BioWDL: RNA-seq

A BioWDL pipeline for processing RNA-seq data, starting with FASTQ files to produce expression measures and VCFs.

Inputs for RNAseq

The following is an overview of all available inputs in RNAseq.

Required inputs

RNAseq.dockerImagesFile
File
A YAML file describing the docker image used for the tasks. The dockerImages.yml provided with the pipeline is recommended.
RNAseq.expression.mergeStringtieGtf.referenceAnnotation
File?
The GTF file to compare with.
RNAseq.hisat2Index
Array[File]+?
The hisat2 index files. Defining this will cause the hisat2 aligner to run. Note that is starIndex is also defined the star results will be used for downstream analyses. May be omitted in starIndex is defined.
RNAseq.outputDir
String — Default: "."
The output directory.
RNAseq.referenceFasta
File
The reference fasta file.
RNAseq.referenceFastaDict
File
Sequence dictionary (.dict) file of the reference.
RNAseq.referenceFastaFai
File
Fasta index (.fai) file of the reference.
RNAseq.sampleConfigFile
File
The samplesheet, including sample ids, library ids, readgroup ids and fastq file locations.
RNAseq.starIndex
Array[File]+?
The star index files. Defining this will cause the star aligner to run and be used for downstream analyses. May be ommited if hisat2Index is defined.
RNAseq.strandedness
String
The strandedness of the RNA sequencing library preparation. One of "None" (unstranded), "FR" (forward-reverse: first read equal transcript) or "RF" (reverse-forward: second read equals transcript).

Other common inputs

RNAseq.adapterForward
String? — Default: "AGATCGGAAGAG"
The adapter to be removed from the reads first or single end reads.
RNAseq.adapterReverse
String? — Default: "AGATCGGAAGAG"
The adapter to be removed from the reads second end reads.
RNAseq.cpatHex
File?
A hexamer frequency table for CPAT. Required if lncRNAdetection is `true`.
RNAseq.cpatLogitModel
File?
A logit model for CPAT. Required if lncRNAdetection is `true`.
RNAseq.dbsnpVCF
File?
dbsnp VCF file used for checking known sites.
RNAseq.dbsnpVCFIndex
File?
Index (.tbi) file for the dbsnp VCF.
RNAseq.detectNovelTranscripts
Boolean — Default: false
Whether or not a transcripts assembly should be used. If set to true Stringtie will be used to create a new GTF file based on the BAM files. This generated GTF file will be used for expression quantification. If `referenceGtfFile` is also provided this reference GTF will be used to guide the assembly.
RNAseq.dgeFiles
Boolean — Default: false
Whether or not input files for DGE should be generated.
RNAseq.expression.stringtieAssembly.geneAbundanceFile
String?
Where the abundance file should be written.
RNAseq.lncRNAdatabases
Array[File] — Default: []
A set of GTF files the assembled GTF file should be compared with. Only used if lncRNAdetection is set to `true`.
RNAseq.lncRNAdetection
Boolean — Default: false
Whether or not lncRNA detection should be run. This will enable detectNovelTranscript (this cannot be disabled by setting detectNovelTranscript to false). This will require cpatLogitModel and cpatHex to be defined.
RNAseq.referenceGtfFile
File?
A reference GTF file. Used for expression quantification or to guide the transcriptome assembly if detectNovelTranscripts is set to `true` (this GTF won't be be used directly for the expression quantification in that case.
RNAseq.refflatFile
File?
A refflat files describing the genes. If this is defined RNAseq metrics will be collected.
RNAseq.runStringtieQuantification
Boolean — Default: true
Option to disable running stringtie for quantification. This does not affect the usage of stringtie for novel transcript detection.
RNAseq.sampleJobs.bamMetrics.ampliconIntervals
File?
An interval list describinig the coordinates of the amplicons sequenced. This should only be used for targeted sequencing or WES. Required if `ampliconIntervals` is defined.
RNAseq.sampleJobs.bamMetrics.targetIntervals
Array[File]+?
An interval list describing the coordinates of the targets sequenced. This should only be used for targeted sequencing or WES. If defined targeted PCR metrics will be collected. Requires `ampliconIntervals` to also be defined.
RNAseq.sampleJobs.qc.contaminations
Array[String]+?
Contaminants/adapters to be removed from the reads.
RNAseq.sampleJobs.qc.readgroupName
String — Default: sub(basename(read1),"(\.fq)?(\.fastq)?(\.gz)?","")
The name of the readgroup.
RNAseq.umiDeduplication
Boolean — Default: false
Whether or not UMI based deduplication should be performed.
RNAseq.variantCalling
Boolean — Default: false
Whether or not variantcalling should be performed.
RNAseq.variantcalling.callAutosomal.excludeIntervalList
Array[File]+?
Bed files or interval lists describing the regions to NOT operate on.
RNAseq.variantcalling.callAutosomal.pedigree
File?
Pedigree file for determining the population "founders".
RNAseq.variantcalling.callAutosomal.ploidy
Int?
The ploidy with which the variants should be called.
RNAseq.variantcalling.callX.excludeIntervalList
Array[File]+?
Bed files or interval lists describing the regions to NOT operate on.
RNAseq.variantcalling.callX.pedigree
File?
Pedigree file for determining the population "founders".
RNAseq.variantcalling.callY.excludeIntervalList
Array[File]+?
Bed files or interval lists describing the regions to NOT operate on.
RNAseq.variantcalling.callY.pedigree
File?
Pedigree file for determining the population "founders".
RNAseq.variantcalling.gvcf
Boolean — Default: false
Whether to call in GVCF mode.
RNAseq.variantcalling.mergeVcf
Boolean — Default: true
Whether to merge scattered VCFs.
RNAseq.variantcalling.Stats.compareVcf
File?
When inputVcf and compareVCF are given, the program generates separate stats for intersection and the complements. By default only sites are compared, samples must be given to include also sample columns.
RNAseq.variantcalling.Stats.compareVcfIndex
File?
Index for the compareVcf.
RNAseq.variantCallingRegions
File?
A bed file describing the regions to operate on for variant calling.

Advanced inputs

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RNAseq.calculateRegions.intersectAutosomalRegions.memory
String — Default: "~{512 + ceil(size([regionsA, regionsB],"M"))}M"
The amount of memory needed for the job.
RNAseq.calculateRegions.intersectAutosomalRegions.timeMinutes
Int — Default: 1 + ceil(size([regionsA, regionsB],"G"))
The maximum amount of time the job will run in minutes.
RNAseq.calculateRegions.intersectX.memory
String — Default: "~{512 + ceil(size([regionsA, regionsB],"M"))}M"
The amount of memory needed for the job.
RNAseq.calculateRegions.intersectX.timeMinutes
Int — Default: 1 + ceil(size([regionsA, regionsB],"G"))
The maximum amount of time the job will run in minutes.
RNAseq.calculateRegions.intersectY.memory
String — Default: "~{512 + ceil(size([regionsA, regionsB],"M"))}M"
The amount of memory needed for the job.
RNAseq.calculateRegions.intersectY.timeMinutes
Int — Default: 1 + ceil(size([regionsA, regionsB],"G"))
The maximum amount of time the job will run in minutes.
RNAseq.calculateRegions.inverseBed.memory
String — Default: "~{512 + ceil(size([inputBed, faidx],"M"))}M"
The amount of memory needed for the job.
RNAseq.calculateRegions.inverseBed.timeMinutes
Int — Default: 1 + ceil(size([inputBed, faidx],"G"))
The maximum amount of time the job will run in minutes.
