#!/usr/bin/env bash

# cutadapt add_sgdemux
# 
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
# 
# The component may contain files which fall under a different license. The
# authors of this component should specify the license in the header of such
# files, or include a separate license file detailing the licenses of all included
# files.
# 
# Component authors:
#  * Toni Verbeiren (author, maintainer)

set -e

if [ -z "$VIASH_TEMP" ]; then
  VIASH_TEMP=${VIASH_TEMP:-$VIASH_TMPDIR}
  VIASH_TEMP=${VIASH_TEMP:-$VIASH_TEMPDIR}
  VIASH_TEMP=${VIASH_TEMP:-$VIASH_TMP}
  VIASH_TEMP=${VIASH_TEMP:-$TMPDIR}
  VIASH_TEMP=${VIASH_TEMP:-$TMP}
  VIASH_TEMP=${VIASH_TEMP:-$TEMPDIR}
  VIASH_TEMP=${VIASH_TEMP:-$TEMP}
  VIASH_TEMP=${VIASH_TEMP:-/tmp}
fi

# define helper functions
# ViashQuote: put quotes around non flag values
# $1     : unquoted string
# return : possibly quoted string
# examples:
#   ViashQuote --foo      # returns --foo
#   ViashQuote bar        # returns 'bar'
#   Viashquote --foo=bar  # returns --foo='bar'
function ViashQuote {
  if [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+=.+$ ]]; then
    echo "$1" | sed "s#=\(.*\)#='\1'#"
  elif [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+$ ]]; then
    echo "$1"
  else
    echo "'$1'"
  fi
}
# ViashRemoveFlags: Remove leading flag
# $1     : string with a possible leading flag
# return : string without possible leading flag
# examples:
#   ViashRemoveFlags --foo=bar  # returns bar
function ViashRemoveFlags {
  echo "$1" | sed 's/^--*[a-zA-Z0-9_\-]*=//'
}
# ViashSourceDir: return the path of a bash file, following symlinks
# usage   : ViashSourceDir ${BASH_SOURCE[0]}
# $1      : Should always be set to ${BASH_SOURCE[0]}
# returns : The absolute path of the bash file
function ViashSourceDir {
  local source="$1"
  while [ -h "$source" ]; do
    local dir="$( cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd )"
    source="$(readlink "$source")"
    [[ $source != /* ]] && source="$dir/$source"
  done
  cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd
}
# ViashFindTargetDir: return the path of the '.build.yaml' file, following symlinks
# usage   : ViashFindTargetDir 'ScriptPath'
# $1      : The location from where to start the upward search
# returns : The absolute path of the '.build.yaml' file
function ViashFindTargetDir {
  local source="$1"
  while [[ "$source" != "" && ! -e "$source/.build.yaml" ]]; do
    source=${source%/*}
  done
  echo $source
}
# see https://en.wikipedia.org/wiki/Syslog#Severity_level
VIASH_LOGCODE_EMERGENCY=0
VIASH_LOGCODE_ALERT=1
VIASH_LOGCODE_CRITICAL=2
VIASH_LOGCODE_ERROR=3
VIASH_LOGCODE_WARNING=4
VIASH_LOGCODE_NOTICE=5
VIASH_LOGCODE_INFO=6
VIASH_LOGCODE_DEBUG=7
VIASH_VERBOSITY=$VIASH_LOGCODE_NOTICE

# ViashLog: Log events depending on the verbosity level
# usage: ViashLog 1 alert Oh no something went wrong!
# $1: required verbosity level
# $2: display tag
# $3+: messages to display
# stdout: Your input, prepended by '[$2] '.
function ViashLog {
  local required_level="$1"
  local display_tag="$2"
  shift 2
  if [ $VIASH_VERBOSITY -ge $required_level ]; then
    >&2 echo "[$display_tag]" "$@"
  fi
}

# ViashEmergency: log events when the system is unstable
# usage: ViashEmergency Oh no something went wrong.
# stdout: Your input, prepended by '[emergency] '.
function ViashEmergency {
  ViashLog $VIASH_LOGCODE_EMERGENCY emergency "$@"
}

# ViashAlert: log events when actions must be taken immediately (e.g. corrupted system database)
# usage: ViashAlert Oh no something went wrong.
# stdout: Your input, prepended by '[alert] '.
function ViashAlert {
  ViashLog $VIASH_LOGCODE_ALERT alert "$@"
}

# ViashCritical: log events when a critical condition occurs
# usage: ViashCritical Oh no something went wrong.
# stdout: Your input, prepended by '[critical] '.
function ViashCritical {
  ViashLog $VIASH_LOGCODE_CRITICAL critical "$@"
}

# ViashError: log events when an error condition occurs
# usage: ViashError Oh no something went wrong.
# stdout: Your input, prepended by '[error] '.
function ViashError {
  ViashLog $VIASH_LOGCODE_ERROR error "$@"
}

# ViashWarning: log potentially abnormal events
# usage: ViashWarning Something may have gone wrong.
# stdout: Your input, prepended by '[warning] '.
function ViashWarning {
  ViashLog $VIASH_LOGCODE_WARNING warning "$@"
}

# ViashNotice: log significant but normal events
# usage: ViashNotice This just happened.
# stdout: Your input, prepended by '[notice] '.
function ViashNotice {
  ViashLog $VIASH_LOGCODE_NOTICE notice "$@"
}

# ViashInfo: log normal events
# usage: ViashInfo This just happened.
# stdout: Your input, prepended by '[info] '.
function ViashInfo {
  ViashLog $VIASH_LOGCODE_INFO info "$@"
}

# ViashDebug: log all events, for debugging purposes
# usage: ViashDebug This just happened.
# stdout: Your input, prepended by '[debug] '.
function ViashDebug {
  ViashLog $VIASH_LOGCODE_DEBUG debug "$@"
}

# find source folder of this component
VIASH_META_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}`

# find the root of the built components & dependencies
VIASH_TARGET_DIR=`ViashFindTargetDir $VIASH_META_RESOURCES_DIR`

# define meta fields
VIASH_META_NAME="cutadapt"
VIASH_META_FUNCTIONALITY_NAME="cutadapt"
VIASH_META_EXECUTABLE="$VIASH_META_RESOURCES_DIR/$VIASH_META_NAME"
VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
VIASH_META_TEMP_DIR="$VIASH_TEMP"


# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
  echo "cutadapt add_sgdemux"
  echo ""
  echo "Cutadapt removes adapter sequences from high-throughput sequencing reads."
  echo ""
  echo "Specify Adapters for R1:"
  echo "    -a, --adapter"
  echo "        type: string, multiple values allowed"
  echo "        Sequence of an adapter ligated to the 3' end (paired data:"
  echo "        of the first read). The adapter and subsequent bases are"
  echo "        trimmed. If a '\$' character is appended ('anchoring'), the"
  echo "        adapter is only found if it is a suffix of the read."
  echo ""
  echo "    -g, --front"
  echo "        type: string, multiple values allowed"
  echo "        Sequence of an adapter ligated to the 5' end (paired data:"
  echo "        of the first read). The adapter and any preceding bases"
  echo "        are trimmed. Partial matches at the 5' end are allowed. If"
  echo "        a '^' character is prepended ('anchoring'), the adapter is"
  echo "        only found if it is a prefix of the read."
  echo ""
  echo "    -b, --anywhere"
  echo "        type: string, multiple values allowed"
  echo "        Sequence of an adapter that may be ligated to the 5' or 3'"
  echo "        end (paired data: of the first read). Both types of"
  echo "        matches as described under -a and -g are allowed. If the"
  echo "        first base of the read is part of the match, the behavior"
  echo "        is as with -g, otherwise as with -a. This option is mostly"
  echo "        for rescuing failed library preparations - do not use if"
  echo "        you know which end your adapter was ligated to!"
  echo ""
  echo "Specify Adapters using Fasta files for R1:"
  echo "    --adapter_fasta"
  echo "        type: file, multiple values allowed, file must exist"
  echo "        Fasta file containing sequences of an adapter ligated to the 3' end"
  echo "        (paired data:"
  echo "        of the first read). The adapter and subsequent bases are"
  echo "        trimmed. If a '\$' character is appended ('anchoring'), the"
  echo "        adapter is only found if it is a suffix of the read."
  echo ""
  echo "    --front_fasta"
  echo "        type: file, file must exist"
  echo "        Fasta file containing sequences of an adapter ligated to the 5' end"
  echo "        (paired data:"
  echo "        of the first read). The adapter and any preceding bases"
  echo "        are trimmed. Partial matches at the 5' end are allowed. If"
  echo "        a '^' character is prepended ('anchoring'), the adapter is"
  echo "        only found if it is a prefix of the read."
  echo ""
  echo "    --anywhere_fasta"
  echo "        type: file, file must exist"
  echo "        Fasta file containing sequences of an adapter that may be ligated to the"
  echo "        5' or 3'"
  echo "        end (paired data: of the first read). Both types of"
  echo "        matches as described under -a and -g are allowed. If the"
  echo "        first base of the read is part of the match, the behavior"
  echo "        is as with -g, otherwise as with -a. This option is mostly"
  echo "        for rescuing failed library preparations - do not use if"
  echo "        you know which end your adapter was ligated to!"
  echo ""
  echo "Specify Adapters for R2:"
  echo "    -A, --adapter_r2"
  echo "        type: string, multiple values allowed"
  echo "        Sequence of an adapter ligated to the 3' end (paired data:"
  echo "        of the first read). The adapter and subsequent bases are"
  echo "        trimmed. If a '\$' character is appended ('anchoring'), the"
  echo "        adapter is only found if it is a suffix of the read."
  echo ""
  echo "    -G, --front_r2"
  echo "        type: string, multiple values allowed"
  echo "        Sequence of an adapter ligated to the 5' end (paired data:"
  echo "        of the first read). The adapter and any preceding bases"
  echo "        are trimmed. Partial matches at the 5' end are allowed. If"
  echo "        a '^' character is prepended ('anchoring'), the adapter is"
  echo "        only found if it is a prefix of the read."
  echo ""
  echo "    -B, --anywhere_r2"
  echo "        type: string, multiple values allowed"
  echo "        Sequence of an adapter that may be ligated to the 5' or 3'"
  echo "        end (paired data: of the first read). Both types of"
  echo "        matches as described under -a and -g are allowed. If the"
  echo "        first base of the read is part of the match, the behavior"
  echo "        is as with -g, otherwise as with -a. This option is mostly"
  echo "        for rescuing failed library preparations - do not use if"
  echo "        you know which end your adapter was ligated to!"
  echo ""
  echo "Specify Adapters using Fasta files for R2:"
  echo "    --adapter_r2_fasta"
  echo "        type: file, file must exist"
  echo "        Fasta file containing sequences of an adapter ligated to the 3' end"
  echo "        (paired data:"
  echo "        of the first read). The adapter and subsequent bases are"
  echo "        trimmed. If a '\$' character is appended ('anchoring'), the"
  echo "        adapter is only found if it is a suffix of the read."
  echo ""
  echo "    --front_r2_fasta"
  echo "        type: file, file must exist"
  echo "        Fasta file containing sequences of an adapter ligated to the 5' end"
  echo "        (paired data:"
  echo "        of the first read). The adapter and any preceding bases"
  echo "        are trimmed. Partial matches at the 5' end are allowed. If"
  echo "        a '^' character is prepended ('anchoring'), the adapter is"
  echo "        only found if it is a prefix of the read."
  echo ""
  echo "    --anywhere_r2_fasta"
  echo "        type: file, file must exist"
  echo "        Fasta file containing sequences of an adapter that may be ligated to the"
  echo "        5' or 3'"
  echo "        end (paired data: of the first read). Both types of"
  echo "        matches as described under -a and -g are allowed. If the"
  echo "        first base of the read is part of the match, the behavior"
  echo "        is as with -g, otherwise as with -a. This option is mostly"
  echo "        for rescuing failed library preparations - do not use if"
  echo "        you know which end your adapter was ligated to!"
  echo ""
  echo "Paired-end options:"
  echo "    --pair_adapters"
  echo "        type: boolean_true"
  echo "        Treat adapters given with -a/-A etc. as pairs. Either both"
  echo "        or none are removed from each read pair."
  echo ""
  echo "    --pair_filter"
  echo "        type: string"
  echo "        choices: [ any, both, first ]"
  echo "        Which of the reads in a paired-end read have to match the"
  echo "        filtering criterion in order for the pair to be filtered."
  echo ""
  echo "    --interleaved"
  echo "        type: boolean_true"
  echo "        Read and/or write interleaved paired-end reads."
  echo ""
  echo "Input parameters:"
  echo "    --input"
  echo "        type: file, required parameter, file must exist"
  echo "        Input fastq file for single-end reads or R1 for paired-end reads."
  echo ""
  echo "    --input_r2"
  echo "        type: file, file must exist"
  echo "        Input fastq file for R2 in the case of paired-end reads."
  echo ""
  echo "    -E, --errors, --error_rate"
  echo "        type: double"
  echo "        example: 0.1"
  echo "        Maximum allowed error rate (if 0 <= E < 1), or absolute"
  echo "        number of errors for full-length adapter match (if E is an"
  echo "        integer >= 1). Error rate = no. of errors divided by"
  echo "        length of matching region. Default: 0.1 (10%)."
  echo ""
  echo "    --no_indels"
  echo "        type: boolean_true"
  echo "        Allow only mismatches in alignments."
  echo ""
  echo "    -n, --times"
  echo "        type: integer"
  echo "        example: 1"
  echo "        Remove up to COUNT adapters from each read. Default: 1."
  echo ""
  echo "    -O, --overlap"
  echo "        type: integer"
  echo "        example: 3"
  echo "        Require MINLENGTH overlap between read and adapter for an"
  echo "        adapter to be found. The default is 3."
  echo ""
  echo "    --match_read_wildcards"
  echo "        type: boolean_true"
  echo "        Interpret IUPAC wildcards in reads."
  echo ""
  echo "    --no_match_adapter_wildcards"
  echo "        type: boolean_true"
  echo "        Do not interpret IUPAC wildcards in adapters."
  echo ""
  echo "    --action"
  echo "        type: string"
  echo "        example: trim"
  echo "        choices: [ trim, retain, mask, lowercase, none ]"
