Inputs for Classification

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

Required inputs

Classification.dockerImagesFile

File
The docker image used for this workflow. Changing this may result in errors which the developers may choose not to address.

Classification.sampleConfigFile

File
Samplesheet describing input fasta/fastq files.

Classification.sampleWorkflow.centrifuge.inputFormat

String — Default: "fastq"
The format of the read file(s).

Classification.sampleWorkflow.centrifuge.minHitLength

Int — Default: 22
Minimum length of partial hits.

Classification.sampleWorkflow.centrifuge.phred64

Boolean — Default: false
If set to true, phred+64 encoding is used.

Classification.sampleWorkflow.centrifugeIndex

Array[File]+
The files of the index for the reference genomes.

Other common inputs

Classification.outputDirectory

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

Classification.sampleWorkflow.centrifuge.excludeTaxIDs

String?
A comma-separated list of taxonomic IDs that will be excluded in classification procedure.

Classification.sampleWorkflow.centrifuge.hostTaxIDs

String?
A comma-separated list of taxonomic IDs that will be preferred in classification procedure.

Classification.sampleWorkflow.centrifuge.reportMaxDistinct

Int?
It searches for at most distinct, primary assignments for each read or pair. </dd>

Classification.sampleWorkflow.centrifuge.trim3

Int?
Trim bases from 3' (right) end of each read before alignment. </dd>

Classification.sampleWorkflow.centrifuge.trim5

Int?
Trim bases from 5' (left) end of each read before alignment. </dd>

Classification.sampleWorkflow.qualityControl.adapterForward

String? — Default: "AGATCGGAAGAG"
The adapter to be removed from the reads first or single end reads.

Classification.sampleWorkflow.qualityControl.adapterReverse

String? — Default: "AGATCGGAAGAG"
The adapter to be removed from the reads second end reads.

Classification.sampleWorkflow.qualityControl.contaminations

Array[String]+?
Contaminants/adapters to be removed from the reads.

</dl> ## Advanced inputs

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Classification.convertDockerImagesFile.dockerImage

String — Default: "quay.io/biocontainers/biowdl-input-converter:0.2.1--py_0"
The docker image used for this task. Changing this may result in errors which the developers may choose not to address.

Classification.convertDockerImagesFile.memory

String — Default: "128M"
The maximum amount of memory the job will need.

Classification.convertDockerImagesFile.timeMinutes

Int — Default: 1
The maximum amount of time the job will run in minutes.

Classification.convertSampleConfig.checkFileMd5sums

Boolean — Default: false
Whether or not the MD5 sums of the files mentioned in the samplesheet should be checked.

Classification.convertSampleConfig.old

Boolean — Default: false
Whether or not the old samplesheet format should be used.

Classification.convertSampleConfig.skipFileCheck

Boolean — Default: true
Whether or not the existance of the files mentioned in the samplesheet should be checked.

Classification.convertSampleConfig.timeMinutes

Int — Default: 1
The maximum amount of time the job will run in minutes.

Classification.multiqcTask.clConfig

String?
Equivalent to MultiQC's `--cl-config` option.

Classification.multiqcTask.comment

String?
Equivalent to MultiQC's `--comment` option.

Classification.multiqcTask.config

File?
Equivalent to MultiQC's `--config` option.

Classification.multiqcTask.dataFormat

String?
Equivalent to MultiQC's `--data-format` option.

Classification.multiqcTask.dirs

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

Classification.multiqcTask.dirsDepth

Int?
Equivalent to MultiQC's `--dirs-depth` option.

Classification.multiqcTask.exclude

Array[String]+?
Equivalent to MultiQC's `--exclude` option.

Classification.multiqcTask.export

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

Classification.multiqcTask.fileList

File?
Equivalent to MultiQC's `--file-list` option.

Classification.multiqcTask.fileName

String?
Equivalent to MultiQC's `--filename` option.

Classification.multiqcTask.flat

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

Classification.multiqcTask.force

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

Classification.multiqcTask.fullNames

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

Classification.multiqcTask.ignore

String?
Equivalent to MultiQC's `--ignore` option.

Classification.multiqcTask.ignoreSamples

String?
Equivalent to MultiQC's `--ignore-samples` option.