RNAseq.calculateRegions.mergeBeds.memory
String — Default: "~{512 + ceil(size(bedFiles,"M"))}M"
The amount of memory needed for the job.
RNAseq.calculateRegions.mergeBeds.outputBed
String — Default: "merged.bed"
The path to write the output to.
RNAseq.calculateRegions.mergeBeds.timeMinutes
Int — Default: 1 + ceil(size(bedFiles,"G"))
The maximum amount of time the job will run in minutes.
RNAseq.calculateRegions.scatterAutosomalRegions.memory
String — Default: "256M"
The amount of memory this job will use.
RNAseq.calculateRegions.scatterAutosomalRegions.prefix
String — Default: "scatters/scatter-"
The prefix of the ouput files. Output will be named like: .bed, in which N is an incrementing number. Default 'scatter-'. </dd>
RNAseq.calculateRegions.scatterAutosomalRegions.splitContigs
Boolean — Default: false
If set, contigs are allowed to be split up over multiple files.
RNAseq.calculateRegions.scatterAutosomalRegions.timeMinutes
Int — Default: 2
The maximum amount of time the job will run in minutes.
RNAseq.collectUmiStats
Boolean — Default: false
Whether or not UMI deduplication stats should be collected. This will potentially cause a massive increase in memory usage of the deduplication step.
RNAseq.convertDockerTagsFile.dockerImage
String — Default: "quay.io/biocontainers/biowdl-input-converter:0.3.0--pyhdfd78af_0"
The docker image used for this task. Changing this may result in errors which the developers may choose not to address.
RNAseq.convertDockerTagsFile.memory
String — Default: "128M"
The maximum amount of memory the job will need.
RNAseq.convertDockerTagsFile.timeMinutes
Int — Default: 1
The maximum amount of time the job will run in minutes.
RNAseq.convertSampleConfig.checkFileMd5sums
Boolean — Default: false
Whether or not the MD5 sums of the files mentioned in the samplesheet should be checked.
RNAseq.convertSampleConfig.dockerImage
String — Default: "quay.io/biocontainers/biowdl-input-converter:0.3.0--pyhdfd78af_0"
The docker image used for this task. Changing this may result in errors which the developers may choose not to address.
RNAseq.convertSampleConfig.memory
String — Default: "128M"
The amount of memory needed for the job.
RNAseq.convertSampleConfig.old
Boolean — Default: false
Whether or not the old samplesheet format should be used.
RNAseq.convertSampleConfig.skipFileCheck
Boolean — Default: true
Whether or not the existance of the files mentioned in the samplesheet should be checked.
RNAseq.convertSampleConfig.timeMinutes
Int — Default: 1
The maximum amount of time the job will run in minutes.
RNAseq.CPAT.memory
String — Default: "4G"
The amount of memory available to the job.
RNAseq.CPAT.startCodons
Array[String]?
Equivalent to CPAT's `--start` option.
RNAseq.CPAT.stopCodons
Array[String]?
Equivalent to CPAT's `--stop` option.
RNAseq.CPAT.timeMinutes
Int — Default: 10 + ceil((size(gene,"G") * 30))
The maximum amount of time the job will run in minutes.
RNAseq.createAnnotation.memory
String — Default: "5G"
The amount of memory this job will use.
RNAseq.createAnnotation.timeMinutes
Int — Default: 30
The maximum amount of time the job will run in minutes.
RNAseq.createDesign.memory
String — Default: "5G"
The amount of memory this job will use.
RNAseq.createDesign.timeMinutes
Int — Default: 30
The maximum amount of time the job will run in minutes.
RNAseq.expression.additionalAttributes
Array[String]+?
Additional attributes which should be taken from the GTF used for quantification and added to the merged expression value tables.
RNAseq.expression.htSeqCount.additionalAttributes
Array[String] — Default: []
Equivalent to the --additional-attr option of htseq-count.
RNAseq.expression.htSeqCount.featureType
String?
Equivalent to the --type option of htseq-count.
RNAseq.expression.htSeqCount.idattr
String?
Equivalent to the --idattr option of htseq-count.
RNAseq.expression.htSeqCount.memory
String — Default: "8G"
The amount of memory the job requires in GB.
RNAseq.expression.htSeqCount.nprocesses
Int — Default: 1
Number of processes to run htseq with.
RNAseq.expression.htSeqCount.order
String — Default: "pos"
Equivalent to the -r option of htseq-count.
RNAseq.expression.htSeqCount.timeMinutes
Int — Default: 1440
The maximum amount of time the job will run in minutes.
RNAseq.expression.mergedHTSeqFragmentsPerGenes.featureAttribute
String?
Equivalent to the -F option of collect-columns.
RNAseq.expression.mergedHTSeqFragmentsPerGenes.featureColumn
Int?
Equivalent to the -f option of collect-columns.
RNAseq.expression.mergedHTSeqFragmentsPerGenes.header
Boolean — Default: false
Equivalent to the -H flag of collect-columns.
RNAseq.expression.mergedHTSeqFragmentsPerGenes.memoryGb
Int — Default: 4 + ceil((0.5 * length(inputTables)))
The maximum amount of memory the job will need in GB.
RNAseq.expression.mergedHTSeqFragmentsPerGenes.separator
Int?
Equivalent to the -s option of collect-columns.
RNAseq.expression.mergedHTSeqFragmentsPerGenes.sumOnDuplicateId
Boolean — Default: false
Equivalent to the -S flag of collect-columns.
RNAseq.expression.mergedHTSeqFragmentsPerGenes.timeMinutes
Int — Default: 10
The maximum amount of time the job will run in minutes.
RNAseq.expression.mergedHTSeqFragmentsPerGenes.valueColumn
Int?
Equivalent to the -c option of collect-columns.
RNAseq.expression.mergedStringtieFPKMs.featureAttribute
String?
Equivalent to the -F option of collect-columns.
RNAseq.expression.mergedStringtieFPKMs.featureColumn
Int?
Equivalent to the -f option of collect-columns.
RNAseq.expression.mergedStringtieFPKMs.memoryGb
Int — Default: 4 + ceil((0.5 * length(inputTables)))
The maximum amount of memory the job will need in GB.
RNAseq.expression.mergedStringtieFPKMs.separator
Int?
Equivalent to the -s option of collect-columns.
RNAseq.expression.mergedStringtieFPKMs.timeMinutes
Int — Default: 10
The maximum amount of time the job will run in minutes.
RNAseq.expression.mergedStringtieTPMs.featureAttribute
String?
Equivalent to the -F option of collect-columns.
RNAseq.expression.mergedStringtieTPMs.featureColumn
Int?
Equivalent to the -f option of collect-columns.
RNAseq.expression.mergedStringtieTPMs.memoryGb
Int — Default: 4 + ceil((0.5 * length(inputTables)))
The maximum amount of memory the job will need in GB.
RNAseq.expression.mergedStringtieTPMs.separator
Int?
Equivalent to the -s option of collect-columns.
RNAseq.expression.mergedStringtieTPMs.timeMinutes
Int — Default: 10
The maximum amount of time the job will run in minutes.
RNAseq.expression.mergeStringtieGtf.A
Boolean — Default: false
Equivalent to gffcompare's `-A` flag.
RNAseq.expression.mergeStringtieGtf.debugMode
Boolean — Default: false
Equivalent to gffcompare's `-D` flag.
RNAseq.expression.mergeStringtieGtf.discardSingleExonReferenceTranscripts
Boolean — Default: false
Equivalent to gffcompare's `-N` flag.
RNAseq.expression.mergeStringtieGtf.discardSingleExonTransfragsAndReferenceTranscripts
Boolean — Default: false
Equivalent to gffcompare's `-M` flag.
