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Inputs for QC
The following is an overview of all available inputs in QC.
Required inputs
- QC.read1
-
File
The first or single end fastq file to be run through cutadapt.
Other common inputs
- QC.adapterForward
-
String?
The adapter to be removed from the reads first or single end reads. - QC.adapterReverse
-
String?
The adapter to be removed from the reads second end reads. - QC.contaminations
-
Array[String]+?
Contaminants/adapters to be removed from the reads. - QC.outputDir
-
String — Default:
"."
The directory to which the outputs will be written. - QC.read2
-
File?
An optional second end fastq file to be run through cutadapt. - QC.readgroupName
-
String — Default:
sub(basename(read1),"(\.fq)?(\.fastq)?(\.gz)?","")
The name of the readgroup.
Advanced inputs
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- QC.Cutadapt.bwa
-
Boolean?
Equivalent to cutadapt's --bwa flag. - QC.Cutadapt.colorspace
-
Boolean?
Equivalent to cutadapt's --colorspace flag. - QC.Cutadapt.compressionLevel
-
Int — Default:
1
The compression level if gzipped output is used. - QC.Cutadapt.cores
-
Int — Default:
4
The number of cores to use. - QC.Cutadapt.cut
-
Int?
Equivalent to cutadapt's --cut option. - QC.Cutadapt.discardTrimmed
-
Boolean?
Equivalent to cutadapt's --quality-cutoff option. - QC.Cutadapt.discardUntrimmed
-
Boolean?
Equivalent to cutadapt's --discard-untrimmed option. - QC.Cutadapt.doubleEncode
-
Boolean?
Equivalent to cutadapt's --double-encode flag. - QC.Cutadapt.errorRate
-
Float?
Equivalent to cutadapt's --error-rate option. - 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. - QC.Cutadapt.frontRead2
-
Array[String] — Default:
[]
A list of 5' ligated adapter sequences to be cut from the given second end fastq file. - QC.Cutadapt.infoFilePath
-
String?
Equivalent to cutadapt's --info-file option. - QC.Cutadapt.interleaved
-
Boolean?
Equivalent to cutadapt's --interleaved flag. - QC.Cutadapt.length
-
Int?
Equivalent to cutadapt's --length option. - QC.Cutadapt.lengthTag
-
String?
Equivalent to cutadapt's --length-tag option. - QC.Cutadapt.maq
-
Boolean?
Equivalent to cutadapt's --maq flag. - QC.Cutadapt.maskAdapter
-
Boolean?
Equivalent to cutadapt's --mask-adapter flag. - QC.Cutadapt.matchReadWildcards
-
Boolean?
Equivalent to cutadapt's --match-read-wildcards flag. - QC.Cutadapt.maximumLength
-
Int?
Equivalent to cutadapt's --maximum-length option. - QC.Cutadapt.maxN
-
Int?
Equivalent to cutadapt's --max-n option. - QC.Cutadapt.memory
-
String — Default:
"5GiB"
The amount of memory this job will use. - QC.Cutadapt.minimumLength
-
Int? — Default:
2
Equivalent to cutadapt's --minimum-length option. - QC.Cutadapt.nextseqTrim
-
String?
Equivalent to cutadapt's --nextseq-trim option. - QC.Cutadapt.noIndels
-
Boolean?
Equivalent to cutadapt's --no-indels flag. - QC.Cutadapt.noMatchAdapterWildcards
-
Boolean?
Equivalent to cutadapt's --no-match-adapter-wildcards flag. - QC.Cutadapt.noTrim
-
Boolean?
Equivalent to cutadapt's --no-trim flag. - QC.Cutadapt.noZeroCap
-
Boolean?
Equivalent to cutadapt's --no-zero-cap flag. - QC.Cutadapt.overlap
-
Int?
Equivalent to cutadapt's --overlap option. - QC.Cutadapt.pairFilter
-
String?
Equivalent to cutadapt's --pair-filter option. - QC.Cutadapt.prefix
-
String?
Equivalent to cutadapt's --prefix option. - QC.Cutadapt.qualityBase
-
Int?
Equivalent to cutadapt's --quality-base option. - QC.Cutadapt.qualityCutoff
-
String?
Equivalent to cutadapt's --quality-cutoff option. - QC.Cutadapt.restFilePath
-
String?
Equivalent to cutadapt's --rest-file option. - QC.Cutadapt.stripF3
-
Boolean?