Classification.multiqcTask.interactive

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

Classification.multiqcTask.lint

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

Classification.multiqcTask.megaQCUpload

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

Classification.multiqcTask.memory

String?
The amount of memory this job will use.

Classification.multiqcTask.module

Array[String]+?
Equivalent to MultiQC's `--module` option.

Classification.multiqcTask.pdf

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

Classification.multiqcTask.sampleNames

File?
Equivalent to MultiQC's `--sample-names` option.

Classification.multiqcTask.tag

String?
Equivalent to MultiQC's `--tag` option.

Classification.multiqcTask.template

String?
Equivalent to MultiQC's `--template` option.

Classification.multiqcTask.timeMinutes

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

Classification.multiqcTask.title

String?
Equivalent to MultiQC's `--title` option.

Classification.multiqcTask.zipDataDir

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

Classification.sampleWorkflow.centrifuge.memory

String — Default: "16G"
The amount of memory available to the job.

Classification.sampleWorkflow.centrifuge.threads

Int — Default: 4
The number of threads to be used.

Classification.sampleWorkflow.kReport.isCountTable

Boolean — Default: false
The format of the file is taxIDCOUNT. </dd>

Classification.sampleWorkflow.kReport.memory

String — Default: "4G"
The amount of memory available to the job.

Classification.sampleWorkflow.kReport.minimumLength

Int?
Require a minimum alignment length to the read.

Classification.sampleWorkflow.kReport.minimumScore

Int?
Require a minimum score for reads to be counted.

Classification.sampleWorkflow.kReport.noLCA

Boolean — Default: false
Do not report the lca of multiple assignments, but report count fractions at the taxa.

Classification.sampleWorkflow.kReport.showZeros

Boolean — Default: false
Show clades that have zero reads.

Classification.sampleWorkflow.kReport.timeMinutes

Int — Default: 10
The maximum amount of time the job will run in minutes.

Classification.sampleWorkflow.krona.memory

String — Default: "4G"
The amount of memory available to the job.

Classification.sampleWorkflow.krona.timeMinutes

Int — Default: 1
The maximum amount of time the job will run in minutes.

Classification.sampleWorkflow.qualityControl.Cutadapt.bwa

Boolean?
Equivalent to cutadapt's --bwa flag.

Classification.sampleWorkflow.qualityControl.Cutadapt.colorspace

Boolean?
Equivalent to cutadapt's --colorspace flag.

Classification.sampleWorkflow.qualityControl.Cutadapt.compressionLevel

Int — Default: 1
The compression level if gzipped output is used.

Classification.sampleWorkflow.qualityControl.Cutadapt.cores

Int — Default: 4
The number of cores to use.

Classification.sampleWorkflow.qualityControl.Cutadapt.cut

Int?
Equivalent to cutadapt's --cut option.

Classification.sampleWorkflow.qualityControl.Cutadapt.discardTrimmed

Boolean?
Equivalent to cutadapt's --quality-cutoff option.

Classification.sampleWorkflow.qualityControl.Cutadapt.discardUntrimmed

Boolean?
Equivalent to cutadapt's --discard-untrimmed option.

Classification.sampleWorkflow.qualityControl.Cutadapt.doubleEncode

Boolean?
Equivalent to cutadapt's --double-encode flag.

Classification.sampleWorkflow.qualityControl.Cutadapt.errorRate

Float?
Equivalent to cutadapt's --error-rate option.

Classification.sampleWorkflow.qualityControl.Cutadapt.front

Array[String] — Default: []
A list of 5' ligated adapter sequences to be cut from the given first or single end fastq file.

Classification.sampleWorkflow.qualityControl.Cutadapt.frontRead2

Array[String] — Default: []
A list of 5' ligated adapter sequences to be cut from the given second end fastq file.

Classification.sampleWorkflow.qualityControl.Cutadapt.infoFilePath

String?
Equivalent to cutadapt's --info-file option.

Classification.sampleWorkflow.qualityControl.Cutadapt.interleaved

Boolean?
Equivalent to cutadapt's --interleaved flag.

Classification.sampleWorkflow.qualityControl.Cutadapt.length

Int?
Equivalent to cutadapt's --length option.

Classification.sampleWorkflow.qualityControl.Cutadapt.lengthTag

String?
Equivalent to cutadapt's --length-tag option.

