Cutadapt¶

cutadapt · 1 contributor · 5 versions

cutadapt -a ADAPTER [options] [-o output.fastq] input.fastq

For paired-end reads:: cutadapt -a ADAPT1 -A ADAPT2 [options] -o out1.fastq -p out2.fastq in1.fastq in2.fastq

Replace “ADAPTER” with the actual sequence of your 3’ adapter. IUPAC wildcard characters are supported. The reverse complement is not automatically searched. All reads from input.fastq will be written to output.fastq with the adapter sequence removed. Adapter matching is error-tolerant. Multiple adapter sequences can be given (use further -a options), but only the best-matching adapter will be removed. Input may also be in FASTA format. Compressed input and output is supported and auto-detected from the file name (.gz, .xz, .bz2). Use the file name ‘-’ for standard input/output. Without the -o option, output is sent to standard output. Citation: Marcel Martin. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.Journal, 17(1):10-12, May 2011. http://dx.doi.org/10.14806/ej.17.1.200 Run “cutadapt - -help” to see all command-line options. See https://cutadapt.readthedocs.io/ for full documentation.

Quickstart¶

from janis_bioinformatics.tools.cutadapt.versions import CutAdapt_2_6

wf = WorkflowBuilder("myworkflow")

wf.step(
    "cutadapt_step",
    CutAdapt_2_6(
        outputPrefix=None,
        fastq=None,
    )
)
wf.output("out", source=cutadapt_step.out)

OR

Install Janis
Ensure Janis is configured to work with Docker or Singularity.
Ensure all reference files are available:

Note

More information about these inputs are available below.

Generate user input files for cutadapt:

# user inputs
janis inputs cutadapt > inputs.yaml

inputs.yaml

fastq:
- fastq_0.fastq.gz
- fastq_1.fastq.gz
outputPrefix: <value>

Run cutadapt with:

janis run [...run options] \
    --inputs inputs.yaml \
    cutadapt

Information¶

ID:	`cutadapt`
URL:	https://cutadapt.readthedocs.io/en/stable/
Versions:	2.6, 2.5, 2.4, 2.1, 1.18
Container:	quay.io/biocontainers/cutadapt:2.6–py36h516909a_0
Authors:	Michael Franklin
Citations:	Martin, Marcel. “Cutadapt Removes Adapter Sequences from High-Throughput Sequencing Reads.” EMBnet.journal, vol. 17, no. 1, EMBnet Stichting, May 2011, p. 10. Crossref, doi:10.14806/ej.17.1.200.
DOI:	DOI:10.14806/ej.17.1.200
Created:	2019-03-21
Updated:	2019-07-23

