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cutadapt.wdl
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cutadapt.wdl
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version 1.0
# Copyright (c) 2017 Leiden University Medical Center
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
task Cutadapt {
input {
File read1
File? read2
String read1output = "cut_r1.fq.gz"
String? read2output
Array[String] adapter = []
Array[String] front = []
Array[String] anywhere = []
Array[String] adapterRead2 = []
Array[String] frontRead2 = []
Array[String] anywhereRead2 = []
String reportPath = "cutadapt_report.txt"
# Cutadapt compresses the zipped output files with a ridiculously
# high compression level (5 or 6).
# This is not the fast compression preset. It takes up to 400% more
# CPU time for a 20% reduction in file size.
# Hence we use compression level 1 here.
Int compressionLevel = 1 # This only affects outputs with the .gz suffix.
Boolean? interleaved
String? pairFilter
Float? errorRate
Boolean? noIndels
Int? times
Int? overlap
Boolean? matchReadWildcards
Boolean? noMatchAdapterWildcards
Boolean? noTrim
Boolean? maskAdapter
Int? cut
String? nextseqTrim
String? qualityCutoff
Int? qualityBase
Int? length
Boolean? trimN
String? lengthTag
String? stripSuffix
String? prefix
String? suffix
Int? minimumLength = 2 # Necessary to prevent creation of empty reads or 1 base reads.
Int? maximumLength
Int? maxN
Boolean? discardTrimmed
Boolean? discardUntrimmed
String? infoFilePath
String? restFilePath
String? wildcardFilePath
String? tooShortOutputPath
String? tooLongOutputPath
String? untrimmedOutputPath
String? tooShortPairedOutputPath
String? tooLongPairedOutputPath
String? untrimmedPairedOutputPath
Boolean? colorspace
Boolean? doubleEncode
Boolean? stripF3
Boolean? maq
Boolean? bwa
Boolean? zeroCap
Boolean? noZeroCap
Boolean revcomp = false
Int cores = 4
String memory = "5GiB"
Int timeMinutes = 1 + ceil(size([read1, read2], "G") * 12.0 / cores)
String dockerImage = "quay.io/biocontainers/cutadapt:4.4--py310h1425a21_0"
}
String realRead2output = select_first([read2output, "cut_r2.fq.gz"])
String read2outputArg = if (defined(read2))
then "mkdir -p $(dirname " + realRead2output + ")"
else ""
# FIXME: Use prefix() function for adapter, adapterRead2, etc.
command {
set -e
~{"mkdir -p $(dirname " + read1output + ")"}
~{read2outputArg}
cutadapt \
~{"--cores=" + cores} \
~{true="-a" false="" length(adapter) > 0} ~{sep=" -a " adapter} \
~{true="-A" false="" length(adapterRead2) > 0} ~{sep=" -A " adapterRead2} \
~{true="-g" false="" length(front) > 0} ~{sep=" -g " front} \
~{true="-G" false="" length(frontRead2) > 0} ~{sep=" -G " frontRead2} \
~{true="-b" false="" length(anywhere) > 0} ~{sep=" -b " anywhere} \
~{true="-B" false="" length(anywhereRead2) > 0} ~{sep=" -B " anywhereRead2} \
--output ~{read1output} ~{if defined(read2) then "-p " + realRead2output else ""} \
--compression-level ~{compressionLevel} \
~{"--to-short-output " + tooShortOutputPath} \
~{"--to-short-paired-output " + tooShortPairedOutputPath} \
~{"--to-long-output " + tooLongOutputPath} \
~{"--to-long-paired-output " + tooLongPairedOutputPath} \
~{"--untrimmed-output " + untrimmedOutputPath} \
~{"--untrimmed-paired-output " + untrimmedPairedOutputPath} \
~{"--pair-filter " + pairFilter} \
~{"--error-rate " + errorRate} \
~{"--times " + times} \
~{"--overlap " + overlap} \
~{"--cut " + cut} \
~{"--nextseq-trim " + nextseqTrim} \
~{"--quality-cutoff " + qualityCutoff} \
~{"--quality-base " + qualityBase} \
~{"--length " + length} \
~{"--length-tag " + lengthTag} \
~{"--strip-suffix " + stripSuffix} \
~{"--prefix " + prefix} \
~{"--suffix " + suffix} \
~{"--minimum-length " + minimumLength} \
~{"--maximum-length " + maximumLength} \
~{"--max-n " + maxN} \
~{true="--discard-untrimmed" false="" discardUntrimmed} \
~{"--info-file " + infoFilePath } \
~{"--rest-file " + restFilePath } \
~{"--wildcard-file " + wildcardFilePath} \
