cutadapt.wdl

version 1.0

task Cutadapt {
    input {
        File read1
        File? read2
        String read1output = "cut_r1.fq.gz"
        String? read2output
        String? format
        Array[String] adapter = []
        Array[String] front = []
        Array[String] anywhere = []
        Array[String] adapterRead2 = []
        Array[String] frontRead2 = []
        Array[String] anywhereRead2 = []
        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? trimPrimer
        Boolean? stripF3
        Boolean? maq
        Boolean? bwa
        Boolean? zeroCap
        Boolean? noZeroCap
        String reportPath = "cutadapt_report.txt"
        #Int compressionLevel = 1  # This only affects outputs with the .gz suffix.
        # --compression-level has a bug in 2.4 https://github.com/marcelm/cutadapt/pull/388
        #~{"--compression-level=" + compressionLevel} \
        Boolean Z = true  # equal to compressionLevel=1  # Fixme: replace once upstream is fixed.
        Int cores = 1
        Int memory = 16  # FIXME: Insane memory. Double-check if needed.
        String dockerImage = "quay.io/biocontainers/cutadapt:2.4--py37h14c3975_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="-Z" false="" Z} \
        ~{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 ""} \
        ~{"--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} \
        ~{read1} \
        ~{read2} \
        ~{"> " + reportPath}
    }

    output{
        File cutRead1 = read1output
        File? cutRead2 = read2output
        File report = reportPath
        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
        docker: dockerImage
    }
}