Outputs¶

name	type	documentation
out	FastqGzPair

Additional configuration (inputs)¶

name	type	prefix	position	documentation
outputPrefix	String			Used for naming purposes
fastq	FastqGzPair		5
adapter	Optional<Array<String>>	-a		Sequence of an adapter ligated to the 3’ end (paired data: of the first read). The adapter and subsequent bases are trimmed. If a ‘$’ character is appended (‘anchoring’), the adapter is only found if it is a suffix of the read.
outputFilename	Optional<Filename>	-o		Write trimmed reads to FILE. FASTQ or FASTA format is chosen depending on input. The summary report is sent to standard output. Use ‘{name}’ in FILE to demultiplex reads into multiple files. Default: write to standard output
secondReadFile	Optional<Filename>	-p		Write second read in a pair to FILE.
cores	Optional<Integer>	–cores		(-j) Number of CPU cores to use. Use 0 to auto-detect. Default: 1
front	Optional<String>	–front		(-g) Sequence of an adapter ligated to the 5’ end (paired data: of the first read). The adapter and any preceding bases are trimmed. Partial matches at the 5’ end are allowed. If a ‘^’ character is prepended (‘anchoring’), the adapter is only found if it is a prefix of the read.
anywhere	Optional<String>	–anywhere		(-b) Sequence of an adapter that may be ligated to the 5’ or 3’ end (paired data: of the first read). Both types of matches as described under -a und -g are allowed. If the first base of the read is part of the match, the behavior is as with -g, otherwise as with -a. This option is mostly for rescuing failed library preparations - do not use if you know which end your adapter was ligated to!
errorRate	Optional<Float>	–error-rate		(-e) Maximum allowed error rate as value between 0 and 1 (no. of errors divided by length of matching region). Default: 0.1 (=10%)
noIndels	Optional<Boolean>	–no-indels		Allow only mismatches in alignments. Default: allow both mismatches and indels
times	Optional<Integer>	–times		(-n) Remove up to COUNT adapters from each read. Default: 1
overlap	Optional<Integer>	–overlap		(-O) Require MINLENGTH overlap between read and adapter for an adapter to be found. Default: 3
matchReadWildcards	Optional<Boolean>	–match-read-wildcards		Interpret IUPAC wildcards in reads. Default: False
noMatchAdapterWildcards	Optional<Boolean>	–no-match-adapter-wildcards		(-N) Do not interpret IUPAC wildcards in adapters.
action	Optional<String>	–action		(trim,mask,lowercase,none} What to do with found adapters. mask: replace with ‘N’ characters; lowercase: convert to lowercase; none: leave unchanged (useful with –discard-untrimmed). Default: trim
cut	Optional<Integer>	–cut		(-u) Remove bases from each read (first read only if paired). If LENGTH is positive, remove bases from the beginning. If LENGTH is negative, remove bases from the end. Can be used twice if LENGTHs have different signs. This is applied before adapter trimming.
nextseqTrim	Optional<String>	–nextseq-trim		NextSeq-specific quality trimming (each read). Trims also dark cycles appearing as high-quality G bases.
qualityCutoff	Optional<Integer>	–quality-cutoff		(]3’CUTOFF, ]3’CUTOFF, -q) Trim low-quality bases from 5’ and/or 3’ ends of each read before adapter removal. Applied to both reads if data is paired. If one value is given, only the 3’ end is trimmed. If two comma-separated cutoffs are given, the 5’ end is trimmed with the first cutoff, the 3’ end with the second.
qualityBase	Optional<Boolean>	–quality-base		Assume that quality values in FASTQ are encoded as ascii(quality + N). This needs to be set to 64 for some old Illumina FASTQ files. Default: 33
length	Optional<Integer>	–length		(-l) Shorten reads to LENGTH. Positive values remove bases at the end while negative ones remove bases at the beginning. This and the following modifications are applied after adapter trimming.
trimN	Optional<Integer>	–trim-n		Trim N’s on ends of reads.