~{true="--match-read-wildcards" false="" matchReadWildcards} \
~{true="--no-match-adapter-wildcards" false="" noMatchAdapterWildcards} \
~{true="--no-trim" false="" noTrim} \
~{true="--mask-adapter" false="" maskAdapter} \
~{true="--no-indels" false="" noIndels} \
~{true="--trim-n" false="" trimN} \
~{true="--interleaved" false="" interleaved} \
~{true="--discard-trimmed" false="" discardTrimmed } \
~{true="--colorspace" false="" colorspace} \
~{true="--double-encode" false="" doubleEncode} \
~{true="--strip-f3" false="" stripF3} \
~{true="--maq" false="" maq} \
~{true="--bwa" false="" bwa} \
~{true="--zero-cap" false="" zeroCap} \
~{true="--no-zero-cap" false="" noZeroCap} \
~{if revcomp then "--revcomp" else ""} \
~{read1} \
~{read2} \
~{"> " + reportPath}
}
output{
File cutRead1 = read1output
File report = reportPath
File? cutRead2 = read2output
File? tooLongOutput=tooLongOutputPath
File? tooShortOutput=tooShortOutputPath
File? untrimmedOutput=untrimmedOutputPath
File? tooLongPairedOutput=tooLongPairedOutputPath
File? tooShortPairedOutput=tooShortPairedOutputPath
File? untrimmedPairedOutput=untrimmedPairedOutputPath
File? infoFile=infoFilePath
File? restFile=restFilePath
File? wildcardFile=wildcardFilePath
}
runtime {
cpu: cores
memory: memory
time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
# inputs
read1: {description: "The first or single end fastq file to be run through cutadapt.", category: "required"}
read2: {description: "An optional second end fastq file to be run through cutadapt.", category: "common"}
read1output: {description: "The name of the resulting first or single end fastq file.", category: "common"}
read2output: {description: "The name of the resulting second end fastq file.", category: "common"}
adapter: {description: "A list of 3' ligated adapter sequences to be cut from the given first or single end fastq file.", category: "common"}
front: {description: "A list of 5' ligated adapter sequences to be cut from the given first or single end fastq file.", category: "advanced"}
anywhere: {description: "A list of 3' or 5' ligated adapter sequences to be cut from the given first or single end fastq file.", category: "advanced"}
adapterRead2: {description: "A list of 3' ligated adapter sequences to be cut from the given second end fastq file.", category: "common"}
frontRead2: {description: "A list of 5' ligated adapter sequences to be cut from the given second end fastq file.", category: "advanced"}
anywhereRead2: {description: "A list of 3' or 5' ligated adapter sequences to be cut from the given second end fastq file.", category: "advanced"}
reportPath: {description: "The name of the file to write cutadapts's stdout to, this contains some metrics.", category: "common"}
compressionLevel: {description: "The compression level if gzipped output is used.", category: "advanced"}
interleaved: {description: "Equivalent to cutadapt's --interleaved flag.", category: "advanced"}
pairFilter: {description: "Equivalent to cutadapt's --pair-filter option.", category: "advanced"}
errorRate: {description: "Equivalent to cutadapt's --error-rate option.", category: "advanced"}
noIndels: {description: "Equivalent to cutadapt's --no-indels flag.", category: "advanced"}
times: {description: "Equivalent to cutadapt's --times option.", category: "advanced"}
overlap: {description: "Equivalent to cutadapt's --overlap option.", category: "advanced"}
matchReadWildcards: {description: "Equivalent to cutadapt's --match-read-wildcards flag.", category: "advanced"}
noMatchAdapterWildcards: {description: "Equivalent to cutadapt's --no-match-adapter-wildcards flag.", category: "advanced"}
noTrim: {description: "Equivalent to cutadapt's --no-trim flag.", category: "advanced"}
maskAdapter: {description: "Equivalent to cutadapt's --mask-adapter flag.", category: "advanced"}
cut: {description: "Equivalent to cutadapt's --cut option.", category: "advanced"}