  echo "        What to do if a match was found. trim: trim adapter and"
  echo "        up- or downstream sequence; retain: trim, but retain"
  echo "        adapter; mask: replace with 'N' characters; lowercase:"
  echo "        convert to lowercase; none: leave unchanged."
  echo "        The default is trim."
  echo ""
  echo "    --rc, --revcomp"
  echo "        type: boolean_true"
  echo "        Check both the read and its reverse complement for adapter"
  echo "        matches. If match is on reverse-complemented version,"
  echo "        output that one."
  echo ""
  echo "Demultiplexing options:"
  echo "    --demultiplex_mode"
  echo "        type: string"
  echo "        choices: [ single, unique_dual, combinatorial_dual ]"
  echo "        Enable demultiplexing and set the mode for it."
  echo "        With mode 'unique_dual', adapters from the first and second read are"
  echo "        used,"
  echo "        and the indexes from the reads are only used in pairs. This implies"
  echo "        --pair_adapters."
  echo "        Enabling mode 'combinatorial_dual' allows all combinations of the sets"
  echo "        of indexes"
  echo "        on R1 and R2. It is necessary to write each read pair to an output"
  echo "        file depending on the adapters found on both R1 and R2."
  echo "        Mode 'single', uses indexes or barcodes located at the 5'"
  echo "        end of the R1 read (single)."
  echo ""
  echo "Read modifications:"
  echo "    -u, --cut"
  echo "        type: integer, multiple values allowed"
  echo "        Remove LEN bases from each read (or R1 if paired; use --cut_r2"
  echo "        option for R2). If LEN is positive, remove bases from the"
  echo "        beginning. If LEN is negative, remove bases from the end."
  echo "        Can be used twice if LENs have different signs. Applied"
  echo "        *before* adapter trimming."
  echo ""
  echo "    --cut_r2"
  echo "        type: integer, multiple values allowed"
  echo "        Remove LEN bases from each read (for R2). If LEN is positive, remove"
  echo "        bases from the"
  echo "        beginning. If LEN is negative, remove bases from the end."
  echo "        Can be used twice if LENs have different signs. Applied"
  echo "        *before* adapter trimming."
  echo ""
  echo "    --nextseq_trim"
  echo "        type: string"
  echo "        NextSeq-specific quality trimming (each read). Trims also"
  echo "        dark cycles appearing as high-quality G bases."
  echo ""
  echo "    -q, --quality_cutoff"
  echo "        type: string"
  echo "        Trim low-quality bases from 5' and/or 3' ends of each read"
  echo "        before adapter removal. Applied to both reads if data is"
  echo "        paired. If one value is given, only the 3' end is trimmed."
  echo "        If two comma-separated cutoffs are given, the 5' end is"
  echo "        trimmed with the first cutoff, the 3' end with the second."
  echo ""
  echo "    -Q, --quality_cutoff_r2"
  echo "        type: string"
  echo "        Quality-trimming cutoff for R2. Default: same as for R1"
  echo ""
  echo "    --quality_base"
  echo "        type: integer"
  echo "        example: 33"
  echo "        Assume that quality values in FASTQ are encoded as"
  echo "        ascii(quality + N). This needs to be set to 64 for some"
  echo "        old Illumina FASTQ files. The default is 33."
  echo ""
  echo "    --poly_a"
  echo "        type: boolean_true"
  echo "        Trim poly-A tails"
  echo ""
  echo "    -l, --length"
  echo "        type: integer"
  echo "        Shorten reads to LENGTH. Positive values remove bases at"
  echo "        the end while negative ones remove bases at the beginning."
  echo "        This and the following modifications are applied after"
  echo "        adapter trimming."
  echo ""
  echo "    --trim_n"
  echo "        type: boolean_true"
  echo "        Trim N's on ends of reads."
  echo ""
  echo "    --length_tag"
  echo "        type: string"
  echo "        example: length="
  echo "        Search for TAG followed by a decimal number in the"
  echo "        description field of the read. Replace the decimal number"
  echo "        with the correct length of the trimmed read. For example,"
  echo "        use --length-tag 'length=' to correct fields like"
  echo "        'length=123'."
  echo ""
  echo "    --strip_suffix"
  echo "        type: string"
  echo "        Remove this suffix from read names if present. Can be"
  echo "        given multiple times."
  echo ""
  echo "    -x, --prefix"
  echo "        type: string"
  echo "        Add this prefix to read names. Use {name} to insert the"
  echo "        name of the matching adapter."
  echo ""
  echo "    -y, --suffix"
  echo "        type: string"
  echo "        Add this suffix to read names; can also include {name}"
  echo ""
  echo "    --rename"
  echo "        type: string"
  echo "        Rename reads using TEMPLATE containing variables such as"
  echo "        {id}, {adapter_name} etc. (see documentation)"
  echo ""
  echo "    -z, --zero_cap"
  echo "        type: boolean_true"
  echo "        Change negative quality values to zero."
  echo ""
  echo "Filtering of processed reads:"
  echo "    Filters are applied after above read modifications. Paired-end reads are"
  echo "    always discarded pairwise (see also --pair_filter)."
  echo ""
  echo "    -m, --minimum_length"
  echo "        type: string"
  echo "        example: 0"
  echo "        Discard reads shorter than LEN. Default is 0."
  echo "        When trimming paired-end reads, the minimum lengths for R1 and R2 can be"
  echo "        specified separately by separating them with a colon (:)."
  echo "        If the colon syntax is not used, the same minimum length applies to both"
  echo "        reads, as discussed above."
  echo "        Also, one of the values can be omitted to impose no restrictions."
  echo "        For example, with -m 17:, the length of R1 must be at least 17, but the"
  echo "        length of R2 is ignored."
  echo ""
  echo "    -M, --maximum_length"
  echo "        type: string"
  echo "        Discard reads longer than LEN. Default: no limit."
  echo "        For paired reads, see the remark for --minimum_length"
  echo ""
  echo "    --max_n"
  echo "        type: string"
  echo "        Discard reads with more than COUNT 'N' bases. If COUNT is"
  echo "        a number between 0 and 1, it is interpreted as a fraction"
  echo "        of the read length."
  echo ""
  echo "    --max_ee, --max_expected_errors"
  echo "        type: long"
  echo "        Discard reads whose expected number of errors (computed"
  echo "        from quality values) exceeds ERRORS."
  echo ""
  echo "    --max_aer, --max_average_error_rate"
  echo "        type: long"
  echo "        as --max_expected_errors (see above), but divided by"
  echo "        length to account for reads of varying length."
  echo ""
  echo "    --discard, --discard_trimmed"
  echo "        type: boolean_true"
  echo "        Discard reads that contain an adapter. Use also -O to"
  echo "        avoid discarding too many randomly matching reads."
  echo ""
  echo "    --trimmed_only, --discard_untrimmed"
  echo "        type: boolean_true"
  echo "        Discard reads that do not contain an adapter."
  echo ""
  echo "    --discard_casava"
  echo "        type: boolean_true"
  echo "        Discard reads that did not pass CASAVA filtering (header"
  echo "        has :Y:)."
  echo ""
  echo "Output parameters:"
  echo "    --report"
  echo "        type: string"
  echo "        example: full"
  echo "        choices: [ full, minimal ]"
  echo "        Which type of report to print: 'full' (default) or 'minimal'."
  echo ""
  echo "    --json"
  echo "        type: boolean_true"
  echo "        Write report in JSON format to this file."
  echo ""
  echo "    --output"
  echo "        type: file, required parameter, multiple values allowed, output, file"
  echo "must exist"
  echo "        example: fastq/*_001.fast[a,q]"
  echo "        Glob pattern for matching the expected output files."
  echo "        Should include \`\$output_dir\`."
  echo ""
  echo "    --fasta"
  echo "        type: boolean_true"
  echo "        Output FASTA to standard output even on FASTQ input."
  echo ""
  echo "    --info_file"
  echo "        type: boolean_true"
  echo "        Write information about each read and its adapter matches"
  echo "        into info.txt in the output directory."
  echo "        See the documentation for the file format."
  echo ""
  echo "Debug:"
  echo "    --debug"
  echo "        type: boolean_true"
  echo "        Print debug information"
}