RNAseq.expression.mergeStringtieGtf.genomeSequences
File?
Equivalent to gffcompare's `-s` option.
RNAseq.expression.mergeStringtieGtf.inputGtfList
File?
Equivalent to gffcompare's `-i` option.
RNAseq.expression.mergeStringtieGtf.K
Boolean — Default: false
Equivalent to gffcompare's `-K` flag.
RNAseq.expression.mergeStringtieGtf.maxDistanceFreeEndsTerminalExons
Int?
Equivalent to gffcompare's `-e` option.
RNAseq.expression.mergeStringtieGtf.maxDistanceGroupingTranscriptStartSites
Int?
Equivalent to gffcompare's `-d` option.
RNAseq.expression.mergeStringtieGtf.memory
String — Default: "4G"
The amount of memory available to the job.
RNAseq.expression.mergeStringtieGtf.namePrefix
String?
Equivalent to gffcompare's `-p` option.
RNAseq.expression.mergeStringtieGtf.noTmap
Boolean — Default: false
Equivalent to gffcompare's `-T` flag.
RNAseq.expression.mergeStringtieGtf.precisionCorrection
Boolean — Default: false
Equivalent to gffcompare's `-Q` flag.
RNAseq.expression.mergeStringtieGtf.snCorrection
Boolean — Default: false
Equivalent to gffcompare's `-R` flag.
RNAseq.expression.mergeStringtieGtf.timeMinutes
Int — Default: 1 + ceil((size(inputGtfFiles,"G") * 30))
The maximum amount of time the job will run in minutes.
RNAseq.expression.mergeStringtieGtf.verbose
Boolean — Default: false
Equivalent to gffcompare's `-V` flag.
RNAseq.expression.mergeStringtieGtf.X
Boolean — Default: false
Equivalent to gffcompare's `-X` flag.
RNAseq.expression.stringtie.memory
String — Default: "2G"
The amount of memory needed for this task in GB.
RNAseq.expression.stringtie.minimumCoverage
Float?
The minimum coverage for a transcript to be shown in the output.
RNAseq.expression.stringtie.threads
Int — Default: 1
The number of threads to use.
RNAseq.expression.stringtie.timeMinutes
Int — Default: 1 + ceil((size(bam,"G") * 60 / threads))
The maximum amount of time the job will run in minutes.
RNAseq.expression.stringtieAssembly.memory
String — Default: "2G"
The amount of memory needed for this task in GB.
RNAseq.expression.stringtieAssembly.minimumCoverage
Float?
The minimum coverage for a transcript to be shown in the output.
RNAseq.expression.stringtieAssembly.threads
Int — Default: 1
The number of threads to use.
RNAseq.expression.stringtieAssembly.timeMinutes
Int — Default: 1 + ceil((size(bam,"G") * 60 / threads))
The maximum amount of time the job will run in minutes.
RNAseq.GffCompare.A
Boolean — Default: false
Equivalent to gffcompare's `-A` flag.
RNAseq.GffCompare.C
Boolean — Default: false
Equivalent to gffcompare's `-C` flag.
RNAseq.GffCompare.debugMode
Boolean — Default: false
Equivalent to gffcompare's `-D` flag.
RNAseq.GffCompare.discardSingleExonReferenceTranscripts
Boolean — Default: false
Equivalent to gffcompare's `-N` flag.
RNAseq.GffCompare.discardSingleExonTransfragsAndReferenceTranscripts
Boolean — Default: false
Equivalent to gffcompare's `-M` flag.
RNAseq.GffCompare.genomeSequences
File?
Equivalent to gffcompare's `-s` option.
RNAseq.GffCompare.inputGtfList
File?
Equivalent to gffcompare's `-i` option.
RNAseq.GffCompare.K
Boolean — Default: false
Equivalent to gffcompare's `-K` flag.
RNAseq.GffCompare.maxDistanceFreeEndsTerminalExons
Int?
Equivalent to gffcompare's `-e` option.
RNAseq.GffCompare.maxDistanceGroupingTranscriptStartSites
Int?
Equivalent to gffcompare's `-d` option.
RNAseq.GffCompare.memory
String — Default: "4G"
The amount of memory available to the job.
RNAseq.GffCompare.namePrefix
String?
Equivalent to gffcompare's `-p` option.
RNAseq.GffCompare.noTmap
Boolean — Default: false
Equivalent to gffcompare's `-T` flag.
RNAseq.GffCompare.outPrefix
String — Default: "gffcmp"
The prefix for the output.
RNAseq.GffCompare.precisionCorrection
Boolean — Default: false
Equivalent to gffcompare's `-Q` flag.
RNAseq.GffCompare.snCorrection
Boolean — Default: false
Equivalent to gffcompare's `-R` flag.
RNAseq.GffCompare.timeMinutes
Int — Default: 1 + ceil((size(inputGtfFiles,"G") * 30))
The maximum amount of time the job will run in minutes.
RNAseq.GffCompare.verbose
Boolean — Default: false
Equivalent to gffcompare's `-V` flag.
RNAseq.GffCompare.X
Boolean — Default: false
Equivalent to gffcompare's `-X` flag.
RNAseq.gffreadTask.CDSFastaPath
String?
The location the CDS fasta should be written to.
RNAseq.gffreadTask.filteredGffPath
String?
The location the filtered GFF should be written to.
RNAseq.gffreadTask.memory
String — Default: "4G"
The amount of memory available to the job.
RNAseq.gffreadTask.outputGtfFormat
Boolean — Default: false
Equivalent to gffread's `-T` flag.
RNAseq.gffreadTask.proteinFastaPath
String?
The location the protein fasta should be written to.
RNAseq.gffreadTask.timeMinutes
Int — Default: 1 + ceil((size(inputGff,"G") * 10))
The maximum amount of time the job will run in minutes.
RNAseq.makeStarIndex.memory
String — Default: "32G"
The amount of memory this job will use.
RNAseq.makeStarIndex.sjdbOverhang
Int?
Equivalent to STAR's `--sjdbOverhang` option.
RNAseq.makeStarIndex.threads
Int — Default: 4
The number of threads to use.
RNAseq.makeStarIndex.timeMinutes
Int — Default: ceil((size(referenceFasta,"G") * 240 / threads))
The maximum amount of time the job will run in minutes.
RNAseq.multiqcTask.clConfig
String?
Equivalent to MultiQC's `--cl-config` option.
RNAseq.multiqcTask.comment
String?
Equivalent to MultiQC's `--comment` option.
RNAseq.multiqcTask.config
File?
Equivalent to MultiQC's `--config` option.
RNAseq.multiqcTask.dataDir
Boolean — Default: false
Whether to output a data dir. Sets `--data-dir` or `--no-data-dir` flag.
RNAseq.multiqcTask.dataFormat
String?
Equivalent to MultiQC's `--data-format` option.
RNAseq.multiqcTask.dirs
Boolean — Default: false
Equivalent to MultiQC's `--dirs` flag.
RNAseq.multiqcTask.dirsDepth
Int?
Equivalent to MultiQC's `--dirs-depth` option.
RNAseq.multiqcTask.exclude
Array[String]+?
Equivalent to MultiQC's `--exclude` option.
RNAseq.multiqcTask.export
Boolean — Default: false
Equivalent to MultiQC's `--export` flag.
RNAseq.multiqcTask.fileList
File?
Equivalent to MultiQC's `--file-list` option.
RNAseq.multiqcTask.fileName
String?
Equivalent to MultiQC's `--filename` option.
RNAseq.multiqcTask.flat
Boolean — Default: false
Equivalent to MultiQC's `--flat` flag.