lengthTag	Optional<Integer>	–length-tag		Search for TAG followed by a decimal number in the description field of the read. Replace the decimal number with the correct length of the trimmed read. For example, use –length-tag ‘length=’ to correct fields like ‘length=123’.
stripSuffix	Optional<String>	–strip-suffix		Remove this suffix from read names if present. Can be given multiple times.
prefix	Optional<String>	–prefix		(-x) Add this prefix to read names. Use {name} to insert the name of the matching adapter.
suffix	Optional<String>	–suffix		(-y) Add this suffix to read names; can also include {name}
zeroCap	Optional<Boolean>	–zero-cap		(-z) Change negative quality values to zero.
minimumLength	Optional<Integer>	–minimum-length		(-m) Discard reads shorter than LEN. Default: 0
maximumLength	Optional<Integer>	–maximum-length		(-M) Discard reads longer than LEN. Default: no limit
maxN	Optional<Float>	–max-n		Discard reads with more than COUNT ‘N’ bases. If COUNT is a number between 0 and 1, it is interpreted as a fraction of the read length.
discardTrimmed	Optional<Boolean>	–discard-trimmed		(–discard) Discard reads that contain an adapter. Use also -O to avoid discarding too many randomly matching reads.
discardUntrimmed	Optional<Boolean>	–discard-untrimmed		(–trimmed-only) Discard reads that do not contain an adapter.
discardCasava	Optional<Boolean>	–discard-casava		Discard reads that did not pass CASAVA filtering (header has :Y:).
quiet	Optional<Boolean>	–quiet		Print only error messages. Which type of report to print: ‘full’ or ‘minimal’. Default: full
compressionLevel	Optional<String>	-Z		Use compression level 1 for gzipped output files (faster, but uses more space)
infoFile	Optional<String>	–info-file		Write information about each read and its adapter matches into FILE. See the documentation for the file format.
restFile	Optional<String>	–rest-file		(-r) When the adapter matches in the middle of a read, write the rest (after the adapter) to FILE.
wildcardFile	Optional<String>	–wildcard-file		When the adapter has N wildcard bases, write adapter bases matching wildcard positions to FILE. (Inaccurate with indels.)
tooShortOutput	Optional<String>	–too-short-output		Write reads that are too short (according to length specified by -m) to FILE. Default: discard reads
tooLongOutput	Optional<String>	–too-long-output		Write reads that are too long (according to length specified by -M) to FILE. Default: discard reads
untrimmedOutput	Optional<String>	–untrimmed-output		Write reads that do not contain any adapter to FILE. Default: output to same file as trimmed reads
removeMiddle3Adapter	Optional<Array<String>>	-A		3’ adapter to be removed from second read in a pair.
removeMiddle5Adapter	Optional<String>	-G		5’ adapter to be removed from second read in a pair.
removeMiddleBothAdapter	Optional<String>	-B		5’/3 adapter to be removed from second read in a pair.
removeNBasesFromSecondRead	Optional<String>	-U		Remove LENGTH bases from second read in a pair.
pairAdapters	Optional<String>	–pair-adapters		Treat adapters given with -a/-A etc. as pairs. Either both or none are removed from each read pair.
pairFilter	Optional<String>	–pair-filter		{any,both,first} Which of the reads in a paired-end read have to match the filtering criterion in order for the pair to be filtered. Default: any
interleaved	Optional<Boolean>	–interleaved		Read and write interleaved paired-end reads.
untrimmedPairedOutput	Optional<String>	–untrimmed-paired-output		Write second read in a pair to this FILE when no adapter was found. Use with –untrimmed-output. Default: output to same file as trimmed reads
tooShortPairedOutput	Optional<String>	–too-short-paired-output		Write second read in a pair to this file if pair is too short. Use also –too-short-output.
tooLongPairedOutput	Optional<String>	–too-long-paired-output		Write second read in a pair to this file if pair is too long. Use also –too-long-output.