# initialise variables
VIASH_MODE='run'
VIASH_ENGINE_ID='docker'

######## Helper functions for setting up Docker images for viash ########
# expects: ViashDockerBuild

# ViashDockerInstallationCheck: check whether Docker is installed correctly
#
# examples:
#   ViashDockerInstallationCheck
function ViashDockerInstallationCheck {
  ViashDebug "Checking whether Docker is installed"
  if [ ! command -v docker &> /dev/null ]; then
    ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
    exit 1
  fi

  ViashDebug "Checking whether the Docker daemon is running"
  local save=$-; set +e
  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
  local out=$?
  [[ $save =~ e ]] && set -e
  if [ $out -ne 0 ]; then
    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
    ViashCritical "- Try running 'dockerd' in the command line"
    ViashCritical "- See https://docs.docker.com/config/daemon/"
    exit 1
  fi
}

# ViashDockerRemoteTagCheck: check whether a Docker image is available 
# on a remote. Assumes `docker login` has been performed, if relevant.
#
# $1                  : image identifier with format `[registry/]image[:tag]`
# exit code $?        : whether or not the image was found
# examples:
#   ViashDockerRemoteTagCheck python:latest
#   echo $?                                     # returns '0'
#   ViashDockerRemoteTagCheck sdaizudceahifu
#   echo $?                                     # returns '1'
function ViashDockerRemoteTagCheck {
  docker manifest inspect $1 > /dev/null 2> /dev/null
}

# ViashDockerLocalTagCheck: check whether a Docker image is available locally
#
# $1                  : image identifier with format `[registry/]image[:tag]`
# exit code $?        : whether or not the image was found
# examples:
#   docker pull python:latest
#   ViashDockerLocalTagCheck python:latest
#   echo $?                                     # returns '0'
#   ViashDockerLocalTagCheck sdaizudceahifu
#   echo $?                                     # returns '1'
function ViashDockerLocalTagCheck {
  [ -n "$(docker images -q $1)" ]
}

# ViashDockerPull: pull a Docker image
#
# $1                  : image identifier with format `[registry/]image[:tag]`
# exit code $?        : whether or not the image was found
# examples:
#   ViashDockerPull python:latest
#   echo $?                                     # returns '0'
#   ViashDockerPull sdaizudceahifu
#   echo $?                                     # returns '1'
function ViashDockerPull {
  ViashNotice "Checking if Docker image is available at '$1'"
  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
    docker pull $1 && return 0 || return 1
  else
    local save=$-; set +e
    docker pull $1 2> /dev/null > /dev/null
    local out=$?
    [[ $save =~ e ]] && set -e
    if [ $out -ne 0 ]; then
      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
    fi
    return $out
  fi
}

# ViashDockerPush: push a Docker image
#
# $1                  : image identifier with format `[registry/]image[:tag]`
# exit code $?        : whether or not the image was found
# examples:
#   ViashDockerPush python:latest
#   echo $?                                     # returns '0'
#   ViashDockerPush sdaizudceahifu
#   echo $?                                     # returns '1'
function ViashDockerPush {
  ViashNotice "Pushing image to '$1'"
  local save=$-; set +e
  local out
  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
    docker push $1
    out=$?
  else
    docker push $1 2> /dev/null > /dev/null
    out=$?
  fi
  [[ $save =~ e ]] && set -e
  if [ $out -eq 0 ]; then
    ViashNotice "Container '$1' push succeeded."
  else
    ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions."
  fi
  return $out
}