RNAseq.multiqcTask.force
Boolean — Default: false
Equivalent to MultiQC's `--force` flag.
RNAseq.multiqcTask.fullNames
Boolean — Default: false
Equivalent to MultiQC's `--fullnames` flag.
RNAseq.multiqcTask.ignore
String?
Equivalent to MultiQC's `--ignore` option.
RNAseq.multiqcTask.ignoreSamples
String?
Equivalent to MultiQC's `--ignore-samples` option.
RNAseq.multiqcTask.interactive
Boolean — Default: true
Equivalent to MultiQC's `--interactive` flag.
RNAseq.multiqcTask.lint
Boolean — Default: false
Equivalent to MultiQC's `--lint` flag.
RNAseq.multiqcTask.megaQCUpload
Boolean — Default: false
Opposite to MultiQC's `--no-megaqc-upload` flag.
RNAseq.multiqcTask.memory
String?
The amount of memory this job will use.
RNAseq.multiqcTask.module
Array[String]+?
Equivalent to MultiQC's `--module` option.
RNAseq.multiqcTask.pdf
Boolean — Default: false
Equivalent to MultiQC's `--pdf` flag.
RNAseq.multiqcTask.sampleNames
File?
Equivalent to MultiQC's `--sample-names` option.
RNAseq.multiqcTask.tag
String?
Equivalent to MultiQC's `--tag` option.
RNAseq.multiqcTask.template
String?
Equivalent to MultiQC's `--template` option.
RNAseq.multiqcTask.timeMinutes
Int — Default: 10 + ceil((size(reports,"G") * 8))
The maximum amount of time the job will run in minutes.
RNAseq.multiqcTask.title
String?
Equivalent to MultiQC's `--title` option.
RNAseq.multiqcTask.zipDataDir
Boolean — Default: true
Equivalent to MultiQC's `--zip-data-dir` flag.
RNAseq.platform
String — Default: "illumina"
The platform used for sequencing.
RNAseq.preprocessing.applyBqsr.javaXmxMb
Int — Default: 2048
The maximum memory available to the program in megabytes. Should be lower than `memoryMb` to accommodate JVM overhead.
RNAseq.preprocessing.applyBqsr.memoryMb
Int — Default: javaXmxMb + 512
The amount of memory this job will use in megabytes.
RNAseq.preprocessing.baseRecalibrator.javaXmxMb
Int — Default: 1024
The maximum memory available to the program in megabytes. Should be lower than `memoryMb` to accommodate JVM overhead.
RNAseq.preprocessing.baseRecalibrator.knownIndelsSitesVCFIndexes
Array[File] — Default: []
The indexed for the known variant VCFs.
RNAseq.preprocessing.baseRecalibrator.knownIndelsSitesVCFs
Array[File] — Default: []
VCF files with known indels.
RNAseq.preprocessing.baseRecalibrator.memoryMb
Int — Default: javaXmxMb + 512
The amount of memory this job will use in megabytes.
RNAseq.preprocessing.gatherBamFiles.compressionLevel
Int?
The compression level of the output BAM.
RNAseq.preprocessing.gatherBamFiles.createMd5File
Boolean — Default: false
???
RNAseq.preprocessing.gatherBamFiles.javaXmxMb
Int — Default: 1024
The maximum memory available to the program in megabytes. Should be lower than `memoryMb` to accommodate JVM overhead.
RNAseq.preprocessing.gatherBamFiles.memoryMb
Int — Default: javaXmxMb + 512
The amount of memory this job will use in megabytes.
RNAseq.preprocessing.gatherBamFiles.timeMinutes
Int — Default: 1 + ceil((size(inputBams,"G") * 1))
The maximum amount of time the job will run in minutes.
RNAseq.preprocessing.gatherBqsr.javaXmxMb
Int — Default: 256
The maximum memory available to the program in megabytes. Should be lower than `memory` to accommodate JVM overhead.
RNAseq.preprocessing.gatherBqsr.memoryMb
Int — Default: 256 + javaXmxMb
The amount of memory this job will use in megabytes.
RNAseq.preprocessing.gatherBqsr.timeMinutes
Int — Default: 1
The maximum amount of time the job will run in minutes.
RNAseq.preprocessing.splitNCigarReads.javaXmx
String — Default: "4G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
RNAseq.preprocessing.splitNCigarReads.memory
String — Default: "5G"
The amount of memory this job will use.
RNAseq.sampleJobs.bamMetrics.ampliconIntervalsLists.javaXmx
String — Default: "3G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
RNAseq.sampleJobs.bamMetrics.ampliconIntervalsLists.memory
String — Default: "4G"
The amount of memory this job will use.
RNAseq.sampleJobs.bamMetrics.ampliconIntervalsLists.timeMinutes
Int — Default: 5
The maximum amount of time the job will run in minutes.
RNAseq.sampleJobs.bamMetrics.collectAlignmentSummaryMetrics
Boolean — Default: true
Equivalent to the `PROGRAM=CollectAlignmentSummaryMetrics` argument in Picard.
RNAseq.sampleJobs.bamMetrics.Flagstat.memory
String — Default: "256M"
The amount of memory needed for the job.
RNAseq.sampleJobs.bamMetrics.Flagstat.timeMinutes
Int — Default: 1 + ceil(size(inputBam,"G"))
The maximum amount of time the job will run in minutes.
RNAseq.sampleJobs.bamMetrics.meanQualityByCycle
Boolean — Default: true
Equivalent to the `PROGRAM=MeanQualityByCycle` argument in Picard.
RNAseq.sampleJobs.bamMetrics.picardMetrics.collectBaseDistributionByCycle
Boolean — Default: true
Equivalent to the `PROGRAM=CollectBaseDistributionByCycle` argument.
RNAseq.sampleJobs.bamMetrics.picardMetrics.collectGcBiasMetrics
Boolean — Default: true
Equivalent to the `PROGRAM=CollectGcBiasMetrics` argument.
RNAseq.sampleJobs.bamMetrics.picardMetrics.collectInsertSizeMetrics
Boolean — Default: true
Equivalent to the `PROGRAM=CollectInsertSizeMetrics` argument.
RNAseq.sampleJobs.bamMetrics.picardMetrics.collectQualityYieldMetrics
Boolean — Default: true
Equivalent to the `PROGRAM=CollectQualityYieldMetrics` argument.
RNAseq.sampleJobs.bamMetrics.picardMetrics.collectSequencingArtifactMetrics
Boolean — Default: true
Equivalent to the `PROGRAM=CollectSequencingArtifactMetrics` argument.
RNAseq.sampleJobs.bamMetrics.picardMetrics.javaXmxMb
Int — Default: 3072
The maximum memory available to the program in megabytes. Should be lower than `memoryMb` to accommodate JVM overhead.
RNAseq.sampleJobs.bamMetrics.picardMetrics.memoryMb
Int — Default: javaXmxMb + 512
The amount of memory this job will use in megabytes.
RNAseq.sampleJobs.bamMetrics.picardMetrics.qualityScoreDistribution
Boolean — Default: true
Equivalent to the `PROGRAM=QualityScoreDistribution` argument.
RNAseq.sampleJobs.bamMetrics.picardMetrics.timeMinutes
Int — Default: 1 + ceil((size(referenceFasta,"G") * 3 * 2)) + ceil((size(inputBam,"G") * 6))
The maximum amount of time the job will run in minutes.
RNAseq.sampleJobs.bamMetrics.rnaSeqMetrics.javaXmx
String — Default: "8G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
RNAseq.sampleJobs.bamMetrics.rnaSeqMetrics.memory
String — Default: "9G"
The amount of memory this job will use.