Workflow Description Language¶

version development

task cutadapt {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    String outputPrefix
    Array[File] fastq
    Array[String]? adapter
    String? outputFilename
    String? secondReadFile
    Int? cores
    String? front
    String? anywhere
    Float? errorRate
    Boolean? noIndels
    Int? times
    Int? overlap
    Boolean? matchReadWildcards
    Boolean? noMatchAdapterWildcards
    String? action
    Int? cut
    String? nextseqTrim
    Int? qualityCutoff
    Boolean? qualityBase
    Int? length
    Int? trimN
    Int? lengthTag
    String? stripSuffix
    String? prefix
    String? suffix
    Boolean? zeroCap
    Int? minimumLength
    Int? maximumLength
    Float? maxN
    Boolean? discardTrimmed
    Boolean? discardUntrimmed
    Boolean? discardCasava
    Boolean? quiet
    String? compressionLevel
    String? infoFile
    String? restFile
    String? wildcardFile
    String? tooShortOutput
    String? tooLongOutput
    String? untrimmedOutput
    Array[String]? removeMiddle3Adapter
    String? removeMiddle5Adapter
    String? removeMiddleBothAdapter
    String? removeNBasesFromSecondRead
    String? pairAdapters
    String? pairFilter
    Boolean? interleaved
    String? untrimmedPairedOutput
    String? tooShortPairedOutput
    String? tooLongPairedOutput
  }
  command <<<
    set -e
    cutadapt \
      ~{if (defined(adapter) && length(select_first([adapter])) > 0) then "-a '" + sep("' -a '", select_first([adapter])) + "'" else ""} \
      -o '~{select_first([outputFilename, "~{outputPrefix}-R1.fastq.gz"])}' \
      -p '~{select_first([secondReadFile, "~{outputPrefix}-R2.fastq.gz"])}' \
      ~{if defined(cores) then ("--cores " + cores) else ''} \
      ~{if defined(front) then ("--front '" + front + "'") else ""} \
      ~{if defined(anywhere) then ("--anywhere '" + anywhere + "'") else ""} \
      ~{if defined(errorRate) then ("--error-rate " + errorRate) else ''} \
      ~{if (defined(noIndels) && select_first([noIndels])) then "--no-indels" else ""} \
      ~{if defined(times) then ("--times " + times) else ''} \
      ~{if defined(overlap) then ("--overlap " + overlap) else ''} \
      ~{if (defined(matchReadWildcards) && select_first([matchReadWildcards])) then "--match-read-wildcards" else ""} \
      ~{if (defined(noMatchAdapterWildcards) && select_first([noMatchAdapterWildcards])) then "--no-match-adapter-wildcards" else ""} \
      ~{if defined(action) then ("--action '" + action + "'") else ""} \
      ~{if defined(cut) then ("--cut " + cut) else ''} \
      ~{if defined(nextseqTrim) then ("--nextseq-trim '" + nextseqTrim + "'") else ""} \
      ~{if defined(qualityCutoff) then ("--quality-cutoff " + qualityCutoff) else ''} \
      ~{if (defined(qualityBase) && select_first([qualityBase])) then "--quality-base" else ""} \
      ~{if defined(length) then ("--length " + length) else ''} \
      ~{if defined(trimN) then ("--trim-n " + trimN) else ''} \
      ~{if defined(lengthTag) then ("--length-tag " + lengthTag) else ''} \
      ~{if defined(stripSuffix) then ("--strip-suffix '" + stripSuffix + "'") else ""} \
      ~{if defined(prefix) then ("--prefix '" + prefix + "'") else ""} \
      ~{if defined(suffix) then ("--suffix '" + suffix + "'") else ""} \
      ~{if (defined(zeroCap) && select_first([zeroCap])) then "--zero-cap" else ""} \
      ~{if defined(minimumLength) then ("--minimum-length " + minimumLength) else ''} \
      ~{if defined(maximumLength) then ("--maximum-length " + maximumLength) else ''} \
      ~{if defined(maxN) then ("--max-n " + maxN) else ''} \
      ~{if (defined(discardTrimmed) && select_first([discardTrimmed])) then "--discard-trimmed" else ""} \
      ~{if (defined(discardUntrimmed) && select_first([discardUntrimmed])) then "--discard-untrimmed" else ""} \
      ~{if (defined(discardCasava) && select_first([discardCasava])) then "--discard-casava" else ""} \
      ~{if (defined(quiet) && select_first([quiet])) then "--quiet" else ""} \
      ~{if defined(compressionLevel) then ("-Z '" + compressionLevel + "'") else ""} \
      ~{if defined(infoFile) then ("--info-file '" + infoFile + "'") else ""} \
      ~{if defined(restFile) then ("--rest-file '" + restFile + "'") else ""} \
      ~{if defined(wildcardFile) then ("--wildcard-file '" + wildcardFile + "'") else ""} \
      ~{if defined(tooShortOutput) then ("--too-short-output '" + tooShortOutput + "'") else ""} \
      ~{if defined(tooLongOutput) then ("--too-long-output '" + tooLongOutput + "'") else ""} \
      ~{if defined(untrimmedOutput) then ("--untrimmed-output '" + untrimmedOutput + "'") else ""} \
      ~{if (defined(removeMiddle3Adapter) && length(select_first([removeMiddle3Adapter])) > 0) then "-A '" + sep("' -A '", select_first([removeMiddle3Adapter])) + "'" else ""} \
      ~{if defined(removeMiddle5Adapter) then ("-G '" + removeMiddle5Adapter + "'") else ""} \
      ~{if defined(removeMiddleBothAdapter) then ("-B '" + removeMiddleBothAdapter + "'") else ""} \
      ~{if defined(removeNBasesFromSecondRead) then ("-U '" + removeNBasesFromSecondRead + "'") else ""} \
      ~{if defined(pairAdapters) then ("--pair-adapters '" + pairAdapters + "'") else ""} \
      ~{if defined(pairFilter) then ("--pair-filter '" + pairFilter + "'") else ""} \
      ~{if (defined(interleaved) && select_first([interleaved])) then "--interleaved" else ""} \
      ~{if defined(untrimmedPairedOutput) then ("--untrimmed-paired-output '" + untrimmedPairedOutput + "'") else ""} \
      ~{if defined(tooShortPairedOutput) then ("--too-short-paired-output '" + tooShortPairedOutput + "'") else ""} \
      ~{if defined(tooLongPairedOutput) then ("--too-long-paired-output '" + tooLongPairedOutput + "'") else ""} \
      ~{if length(fastq) > 0 then "'" + sep("' '", fastq) + "'" else ""}
  >>>
  runtime {
    cpu: select_first([runtime_cpu, 5, 1])
    disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
    docker: "quay.io/biocontainers/cutadapt:2.6--py36h516909a_0"
    duration: select_first([runtime_seconds, 86400])
    memory: "~{select_first([runtime_memory, 4, 4])}G"
    preemptible: 2
  }
  output {
    Array[File] out = [(outputPrefix + "-R1.fastq.gz"), (outputPrefix + "-R2.fastq.gz")]
  }
}