# ViashDockerPullElseBuild: pull a Docker image, else build it
#
# $1                  : image identifier with format `[registry/]image[:tag]`
# ViashDockerBuild    : a Bash function which builds a docker image, takes image identifier as argument.
# examples:
#   ViashDockerPullElseBuild mynewcomponent
function ViashDockerPullElseBuild {
  local save=$-; set +e
  ViashDockerPull $1
  local out=$?
  [[ $save =~ e ]] && set -e
  if [ $out -ne 0 ]; then
    ViashDockerBuild $@
  fi
}

# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
#
# $1          : image identifier with format `[registry/]image[:tag]`
# $2          : docker setup strategy, see DockerSetupStrategy.scala
# examples:
#   ViashDockerSetup mynewcomponent alwaysbuild
function ViashDockerSetup {
  local image_id="$1"
  local setup_strategy="$2"
  if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
    ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
  elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then
    ViashDockerPull $image_id
  elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then
    ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
  elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then
    ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
  elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then
    ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
  elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then
    local save=$-; set +e
    ViashDockerLocalTagCheck $image_id
    local outCheck=$?
    [[ $save =~ e ]] && set -e
    if [ $outCheck -eq 0 ]; then
      ViashInfo "Image $image_id already exists"
    elif [ "$setup_strategy" == "ifneedbebuild" ]; then
      ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
    elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then
      ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
    elif [ "$setup_strategy" == "ifneedbepull" ]; then
      ViashDockerPull $image_id
    elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then
      ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
    elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then
      ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
    else
      ViashError "Unrecognised Docker strategy: $setup_strategy"
      exit 1
    fi
  elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then
    ViashDockerPush "$image_id"
  elif [ "$setup_strategy" == "pushifnotpresent" -o "$setup_strategy" == "gentlepush" -o "$setup_strategy" == "maybepush" ]; then
    local save=$-; set +e
    ViashDockerRemoteTagCheck $image_id
    local outCheck=$?
    [[ $save =~ e ]] && set -e
    if [ $outCheck -eq 0 ]; then
      ViashNotice "Container '$image_id' exists, doing nothing."
    else
      ViashNotice "Container '$image_id' does not yet exist."
      ViashDockerPush "$image_id"
    fi
  elif [ "$setup_strategy" == "donothing" -o "$setup_strategy" == "meh" ]; then
    ViashNotice "Skipping setup."
  else
    ViashError "Unrecognised Docker strategy: $setup_strategy"
    exit 1
  fi
}

# ViashDockerCheckCommands: Check whether a docker container has the required commands
#
# $1                  : image identifier with format `[registry/]image[:tag]`
# $@                  : commands to verify being present
# examples:
#   ViashDockerCheckCommands bash:4.0 bash ps foo
function ViashDockerCheckCommands {
  local image_id="$1"
  shift 1
  local commands="$@"
  local save=$-; set +e
  local missing # mark 'missing' as local in advance, otherwise the exit code of the command will be missing and always be '0'
  missing=$(docker run --rm --entrypoint=sh "$image_id" -c "for command in $commands; do command -v \$command >/dev/null 2>&1; if [ \$? -ne 0 ]; then echo \$command; exit 1; fi; done")
  local outCheck=$?
  [[ $save =~ e ]] && set -e
  if [ $outCheck -ne 0 ]; then
  	ViashError "Docker container '$image_id' does not contain command '$missing'."
  	exit 1
  fi
}

# ViashDockerBuild: build a docker image
# $1                               : image identifier with format `[registry/]image[:tag]`
# $...                             : additional arguments to pass to docker build
# $VIASH_META_TEMP_DIR             : temporary directory to store dockerfile & optional resources in
# $VIASH_META_NAME                 : name of the component
# $VIASH_META_RESOURCES_DIR        : directory containing the resources
# $VIASH_VERBOSITY                 : verbosity level
# exit code $?                     : whether or not the image was built successfully
function ViashDockerBuild {
  local image_id="$1"
  shift 1

  # create temporary directory to store dockerfile & optional resources in
  local tmpdir=$(mktemp -d "$VIASH_META_TEMP_DIR/dockerbuild-$VIASH_META_NAME-XXXXXX")
  local dockerfile="$tmpdir/Dockerfile"
  function clean_up {
    rm -rf "$tmpdir"
  }
  trap clean_up EXIT

  # store dockerfile and resources
  ViashDockerfile "$VIASH_ENGINE_ID" > "$dockerfile"

  # generate the build command
  local docker_build_cmd="docker build -t '$image_id' $@ '$VIASH_META_RESOURCES_DIR' -f '$dockerfile'"

  # build the container
  ViashNotice "Building container '$image_id' with Dockerfile"
  ViashInfo "$docker_build_cmd"
  local save=$-; set +e
  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
    eval $docker_build_cmd
  else
    eval $docker_build_cmd &> "$tmpdir/docker_build.log"
  fi

  # check exit code
  local out=$?
  [[ $save =~ e ]] && set -e
  if [ $out -ne 0 ]; then
    ViashError "Error occurred while building container '$image_id'"
    if [ $VIASH_VERBOSITY -lt $VIASH_LOGCODE_INFO ]; then
      ViashError "Transcript: --------------------------------"
      cat "$tmpdir/docker_build.log"
      ViashError "End of transcript --------------------------"
    fi
    exit 1
  fi
}

######## End of helper functions for setting up Docker images for viash ########

# ViashDockerFile: print the dockerfile to stdout
# $1    : engine identifier
# return : dockerfile required to run this component
# examples:
#   ViashDockerFile
function ViashDockerfile {
  local engine_id="$1"

  if [[ "$engine_id" == "docker" ]]; then
    cat << 'VIASHDOCKER'
FROM python:3.12
ENTRYPOINT []
RUN pip install --upgrade pip && \
  pip install --upgrade --no-cache-dir "cutadapt"

RUN cutadapt --version | sed 's/\(.*\)/cutadapt: "\1"/' > /var/software_versions.txt

LABEL org.opencontainers.image.authors="Toni Verbeiren"
LABEL org.opencontainers.image.description="Companion container for running component cutadapt"
LABEL org.opencontainers.image.created="2024-11-14T12:50:40Z"
LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt"
LABEL org.opencontainers.image.revision="402ad6a813c0d0b141bbf8f9a3aab9c270a74812"
LABEL org.opencontainers.image.version="add_sgdemux"