Equivalent to cutadapt's --strip-f3 flag. - QC.Cutadapt.stripSuffix
-
String?
Equivalent to cutadapt's --strip-suffix option. - QC.Cutadapt.suffix
-
String?
Equivalent to cutadapt's --suffix option. - 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. - QC.Cutadapt.times
-
Int?
Equivalent to cutadapt's --times option. - QC.Cutadapt.tooLongOutputPath
-
String?
Equivalent to cutadapt's --too-long-output option. - QC.Cutadapt.tooLongPairedOutputPath
-
String?
Equivalent to cutadapt's --too-long-paired-output option. - QC.Cutadapt.tooShortOutputPath
-
String?
Equivalent to cutadapt's --too-short-output option. - QC.Cutadapt.tooShortPairedOutputPath
-
String?
Equivalent to cutadapt's --too-short-paired-output option. - QC.Cutadapt.trimN
-
Boolean?
Equivalent to cutadapt's --trim-n flag. - QC.Cutadapt.untrimmedOutputPath
-
String?
Equivalent to cutadapt's --untrimmed-output option. - QC.Cutadapt.untrimmedPairedOutputPath
-
String?
Equivalent to cutadapt's --untrimmed-paired-output option. - QC.Cutadapt.wildcardFilePath
-
String?
Equivalent to cutadapt's --wildcard-file option. - QC.Cutadapt.zeroCap
-
Boolean?
Equivalent to cutadapt's --zero-cap flag. - QC.dockerImages
-
Map[String,String] — Default:
{"fastqc": "quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0", "cutadapt": "quay.io/biocontainers/cutadapt:4.4--py310h1425a21_0"}
The docker images used. Changing this may result in errors which the developers may choose not to address. - QC.extractFastqcZip
-
Boolean — Default:
false
Whether to extract Fastqc's report zip files. - QC.FastqcRead1.adapters
-
File?
Equivalent to fastqc's --adapters option. - QC.FastqcRead1.casava
-
Boolean — Default:
false
Equivalent to fastqc's --casava flag. - QC.FastqcRead1.contaminants
-
File?
Equivalent to fastqc's --contaminants option. - QC.FastqcRead1.dir
-
String?
Equivalent to fastqc's --dir option. - QC.FastqcRead1.format
-
String?
Equivalent to fastqc's --format option. - QC.FastqcRead1.javaXmx
-
String — Default:
"1750M"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead. - QC.FastqcRead1.kmers
-
Int?
Equivalent to fastqc's --kmers option. - QC.FastqcRead1.limits
-
File?
Equivalent to fastqc's --limits option. - QC.FastqcRead1.memory
-
String — Default:
"2GiB"
The amount of memory this job will use. - QC.FastqcRead1.minLength
-
Int?
Equivalent to fastqc's --min_length option. - QC.FastqcRead1.nano
-
Boolean — Default:
false
Equivalent to fastqc's --nano flag. - QC.FastqcRead1.noFilter
-
Boolean — Default:
false
Equivalent to fastqc's --nofilter flag. - QC.FastqcRead1.nogroup
-
Boolean — Default:
false
Equivalent to fastqc's --nogroup flag. - QC.FastqcRead1.threads
-
Int — Default:
1
The number of cores to use. - QC.FastqcRead1.timeMinutes
-
Int — Default:
1 + ceil(size(seqFile,"G")) * 4
The maximum amount of time the job will run in minutes. - QC.FastqcRead1After.adapters
-
File?
Equivalent to fastqc's --adapters option. - QC.FastqcRead1After.casava
-
Boolean — Default:
false
Equivalent to fastqc's --casava flag. - QC.FastqcRead1After.contaminants
-
File?
Equivalent to fastqc's --contaminants option. - QC.FastqcRead1After.dir
-
String?
Equivalent to fastqc's --dir option. - QC.FastqcRead1After.format
-
String?
Equivalent to fastqc's --format option. - QC.FastqcRead1After.javaXmx
-
String — Default:
"1750M"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead. - QC.FastqcRead1After.kmers
-
Int?
Equivalent to fastqc's --kmers option. - QC.FastqcRead1After.limits
-
File?
Equivalent to fastqc's --limits option. - QC.FastqcRead1After.memory
-
String — Default:
"2GiB"
The amount of memory this job will use. - QC.FastqcRead1After.minLength
-
Int?