Common Workflow Language¶

#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: Cutadapt
doc: |
  cutadapt version 2.4
  Copyright (C) 2010-2019 Marcel Martin <marcel.martin@scilifelab.se>
  cutadapt removes adapter sequences from high-throughput sequencing reads.
  Usage:
      cutadapt -a ADAPTER [options] [-o output.fastq] input.fastq
  For paired-end reads:
      cutadapt -a ADAPT1 -A ADAPT2 [options] -o out1.fastq -p out2.fastq in1.fastq in2.fastq
  Replace "ADAPTER" with the actual sequence of your 3' adapter. IUPAC wildcard
  characters are supported. The reverse complement is *not* automatically
  searched. All reads from input.fastq will be written to output.fastq with the
  adapter sequence removed. Adapter matching is error-tolerant. Multiple adapter
  sequences can be given (use further -a options), but only the best-matching
  adapter will be removed.
  Input may also be in FASTA format. Compressed input and output is supported and
  auto-detected from the file name (.gz, .xz, .bz2). Use the file name '-' for
  standard input/output. Without the -o option, output is sent to standard output.
  Citation:
  Marcel Martin. Cutadapt removes adapter sequences from high-throughput
  sequencing reads. EMBnet.Journal, 17(1):10-12, May 2011.
  http://dx.doi.org/10.14806/ej.17.1.200
  Run "cutadapt - -help" to see all command-line options.
  See https://cutadapt.readthedocs.io/ for full documentation.

requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
  dockerPull: quay.io/biocontainers/cutadapt:2.6--py36h516909a_0

