Please be aware that the page you are currently viewing is not for the latest available version!
Inputs for QC
The following is an overview of all available inputs in QC.
Required inputs
- QC.read1
-
File — Default:
None
The first or single end fastq file to be run through cutadapt.
Other common inputs
- QC.adapterForward
-
String? — Default:
"AGATCGGAAGAG"
The adapter to be removed from the reads first or single end reads. - QC.adapterReverse
-
String? — Default:
"AGATCGGAAGAG"
The adapter to be removed from the reads second end reads. - QC.contaminations
-
Array[String]+? — Default:
None
Contaminants/adapters to be removed from the reads. - QC.outputDir
-
String — Default:
"."
The directory to which the outputs will be written. - QC.read2
-
File? — Default:
None
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
Show/Hide
- QC.Cutadapt.bwa
-
Boolean? — Default:
None
Equivalent to cutadapt's --bwa flag. - QC.Cutadapt.colorspace
-
Boolean? — Default:
None
Equivalent to cutadapt's --colorspace flag. - QC.Cutadapt.cores
-
Int — Default:
1
The number of cores to use. - QC.Cutadapt.cut
-
Int? — Default:
None
Equivalent to cutadapt's --cut option. - QC.Cutadapt.discardTrimmed
-
Boolean? — Default:
None
Equivalent to cutadapt's --quality-cutoff option. - QC.Cutadapt.discardUntrimmed
-
Boolean? — Default:
None
Equivalent to cutadapt's --discard-untrimmed option. - QC.Cutadapt.doubleEncode
-
Boolean? — Default:
None
Equivalent to cutadapt's --double-encode flag. - QC.Cutadapt.errorRate
-
Float? — Default:
None
Equivalent to cutadapt's --error-rate option. - QC.Cutadapt.format
-
String? — Default:
None
Equivalent to cutadapt's --format 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? — Default:
None
Equivalent to cutadapt's --info-file option. - QC.Cutadapt.interleaved
-
Boolean? — Default:
None
Equivalent to cutadapt's --interleaved flag. - QC.Cutadapt.length
-
Int? — Default:
None
Equivalent to cutadapt's --length option. - QC.Cutadapt.lengthTag
-
String? — Default:
None
Equivalent to cutadapt's --length-tag option. - QC.Cutadapt.maq
-
Boolean? — Default:
None
Equivalent to cutadapt's --maq flag. - QC.Cutadapt.maskAdapter
-
Boolean? — Default:
None
Equivalent to cutadapt's --mask-adapter flag. - QC.Cutadapt.matchReadWildcards
-
Boolean? — Default:
None
Equivalent to cutadapt's --match-read-wildcards flag. - QC.Cutadapt.maximumLength
-
Int? — Default:
None
Equivalent to cutadapt's --maximum-length option. - QC.Cutadapt.maxN
-
Int? — Default:
None
Equivalent to cutadapt's --max-n option. - QC.Cutadapt.memory
-
String — Default:
"4G"
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? — Default:
None
Equivalent to cutadapt's --nextseq-trim option. - QC.Cutadapt.noIndels
-
Boolean? — Default:
None
Equivalent to cutadapt's --no-indels flag. - QC.Cutadapt.noMatchAdapterWildcards
-
Boolean? — Default:
None
Equivalent to cutadapt's --no-match-adapter-wildcards flag. - QC.Cutadapt.noTrim
-
Boolean? — Default:
None
Equivalent to cutadapt's --no-trim flag. - QC.Cutadapt.noZeroCap
-
Boolean? — Default:
None
Equivalent to cutadapt's --no-zero-cap flag. - QC.Cutadapt.overlap
-
Int? — Default:
None
Equivalent to cutadapt's --overlap option. - QC.Cutadapt.pairFilter
-
String? — Default:
None
Equivalent to cutadapt's --pair-filter option. - QC.Cutadapt.prefix
-
String? — Default:
None
Equivalent to cutadapt's --prefix option. - QC.Cutadapt.qualityBase
-
Int? — Default:
None
Equivalent to cutadapt's --quality-base option. - QC.Cutadapt.qualityCutoff
-
String? — Default:
None
Equivalent to cutadapt's --quality-cutoff option. - QC.Cutadapt.restFilePath
-
String? — Default:
None
Equivalent to cutadapt's --rest-file option. - QC.Cutadapt.stripF3
-
Boolean? — Default:
None
Equivalent to cutadapt's --strip-f3 flag. - QC.Cutadapt.stripSuffix
-
String? — Default:
None
Equivalent to cutadapt's --strip-suffix option. - QC.Cutadapt.suffix
-
String? — Default:
None
Equivalent to cutadapt's --suffix option. - QC.Cutadapt.times
-
Int? — Default:
None
Equivalent to cutadapt's --times option. - QC.Cutadapt.tooLongOutputPath
-
String? — Default:
None
Equivalent to cutadapt's --too-long-output option. - QC.Cutadapt.tooLongPairedOutputPath
-
String? — Default:
None
Equivalent to cutadapt's --too-long-paired-output option. - QC.Cutadapt.tooShortOutputPath
-
String? — Default:
None
Equivalent to cutadapt's --too-short-output option. - QC.Cutadapt.tooShortPairedOutputPath
-
String? — Default:
None
Equivalent to cutadapt's --too-short-paired-output option. - QC.Cutadapt.trimN
-
Boolean? — Default:
None