Classification.sampleWorkflow.qualityControl.Cutadapt.maq

Boolean?
Equivalent to cutadapt's --maq flag.

Classification.sampleWorkflow.qualityControl.Cutadapt.maskAdapter

Boolean?
Equivalent to cutadapt's --mask-adapter flag.

Classification.sampleWorkflow.qualityControl.Cutadapt.matchReadWildcards

Boolean?
Equivalent to cutadapt's --match-read-wildcards flag.

Classification.sampleWorkflow.qualityControl.Cutadapt.maximumLength

Int?
Equivalent to cutadapt's --maximum-length option.

Classification.sampleWorkflow.qualityControl.Cutadapt.maxN

Int?
Equivalent to cutadapt's --max-n option.

Classification.sampleWorkflow.qualityControl.Cutadapt.memory

String — Default: "~{300 + 100 * cores}M"
The amount of memory this job will use.

Classification.sampleWorkflow.qualityControl.Cutadapt.minimumLength

Int? — Default: 2
Equivalent to cutadapt's --minimum-length option.

Classification.sampleWorkflow.qualityControl.Cutadapt.nextseqTrim

String?
Equivalent to cutadapt's --nextseq-trim option.

Classification.sampleWorkflow.qualityControl.Cutadapt.noIndels

Boolean?
Equivalent to cutadapt's --no-indels flag.

Classification.sampleWorkflow.qualityControl.Cutadapt.noMatchAdapterWildcards

Boolean?
Equivalent to cutadapt's --no-match-adapter-wildcards flag.

Classification.sampleWorkflow.qualityControl.Cutadapt.noTrim

Boolean?
Equivalent to cutadapt's --no-trim flag.

Classification.sampleWorkflow.qualityControl.Cutadapt.noZeroCap

Boolean?
Equivalent to cutadapt's --no-zero-cap flag.

Classification.sampleWorkflow.qualityControl.Cutadapt.overlap

Int?
Equivalent to cutadapt's --overlap option.

Classification.sampleWorkflow.qualityControl.Cutadapt.pairFilter

String?
Equivalent to cutadapt's --pair-filter option.

Classification.sampleWorkflow.qualityControl.Cutadapt.prefix

String?
Equivalent to cutadapt's --prefix option.

Classification.sampleWorkflow.qualityControl.Cutadapt.qualityBase

Int?
Equivalent to cutadapt's --quality-base option.

Classification.sampleWorkflow.qualityControl.Cutadapt.qualityCutoff

String?
Equivalent to cutadapt's --quality-cutoff option.

Classification.sampleWorkflow.qualityControl.Cutadapt.restFilePath

String?
Equivalent to cutadapt's --rest-file option.

Classification.sampleWorkflow.qualityControl.Cutadapt.stripF3

Boolean?
Equivalent to cutadapt's --strip-f3 flag.

Classification.sampleWorkflow.qualityControl.Cutadapt.stripSuffix

String?
Equivalent to cutadapt's --strip-suffix option.

Classification.sampleWorkflow.qualityControl.Cutadapt.suffix

String?
Equivalent to cutadapt's --suffix option.

Classification.sampleWorkflow.qualityControl.Cutadapt.timeMinutes

Int — Default: 1 + ceil((size([read1, read2],"G") * 12.0 / cores))
The maximum amount of time the job will run in minutes.

Classification.sampleWorkflow.qualityControl.Cutadapt.times

Int?
Equivalent to cutadapt's --times option.

Classification.sampleWorkflow.qualityControl.Cutadapt.tooLongOutputPath

String?
Equivalent to cutadapt's --too-long-output option.

Classification.sampleWorkflow.qualityControl.Cutadapt.tooLongPairedOutputPath

String?
Equivalent to cutadapt's --too-long-paired-output option.

Classification.sampleWorkflow.qualityControl.Cutadapt.tooShortOutputPath

String?
Equivalent to cutadapt's --too-short-output option.

Classification.sampleWorkflow.qualityControl.Cutadapt.tooShortPairedOutputPath

String?
Equivalent to cutadapt's --too-short-paired-output option.

Classification.sampleWorkflow.qualityControl.Cutadapt.trimN

Boolean?
Equivalent to cutadapt's --trim-n flag.