RNAseq.sampleJobs.bamMetrics.rnaSeqMetrics.timeMinutes
Int — Default: 1 + ceil((size(inputBam,"G") * 12))
The maximum amount of time the job will run in minutes.
RNAseq.sampleJobs.bamMetrics.targetIntervalsLists.javaXmx
String — Default: "3G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
RNAseq.sampleJobs.bamMetrics.targetIntervalsLists.memory
String — Default: "4G"
The amount of memory this job will use.
RNAseq.sampleJobs.bamMetrics.targetIntervalsLists.timeMinutes
Int — Default: 5
The maximum amount of time the job will run in minutes.
RNAseq.sampleJobs.bamMetrics.targetMetrics.javaXmx
String — Default: "3G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
RNAseq.sampleJobs.bamMetrics.targetMetrics.memory
String — Default: "4G"
The amount of memory this job will use.
RNAseq.sampleJobs.bamMetrics.targetMetrics.timeMinutes
Int — Default: 1 + ceil((size(inputBam,"G") * 6))
The maximum amount of time the job will run in minutes.
RNAseq.sampleJobs.hisat2.compressionLevel
Int — Default: 1
The compression level of the output BAM.
RNAseq.sampleJobs.hisat2.downstreamTranscriptomeAssembly
Boolean — Default: true
Equivalent to hisat2's `--dta` flag.
RNAseq.sampleJobs.hisat2.memoryGb
Int?
The amount of memory this job will use in gigabytes.
RNAseq.sampleJobs.hisat2.sortMemoryPerThreadGb
Int — Default: 2
The amount of memory for each sorting thread in gigabytes.
RNAseq.sampleJobs.hisat2.sortThreads
Int?
The number of threads to use for sorting.
RNAseq.sampleJobs.hisat2.threads
Int — Default: 4
The number of threads to use.
RNAseq.sampleJobs.hisat2.timeMinutes
Int — Default: 1 + ceil((size([inputR1, inputR2],"G") * 180 / threads))
The maximum amount of time the job will run in minutes.
RNAseq.sampleJobs.markDuplicates.compressionLevel
Int — Default: 1
The compression level at which the BAM files are written.
RNAseq.sampleJobs.markDuplicates.createMd5File
Boolean — Default: false
Whether to create a md5 file for the created BAM file.
RNAseq.sampleJobs.markDuplicates.javaXmxMb
Int — Default: 6656
The maximum memory available to the program in megabytes. Should be lower than `memoryMb` to accommodate JVM overhead.
RNAseq.sampleJobs.markDuplicates.memoryMb
String — Default: javaXmxMb + 512
The amount of memory this job will use in megabytes.
RNAseq.sampleJobs.markDuplicates.read_name_regex
String?
Equivalent to the `READ_NAME_REGEX` option of MarkDuplicates.
RNAseq.sampleJobs.markDuplicates.timeMinutes
Int — Default: 1 + ceil((size(inputBams,"G") * 8))
The maximum amount of time the job will run in minutes.
RNAseq.sampleJobs.markDuplicates.useJdkDeflater
Boolean — Default: true
True, uses the java deflator to compress the BAM files. False uses the optimized intel deflater.
RNAseq.sampleJobs.markDuplicates.useJdkInflater
Boolean — Default: true
True, uses the java inflater. False, uses the optimized intel inflater.
RNAseq.sampleJobs.postUmiDedupMarkDuplicates.compressionLevel
Int — Default: 1
The compression level at which the BAM files are written.
RNAseq.sampleJobs.postUmiDedupMarkDuplicates.createMd5File
Boolean — Default: false
Whether to create a md5 file for the created BAM file.
RNAseq.sampleJobs.postUmiDedupMarkDuplicates.javaXmxMb
Int — Default: 6656
The maximum memory available to the program in megabytes. Should be lower than `memoryMb` to accommodate JVM overhead.
RNAseq.sampleJobs.postUmiDedupMarkDuplicates.memoryMb
String — Default: javaXmxMb + 512
The amount of memory this job will use in megabytes.
RNAseq.sampleJobs.postUmiDedupMarkDuplicates.read_name_regex
String?
Equivalent to the `READ_NAME_REGEX` option of MarkDuplicates.
RNAseq.sampleJobs.postUmiDedupMarkDuplicates.timeMinutes
Int — Default: 1 + ceil((size(inputBams,"G") * 8))
The maximum amount of time the job will run in minutes.
RNAseq.sampleJobs.postUmiDedupMarkDuplicates.useJdkDeflater
Boolean — Default: true
True, uses the java deflator to compress the BAM files. False uses the optimized intel deflater.
RNAseq.sampleJobs.postUmiDedupMarkDuplicates.useJdkInflater
Boolean — Default: true
True, uses the java inflater. False, uses the optimized intel inflater.
RNAseq.sampleJobs.qc.Cutadapt.bwa
Boolean?
Equivalent to cutadapt's --bwa flag.
RNAseq.sampleJobs.qc.Cutadapt.colorspace
Boolean?
Equivalent to cutadapt's --colorspace flag.
RNAseq.sampleJobs.qc.Cutadapt.compressionLevel
Int — Default: 1
The compression level if gzipped output is used.
RNAseq.sampleJobs.qc.Cutadapt.cores
Int — Default: 4
The number of cores to use.
RNAseq.sampleJobs.qc.Cutadapt.cut
Int?
Equivalent to cutadapt's --cut option.
RNAseq.sampleJobs.qc.Cutadapt.discardTrimmed
Boolean?
Equivalent to cutadapt's --quality-cutoff option.
RNAseq.sampleJobs.qc.Cutadapt.discardUntrimmed
Boolean?
Equivalent to cutadapt's --discard-untrimmed option.
RNAseq.sampleJobs.qc.Cutadapt.doubleEncode
Boolean?
Equivalent to cutadapt's --double-encode flag.
RNAseq.sampleJobs.qc.Cutadapt.errorRate
Float?
Equivalent to cutadapt's --error-rate option.
RNAseq.sampleJobs.qc.Cutadapt.front
Array[String] — Default: []
A list of 5' ligated adapter sequences to be cut from the given first or single end fastq file.
RNAseq.sampleJobs.qc.Cutadapt.frontRead2
Array[String] — Default: []
A list of 5' ligated adapter sequences to be cut from the given second end fastq file.
RNAseq.sampleJobs.qc.Cutadapt.infoFilePath
String?
Equivalent to cutadapt's --info-file option.
RNAseq.sampleJobs.qc.Cutadapt.interleaved
Boolean?
Equivalent to cutadapt's --interleaved flag.
RNAseq.sampleJobs.qc.Cutadapt.length
Int?
Equivalent to cutadapt's --length option.
RNAseq.sampleJobs.qc.Cutadapt.lengthTag
String?
Equivalent to cutadapt's --length-tag option.
RNAseq.sampleJobs.qc.Cutadapt.maq
Boolean?
Equivalent to cutadapt's --maq flag.
RNAseq.sampleJobs.qc.Cutadapt.maskAdapter
Boolean?
Equivalent to cutadapt's --mask-adapter flag.
RNAseq.sampleJobs.qc.Cutadapt.matchReadWildcards
Boolean?
Equivalent to cutadapt's --match-read-wildcards flag.
RNAseq.sampleJobs.qc.Cutadapt.maximumLength
Int?
Equivalent to cutadapt's --maximum-length option.
RNAseq.sampleJobs.qc.Cutadapt.maxN
Int?
Equivalent to cutadapt's --max-n option.
RNAseq.sampleJobs.qc.Cutadapt.memory
String — Default: "5G"
The amount of memory this job will use.
RNAseq.sampleJobs.qc.Cutadapt.minimumLength
Int? — Default: 2
Equivalent to cutadapt's --minimum-length option.