VIASHDOCKER
  fi
}

# ViashDockerBuildArgs: return the arguments to pass to docker build
# $1    : engine identifier
# return : arguments to pass to docker build
function ViashDockerBuildArgs {
  local engine_id="$1"

  if [[ "$engine_id" == "docker" ]]; then
    echo ""
  fi
}

# ViashAbsolutePath: generate absolute path from relative path
# borrowed from https://stackoverflow.com/a/21951256
# $1     : relative filename
# return : absolute path
# examples:
#   ViashAbsolutePath some_file.txt   # returns /path/to/some_file.txt
#   ViashAbsolutePath /foo/bar/..     # returns /foo
function ViashAbsolutePath {
  local thePath
  local parr
  local outp
  local len
  if [[ ! "$1" =~ ^/ ]]; then
    thePath="$PWD/$1"
  else
    thePath="$1"
  fi
  echo "$thePath" | (
    IFS=/
    read -a parr
    declare -a outp
    for i in "${parr[@]}"; do
      case "$i" in
      ''|.) continue ;;
      ..)
        len=${#outp[@]}
        if ((len==0)); then
          continue
        else
          unset outp[$((len-1))]
        fi
        ;;
      *)
        len=${#outp[@]}
        outp[$len]="$i"
      ;;
      esac
    done
    echo /"${outp[*]}"
  )
}
# ViashDockerAutodetectMount: auto configuring docker mounts from parameters
# $1                             : The parameter value
# returns                        : New parameter
# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
# examples:
#   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
#   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
function ViashDockerAutodetectMount {
  local abs_path=$(ViashAbsolutePath "$1")
  local mount_source
  local base_name
  if [ -d "$abs_path" ]; then
    mount_source="$abs_path"
    base_name=""
  else
    mount_source=`dirname "$abs_path"`
    base_name=`basename "$abs_path"`
  fi
  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
  if [ -z "$base_name" ]; then
    echo "$mount_target"
  else
    echo "$mount_target/$base_name"
  fi
}
function ViashDockerAutodetectMountArg {
  local abs_path=$(ViashAbsolutePath "$1")
  local mount_source
  local base_name
  if [ -d "$abs_path" ]; then
    mount_source="$abs_path"
    base_name=""
  else
    mount_source=`dirname "$abs_path"`
    base_name=`basename "$abs_path"`
  fi
  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
  echo "--volume=\"$mount_source:$mount_target\""
}
function ViashDockerStripAutomount {
  local abs_path=$(ViashAbsolutePath "$1")
  echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
}
# initialise variables
VIASH_DIRECTORY_MOUNTS=()

# configure default docker automount prefix if it is unset
if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
  VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
fi

# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)