Equivalent to cutadapt's --trim-n flag. - QC.Cutadapt.trimPrimer
-
Boolean? — Default:
None
Equivalent to cutadapt's --trim-primer flag. - QC.Cutadapt.untrimmedOutputPath
-
String? — Default:
None
Equivalent to cutadapt's --untrimmed-output option. - QC.Cutadapt.untrimmedPairedOutputPath
-
String? — Default:
None
Equivalent to cutadapt's --untrimmed-paired-output option. - QC.Cutadapt.wildcardFilePath
-
String? — Default:
None
Equivalent to cutadapt's --wildcard-file option. - QC.Cutadapt.Z
-
Boolean — Default:
true
Equivalent to cutadapt's -Z flag. - QC.Cutadapt.zeroCap
-
Boolean? — Default:
None
Equivalent to cutadapt's --zero-cap flag. - QC.dockerImages
-
Map[String,String] — Default:
{"fastqc": "quay.io/biocontainers/fastqc:0.11.7--4", "cutadapt": "quay.io/biocontainers/cutadapt:2.4--py37h14c3975_0"}
The docker image used for this task. Changing this may result in errors which the developers may choose not to address. - QC.FastqcRead1.adapters
-
File? — Default:
None
Equivalent to fastqc's --adapters option. - QC.FastqcRead1.casava
-
Boolean — Default:
false
Equivalent to fastqc's --casava flag. - QC.FastqcRead1.contaminants
-
File? — Default:
None
Equivalent to fastqc's --contaminants option. - QC.FastqcRead1.dir
-
String? — Default:
None
Equivalent to fastqc's --dir option. - QC.FastqcRead1.extract
-
Boolean — Default:
false
Equivalent to fastqc's --extract flag. - QC.FastqcRead1.format
-
String? — Default:
None
Equivalent to fastqc's --format option. - QC.FastqcRead1.kmers
-
Int? — Default:
None
Equivalent to fastqc's --kmers option. - QC.FastqcRead1.limits
-
File? — Default:
None
Equivalent to fastqc's --limits option. - QC.FastqcRead1.minLength
-
Int? — Default:
None
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.FastqcRead1After.adapters
-
File? — Default:
None
Equivalent to fastqc's --adapters option. - QC.FastqcRead1After.casava
-
Boolean — Default:
false
Equivalent to fastqc's --casava flag. - QC.FastqcRead1After.contaminants
-
File? — Default:
None
Equivalent to fastqc's --contaminants option. - QC.FastqcRead1After.dir
-
String? — Default:
None
Equivalent to fastqc's --dir option. - QC.FastqcRead1After.extract
-
Boolean — Default:
false
Equivalent to fastqc's --extract flag. - QC.FastqcRead1After.format
-
String? — Default:
None
Equivalent to fastqc's --format option. - QC.FastqcRead1After.kmers
-
Int? — Default:
None
Equivalent to fastqc's --kmers option. - QC.FastqcRead1After.limits
-
File? — Default:
None
Equivalent to fastqc's --limits option. - QC.FastqcRead1After.minLength
-
Int? — Default:
None
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.FastqcRead2.adapters
-
File? — Default:
None
Equivalent to fastqc's --adapters option. - QC.FastqcRead2.casava
-
Boolean — Default:
false
Equivalent to fastqc's --casava flag. - QC.FastqcRead2.contaminants
-
File? — Default:
None
Equivalent to fastqc's --contaminants option. - QC.FastqcRead2.dir
-
String? — Default:
None
Equivalent to fastqc's --dir option. - QC.FastqcRead2.extract
-
Boolean — Default:
false
Equivalent to fastqc's --extract flag. - QC.FastqcRead2.format
-
String? — Default:
None
Equivalent to fastqc's --format option. - QC.FastqcRead2.kmers
-
Int? — Default:
None
Equivalent to fastqc's --kmers option. - QC.FastqcRead2.limits
-
File? — Default:
None
Equivalent to fastqc's --limits option. - QC.FastqcRead2.minLength
-
Int? — Default:
None
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.FastqcRead2After.adapters
-
File? — Default:
None
Equivalent to fastqc's --adapters option. - QC.FastqcRead2After.casava
-
Boolean — Default:
false
Equivalent to fastqc's --casava flag. - QC.FastqcRead2After.contaminants
-
File? — Default:
None
Equivalent to fastqc's --contaminants option. - QC.FastqcRead2After.dir
-
String? — Default:
None
Equivalent to fastqc's --dir option. - QC.FastqcRead2After.extract
-
Boolean — Default:
false
Equivalent to fastqc's --extract flag. - QC.FastqcRead2After.format
-
String? — Default:
None
Equivalent to fastqc's --format option. - QC.FastqcRead2After.kmers
-
Int? — Default:
None
Equivalent to fastqc's --kmers option. - QC.FastqcRead2After.limits
-
File? — Default:
None
Equivalent to fastqc's --limits option. - QC.FastqcRead2After.minLength
-
Int? — Default:
None
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.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.NoneFile
- QC.FastqcRead1.NoneArray
- QC.FastqcRead2.NoneFile
- QC.FastqcRead2.NoneArray
- QC.FastqcRead1After.NoneFile
- QC.FastqcRead1After.NoneArray
- QC.FastqcRead2After.NoneFile
- QC.FastqcRead2After.NoneArray