BioWDL: Expression-Quantification

A BioWDL workflow for quantifying expression.

Inputs for MultiBamExpressionQuantification

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

Required inputs

MultiBamExpressionQuantification.bams
Array[Pair[String,struct(file : File, index : File, md5sum : String?)]]+
A list of pairs in which the left item is a sample Id and the right item an object containing the paths to that samples BAM file and its index.
MultiBamExpressionQuantification.mergeStringtieGtf.referenceAnnotation
File?
The GTF file to compare with.
MultiBamExpressionQuantification.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

MultiBamExpressionQuantification.detectNovelTranscripts
Boolean — Default: if defined(referenceGtfFile) then false else true
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.
MultiBamExpressionQuantification.outputDir
String — Default: "."
The directory to which the outputs will be written.
MultiBamExpressionQuantification.referenceGtfFile
File?
A reference GTF file. If detectNovelTranscripts is set to true then this reference GTF will be used as a guide during transcript assembly, otherwise this GTF file is used directly as the annotation source for read counting. If undefined `detectNovelTranscripts` will be set to true by default.
MultiBamExpressionQuantification.runStringtieQuantification
Boolean — Default: true
Option to disable running stringtie for quantification. This does not affect the usage of stringtie for novel transcript detection.
MultiBamExpressionQuantification.stringtieAssembly.geneAbundanceFile
String?
Where the abundance file should be written.

