Creating sample-bam list instead of joining
This should save us at least one day in the trio decoy processing.
This commit is contained in:
Mauricio Carneiro
parent
04d8bcaf19
commit
136f0eb685
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@ -218,7 +218,6 @@ class DataProcessingPipeline extends QScript {
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return revertedBAM
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}
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/****************************************************************************
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* Main script
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****************************************************************************/
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@ -271,13 +270,12 @@ class DataProcessingPipeline extends QScript {
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val postValidateLog = swapExt(bam, ".bam", ".post.validation")
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//todo -- update the validation to work with .list files
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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) {
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// add(validate(bam, preValidateLog),
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// validate(recalBam, postValidateLog))
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// }
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if (!noValidation && sampleFile.endsWith(".bam")) { // todo -- implement validation for .list BAM files
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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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@ -390,7 +388,7 @@ class DataProcessingPipeline extends QScript {
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}
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case class dedup (inBam: File, outBam: File, metricsFile: File) extends MarkDuplicates with ExternalCommonArgs {
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this.input = List(inBam)
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this.input :+= inBam
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this.output = outBam
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this.metrics = metricsFile
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this.memoryLimit = 16
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@ -406,7 +404,7 @@ class DataProcessingPipeline extends QScript {
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}
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case class sortSam (inSam: File, outBam: File, sortOrderP: SortOrder) extends SortSam with ExternalCommonArgs {
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this.input = List(inSam)
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this.input :+= inSam
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this.output = outBam
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this.sortOrder = sortOrderP
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this.analysisName = queueLogDir + outBam + ".sortSam"
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@ -414,7 +412,7 @@ class DataProcessingPipeline extends QScript {
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}
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case class validate (inBam: File, outLog: File) extends ValidateSamFile with ExternalCommonArgs {
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this.input = List(inBam)
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this.input :+= inBam
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this.output = outLog
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this.REFERENCE_SEQUENCE = qscript.reference
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this.isIntermediate = false
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@ -424,8 +422,7 @@ class DataProcessingPipeline extends QScript {
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case class addReadGroup (inBam: File, outBam: File, readGroup: ReadGroup) extends AddOrReplaceReadGroups with ExternalCommonArgs {
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@Output(doc="output bai file") var bai = swapExt(outBam, ".bam", ".bai")
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this.input = List(inBam)
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this.input :+= inBam
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this.output = outBam
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this.RGID = readGroup.id
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this.RGCN = readGroup.cn
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@ -15,7 +15,7 @@ class AddOrReplaceReadGroups extends org.broadinstitute.sting.queue.function.Jav
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javaMainClass = "net.sf.picard.sam.AddOrReplaceReadGroups"
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@Input(doc="The input SAM or BAM files to analyze. Must be coordinate sorted.", shortName = "input", fullName = "input_bam_files", required = true)
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var input: List[File] = _
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var input: List[File] = Nil
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@Output(doc="The output BAM file with the modified/added read groups", shortName = "output", fullName = "output_bam_file", required = true)
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var output: File = _
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@ -15,7 +15,7 @@ class MarkDuplicates extends org.broadinstitute.sting.queue.function.JavaCommand
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javaMainClass = "net.sf.picard.sam.MarkDuplicates"
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@Input(doc="The input SAM or BAM files to analyze. Must be coordinate sorted.", shortName = "input", fullName = "input_bam_files", required = true)
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var input: List[File] = _
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var input: List[File] = Nil
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@Output(doc="The output file to write marked records to", shortName = "output", fullName = "output_bam_file", required = true)
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var output: File = _
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@ -16,7 +16,7 @@ class MergeSamFiles extends org.broadinstitute.sting.queue.function.JavaCommandL
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javaMainClass = "net.sf.picard.sam.MergeSamFiles"
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@Input(doc="The input SAM or BAM files to analyze. Must be coordinate sorted.", shortName = "input", fullName = "input_bam_files", required = true)
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var input: List[File] = _
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var input: List[File] = Nil
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@Output(doc="The output merged BAM file", shortName = "output", fullName = "output_bam_file", required = true)
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var output: File = _
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@ -16,7 +16,7 @@ class SortSam extends org.broadinstitute.sting.queue.function.JavaCommandLineFun
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javaMainClass = "net.sf.picard.sam.SortSam"
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@Input(doc="The input SAM or BAM files to sort.", shortName = "input", fullName = "input_bam_files", required = true)
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var input: List[File] = _
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var input: List[File] = Nil
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@Output(doc="The sorted BAM or SAM output file.", shortName = "output", fullName = "output_bam_file", required = true)
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var output: File = _
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@ -17,7 +17,7 @@ class ValidateSamFile extends org.broadinstitute.sting.queue.function.JavaComman
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javaMainClass = "net.sf.picard.sam.ValidateSamFile"
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@Input(doc="The input SAM or BAM files to analyze. Must be coordinate sorted.", shortName = "input", fullName = "input_bam_files", required = true)
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var input: List[File] = _
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var input: List[File] = Nil
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@Output(doc="Send output to a file instead of stdout", shortName = "output", fullName = "output_file", required = false)
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var output: File = _
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@ -26,7 +26,7 @@ class ValidateSamFile extends org.broadinstitute.sting.queue.function.JavaComman
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var MODE: Mode = Mode.VERBOSE
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@Argument(doc="List of validation error types to ignore.", shortName = "ignore", fullName = "ignore_error_types", required = false)
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var IGNORE: List[String] = _
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var IGNORE: List[String] = Nil
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@Argument(doc = "The maximum number of lines output in verbose mode.", shortName = "max", fullName = "max_output", required = false)
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var MAX_OUTPUT: Int = 100
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