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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.
- MultiBamExpressionQuantification.mergeStringtieGtf.noneFile