Classification.sampleWorkflow.qualityControl.Cutadapt.untrimmedOutputPath

String?
Equivalent to cutadapt's --untrimmed-output option.

Classification.sampleWorkflow.qualityControl.Cutadapt.untrimmedPairedOutputPath

String?
Equivalent to cutadapt's --untrimmed-paired-output option.

Classification.sampleWorkflow.qualityControl.Cutadapt.wildcardFilePath

String?
Equivalent to cutadapt's --wildcard-file option.

Classification.sampleWorkflow.qualityControl.Cutadapt.zeroCap

Boolean?
Equivalent to cutadapt's --zero-cap flag.

Classification.sampleWorkflow.qualityControl.extractFastqcZip

Boolean — Default: false
Whether to extract Fastqc's report zip files

Classification.sampleWorkflow.qualityControl.FastqcRead1.adapters

File?
Equivalent to fastqc's --adapters option.

Classification.sampleWorkflow.qualityControl.FastqcRead1.casava

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

Classification.sampleWorkflow.qualityControl.FastqcRead1.contaminants

File?
Equivalent to fastqc's --contaminants option.

Classification.sampleWorkflow.qualityControl.FastqcRead1.dir

String?
Equivalent to fastqc's --dir option.

Classification.sampleWorkflow.qualityControl.FastqcRead1.format

String?
Equivalent to fastqc's --format option.

Classification.sampleWorkflow.qualityControl.FastqcRead1.javaXmx

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

Classification.sampleWorkflow.qualityControl.FastqcRead1.kmers

Int?
Equivalent to fastqc's --kmers option.

Classification.sampleWorkflow.qualityControl.FastqcRead1.limits

File?
Equivalent to fastqc's --limits option.

Classification.sampleWorkflow.qualityControl.FastqcRead1.memory

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

Classification.sampleWorkflow.qualityControl.FastqcRead1.minLength

Int?
Equivalent to fastqc's --min_length option.

Classification.sampleWorkflow.qualityControl.FastqcRead1.nano

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

Classification.sampleWorkflow.qualityControl.FastqcRead1.noFilter

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

Classification.sampleWorkflow.qualityControl.FastqcRead1.nogroup

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

Classification.sampleWorkflow.qualityControl.FastqcRead1.threads

Int — Default: 1
The number of cores to use.

Classification.sampleWorkflow.qualityControl.FastqcRead1.timeMinutes

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

Classification.sampleWorkflow.qualityControl.FastqcRead1After.adapters

File?
Equivalent to fastqc's --adapters option.

Classification.sampleWorkflow.qualityControl.FastqcRead1After.casava

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

Classification.sampleWorkflow.qualityControl.FastqcRead1After.contaminants

File?
Equivalent to fastqc's --contaminants option.

Classification.sampleWorkflow.qualityControl.FastqcRead1After.dir

String?
Equivalent to fastqc's --dir option.

Classification.sampleWorkflow.qualityControl.FastqcRead1After.format

String?
Equivalent to fastqc's --format option.

Classification.sampleWorkflow.qualityControl.FastqcRead1After.javaXmx

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

Classification.sampleWorkflow.qualityControl.FastqcRead1After.kmers

Int?
Equivalent to fastqc's --kmers option.

Classification.sampleWorkflow.qualityControl.FastqcRead1After.limits

File?
Equivalent to fastqc's --limits option.

Classification.sampleWorkflow.qualityControl.FastqcRead1After.memory

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

Classification.sampleWorkflow.qualityControl.FastqcRead1After.minLength

Int?
Equivalent to fastqc's --min_length option.

Classification.sampleWorkflow.qualityControl.FastqcRead1After.nano

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

Classification.sampleWorkflow.qualityControl.FastqcRead1After.noFilter

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

Classification.sampleWorkflow.qualityControl.FastqcRead1After.nogroup

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

Classification.sampleWorkflow.qualityControl.FastqcRead1After.threads

Int — Default: 1
The number of cores to use.

Classification.sampleWorkflow.qualityControl.FastqcRead1After.timeMinutes

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

Classification.sampleWorkflow.qualityControl.FastqcRead2.adapters

File?
Equivalent to fastqc's --adapters option.

