SubreadsProcessing.bam2FastqLima.compressionLevel
Int — Default: 1
Gzip compression level [1-9]

SubreadsProcessing.bam2FastqLima.memory
String — Default: "2G"
The amount of memory available to the job.

SubreadsProcessing.bam2FastqLima.seqIdPrefix
String? — Default: None
Prefix for sequence IDs in headers.

SubreadsProcessing.bam2FastqLima.splitByBarcode
Boolean — Default: false
Split output into multiple fastq files, by barcode pairs.

SubreadsProcessing.bam2FastqLima.timeMinutes
Int — Default: 15
The maximum amount of time the job will run in minutes.

SubreadsProcessing.bam2FastqRefine.compressionLevel
Int — Default: 1
Gzip compression level [1-9]

SubreadsProcessing.bam2FastqRefine.memory
String — Default: "2G"
The amount of memory available to the job.

SubreadsProcessing.bam2FastqRefine.seqIdPrefix
String? — Default: None
Prefix for sequence IDs in headers.

SubreadsProcessing.bam2FastqRefine.splitByBarcode
Boolean — Default: false
Split output into multiple fastq files, by barcode pairs.

SubreadsProcessing.bam2FastqRefine.timeMinutes
Int — Default: 15
The maximum amount of time the job will run in minutes.

SubreadsProcessing.ccs.byStrand
Boolean — Default: false
Generate a consensus for each strand.

SubreadsProcessing.ccs.logLevel
String — Default: "WARN"
Set log level. Valid choices: (TRACE, DEBUG, INFO, WARN, FATAL).

SubreadsProcessing.ccs.maxLength
Int — Default: 50000
Maximum draft length before polishing.

SubreadsProcessing.ccs.memory
String — Default: "2G"
The amount of memory available to the job.

SubreadsProcessing.ccs.minLength
Int — Default: 10
Minimum draft length before polishing.

SubreadsProcessing.ccs.minPasses
Int — Default: 3
Minimum number of full-length subreads required to generate ccs for a ZMW.

SubreadsProcessing.ccs.timeMinutes
Int — Default: 1440
The maximum amount of time the job will run in minutes.

SubreadsProcessing.ccsCores
Int — Default: 2
The number of CPU cores to be used by ccs.

SubreadsProcessing.ccsMode
Boolean — Default: true
Ccs mode, use optimal alignment options.

SubreadsProcessing.dockerImages
Map[String,String] — Default: {"bam2fastx": "quay.io/biocontainers/bam2fastx:1.3.0--he1c1bb9_8", "biowdl-input-converter": "quay.io/biocontainers/biowdl-input-converter:0.2.1--py_0", "ccs": "quay.io/biocontainers/pbccs:4.2.0--1", "fastqc": "quay.io/biocontainers/fastqc:0.11.9--0", "isoseq3": "quay.io/biocontainers/isoseq3:3.3.0--0", "lima": "quay.io/biocontainers/lima:1.11.0--0", "multiqc": "quay.io/biocontainers/multiqc:1.9--pyh9f0ad1d_0"}
The docker image(s) used for this workflow. Changing this may result in errors which the developers may choose not to address.

SubreadsProcessing.fastqcLima.adapters
File? — Default: None
Equivalent to fastqc's --adapters option.

SubreadsProcessing.fastqcLima.casava
Boolean — Default: false
Equivalent to fastqc's --casava flag.

SubreadsProcessing.fastqcLima.contaminants
File? — Default: None
Equivalent to fastqc's --contaminants option.

SubreadsProcessing.fastqcLima.dir
String? — Default: None
Equivalent to fastqc's --dir option.

SubreadsProcessing.fastqcLima.extract
Boolean — Default: false
Equivalent to fastqc's --extract flag.

SubreadsProcessing.fastqcLima.javaXmx
String — Default: "1750M"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.

SubreadsProcessing.fastqcLima.kmers
Int? — Default: None
Equivalent to fastqc's --kmers option.

SubreadsProcessing.fastqcLima.limits
File? — Default: None
Equivalent to fastqc's --limits option.

SubreadsProcessing.fastqcLima.memory
String — Default: "2G"
The amount of memory this job will use.

SubreadsProcessing.fastqcLima.minLength
Int? — Default: None
Equivalent to fastqc's --min_length option.

SubreadsProcessing.fastqcLima.nano
Boolean — Default: false
Equivalent to fastqc's --nano flag.

SubreadsProcessing.fastqcLima.noFilter
Boolean — Default: false
Equivalent to fastqc's --nofilter flag.

