output_dir = outPath . toString
this . analysisName = queueLogDir + inRecalFile + ".analyze_covariates"
this . jobName = queueLogDir + inRecalFile + ".analyze_covariates"
}
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case class dedup ( inBam : File , outBam : File , metricsFile : File ) extends MarkDuplicates {
this . input = List ( inBam )
this . output = outBam
this . metrics = metricsFile
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this . memoryLimit = 6
this . isIntermediate = true
this . analysisName = queueLogDir + outBam + ".dedup"
this . jobName = queueLogDir + outBam + ".dedup"
}
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case class joinBams ( inBams : List [ File ] , outBam : File ) extends MergeSamFiles {
this . input = inBams
this . output = outBam
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this . memoryLimit = 4
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this . isIntermediate = true
this . analysisName = queueLogDir + outBam + ".joinBams"
this . jobName = queueLogDir + outBam + ".joinBams"
}
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case class sortSam ( inSam : File , outBam : File ) extends SortSam {
this . input = List ( inSam )
this . output = outBam
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this . memoryLimit = 4
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this . isIntermediate = true
this . analysisName = queueLogDir + outBam + ".sortSam"
this . jobName = queueLogDir + outBam + ".sortSam"
}
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case class validate ( inBam : File , outLog : File ) extends ValidateSamFile {
this . input = List ( inBam )
this . output = outLog
this . maxRecordsInRam = 100000
this . REFERENCE_SEQUENCE = qscript . reference
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this . memoryLimit = 4
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this . isIntermediate = false
this . analysisName = queueLogDir + outLog + ".validate"
this . jobName = queueLogDir + outLog + ".validate"
}
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case class addReadGroup ( inBam : File , outBam : File , readGroup : ReadGroup ) extends AddOrReplaceReadGroups {
this . input = List ( inBam )
this . output = outBam
this . RGID = readGroup . id
this . RGCN = readGroup . cn
this . RGDS = readGroup . ds
this . RGLB = readGroup . lb
this . RGPL = readGroup . pl
this . RGPU = readGroup . pu
this . RGSM = readGroup . sm
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this . memoryLimit = 4
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this . isIntermediate = true
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this . analysisName = queueLogDir + outBam + ".rg"
this . jobName = queueLogDir + outBam + ".rg"
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}
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trait BWACommonArgs extends CommandLineFunction {
this . memoryLimit = 4
this . isIntermediate = true
}
case class bwa_aln_se ( inBam : File , outSai : File ) extends CommandLineFunction with BWACommonArgs {
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@Input ( doc = "bam file to be aligned" ) var bam = inBam
@Output ( doc = "output sai file" ) var sai = outSai
def commandLine = bwaPath + " aln -q 5 " + reference + " -b " + bam + " > " + sai
this . analysisName = queueLogDir + outSai + ".bwa_aln_se"
this . jobName = queueLogDir + outSai + ".bwa_aln_se"
}
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case class bwa_aln_pe ( inBam : File , outSai1 : File , index : Int ) extends CommandLineFunction with BWACommonArgs {
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@Input ( doc = "bam file to be aligned" ) var bam = inBam
@Output ( doc = "output sai file for 1st mating pair" ) var sai = outSai1
def commandLine = bwaPath + " aln -q 5 " + reference + " -b" + index + " " + bam + " > " + sai
this . analysisName = queueLogDir + outSai1 + ".bwa_aln_pe1"
this . jobName = queueLogDir + outSai1 + ".bwa_aln_pe1"
}
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case class bwa_sam_se ( inBam : File , inSai : File , outBam : File ) extends CommandLineFunction with BWACommonArgs {
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@Input ( doc = "bam file to be aligned" ) var bam = inBam
@Input ( doc = "bwa alignment index file" ) var sai = inSai
@Output ( doc = "output aligned bam file" ) var alignedBam = outBam
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def commandLine = bwaPath + " samse " + reference + " " + sai + " " + bam + " > " + alignedBam
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this . analysisName = queueLogDir + outBam + ".bwa_sam_se"
this . jobName = queueLogDir + outBam + ".bwa_sam_se"
}
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case class bwa_sam_pe ( inBam : File , inSai1 : File , inSai2 : File , outBam : File ) extends CommandLineFunction with BWACommonArgs {
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@Input ( doc = "bam file to be aligned" ) var bam = inBam
@Input ( doc = "bwa alignment index file for 1st mating pair" ) var sai1 = inSai1
@Input ( doc = "bwa alignment index file for 2nd mating pair" ) var sai2 = inSai2
@Output ( doc = "output aligned bam file" ) var alignedBam = outBam
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def commandLine = bwaPath + " sampe " + reference + " " + sai1 + " " + sai2 + " " + bam + " " + bam + " > " + alignedBam
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this . analysisName = queueLogDir + outBam + ".bwa_sam_pe"
this . jobName = queueLogDir + outBam + ".bwa_sam_pe"
}
case class writeList ( inBams : List [ File ] , outBamList : File ) extends ListWriterFunction {
this . inputFiles = inBams
this . listFile = outBamList
this . analysisName = queueLogDir + outBamList + ".bamList"
this . jobName = queueLogDir + outBamList + ".bamList"
}
}