Classification.sampleWorkflow.qualityControl.FastqcRead2.casava

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

Classification.sampleWorkflow.qualityControl.FastqcRead2.contaminants

File?
Equivalent to fastqc's --contaminants option.

Classification.sampleWorkflow.qualityControl.FastqcRead2.dir

String?
Equivalent to fastqc's --dir option.

Classification.sampleWorkflow.qualityControl.FastqcRead2.format

String?
Equivalent to fastqc's --format option.

Classification.sampleWorkflow.qualityControl.FastqcRead2.javaXmx

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

Classification.sampleWorkflow.qualityControl.FastqcRead2.kmers

Int?
Equivalent to fastqc's --kmers option.

Classification.sampleWorkflow.qualityControl.FastqcRead2.limits

File?
Equivalent to fastqc's --limits option.

Classification.sampleWorkflow.qualityControl.FastqcRead2.memory

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

Classification.sampleWorkflow.qualityControl.FastqcRead2.minLength

Int?
Equivalent to fastqc's --min_length option.

Classification.sampleWorkflow.qualityControl.FastqcRead2.nano

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

Classification.sampleWorkflow.qualityControl.FastqcRead2.noFilter

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

Classification.sampleWorkflow.qualityControl.FastqcRead2.nogroup

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

Classification.sampleWorkflow.qualityControl.FastqcRead2.threads

Int — Default: 1
The number of cores to use.

Classification.sampleWorkflow.qualityControl.FastqcRead2.timeMinutes

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

Classification.sampleWorkflow.qualityControl.FastqcRead2After.adapters

File?
Equivalent to fastqc's --adapters option.

Classification.sampleWorkflow.qualityControl.FastqcRead2After.casava

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

Classification.sampleWorkflow.qualityControl.FastqcRead2After.contaminants

File?
Equivalent to fastqc's --contaminants option.

Classification.sampleWorkflow.qualityControl.FastqcRead2After.dir

String?
Equivalent to fastqc's --dir option.

Classification.sampleWorkflow.qualityControl.FastqcRead2After.format

String?
Equivalent to fastqc's --format option.

Classification.sampleWorkflow.qualityControl.FastqcRead2After.javaXmx

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

Classification.sampleWorkflow.qualityControl.FastqcRead2After.kmers

Int?
Equivalent to fastqc's --kmers option.

Classification.sampleWorkflow.qualityControl.FastqcRead2After.limits

File?
Equivalent to fastqc's --limits option.

Classification.sampleWorkflow.qualityControl.FastqcRead2After.memory

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

Classification.sampleWorkflow.qualityControl.FastqcRead2After.minLength

Int?
Equivalent to fastqc's --min_length option.

Classification.sampleWorkflow.qualityControl.FastqcRead2After.nano

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

Classification.sampleWorkflow.qualityControl.FastqcRead2After.noFilter

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

Classification.sampleWorkflow.qualityControl.FastqcRead2After.nogroup

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

Classification.sampleWorkflow.qualityControl.FastqcRead2After.threads

Int — Default: 1
The number of cores to use.

Classification.sampleWorkflow.qualityControl.FastqcRead2After.timeMinutes

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

Classification.sampleWorkflow.qualityControl.runAdapterClipping

Boolean — Default: defined(adapterForward) || defined(adapterReverse) || length(select_first([contaminations, []])) > 0
Whether or not adapters should be removed from the reads.

</dl> </details> ## Do not set these inputs! The following inputs should ***not*** be set, even though womtool may show them as being available inputs. * Classification.sampleWorkflow.qualityControl.FastqcRead1.NoneFile * Classification.sampleWorkflow.qualityControl.FastqcRead1.NoneArray * Classification.sampleWorkflow.qualityControl.FastqcRead2.NoneFile * Classification.sampleWorkflow.qualityControl.FastqcRead2.NoneArray * Classification.sampleWorkflow.qualityControl.FastqcRead1After.NoneFile * Classification.sampleWorkflow.qualityControl.FastqcRead1After.NoneArray * Classification.sampleWorkflow.qualityControl.FastqcRead2After.NoneFile * Classification.sampleWorkflow.qualityControl.FastqcRead2After.NoneArray * Classification.multiqcTask.finished * Classification.multiqcTask.dependencies