SubreadsProcessing.fastqcLima.nogroup
Boolean — Default: false
Equivalent to fastqc's --nogroup flag.

SubreadsProcessing.fastqcLima.timeMinutes
Int — Default: 1 + ceil(size(seqFile,"G")) * 4
The maximum amount of time the job will run in minutes.

SubreadsProcessing.fastqcRefine.adapters
File? — Default: None
Equivalent to fastqc's --adapters option.

SubreadsProcessing.fastqcRefine.casava
Boolean — Default: false
Equivalent to fastqc's --casava flag.

SubreadsProcessing.fastqcRefine.contaminants
File? — Default: None
Equivalent to fastqc's --contaminants option.

SubreadsProcessing.fastqcRefine.dir
String? — Default: None
Equivalent to fastqc's --dir option.

SubreadsProcessing.fastqcRefine.extract
Boolean — Default: false
Equivalent to fastqc's --extract flag.

SubreadsProcessing.fastqcRefine.javaXmx
String — Default: "1750M"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.

SubreadsProcessing.fastqcRefine.kmers
Int? — Default: None
Equivalent to fastqc's --kmers option.

SubreadsProcessing.fastqcRefine.limits
File? — Default: None
Equivalent to fastqc's --limits option.

SubreadsProcessing.fastqcRefine.memory
String — Default: "2G"
The amount of memory this job will use.

SubreadsProcessing.fastqcRefine.minLength
Int? — Default: None
Equivalent to fastqc's --min_length option.

SubreadsProcessing.fastqcRefine.nano
Boolean — Default: false
Equivalent to fastqc's --nano flag.

SubreadsProcessing.fastqcRefine.noFilter
Boolean — Default: false
Equivalent to fastqc's --nofilter flag.

SubreadsProcessing.fastqcRefine.nogroup
Boolean — Default: false
Equivalent to fastqc's --nogroup flag.

SubreadsProcessing.fastqcRefine.timeMinutes
Int — Default: 1 + ceil(size(seqFile,"G")) * 4
The maximum amount of time the job will run in minutes.

SubreadsProcessing.libraryDesign
String — Default: "same"
Barcode structure of the library design.

SubreadsProcessing.lima.guess
Int — Default: 0
Try to guess the used barcodes, using the provided mean score threshold, 0 means guessing deactivated.

SubreadsProcessing.lima.guessMinCount
Int — Default: 0
Minimum number of ZMWs observed to whitelist barcodes.

SubreadsProcessing.lima.logLevel
String — Default: "WARN"
Set log level. Valid choices: (TRACE, DEBUG, INFO, WARN, FATAL).

SubreadsProcessing.lima.maxInputLength
Int — Default: 0
Maximum input sequence length, 0 means deactivated.

SubreadsProcessing.lima.maxScoredAdapters
Int — Default: 0
Analyze at maximum the provided number of adapters per ZMW, 0 means deactivated.

SubreadsProcessing.lima.maxScoredBarcodePairs
Int — Default: 0
Only use up to N barcode pair regions to find the barcode, 0 means use all.

SubreadsProcessing.lima.maxScoredBarcodes
Int — Default: 0
Analyze at maximum the provided number of barcodes per ZMW, 0 means deactivated.

SubreadsProcessing.lima.memory
String — Default: "2G"
The amount of memory available to the job.

SubreadsProcessing.lima.minEndScore
Int — Default: 0
Minimum end barcode score threshold is applied to the individual leading and trailing ends.

SubreadsProcessing.lima.minRefSpan
Float — Default: 0.5
Minimum reference span relative to the barcode length.

SubreadsProcessing.lima.minScoringRegion
Int — Default: 1
Minimum number of barcode regions with sufficient relative span to the barcode length.

SubreadsProcessing.lima.minSignalIncrease
Int — Default: 10
The minimal score difference, between first and combined, required to call a barcode pair different.

SubreadsProcessing.lima.peek
Int — Default: 0
Demux the first N ZMWs and return the mean score, 0 means peeking deactivated.

SubreadsProcessing.lima.peekGuess
Boolean — Default: false
Try to infer the used barcodes subset, by peeking at the first 50,000 ZMWs.

SubreadsProcessing.lima.scoredAdapterRatio
Float — Default: 0.25
Minimum ratio of scored vs sequenced adapters.

SubreadsProcessing.lima.scoreFullPass
Boolean — Default: false
Only use subreads flanked by adapters for barcode identification.

SubreadsProcessing.lima.timeMinutes
Int — Default: 30
The maximum amount of time the job will run in minutes.