# initialise array
VIASH_POSITIONAL_ARGS=''

while [[ $# -gt 0 ]]; do
    case "$1" in
        -h|--help)
            ViashHelp
            exit
            ;;
        ---v|---verbose)
            let "VIASH_VERBOSITY=VIASH_VERBOSITY+1"
            shift 1
            ;;
        ---verbosity)
            VIASH_VERBOSITY="$2"
            shift 2
            ;;
        ---verbosity=*)
            VIASH_VERBOSITY="$(ViashRemoveFlags "$1")"
            shift 1
            ;;
        --version)
            echo "cutadapt add_sgdemux"
            exit
            ;;
        --adapter)
            if [ -z "$VIASH_PAR_ADAPTER" ]; then
              VIASH_PAR_ADAPTER="$2"
            else
              VIASH_PAR_ADAPTER="$VIASH_PAR_ADAPTER;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --adapter. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --adapter=*)
            if [ -z "$VIASH_PAR_ADAPTER" ]; then
              VIASH_PAR_ADAPTER=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_ADAPTER="$VIASH_PAR_ADAPTER;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        -a)
            if [ -z "$VIASH_PAR_ADAPTER" ]; then
              VIASH_PAR_ADAPTER="$2"
            else
              VIASH_PAR_ADAPTER="$VIASH_PAR_ADAPTER;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -a. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --front)
            if [ -z "$VIASH_PAR_FRONT" ]; then
              VIASH_PAR_FRONT="$2"
            else
              VIASH_PAR_FRONT="$VIASH_PAR_FRONT;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --front. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --front=*)
            if [ -z "$VIASH_PAR_FRONT" ]; then
              VIASH_PAR_FRONT=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_FRONT="$VIASH_PAR_FRONT;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        -g)
            if [ -z "$VIASH_PAR_FRONT" ]; then
              VIASH_PAR_FRONT="$2"
            else
              VIASH_PAR_FRONT="$VIASH_PAR_FRONT;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -g. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --anywhere)
            if [ -z "$VIASH_PAR_ANYWHERE" ]; then
              VIASH_PAR_ANYWHERE="$2"
            else
              VIASH_PAR_ANYWHERE="$VIASH_PAR_ANYWHERE;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --anywhere. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --anywhere=*)
            if [ -z "$VIASH_PAR_ANYWHERE" ]; then
              VIASH_PAR_ANYWHERE=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_ANYWHERE="$VIASH_PAR_ANYWHERE;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        -b)
            if [ -z "$VIASH_PAR_ANYWHERE" ]; then
              VIASH_PAR_ANYWHERE="$2"
            else
              VIASH_PAR_ANYWHERE="$VIASH_PAR_ANYWHERE;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -b. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --adapter_fasta)
            if [ -z "$VIASH_PAR_ADAPTER_FASTA" ]; then
              VIASH_PAR_ADAPTER_FASTA="$2"
            else
              VIASH_PAR_ADAPTER_FASTA="$VIASH_PAR_ADAPTER_FASTA;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --adapter_fasta. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --adapter_fasta=*)
            if [ -z "$VIASH_PAR_ADAPTER_FASTA" ]; then
              VIASH_PAR_ADAPTER_FASTA=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_ADAPTER_FASTA="$VIASH_PAR_ADAPTER_FASTA;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --front_fasta)
            [ -n "$VIASH_PAR_FRONT_FASTA" ] && ViashError Bad arguments for option \'--front_fasta\': \'$VIASH_PAR_FRONT_FASTA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FRONT_FASTA="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --front_fasta. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --front_fasta=*)
            [ -n "$VIASH_PAR_FRONT_FASTA" ] && ViashError Bad arguments for option \'--front_fasta=*\': \'$VIASH_PAR_FRONT_FASTA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FRONT_FASTA=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --anywhere_fasta)
            [ -n "$VIASH_PAR_ANYWHERE_FASTA" ] && ViashError Bad arguments for option \'--anywhere_fasta\': \'$VIASH_PAR_ANYWHERE_FASTA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ANYWHERE_FASTA="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --anywhere_fasta. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --anywhere_fasta=*)
            [ -n "$VIASH_PAR_ANYWHERE_FASTA" ] && ViashError Bad arguments for option \'--anywhere_fasta=*\': \'$VIASH_PAR_ANYWHERE_FASTA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ANYWHERE_FASTA=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --adapter_r2)
            if [ -z "$VIASH_PAR_ADAPTER_R2" ]; then
              VIASH_PAR_ADAPTER_R2="$2"
            else
              VIASH_PAR_ADAPTER_R2="$VIASH_PAR_ADAPTER_R2;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --adapter_r2. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --adapter_r2=*)
            if [ -z "$VIASH_PAR_ADAPTER_R2" ]; then
              VIASH_PAR_ADAPTER_R2=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_ADAPTER_R2="$VIASH_PAR_ADAPTER_R2;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        -A)
            if [ -z "$VIASH_PAR_ADAPTER_R2" ]; then
              VIASH_PAR_ADAPTER_R2="$2"
            else
              VIASH_PAR_ADAPTER_R2="$VIASH_PAR_ADAPTER_R2;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -A. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --front_r2)
            if [ -z "$VIASH_PAR_FRONT_R2" ]; then
              VIASH_PAR_FRONT_R2="$2"
            else
              VIASH_PAR_FRONT_R2="$VIASH_PAR_FRONT_R2;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --front_r2. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --front_r2=*)
            if [ -z "$VIASH_PAR_FRONT_R2" ]; then
              VIASH_PAR_FRONT_R2=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_FRONT_R2="$VIASH_PAR_FRONT_R2;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        -G)
            if [ -z "$VIASH_PAR_FRONT_R2" ]; then
              VIASH_PAR_FRONT_R2="$2"
            else
              VIASH_PAR_FRONT_R2="$VIASH_PAR_FRONT_R2;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -G. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --anywhere_r2)
            if [ -z "$VIASH_PAR_ANYWHERE_R2" ]; then
              VIASH_PAR_ANYWHERE_R2="$2"
            else
              VIASH_PAR_ANYWHERE_R2="$VIASH_PAR_ANYWHERE_R2;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --anywhere_r2. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --anywhere_r2=*)
            if [ -z "$VIASH_PAR_ANYWHERE_R2" ]; then
              VIASH_PAR_ANYWHERE_R2=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_ANYWHERE_R2="$VIASH_PAR_ANYWHERE_R2;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        -B)
            if [ -z "$VIASH_PAR_ANYWHERE_R2" ]; then
              VIASH_PAR_ANYWHERE_R2="$2"
            else
              VIASH_PAR_ANYWHERE_R2="$VIASH_PAR_ANYWHERE_R2;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -B. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --adapter_r2_fasta)
            [ -n "$VIASH_PAR_ADAPTER_R2_FASTA" ] && ViashError Bad arguments for option \'--adapter_r2_fasta\': \'$VIASH_PAR_ADAPTER_R2_FASTA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ADAPTER_R2_FASTA="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --adapter_r2_fasta. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --adapter_r2_fasta=*)
            [ -n "$VIASH_PAR_ADAPTER_R2_FASTA" ] && ViashError Bad arguments for option \'--adapter_r2_fasta=*\': \'$VIASH_PAR_ADAPTER_R2_FASTA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ADAPTER_R2_FASTA=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --front_r2_fasta)
            [ -n "$VIASH_PAR_FRONT_R2_FASTA" ] && ViashError Bad arguments for option \'--front_r2_fasta\': \'$VIASH_PAR_FRONT_R2_FASTA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FRONT_R2_FASTA="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --front_r2_fasta. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --front_r2_fasta=*)
            [ -n "$VIASH_PAR_FRONT_R2_FASTA" ] && ViashError Bad arguments for option \'--front_r2_fasta=*\': \'$VIASH_PAR_FRONT_R2_FASTA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FRONT_R2_FASTA=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --anywhere_r2_fasta)
            [ -n "$VIASH_PAR_ANYWHERE_R2_FASTA" ] && ViashError Bad arguments for option \'--anywhere_r2_fasta\': \'$VIASH_PAR_ANYWHERE_R2_FASTA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ANYWHERE_R2_FASTA="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --anywhere_r2_fasta. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --anywhere_r2_fasta=*)
            [ -n "$VIASH_PAR_ANYWHERE_R2_FASTA" ] && ViashError Bad arguments for option \'--anywhere_r2_fasta=*\': \'$VIASH_PAR_ANYWHERE_R2_FASTA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ANYWHERE_R2_FASTA=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --pair_adapters)
            [ -n "$VIASH_PAR_PAIR_ADAPTERS" ] && ViashError Bad arguments for option \'--pair_adapters\': \'$VIASH_PAR_PAIR_ADAPTERS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PAIR_ADAPTERS=true
            shift 1
            ;;
        --pair_filter)
            [ -n "$VIASH_PAR_PAIR_FILTER" ] && ViashError Bad arguments for option \'--pair_filter\': \'$VIASH_PAR_PAIR_FILTER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PAIR_FILTER="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --pair_filter. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --pair_filter=*)