RNAseq.sampleJobs.qc.Cutadapt.nextseqTrim
String?
Equivalent to cutadapt's --nextseq-trim option.
RNAseq.sampleJobs.qc.Cutadapt.noIndels
Boolean?
Equivalent to cutadapt's --no-indels flag.
RNAseq.sampleJobs.qc.Cutadapt.noMatchAdapterWildcards
Boolean?
Equivalent to cutadapt's --no-match-adapter-wildcards flag.
RNAseq.sampleJobs.qc.Cutadapt.noTrim
Boolean?
Equivalent to cutadapt's --no-trim flag.
RNAseq.sampleJobs.qc.Cutadapt.noZeroCap
Boolean?
Equivalent to cutadapt's --no-zero-cap flag.
RNAseq.sampleJobs.qc.Cutadapt.overlap
Int?
Equivalent to cutadapt's --overlap option.
RNAseq.sampleJobs.qc.Cutadapt.pairFilter
String?
Equivalent to cutadapt's --pair-filter option.
RNAseq.sampleJobs.qc.Cutadapt.prefix
String?
Equivalent to cutadapt's --prefix option.
RNAseq.sampleJobs.qc.Cutadapt.qualityBase
Int?
Equivalent to cutadapt's --quality-base option.
RNAseq.sampleJobs.qc.Cutadapt.qualityCutoff
String?
Equivalent to cutadapt's --quality-cutoff option.
RNAseq.sampleJobs.qc.Cutadapt.restFilePath
String?
Equivalent to cutadapt's --rest-file option.
RNAseq.sampleJobs.qc.Cutadapt.stripF3
Boolean?
Equivalent to cutadapt's --strip-f3 flag.
RNAseq.sampleJobs.qc.Cutadapt.stripSuffix
String?
Equivalent to cutadapt's --strip-suffix option.
RNAseq.sampleJobs.qc.Cutadapt.suffix
String?
Equivalent to cutadapt's --suffix option.
RNAseq.sampleJobs.qc.Cutadapt.timeMinutes
Int — Default: 1 + ceil((size([read1, read2],"G") * 12.0 / cores))
The maximum amount of time the job will run in minutes.
RNAseq.sampleJobs.qc.Cutadapt.times
Int?
Equivalent to cutadapt's --times option.
RNAseq.sampleJobs.qc.Cutadapt.tooLongOutputPath
String?
Equivalent to cutadapt's --too-long-output option.
RNAseq.sampleJobs.qc.Cutadapt.tooLongPairedOutputPath
String?
Equivalent to cutadapt's --too-long-paired-output option.
RNAseq.sampleJobs.qc.Cutadapt.tooShortOutputPath
String?
Equivalent to cutadapt's --too-short-output option.
RNAseq.sampleJobs.qc.Cutadapt.tooShortPairedOutputPath
String?
Equivalent to cutadapt's --too-short-paired-output option.
RNAseq.sampleJobs.qc.Cutadapt.trimN
Boolean?
Equivalent to cutadapt's --trim-n flag.
RNAseq.sampleJobs.qc.Cutadapt.untrimmedOutputPath
String?
Equivalent to cutadapt's --untrimmed-output option.
RNAseq.sampleJobs.qc.Cutadapt.untrimmedPairedOutputPath
String?
Equivalent to cutadapt's --untrimmed-paired-output option.
RNAseq.sampleJobs.qc.Cutadapt.wildcardFilePath
String?
Equivalent to cutadapt's --wildcard-file option.
RNAseq.sampleJobs.qc.Cutadapt.zeroCap
Boolean?
Equivalent to cutadapt's --zero-cap flag.
RNAseq.sampleJobs.qc.extractFastqcZip
Boolean — Default: false
Whether to extract Fastqc's report zip files.
RNAseq.sampleJobs.qc.FastqcRead1.adapters
File?
Equivalent to fastqc's --adapters option.
RNAseq.sampleJobs.qc.FastqcRead1.casava
Boolean — Default: false
Equivalent to fastqc's --casava flag.
RNAseq.sampleJobs.qc.FastqcRead1.contaminants
File?
Equivalent to fastqc's --contaminants option.
RNAseq.sampleJobs.qc.FastqcRead1.dir
String?
Equivalent to fastqc's --dir option.
RNAseq.sampleJobs.qc.FastqcRead1.format
String?
Equivalent to fastqc's --format option.
RNAseq.sampleJobs.qc.FastqcRead1.javaXmx
String — Default: "1750M"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
RNAseq.sampleJobs.qc.FastqcRead1.kmers
Int?
Equivalent to fastqc's --kmers option.
RNAseq.sampleJobs.qc.FastqcRead1.limits
File?
Equivalent to fastqc's --limits option.
RNAseq.sampleJobs.qc.FastqcRead1.memory
String — Default: "2G"
The amount of memory this job will use.
RNAseq.sampleJobs.qc.FastqcRead1.minLength
Int?
Equivalent to fastqc's --min_length option.
RNAseq.sampleJobs.qc.FastqcRead1.nano
Boolean — Default: false
Equivalent to fastqc's --nano flag.
RNAseq.sampleJobs.qc.FastqcRead1.noFilter
Boolean — Default: false
Equivalent to fastqc's --nofilter flag.
RNAseq.sampleJobs.qc.FastqcRead1.nogroup
Boolean — Default: false
Equivalent to fastqc's --nogroup flag.
RNAseq.sampleJobs.qc.FastqcRead1.threads
Int — Default: 1
The number of cores to use.
RNAseq.sampleJobs.qc.FastqcRead1.timeMinutes
Int — Default: 1 + ceil(size(seqFile,"G")) * 4
The maximum amount of time the job will run in minutes.
RNAseq.sampleJobs.qc.FastqcRead1After.adapters
File?
Equivalent to fastqc's --adapters option.
RNAseq.sampleJobs.qc.FastqcRead1After.casava
Boolean — Default: false
Equivalent to fastqc's --casava flag.
RNAseq.sampleJobs.qc.FastqcRead1After.contaminants
File?
Equivalent to fastqc's --contaminants option.
RNAseq.sampleJobs.qc.FastqcRead1After.dir
String?
Equivalent to fastqc's --dir option.
RNAseq.sampleJobs.qc.FastqcRead1After.format
String?
Equivalent to fastqc's --format option.
RNAseq.sampleJobs.qc.FastqcRead1After.javaXmx
String — Default: "1750M"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
RNAseq.sampleJobs.qc.FastqcRead1After.kmers
Int?
Equivalent to fastqc's --kmers option.
RNAseq.sampleJobs.qc.FastqcRead1After.limits
File?
Equivalent to fastqc's --limits option.
RNAseq.sampleJobs.qc.FastqcRead1After.memory
String — Default: "2G"
The amount of memory this job will use.
RNAseq.sampleJobs.qc.FastqcRead1After.minLength
Int?
Equivalent to fastqc's --min_length option.
RNAseq.sampleJobs.qc.FastqcRead1After.nano
Boolean — Default: false
Equivalent to fastqc's --nano flag.
RNAseq.sampleJobs.qc.FastqcRead1After.noFilter
Boolean — Default: false
Equivalent to fastqc's --nofilter flag.
RNAseq.sampleJobs.qc.FastqcRead1After.nogroup
Boolean — Default: false
Equivalent to fastqc's --nogroup flag.
RNAseq.sampleJobs.qc.FastqcRead1After.threads
Int — Default: 1
The number of cores to use.
RNAseq.sampleJobs.qc.FastqcRead1After.timeMinutes
Int — Default: 1 + ceil(size(seqFile,"G")) * 4
The maximum amount of time the job will run in minutes.