Equivalent to fastqc's --min_length option. - QC.FastqcRead1After.nano
-
Boolean — Default:
false
Equivalent to fastqc's --nano flag. - QC.FastqcRead1After.noFilter
-
Boolean — Default:
false
Equivalent to fastqc's --nofilter flag. - QC.FastqcRead1After.nogroup
-
Boolean — Default:
false
Equivalent to fastqc's --nogroup flag. - QC.FastqcRead1After.threads
-
Int — Default:
1
The number of cores to use. - QC.FastqcRead1After.timeMinutes
-
Int — Default:
1 + ceil(size(seqFile,"G")) * 4
The maximum amount of time the job will run in minutes. - QC.FastqcRead2.adapters
-
File?
Equivalent to fastqc's --adapters option. - QC.FastqcRead2.casava
-
Boolean — Default:
false
Equivalent to fastqc's --casava flag. - QC.FastqcRead2.contaminants
-
File?
Equivalent to fastqc's --contaminants option. - QC.FastqcRead2.dir
-
String?
Equivalent to fastqc's --dir option. - QC.FastqcRead2.format
-
String?
Equivalent to fastqc's --format option. - QC.FastqcRead2.javaXmx
-
String — Default:
"1750M"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead. - QC.FastqcRead2.kmers
-
Int?
Equivalent to fastqc's --kmers option. - QC.FastqcRead2.limits
-
File?
Equivalent to fastqc's --limits option. - QC.FastqcRead2.memory
-
String — Default:
"2GiB"
The amount of memory this job will use. - QC.FastqcRead2.minLength
-
Int?
Equivalent to fastqc's --min_length option. - QC.FastqcRead2.nano
-
Boolean — Default:
false
Equivalent to fastqc's --nano flag. - QC.FastqcRead2.noFilter
-
Boolean — Default:
false
Equivalent to fastqc's --nofilter flag. - QC.FastqcRead2.nogroup
-
Boolean — Default:
false
Equivalent to fastqc's --nogroup flag. - QC.FastqcRead2.threads
-
Int — Default:
1
The number of cores to use. - QC.FastqcRead2.timeMinutes
-
Int — Default:
1 + ceil(size(seqFile,"G")) * 4
The maximum amount of time the job will run in minutes. - QC.FastqcRead2After.adapters
-
File?
Equivalent to fastqc's --adapters option. - QC.FastqcRead2After.casava
-
Boolean — Default:
false
Equivalent to fastqc's --casava flag. - QC.FastqcRead2After.contaminants
-
File?
Equivalent to fastqc's --contaminants option. - QC.FastqcRead2After.dir
-
String?
Equivalent to fastqc's --dir option. - QC.FastqcRead2After.format
-
String?
Equivalent to fastqc's --format option. - QC.FastqcRead2After.javaXmx
-
String — Default:
"1750M"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead. - QC.FastqcRead2After.kmers
-
Int?
Equivalent to fastqc's --kmers option. - QC.FastqcRead2After.limits
-
File?
Equivalent to fastqc's --limits option. - QC.FastqcRead2After.memory
-
String — Default:
"2GiB"
The amount of memory this job will use. - QC.FastqcRead2After.minLength
-
Int?
Equivalent to fastqc's --min_length option. - QC.FastqcRead2After.nano
-
Boolean — Default:
false
Equivalent to fastqc's --nano flag. - QC.FastqcRead2After.noFilter
-
Boolean — Default:
false
Equivalent to fastqc's --nofilter flag. - QC.FastqcRead2After.nogroup
-
Boolean — Default:
false
Equivalent to fastqc's --nogroup flag. - QC.FastqcRead2After.threads
-
Int — Default:
1
The number of cores to use. - QC.FastqcRead2After.timeMinutes
-
Int — Default:
1 + ceil(size(seqFile,"G")) * 4
The maximum amount of time the job will run in minutes. - QC.runAdapterClipping
-
Boolean — Default:
defined(adapterForward) || defined(adapterReverse) || length(select_first([contaminations, []])) > 0
Whether or not adapters should be removed from the reads.
Do not set these inputs!
The following inputs should not be set, even though womtool may show them as being available inputs.
- QC.FastqcRead1.noneArray
- QC.FastqcRead1.noneFile
- QC.FastqcRead2.noneArray
- QC.FastqcRead2.noneFile
- QC.FastqcRead1After.noneArray
- QC.FastqcRead1After.noneFile
- QC.FastqcRead2After.noneArray
- QC.FastqcRead2After.noneFile