Advanced inputs

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MultiBamExpressionQuantification.additionalAttributes
Array[String]+?
Additional attributes which should be taken from the GTF used for quantification and added to the merged expression value tables.
MultiBamExpressionQuantification.dockerImages
Map[String,String] — Default: {"htseq": "quay.io/biocontainers/htseq:0.12.4--py37h0498b6d_2", "stringtie": "quay.io/biocontainers/stringtie:1.3.6--h92e31bf_0", "collect-columns": "quay.io/biocontainers/collect-columns:1.0.0--py_0", "gffcompare": "quay.io/biocontainers/gffcompare:0.10.6--h2d50403_0"}
The docker images used. Changing this may result in errors which the developers may choose not to address.
MultiBamExpressionQuantification.htSeqCount.additionalAttributes
Array[String] — Default: []
Equivalent to the --additional-attr option of htseq-count.
MultiBamExpressionQuantification.htSeqCount.featureType
String?
Equivalent to the --type option of htseq-count.
MultiBamExpressionQuantification.htSeqCount.idattr
String?
Equivalent to the --idattr option of htseq-count.
MultiBamExpressionQuantification.htSeqCount.memory
String — Default: "8G"
The amount of memory the job requires in GB.
MultiBamExpressionQuantification.htSeqCount.nprocesses
Int — Default: 1
Number of processes to run htseq with.
MultiBamExpressionQuantification.htSeqCount.order
String — Default: "pos"
Equivalent to the -r option of htseq-count.
MultiBamExpressionQuantification.htSeqCount.timeMinutes
Int — Default: 1440
The maximum amount of time the job will run in minutes.
MultiBamExpressionQuantification.mergedHTSeqFragmentsPerGenes.featureAttribute
String?
Equivalent to the -F option of collect-columns.
MultiBamExpressionQuantification.mergedHTSeqFragmentsPerGenes.featureColumn
Int?
Equivalent to the -f option of collect-columns.
MultiBamExpressionQuantification.mergedHTSeqFragmentsPerGenes.header
Boolean — Default: false
Equivalent to the -H flag of collect-columns.
MultiBamExpressionQuantification.mergedHTSeqFragmentsPerGenes.memoryGb
Int — Default: 4 + ceil((0.5 * length(inputTables)))
The maximum amount of memory the job will need in GB.
MultiBamExpressionQuantification.mergedHTSeqFragmentsPerGenes.separator
Int?
Equivalent to the -s option of collect-columns.
MultiBamExpressionQuantification.mergedHTSeqFragmentsPerGenes.sumOnDuplicateId
Boolean — Default: false
Equivalent to the -S flag of collect-columns.
MultiBamExpressionQuantification.mergedHTSeqFragmentsPerGenes.timeMinutes
Int — Default: 10
The maximum amount of time the job will run in minutes.
MultiBamExpressionQuantification.mergedHTSeqFragmentsPerGenes.valueColumn
Int?
Equivalent to the -c option of collect-columns.
MultiBamExpressionQuantification.mergedStringtieFPKMs.featureAttribute
String?
Equivalent to the -F option of collect-columns.
MultiBamExpressionQuantification.mergedStringtieFPKMs.featureColumn
Int?
Equivalent to the -f option of collect-columns.
MultiBamExpressionQuantification.mergedStringtieFPKMs.memoryGb
Int — Default: 4 + ceil((0.5 * length(inputTables)))
The maximum amount of memory the job will need in GB.
MultiBamExpressionQuantification.mergedStringtieFPKMs.separator
Int?
Equivalent to the -s option of collect-columns.
MultiBamExpressionQuantification.mergedStringtieFPKMs.timeMinutes
Int — Default: 10
The maximum amount of time the job will run in minutes.
MultiBamExpressionQuantification.mergedStringtieTPMs.featureAttribute
String?
Equivalent to the -F option of collect-columns.
MultiBamExpressionQuantification.mergedStringtieTPMs.featureColumn
Int?
Equivalent to the -f option of collect-columns.
MultiBamExpressionQuantification.mergedStringtieTPMs.memoryGb
Int — Default: 4 + ceil((0.5 * length(inputTables)))
The maximum amount of memory the job will need in GB.
MultiBamExpressionQuantification.mergedStringtieTPMs.separator
Int?
Equivalent to the -s option of collect-columns.
MultiBamExpressionQuantification.mergedStringtieTPMs.timeMinutes
Int — Default: 10
The maximum amount of time the job will run in minutes.
MultiBamExpressionQuantification.mergeStringtieGtf.A
Boolean — Default: false
Equivalent to gffcompare's `-A` flag.
MultiBamExpressionQuantification.mergeStringtieGtf.debugMode
Boolean — Default: false
Equivalent to gffcompare's `-D` flag.
MultiBamExpressionQuantification.mergeStringtieGtf.discardSingleExonReferenceTranscripts
Boolean — Default: false
Equivalent to gffcompare's `-N` flag.
MultiBamExpressionQuantification.mergeStringtieGtf.discardSingleExonTransfragsAndReferenceTranscripts
Boolean — Default: false
Equivalent to gffcompare's `-M` flag.
MultiBamExpressionQuantification.mergeStringtieGtf.genomeSequences
File?
Equivalent to gffcompare's `-s` option.
MultiBamExpressionQuantification.mergeStringtieGtf.inputGtfList
File?
Equivalent to gffcompare's `-i` option.
MultiBamExpressionQuantification.mergeStringtieGtf.K
Boolean — Default: false
Equivalent to gffcompare's `-K` flag.
MultiBamExpressionQuantification.mergeStringtieGtf.maxDistanceFreeEndsTerminalExons
Int?
Equivalent to gffcompare's `-e` option.
MultiBamExpressionQuantification.mergeStringtieGtf.maxDistanceGroupingTranscriptStartSites
Int?
Equivalent to gffcompare's `-d` option.
MultiBamExpressionQuantification.mergeStringtieGtf.memory
String — Default: "4G"
The amount of memory available to the job.
MultiBamExpressionQuantification.mergeStringtieGtf.namePrefix
String?
Equivalent to gffcompare's `-p` option.
MultiBamExpressionQuantification.mergeStringtieGtf.noTmap
Boolean — Default: false
Equivalent to gffcompare's `-T` flag.
MultiBamExpressionQuantification.mergeStringtieGtf.precisionCorrection
Boolean — Default: false
Equivalent to gffcompare's `-Q` flag.
MultiBamExpressionQuantification.mergeStringtieGtf.snCorrection
Boolean — Default: false
Equivalent to gffcompare's `-R` flag.
MultiBamExpressionQuantification.mergeStringtieGtf.timeMinutes
Int — Default: 1 + ceil((size(inputGtfFiles,"G") * 30))
The maximum amount of time the job will run in minutes.
MultiBamExpressionQuantification.mergeStringtieGtf.verbose
Boolean — Default: false
Equivalent to gffcompare's `-V` flag.
MultiBamExpressionQuantification.mergeStringtieGtf.X
Boolean — Default: false
Equivalent to gffcompare's `-X` flag.
MultiBamExpressionQuantification.stringtie.memory
String — Default: "2G"
The amount of memory needed for this task in GB.
MultiBamExpressionQuantification.stringtie.minimumCoverage
Float?
The minimum coverage for a transcript to be shown in the output.
MultiBamExpressionQuantification.stringtie.threads
Int — Default: 1
The number of threads to use.
MultiBamExpressionQuantification.stringtie.timeMinutes
Int — Default: 1 + ceil((size(bam,"G") * 60 / threads))
The maximum amount of time the job will run in minutes.
MultiBamExpressionQuantification.stringtieAssembly.memory
String — Default: "2G"
The amount of memory needed for this task in GB.
MultiBamExpressionQuantification.stringtieAssembly.minimumCoverage
Float?
The minimum coverage for a transcript to be shown in the output.
MultiBamExpressionQuantification.stringtieAssembly.threads
Int — Default: 1
The number of threads to use.
MultiBamExpressionQuantification.stringtieAssembly.timeMinutes
Int — Default: 1 + ceil((size(bam,"G") * 60 / threads))
The maximum amount of time the job will run in minutes.

Do not set these inputs!

The following inputs should not be set, even though womtool may show them as being available inputs.