RNAseq.sampleJobs.qc.FastqcRead2.adapters
File?
Equivalent to fastqc's --adapters option.
RNAseq.sampleJobs.qc.FastqcRead2.casava
Boolean — Default: false
Equivalent to fastqc's --casava flag.
RNAseq.sampleJobs.qc.FastqcRead2.contaminants
File?
Equivalent to fastqc's --contaminants option.
RNAseq.sampleJobs.qc.FastqcRead2.dir
String?
Equivalent to fastqc's --dir option.
RNAseq.sampleJobs.qc.FastqcRead2.format
String?
Equivalent to fastqc's --format option.
RNAseq.sampleJobs.qc.FastqcRead2.javaXmx
String — Default: "1750M"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
RNAseq.sampleJobs.qc.FastqcRead2.kmers
Int?
Equivalent to fastqc's --kmers option.
RNAseq.sampleJobs.qc.FastqcRead2.limits
File?
Equivalent to fastqc's --limits option.
RNAseq.sampleJobs.qc.FastqcRead2.memory
String — Default: "2G"
The amount of memory this job will use.
RNAseq.sampleJobs.qc.FastqcRead2.minLength
Int?
Equivalent to fastqc's --min_length option.
RNAseq.sampleJobs.qc.FastqcRead2.nano
Boolean — Default: false
Equivalent to fastqc's --nano flag.
RNAseq.sampleJobs.qc.FastqcRead2.noFilter
Boolean — Default: false
Equivalent to fastqc's --nofilter flag.
RNAseq.sampleJobs.qc.FastqcRead2.nogroup
Boolean — Default: false
Equivalent to fastqc's --nogroup flag.
RNAseq.sampleJobs.qc.FastqcRead2.threads
Int — Default: 1
The number of cores to use.
RNAseq.sampleJobs.qc.FastqcRead2.timeMinutes
Int — Default: 1 + ceil(size(seqFile,"G")) * 4
The maximum amount of time the job will run in minutes.
RNAseq.sampleJobs.qc.FastqcRead2After.adapters
File?
Equivalent to fastqc's --adapters option.
RNAseq.sampleJobs.qc.FastqcRead2After.casava
Boolean — Default: false
Equivalent to fastqc's --casava flag.
RNAseq.sampleJobs.qc.FastqcRead2After.contaminants
File?
Equivalent to fastqc's --contaminants option.
RNAseq.sampleJobs.qc.FastqcRead2After.dir
String?
Equivalent to fastqc's --dir option.
RNAseq.sampleJobs.qc.FastqcRead2After.format
String?
Equivalent to fastqc's --format option.
RNAseq.sampleJobs.qc.FastqcRead2After.javaXmx
String — Default: "1750M"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
RNAseq.sampleJobs.qc.FastqcRead2After.kmers
Int?
Equivalent to fastqc's --kmers option.
RNAseq.sampleJobs.qc.FastqcRead2After.limits
File?
Equivalent to fastqc's --limits option.
RNAseq.sampleJobs.qc.FastqcRead2After.memory
String — Default: "2G"
The amount of memory this job will use.
RNAseq.sampleJobs.qc.FastqcRead2After.minLength
Int?
Equivalent to fastqc's --min_length option.
RNAseq.sampleJobs.qc.FastqcRead2After.nano
Boolean — Default: false
Equivalent to fastqc's --nano flag.
RNAseq.sampleJobs.qc.FastqcRead2After.noFilter
Boolean — Default: false
Equivalent to fastqc's --nofilter flag.
RNAseq.sampleJobs.qc.FastqcRead2After.nogroup
Boolean — Default: false
Equivalent to fastqc's --nogroup flag.
RNAseq.sampleJobs.qc.FastqcRead2After.threads
Int — Default: 1
The number of cores to use.
RNAseq.sampleJobs.qc.FastqcRead2After.timeMinutes
Int — Default: 1 + ceil(size(seqFile,"G")) * 4
The maximum amount of time the job will run in minutes.
RNAseq.sampleJobs.qc.runAdapterClipping
Boolean — Default: defined(adapterForward) || defined(adapterReverse) || length(select_first([contaminations, []])) > 0
Whether or not adapters should be removed from the reads.
RNAseq.sampleJobs.star.limitBAMsortRAM
Int?
Equivalent to star's `--limitBAMsortRAM` option.
RNAseq.sampleJobs.star.memory
String?
The amount of memory this job will use.
RNAseq.sampleJobs.star.outBAMcompression
Int — Default: 1
The compression level of the output BAM.
RNAseq.sampleJobs.star.outFilterMatchNmin
Int?
Equivalent to star's `--outFilterMatchNmin` option.
RNAseq.sampleJobs.star.outFilterMatchNminOverLread
Float?
Equivalent to star's `--outFilterMatchNminOverLread` option.
RNAseq.sampleJobs.star.outFilterScoreMin
Int?
Equivalent to star's `--outFilterScoreMin` option.
RNAseq.sampleJobs.star.outFilterScoreMinOverLread
Float?
Equivalent to star's `--outFilterScoreMinOverLread` option.
RNAseq.sampleJobs.star.outSAMunmapped
String? — Default: "Within KeepPairs"
Equivalent to star's `--outSAMunmapped` option.
RNAseq.sampleJobs.star.outStd
String?
Equivalent to star's `--outStd` option.
RNAseq.sampleJobs.star.runThreadN
Int — Default: 4
The number of threads to use.
RNAseq.sampleJobs.star.timeMinutes
Int — Default: 1 + ceil(size(indexFiles,"G")) + ceil((size(flatten([inputR1, inputR2]),"G") * 300 / runThreadN))
The maximum amount of time the job will run in minutes.
RNAseq.sampleJobs.star.twopassMode
String? — Default: "Basic"
Equivalent to star's `--twopassMode` option.
RNAseq.sampleJobs.umiDedup.memory
String — Default: "25G"
The amount of memory required for the task.
RNAseq.sampleJobs.umiDedup.timeMinutes
Int — Default: 30 + ceil((size(inputBam,"G") * 30))
The maximum amount of time the job will run in minutes.
RNAseq.sampleJobs.umiDedup.tmpDir
String — Default: "./umiToolsDedupTmpDir"
Temporary directory.
RNAseq.sampleJobs.umiDedup.umiSeparator
String?
Seperator used for UMIs in the read names.
RNAseq.scatterList.memory
String — Default: "256M"
The amount of memory this job will use.
RNAseq.scatterList.prefix
String — Default: "scatters/scatter-"
The prefix of the ouput files. Output will be named like: .bed, in which N is an incrementing number. Default 'scatter-'. </dd>
RNAseq.scatterList.splitContigs
Boolean — Default: false
If set, contigs are allowed to be split up over multiple files.
RNAseq.scatterList.timeMinutes
Int — Default: 2
The maximum amount of time the job will run in minutes.
RNAseq.scatterSize
Int?
The size of the scattered regions in bases for the GATK subworkflows. Scattering is used to speed up certain processes. The genome will be seperated into multiple chunks (scatters) which will be processed in their own job, allowing for parallel processing. Higher values will result in a lower number of jobs. The optimal value here will depend on the available resources.
RNAseq.scatterSizeMillions
Int — Default: 1000
Same as scatterSize, but is multiplied by 1000000 to get scatterSize. This allows for setting larger values more easily.
RNAseq.variantcalling.callAutosomal.contamination
Float?
Equivalent to HaplotypeCaller's `-contamination` option.
RNAseq.variantcalling.callAutosomal.emitRefConfidence
String — Default: if gvcf then "GVCF" else "NONE"
Whether to include reference calls. Three modes: 'NONE', 'BP_RESOLUTION' and 'GVCF'.