inputs:
- id: outputPrefix
  label: outputPrefix
  doc: Used for naming purposes
  type: string
- id: fastq
  label: fastq
  type:
    type: array
    items: File
  inputBinding:
    position: 5
- id: adapter
  label: adapter
  doc: |-
    Sequence of an adapter ligated to the 3' end (paired data: of the first read). The adapter and subsequent bases are trimmed. If a '$' character is appended ('anchoring'), the adapter is only found if it is a suffix of the read.
  type:
  - type: array
    inputBinding:
      prefix: -a
    items: string
  - 'null'
  inputBinding: {}
- id: outputFilename
  label: outputFilename
  doc: |-
    Write trimmed reads to FILE. FASTQ or FASTA format is chosen depending on input. The summary report is sent to standard output. Use '{name}' in FILE to demultiplex reads into multiple files. Default: write to standard output
  type:
  - string
  - 'null'
  default: generated-R1.fastq.gz
  inputBinding:
    prefix: -o
    valueFrom: $(inputs.outputPrefix)-R1.fastq.gz
- id: secondReadFile
  label: secondReadFile
  doc: Write second read in a pair to FILE.
  type:
  - string
  - 'null'
  default: generated-R2.fastq.gz
  inputBinding:
    prefix: -p
    valueFrom: $(inputs.outputPrefix)-R2.fastq.gz
- id: cores
  label: cores
  doc: '(-j)  Number of CPU cores to use. Use 0 to auto-detect. Default: 1'
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --cores
    separate: true
- id: front
  label: front
  doc: |-
    (-g)  Sequence of an adapter ligated to the 5' end (paired data: of the first read). The adapter and any preceding bases are trimmed. Partial matches at the 5' end are allowed. If a '^' character is prepended ('anchoring'), the adapter is only found if it is a prefix of the read.
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --front
    separate: true
- id: anywhere
  label: anywhere
  doc: |-
    (-b)  Sequence of an adapter that may be ligated to the 5' or 3' end (paired data: of the first read). Both types of matches as described under -a und -g are allowed. If the first base of the read is part of the match, the behavior is as with -g, otherwise as with -a. This option is mostly for rescuing failed library preparations - do not use if you know which end your adapter was ligated to!
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --anywhere
    separate: true
- id: errorRate
  label: errorRate
  doc: |-
    (-e)  Maximum allowed error rate as value between 0 and 1 (no. of errors divided by length of matching region). Default: 0.1 (=10%)
  type:
  - float
  - 'null'
  inputBinding:
    prefix: --error-rate
    separate: true
- id: noIndels
  label: noIndels
  doc: 'Allow only mismatches in alignments. Default: allow both mismatches and indels'
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --no-indels
    separate: true
- id: times
  label: times
  doc: '(-n)  Remove up to COUNT adapters from each read. Default: 1'
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --times
    separate: true
- id: overlap
  label: overlap
  doc: |-
    (-O)  Require MINLENGTH overlap between read and adapter for an adapter to be found. Default: 3
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --overlap
    separate: true
- id: matchReadWildcards
  label: matchReadWildcards
  doc: ' Interpret IUPAC wildcards in reads. Default: False'
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --match-read-wildcards
    separate: true
- id: noMatchAdapterWildcards
  label: noMatchAdapterWildcards
  doc: (-N)  Do not interpret IUPAC wildcards in adapters.
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --no-match-adapter-wildcards
    separate: true
- id: action
  label: action
  doc: |-
    (trim,mask,lowercase,none}  What to do with found adapters. mask: replace with 'N' characters; lowercase: convert to lowercase; none: leave unchanged (useful with --discard-untrimmed). Default: trim
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --action
    separate: true
- id: cut
  label: cut
  doc: |-
    (-u)  Remove bases from each read (first read only if paired). If LENGTH is positive, remove bases from the beginning. If LENGTH is negative, remove bases from the end. Can be used twice if LENGTHs have different signs. This is applied *before* adapter trimming.
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --cut
    separate: true
- id: nextseqTrim
  label: nextseqTrim
  doc: |2-
     NextSeq-specific quality trimming (each read). Trims also dark cycles appearing as high-quality G bases.
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --nextseq-trim
    separate: true
- id: qualityCutoff
  label: qualityCutoff
  doc: |-
    (]3'CUTOFF, ]3'CUTOFF, -q)  Trim low-quality bases from 5' and/or 3' ends of each read before adapter removal. Applied to both reads if data is paired. If one value is given, only the 3' end is trimmed. If two comma-separated cutoffs are given, the 5' end is trimmed with the first cutoff, the 3' end with the second.
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --quality-cutoff
    separate: true
- id: qualityBase
  label: qualityBase
  doc: |-
    Assume that quality values in FASTQ are encoded as ascii(quality + N). This needs to be set to 64 for some old Illumina FASTQ files. Default: 33
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --quality-base
    separate: true
- id: length
  label: length
  doc: |-
    (-l)  Shorten reads to LENGTH. Positive values remove bases at the end while negative ones remove bases at the beginning. This and the following modifications are applied after adapter trimming.
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --length
    separate: true
- id: trimN
  label: trimN
  doc: Trim N's on ends of reads.
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --trim-n
    separate: true
- id: lengthTag
  label: lengthTag
  doc: |-
    Search for TAG followed by a decimal number in the description field of the read. Replace the decimal number with the correct length of the trimmed read. For example, use --length-tag 'length=' to correct fields like 'length=123'.
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --length-tag
    separate: true
- id: stripSuffix
  label: stripSuffix
  doc: ' Remove this suffix from read names if present. Can be given multiple times.'
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --strip-suffix
    separate: true
- id: prefix
  label: prefix
  doc: |-
    (-x)  Add this prefix to read names. Use {name} to insert the name of the matching adapter.
