Fixed list dependency
Instead of creating a bam list file, I dynamically create a scala list and pass as parameters. This way the intermediate bam files don't get deleted before they should.
This commit is contained in:
Mauricio Carneiro
parent
219252a566
commit
cd12f7f286
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@ -106,7 +106,7 @@ class DataProcessingPipeline extends QScript {
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// Because the realignment only happens after these scripts are executed, in case you are using
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// bwa realignment, this function will operate over the original bam files and output over the
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// (to be realigned) bam files.
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def createSampleFiles(bamFiles: List[File], realignedBamFiles: List[File]): Map[String, File] = {
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def createSampleFiles(bamFiles: List[File], realignedBamFiles: List[File]): Map[String, List[File]] = {
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// Creating a table with SAMPLE information from each input BAM file
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val sampleTable = scala.collection.mutable.Map.empty[String, List[File]]
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@ -131,24 +131,25 @@ class DataProcessingPipeline extends QScript {
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sampleTable(sample) :+= rBam
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}
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}
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return sampleTable.toMap
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println("\n\n*** INPUT FILES ***\n")
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// Creating one file for each sample in the dataset
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val sampleBamFiles = scala.collection.mutable.Map.empty[String, File]
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for ((sample, flist) <- sampleTable) {
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println(sample + ":")
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for (f <- flist)
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println (f)
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println()
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val sampleFileName = new File(qscript.outputDir + qscript.projectName + "." + sample + ".list")
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sampleBamFiles(sample) = sampleFileName
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add(writeList(flist, sampleFileName))
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}
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println("*** INPUT FILES ***\n\n")
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return sampleBamFiles.toMap
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// println("\n\n*** INPUT FILES ***\n")
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// // Creating one file for each sample in the dataset
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// val sampleBamFiles = scala.collection.mutable.Map.empty[String, File]
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// for ((sample, flist) <- sampleTable) {
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//
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// println(sample + ":")
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// for (f <- flist)
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// println (f)
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// println()
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//
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// val sampleFileName = new File(qscript.outputDir + qscript.projectName + "." + sample + ".list")
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// sampleBamFiles(sample) = sampleFileName
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// //add(writeList(flist, sampleFileName))
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// }
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// println("*** INPUT FILES ***\n\n")
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//
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// return sampleBamFiles.toMap
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}
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// Rebuilds the Read Group string to give BWA
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@ -224,7 +225,10 @@ class DataProcessingPipeline extends QScript {
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def script = {
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// final output list of processed bam files
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var cohortList: List[File] = List()
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// sets the model for the Indel Realigner
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cleanModelEnum = getIndelCleaningModel()
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// keep a record of the number of contigs in the first bam file in the list
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@ -233,28 +237,19 @@ class DataProcessingPipeline extends QScript {
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val realignedBAMs = if (useBWApe || useBWAse) {performAlignment(bams)} else {revertBams(bams)}
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// Generate a BAM file per sample joining all per lane files if necessary
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val sampleBAMFiles: Map[String, File] = createSampleFiles(bams, realignedBAMs)
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// generate a BAM file per sample joining all per lane files if necessary
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val sampleBAMFiles: Map[String, List[File]] = createSampleFiles(bams, realignedBAMs)
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// Final output list of processed bam files
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var cohortList: List[File] = List()
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// Simple progress report
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println("\nFound the following samples: ")
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for ((sample, file) <- sampleBAMFiles)
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println("\t" + sample + " -> " + file)
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println("\n")
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// If this is a 'knowns only' indel realignment run, do it only once for all samples.
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// if this is a 'knowns only' indel realignment run, do it only once for all samples.
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val globalIntervals = new File(outputDir + projectName + ".intervals")
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if (cleaningModel == ConsensusDeterminationModel.KNOWNS_ONLY)
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add(target(null, globalIntervals))
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// Put each sample through the pipeline
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for ((sample, sampleFile) <- sampleBAMFiles) {
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val bam = if (sampleFile.endsWith(".list")) {swapExt(sampleFile, ".list", ".bam")} else {sampleFile}
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// put each sample through the pipeline
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for ((sample, bamList) <- sampleBAMFiles) {
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// BAM files generated by the pipeline
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val bam = new File(qscript.projectName + "." + sample + ".bam")
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val cleanedBam = swapExt(bam, ".bam", ".clean.bam")
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val dedupedBam = swapExt(bam, ".bam", ".clean.dedup.bam")
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val recalBam = swapExt(bam, ".bam", ".clean.dedup.recal.bam")
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@ -272,15 +267,16 @@ class DataProcessingPipeline extends QScript {
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// Validation is an optional step for the BAM file generated after
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// alignment and the final bam file of the pipeline.
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if (!noValidation && sampleFile.endsWith(".bam")) { // todo -- implement validation for .list BAM files
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if (!noValidation) {
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for (sampleFile <- bamList)
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add(validate(sampleFile, preValidateLog),
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validate(recalBam, postValidateLog))
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}
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if (cleaningModel != ConsensusDeterminationModel.KNOWNS_ONLY)
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add(target(sampleFile, targetIntervals))
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add(target(bamList, targetIntervals))
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add(clean(sampleFile, targetIntervals, cleanedBam),
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add(clean(bamList, targetIntervals, cleanedBam),
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dedup(cleanedBam, dedupedBam, metricsFile),
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cov(dedupedBam, preRecalFile),
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recal(dedupedBam, preRecalFile, recalBam),
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@ -320,9 +316,9 @@ class DataProcessingPipeline extends QScript {
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this.maxRecordsInRam = 100000
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}
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case class target (inBams: File, outIntervals: File) extends RealignerTargetCreator with CommandLineGATKArgs {
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case class target (inBams: List[File], outIntervals: File) extends RealignerTargetCreator with CommandLineGATKArgs {
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if (cleanModelEnum != ConsensusDeterminationModel.KNOWNS_ONLY)
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this.input_file :+= inBams
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this.input_file = inBams
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this.out = outIntervals
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this.mismatchFraction = 0.0
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this.known :+= qscript.dbSNP
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@ -333,8 +329,8 @@ class DataProcessingPipeline extends QScript {
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this.jobName = queueLogDir + outIntervals + ".target"
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}
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case class clean (inBams: File, tIntervals: File, outBam: File) extends IndelRealigner with CommandLineGATKArgs {
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this.input_file :+= inBams
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case class clean (inBams: List[File], tIntervals: File, outBam: File) extends IndelRealigner with CommandLineGATKArgs {
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this.input_file = inBams
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this.targetIntervals = tIntervals
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this.out = outBam
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this.known :+= qscript.dbSNP
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