SubreadsProcessing.limaCores
Int — Default: 2
The number of CPU cores to be used by lima.

SubreadsProcessing.multiqcTask.clConfig
String? — Default: None
Equivalent to MultiQC's `--cl-config` option.

SubreadsProcessing.multiqcTask.comment
String? — Default: None
Equivalent to MultiQC's `--comment` option.

SubreadsProcessing.multiqcTask.config
File? — Default: None
Equivalent to MultiQC's `--config` option.

SubreadsProcessing.multiqcTask.dataFormat
String? — Default: None
Equivalent to MultiQC's `--data-format` option.

SubreadsProcessing.multiqcTask.dirs
Boolean — Default: false
Equivalent to MultiQC's `--dirs` flag.

SubreadsProcessing.multiqcTask.dirsDepth
Int? — Default: None
Equivalent to MultiQC's `--dirs-depth` option.

SubreadsProcessing.multiqcTask.exclude
Array[String]+? — Default: None
Equivalent to MultiQC's `--exclude` option.

SubreadsProcessing.multiqcTask.export
Boolean — Default: false
Equivalent to MultiQC's `--export` flag.

SubreadsProcessing.multiqcTask.fileList
File? — Default: None
Equivalent to MultiQC's `--file-list` option.

SubreadsProcessing.multiqcTask.fileName
String? — Default: None
Equivalent to MultiQC's `--filename` option.

SubreadsProcessing.multiqcTask.flat
Boolean — Default: false
Equivalent to MultiQC's `--flat` flag.

SubreadsProcessing.multiqcTask.force
Boolean — Default: false
Equivalent to MultiQC's `--force` flag.

SubreadsProcessing.multiqcTask.fullNames
Boolean — Default: false
Equivalent to MultiQC's `--fullnames` flag.

SubreadsProcessing.multiqcTask.ignore
String? — Default: None
Equivalent to MultiQC's `--ignore` option.

SubreadsProcessing.multiqcTask.ignoreSamples
String? — Default: None
Equivalent to MultiQC's `--ignore-samples` option.

SubreadsProcessing.multiqcTask.interactive
Boolean — Default: true
Equivalent to MultiQC's `--interactive` flag.

SubreadsProcessing.multiqcTask.lint
Boolean — Default: false
Equivalent to MultiQC's `--lint` flag.

SubreadsProcessing.multiqcTask.megaQCUpload
Boolean — Default: false
Opposite to MultiQC's `--no-megaqc-upload` flag.

SubreadsProcessing.multiqcTask.memory
String? — Default: None
The amount of memory this job will use.

SubreadsProcessing.multiqcTask.module
Array[String]+? — Default: None
Equivalent to MultiQC's `--module` option.

SubreadsProcessing.multiqcTask.pdf
Boolean — Default: false
Equivalent to MultiQC's `--pdf` flag.

SubreadsProcessing.multiqcTask.sampleNames
File? — Default: None
Equivalent to MultiQC's `--sample-names` option.

SubreadsProcessing.multiqcTask.tag
String? — Default: None
Equivalent to MultiQC's `--tag` option.

SubreadsProcessing.multiqcTask.template
String? — Default: None
Equivalent to MultiQC's `--template` option.

SubreadsProcessing.multiqcTask.timeMinutes
Int — Default: 2 + ceil((size(reports,"G") * 8))
The maximum amount of time the job will run in minutes.

SubreadsProcessing.multiqcTask.title
String? — Default: None
Equivalent to MultiQC's `--title` option.

SubreadsProcessing.multiqcTask.zipDataDir
Boolean — Default: true
Equivalent to MultiQC's `--zip-data-dir` flag.

SubreadsProcessing.outputDirectory
String — Default: "."
The directory to which the outputs will be written.

SubreadsProcessing.refine.cores
Int — Default: 2
The number of cores to be used.

SubreadsProcessing.refine.logLevel
String — Default: "WARN"
Set log level. Valid choices: (TRACE, DEBUG, INFO, WARN, FATAL).

SubreadsProcessing.refine.memory
String — Default: "2G"
The amount of memory available to the job.

SubreadsProcessing.refine.minPolyALength
Int — Default: 20
Minimum poly(A) tail length.

SubreadsProcessing.refine.timeMinutes
Int — Default: 30
The maximum amount of time the job will run in minutes.

SubreadsProcessing.runIsoseq3Refine
Boolean — Default: false
Run isoseq3 refine for de-novo transcript reconstruction. Do not set this to true when analysing dna reads.

SubreadsProcessing.splitBamNamed
Boolean — Default: true
Split bam file(s) by resolved barcode pair name.