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --prefix
    separate: true
- id: suffix
  label: suffix
  doc: (-y)  Add this suffix to read names; can also include {name}
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --suffix
    separate: true
- id: zeroCap
  label: zeroCap
  doc: (-z) Change negative quality values to zero.
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --zero-cap
    separate: true
- id: minimumLength
  label: minimumLength
  doc: '(-m)  Discard reads shorter than LEN. Default: 0'
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --minimum-length
    separate: true
- id: maximumLength
  label: maximumLength
  doc: '(-M)  Discard reads longer than LEN. Default: no limit'
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --maximum-length
    separate: true
- id: maxN
  label: maxN
  doc: |-
    Discard reads with more than COUNT 'N' bases. If COUNT is a number between 0 and 1, it is interpreted as a fraction of the read length.
  type:
  - float
  - 'null'
  inputBinding:
    prefix: --max-n
    separate: true
- id: discardTrimmed
  label: discardTrimmed
  doc: |-
    (--discard)  Discard reads that contain an adapter. Use also -O to avoid discarding too many randomly matching reads.
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --discard-trimmed
    separate: true
- id: discardUntrimmed
  label: discardUntrimmed
  doc: (--trimmed-only)  Discard reads that do not contain an adapter.
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --discard-untrimmed
    separate: true
- id: discardCasava
  label: discardCasava
  doc: Discard reads that did not pass CASAVA filtering (header has :Y:).
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --discard-casava
    separate: true
- id: quiet
  label: quiet
  doc: |-
    Print only error messages. Which type of report to print: 'full' or 'minimal'. Default: full
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --quiet
    separate: true
- id: compressionLevel
  label: compressionLevel
  doc: Use compression level 1 for gzipped output files (faster, but uses more space)
  type:
  - string
  - 'null'
  inputBinding:
    prefix: -Z
    separate: true
- id: infoFile
  label: infoFile
  doc: |-
    Write information about each read and its adapter matches into FILE. See the documentation for the file format.
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --info-file
    separate: true
- id: restFile
  label: restFile
  doc: |-
    (-r)  When the adapter matches in the middle of a read, write the rest (after the adapter) to FILE.
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --rest-file
    separate: true
- id: wildcardFile
  label: wildcardFile
  doc: |-
    When the adapter has N wildcard bases, write adapter bases matching wildcard positions to FILE. (Inaccurate with indels.)
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --wildcard-file
    separate: true
- id: tooShortOutput
  label: tooShortOutput
  doc: |2-
     Write reads that are too short (according to length specified by -m) to FILE. Default: discard reads
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --too-short-output
    separate: true
- id: tooLongOutput
  label: tooLongOutput
  doc: |2-
     Write reads that are too long (according to length specified by -M) to FILE. Default: discard reads
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --too-long-output
    separate: true
- id: untrimmedOutput
  label: untrimmedOutput
  doc: |2-
     Write reads that do not contain any adapter to FILE. Default: output to same file as trimmed reads
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --untrimmed-output
    separate: true
- id: removeMiddle3Adapter
  label: removeMiddle3Adapter
  doc: 3' adapter to be removed from second read in a pair.
  type:
  - type: array
    inputBinding:
      prefix: -A
      separate: true
    items: string
  - 'null'
  inputBinding: {}
- id: removeMiddle5Adapter
  label: removeMiddle5Adapter
  doc: 5' adapter to be removed from second read in a pair.
  type:
  - string
  - 'null'
  inputBinding:
    prefix: -G
    separate: true
- id: removeMiddleBothAdapter
  label: removeMiddleBothAdapter
  doc: 5'/3 adapter to be removed from second read in a pair.
  type:
  - string
  - 'null'
  inputBinding:
    prefix: -B
    separate: true
- id: removeNBasesFromSecondRead
  label: removeNBasesFromSecondRead
  doc: Remove LENGTH bases from second read in a pair.
  type:
  - string
  - 'null'
  inputBinding:
    prefix: -U
    separate: true
- id: pairAdapters
  label: pairAdapters
  doc: |-
    Treat adapters given with -a/-A etc. as pairs. Either both or none are removed from each read pair.
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --pair-adapters
    separate: true
- id: pairFilter
  label: pairFilter
  doc: |-
    {any,both,first} Which of the reads in a paired-end read have to match the filtering criterion in order for the pair to be filtered. Default: any
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --pair-filter
    separate: true
- id: interleaved
  label: interleaved
  doc: Read and write interleaved paired-end reads.
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --interleaved
    separate: true
- id: untrimmedPairedOutput
  label: untrimmedPairedOutput
  doc: |2-
     Write second read in a pair to this FILE when no adapter was found. Use with --untrimmed-output. Default: output to same file as trimmed reads
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --untrimmed-paired-output
    separate: true
- id: tooShortPairedOutput
  label: tooShortPairedOutput
  doc: |2-
     Write second read in a pair to this file if pair is too short. Use also --too-short-output.
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --too-short-paired-output
    separate: true
- id: tooLongPairedOutput
  label: tooLongPairedOutput
  doc: |2-
     Write second read in a pair to this file if pair is too long. Use also --too-long-output.
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --too-long-paired-output
    separate: true

outputs:
- id: out
  label: out
  type:
    type: array
    items: File
  outputBinding:
    glob:
    - $((inputs.outputPrefix + "-R1.fastq.gz"))
    - $((inputs.outputPrefix + "-R2.fastq.gz"))
    loadContents: false
stdout: _stdout
stderr: _stderr

baseCommand: cutadapt
arguments: []

hints:
- class: ToolTimeLimit
  timelimit: |-
    $([inputs.runtime_seconds, 86400].filter(function (inner) { return inner != null })[0])
id: cutadapt