nextseqTrim: {description: "Equivalent to cutadapt's --nextseq-trim option.", category: "advanced"}
qualityCutoff: {description: "Equivalent to cutadapt's --quality-cutoff option.", category: "advanced"}
qualityBase: {description: "Equivalent to cutadapt's --quality-base option.", category: "advanced"}
length: {description: "Equivalent to cutadapt's --length option.", category: "advanced"}
trimN: {description: "Equivalent to cutadapt's --trim-n flag.", category: "advanced"}
lengthTag: {description: "Equivalent to cutadapt's --length-tag option.", category: "advanced"}
stripSuffix: {description: "Equivalent to cutadapt's --strip-suffix option.", category: "advanced"}
prefix: {description: "Equivalent to cutadapt's --prefix option.", category: "advanced"}
suffix: {description: "Equivalent to cutadapt's --suffix option.", category: "advanced"}
minimumLength: {description: "Equivalent to cutadapt's --minimum-length option.", category: "advanced"}
maximumLength: {description: "Equivalent to cutadapt's --maximum-length option.", category: "advanced"}
maxN: {description: "Equivalent to cutadapt's --max-n option.", category: "advanced"}
discardTrimmed: {description: "Equivalent to cutadapt's --quality-cutoff option.", category: "advanced"}
discardUntrimmed: {description: "Equivalent to cutadapt's --discard-untrimmed option.", category: "advanced"}
infoFilePath: {description: "Equivalent to cutadapt's --info-file option.", category: "advanced"}
restFilePath: {description: "Equivalent to cutadapt's --rest-file option.", category: "advanced"}
wildcardFilePath: {description: "Equivalent to cutadapt's --wildcard-file option.", category: "advanced"}
tooShortOutputPath: {description: "Equivalent to cutadapt's --too-short-output option.", category: "advanced"}
tooLongOutputPath: {description: "Equivalent to cutadapt's --too-long-output option.", category: "advanced"}
untrimmedOutputPath: {description: "Equivalent to cutadapt's --untrimmed-output option.", category: "advanced"}
tooShortPairedOutputPath: {description: "Equivalent to cutadapt's --too-short-paired-output option.", category: "advanced"}
tooLongPairedOutputPath: {description: "Equivalent to cutadapt's --too-long-paired-output option.", category: "advanced"}
untrimmedPairedOutputPath: {description: "Equivalent to cutadapt's --untrimmed-paired-output option.", category: "advanced"}
colorspace: {description: "Equivalent to cutadapt's --colorspace flag.", category: "advanced"}
doubleEncode: {description: "Equivalent to cutadapt's --double-encode flag.", category: "advanced"}
stripF3: {description: "Equivalent to cutadapt's --strip-f3 flag.", category: "advanced"}
maq: {description: "Equivalent to cutadapt's --maq flag.", category: "advanced"}
bwa: {description: "Equivalent to cutadapt's --bwa flag.", category: "advanced"}
zeroCap: {description: "Equivalent to cutadapt's --zero-cap flag.", category: "advanced"}
noZeroCap: {description: "Equivalent to cutadapt's --no-zero-cap flag.", category: "advanced"}
revcomp: {description: "Equivalent to cutadapt's --revcomp flag.", category: "advanced"}
cores: {description: "The number of cores to use.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
# outputs
cutRead1: {description: "Trimmed read one."}
report: {description: "Per-adapter statistics file."}
cutRead2: {description: "Trimmed read two in pair."}
tooLongOutput: {description: "Reads that are too long according to -M."}
tooShortOutput: {description: "Reads that are too short according to -m."}
untrimmedOutput: {description: "All reads without adapters (instead of the regular output file)."}
tooLongPairedOutput: {description: "Second reads in a pair."}
tooShortPairedOutput: {description: "Second reads in a pair."}
untrimmedPairedOutput: {description: "The second reads in a pair that were not trimmed."}
infoFile: {description: "Detailed information about where adapters were found in each read."}
restFile: {description: "The rest file."}
wildcardFile: {description: "The wildcard file."}
}
}