RNAseq.variantcalling.callAutosomal.javaXmxMb
Int — Default: 4096
The maximum memory available to the program in megabytes. Should be lower than `memoryMb` to accommodate JVM overhead.
RNAseq.variantcalling.callAutosomal.memoryMb
Int — Default: javaXmxMb + 512
The amount of memory this job will use in megabytes.
RNAseq.variantcalling.callAutosomal.outputMode
String?
Specifies which type of calls we should output. Same as HaplotypeCaller's `--output-mode` option.
RNAseq.variantcalling.callX.contamination
Float?
Equivalent to HaplotypeCaller's `-contamination` option.
RNAseq.variantcalling.callX.emitRefConfidence
String — Default: if gvcf then "GVCF" else "NONE"
Whether to include reference calls. Three modes: 'NONE', 'BP_RESOLUTION' and 'GVCF'.
RNAseq.variantcalling.callX.javaXmxMb
Int — Default: 4096
The maximum memory available to the program in megabytes. Should be lower than `memoryMb` to accommodate JVM overhead.
RNAseq.variantcalling.callX.memoryMb
Int — Default: javaXmxMb + 512
The amount of memory this job will use in megabytes.
RNAseq.variantcalling.callX.outputMode
String?
Specifies which type of calls we should output. Same as HaplotypeCaller's `--output-mode` option.
RNAseq.variantcalling.callY.contamination
Float?
Equivalent to HaplotypeCaller's `-contamination` option.
RNAseq.variantcalling.callY.emitRefConfidence
String — Default: if gvcf then "GVCF" else "NONE"
Whether to include reference calls. Three modes: 'NONE', 'BP_RESOLUTION' and 'GVCF'.
RNAseq.variantcalling.callY.javaXmxMb
Int — Default: 4096
The maximum memory available to the program in megabytes. Should be lower than `memoryMb` to accommodate JVM overhead.
RNAseq.variantcalling.callY.memoryMb
Int — Default: javaXmxMb + 512
The amount of memory this job will use in megabytes.
RNAseq.variantcalling.callY.outputMode
String?
Specifies which type of calls we should output. Same as HaplotypeCaller's `--output-mode` option.
RNAseq.variantcalling.mergeSingleSampleGvcf.intervals
Array[File] — Default: []
Bed files or interval lists describing the regions to operate on.
RNAseq.variantcalling.mergeSingleSampleGvcf.javaXmx
String — Default: "4G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
RNAseq.variantcalling.mergeSingleSampleGvcf.memory
String — Default: "5G"
The amount of memory this job will use.
RNAseq.variantcalling.mergeSingleSampleGvcf.timeMinutes
Int — Default: 1 + ceil((size(gvcfFiles,"G") * 8))
The maximum amount of time the job will run in minutes.
RNAseq.variantcalling.mergeSingleSampleVcf.compressionLevel
Int — Default: 1
The compression level at which the BAM files are written.
RNAseq.variantcalling.mergeSingleSampleVcf.javaXmx
String — Default: "4G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
RNAseq.variantcalling.mergeSingleSampleVcf.memory
String — Default: "5G"
The amount of memory this job will use.
RNAseq.variantcalling.mergeSingleSampleVcf.timeMinutes
Int — Default: 1 + ceil(size(inputVCFs,"G")) * 2
The maximum amount of time the job will run in minutes.
RNAseq.variantcalling.mergeSingleSampleVcf.useJdkDeflater
Boolean — Default: true
True, uses the java deflator to compress the BAM files. False uses the optimized intel deflater.
RNAseq.variantcalling.mergeSingleSampleVcf.useJdkInflater
Boolean — Default: true
True, uses the java inflater. False, uses the optimized intel inflater.
RNAseq.variantcalling.Stats.afBins
String?
Allele frequency bins, a list (0.1,0.5,1) or a file (0.1 0.5 1).
RNAseq.variantcalling.Stats.applyFilters
String?
Require at least one of the listed FILTER strings (e.g. "PASS,.").
RNAseq.variantcalling.Stats.collapse
String?
Treat as identical records with <snps|indels|both|all|some|none>, see man page for details.
RNAseq.variantcalling.Stats.depth
String?
Depth distribution: min,max,bin size [0,500,1].
RNAseq.variantcalling.Stats.exclude
String?
Exclude sites for which the expression is true (see man page for details).
RNAseq.variantcalling.Stats.exons
File?
Tab-delimited file with exons for indel frameshifts (chr,from,to; 1-based, inclusive, bgzip compressed).
RNAseq.variantcalling.Stats.firstAlleleOnly
Boolean — Default: false
Include only 1st allele at multiallelic sites.
RNAseq.variantcalling.Stats.include
String?
Select sites for which the expression is true (see man page for details).
RNAseq.variantcalling.Stats.memory
String — Default: "256M"
The amount of memory this job will use.
RNAseq.variantcalling.Stats.regions
String?
Restrict to comma-separated list of regions.
RNAseq.variantcalling.Stats.samplesFile
File?
File of samples to include.
RNAseq.variantcalling.Stats.splitByID
Boolean — Default: false
Collect stats for sites with ID separately (known vs novel).
RNAseq.variantcalling.Stats.targets
String?
Similar to regions but streams rather than index-jumps.
RNAseq.variantcalling.Stats.targetsFile
File?
Similar to regionsFile but streams rather than index-jumps.
RNAseq.variantcalling.Stats.threads
Int — Default: 0
Number of extra decompression threads [0].
RNAseq.variantcalling.Stats.timeMinutes
Int — Default: 1 + 2 * ceil(size(select_all([inputVcf, compareVcf]),"G"))
The maximum amount of time the job will run in minutes.
RNAseq.variantcalling.Stats.userTsTv
String?
<TAG[:min:max:n]>. Collect Ts/Tv stats for any tag using the given binning [0:1:100].
RNAseq.variantcalling.Stats.verbose
Boolean — Default: false
Produce verbose per-site and per-sample output.
RNAseq.variantcalling.statsRegions
File?
Which regions need to be analysed by the stats tools.
RNAseq.variantcalling.timeMinutes
Int — Default: ceil((size(bam,"G") * 120))
The time in minutes expected for each haplotype caller task. Will be exposed as the time_minutes runtime attribute.
RNAseq.XNonParRegions
File?
Bed file with the non-PAR regions of X for variant calling.
RNAseq.YNonParRegions
File?
Bed file with the non-PAR regions of Y for variant calling.
</dl> </details> ## Other inputs
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RNAseq.makeStarIndex.genomeDir
String — Default: "STAR_index"
The directory the STAR index should be written to.
## Do not set these inputs! The following inputs should ***not*** be set, even though womtool may show them as being available inputs. * RNAseq.sampleJobs.star.outSAMtype * RNAseq.sampleJobs.star.readFilesCommand * RNAseq.sampleJobs.DONOTDEFINE * RNAseq.sampleJobs.qc.FastqcRead1.noneFile * RNAseq.sampleJobs.qc.FastqcRead1.noneArray * RNAseq.sampleJobs.qc.FastqcRead2.noneFile * RNAseq.sampleJobs.qc.FastqcRead2.noneArray * RNAseq.sampleJobs.qc.FastqcRead1After.noneFile * RNAseq.sampleJobs.qc.FastqcRead1After.noneArray * RNAseq.sampleJobs.qc.FastqcRead2After.noneFile * RNAseq.sampleJobs.qc.FastqcRead2After.noneArray * RNAseq.expression.mergeStringtieGtf.noneFile * RNAseq.GffCompare.noneFile