            [ -n "$VIASH_PAR_PAIR_FILTER" ] && ViashError Bad arguments for option \'--pair_filter=*\': \'$VIASH_PAR_PAIR_FILTER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PAIR_FILTER=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --interleaved)
            [ -n "$VIASH_PAR_INTERLEAVED" ] && ViashError Bad arguments for option \'--interleaved\': \'$VIASH_PAR_INTERLEAVED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INTERLEAVED=true
            shift 1
            ;;
        --input)
            [ -n "$VIASH_PAR_INPUT" ] && ViashError Bad arguments for option \'--input\': \'$VIASH_PAR_INPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INPUT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --input. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --input=*)
            [ -n "$VIASH_PAR_INPUT" ] && ViashError Bad arguments for option \'--input=*\': \'$VIASH_PAR_INPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INPUT=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --input_r2)
            [ -n "$VIASH_PAR_INPUT_R2" ] && ViashError Bad arguments for option \'--input_r2\': \'$VIASH_PAR_INPUT_R2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INPUT_R2="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --input_r2. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --input_r2=*)
            [ -n "$VIASH_PAR_INPUT_R2" ] && ViashError Bad arguments for option \'--input_r2=*\': \'$VIASH_PAR_INPUT_R2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INPUT_R2=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --error_rate)
            [ -n "$VIASH_PAR_ERROR_RATE" ] && ViashError Bad arguments for option \'--error_rate\': \'$VIASH_PAR_ERROR_RATE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ERROR_RATE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --error_rate. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --error_rate=*)
            [ -n "$VIASH_PAR_ERROR_RATE" ] && ViashError Bad arguments for option \'--error_rate=*\': \'$VIASH_PAR_ERROR_RATE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ERROR_RATE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -E)
            [ -n "$VIASH_PAR_ERROR_RATE" ] && ViashError Bad arguments for option \'-E\': \'$VIASH_PAR_ERROR_RATE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ERROR_RATE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -E. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --errors)
            [ -n "$VIASH_PAR_ERROR_RATE" ] && ViashError Bad arguments for option \'--errors\': \'$VIASH_PAR_ERROR_RATE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ERROR_RATE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --errors. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --no_indels)
            [ -n "$VIASH_PAR_NO_INDELS" ] && ViashError Bad arguments for option \'--no_indels\': \'$VIASH_PAR_NO_INDELS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_NO_INDELS=true
            shift 1
            ;;
        --times)
            [ -n "$VIASH_PAR_TIMES" ] && ViashError Bad arguments for option \'--times\': \'$VIASH_PAR_TIMES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_TIMES="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --times. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --times=*)
            [ -n "$VIASH_PAR_TIMES" ] && ViashError Bad arguments for option \'--times=*\': \'$VIASH_PAR_TIMES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_TIMES=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -n)
            [ -n "$VIASH_PAR_TIMES" ] && ViashError Bad arguments for option \'-n\': \'$VIASH_PAR_TIMES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_TIMES="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -n. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --overlap)
            [ -n "$VIASH_PAR_OVERLAP" ] && ViashError Bad arguments for option \'--overlap\': \'$VIASH_PAR_OVERLAP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OVERLAP="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --overlap. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --overlap=*)
            [ -n "$VIASH_PAR_OVERLAP" ] && ViashError Bad arguments for option \'--overlap=*\': \'$VIASH_PAR_OVERLAP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OVERLAP=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -O)
            [ -n "$VIASH_PAR_OVERLAP" ] && ViashError Bad arguments for option \'-O\': \'$VIASH_PAR_OVERLAP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OVERLAP="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -O. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --match_read_wildcards)
            [ -n "$VIASH_PAR_MATCH_READ_WILDCARDS" ] && ViashError Bad arguments for option \'--match_read_wildcards\': \'$VIASH_PAR_MATCH_READ_WILDCARDS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MATCH_READ_WILDCARDS=true
            shift 1
            ;;
        --no_match_adapter_wildcards)
            [ -n "$VIASH_PAR_NO_MATCH_ADAPTER_WILDCARDS" ] && ViashError Bad arguments for option \'--no_match_adapter_wildcards\': \'$VIASH_PAR_NO_MATCH_ADAPTER_WILDCARDS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_NO_MATCH_ADAPTER_WILDCARDS=true
            shift 1
            ;;
        --action)
            [ -n "$VIASH_PAR_ACTION" ] && ViashError Bad arguments for option \'--action\': \'$VIASH_PAR_ACTION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ACTION="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --action. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --action=*)
            [ -n "$VIASH_PAR_ACTION" ] && ViashError Bad arguments for option \'--action=*\': \'$VIASH_PAR_ACTION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ACTION=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --revcomp)
            [ -n "$VIASH_PAR_REVCOMP" ] && ViashError Bad arguments for option \'--revcomp\': \'$VIASH_PAR_REVCOMP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_REVCOMP=true
            shift 1
            ;;
        --rc)
            [ -n "$VIASH_PAR_REVCOMP" ] && ViashError Bad arguments for option \'--rc\': \'$VIASH_PAR_REVCOMP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_REVCOMP=true
            shift 1
            ;;
        --demultiplex_mode)
            [ -n "$VIASH_PAR_DEMULTIPLEX_MODE" ] && ViashError Bad arguments for option \'--demultiplex_mode\': \'$VIASH_PAR_DEMULTIPLEX_MODE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_DEMULTIPLEX_MODE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --demultiplex_mode. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --demultiplex_mode=*)
            [ -n "$VIASH_PAR_DEMULTIPLEX_MODE" ] && ViashError Bad arguments for option \'--demultiplex_mode=*\': \'$VIASH_PAR_DEMULTIPLEX_MODE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_DEMULTIPLEX_MODE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --cut)
            if [ -z "$VIASH_PAR_CUT" ]; then
              VIASH_PAR_CUT="$2"
            else
              VIASH_PAR_CUT="$VIASH_PAR_CUT;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --cut. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --cut=*)
            if [ -z "$VIASH_PAR_CUT" ]; then
              VIASH_PAR_CUT=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_CUT="$VIASH_PAR_CUT;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        -u)
            if [ -z "$VIASH_PAR_CUT" ]; then
              VIASH_PAR_CUT="$2"
            else
              VIASH_PAR_CUT="$VIASH_PAR_CUT;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -u. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --cut_r2)
            if [ -z "$VIASH_PAR_CUT_R2" ]; then
              VIASH_PAR_CUT_R2="$2"
            else
              VIASH_PAR_CUT_R2="$VIASH_PAR_CUT_R2;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --cut_r2. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --cut_r2=*)
            if [ -z "$VIASH_PAR_CUT_R2" ]; then
              VIASH_PAR_CUT_R2=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_CUT_R2="$VIASH_PAR_CUT_R2;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --nextseq_trim)
            [ -n "$VIASH_PAR_NEXTSEQ_TRIM" ] && ViashError Bad arguments for option \'--nextseq_trim\': \'$VIASH_PAR_NEXTSEQ_TRIM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_NEXTSEQ_TRIM="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --nextseq_trim. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --nextseq_trim=*)
            [ -n "$VIASH_PAR_NEXTSEQ_TRIM" ] && ViashError Bad arguments for option \'--nextseq_trim=*\': \'$VIASH_PAR_NEXTSEQ_TRIM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_NEXTSEQ_TRIM=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --quality_cutoff)
            [ -n "$VIASH_PAR_QUALITY_CUTOFF" ] && ViashError Bad arguments for option \'--quality_cutoff\': \'$VIASH_PAR_QUALITY_CUTOFF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_QUALITY_CUTOFF="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --quality_cutoff. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --quality_cutoff=*)
            [ -n "$VIASH_PAR_QUALITY_CUTOFF" ] && ViashError Bad arguments for option \'--quality_cutoff=*\': \'$VIASH_PAR_QUALITY_CUTOFF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_QUALITY_CUTOFF=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -q)
            [ -n "$VIASH_PAR_QUALITY_CUTOFF" ] && ViashError Bad arguments for option \'-q\': \'$VIASH_PAR_QUALITY_CUTOFF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_QUALITY_CUTOFF="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -q. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --quality_cutoff_r2)
            [ -n "$VIASH_PAR_QUALITY_CUTOFF_R2" ] && ViashError Bad arguments for option \'--quality_cutoff_r2\': \'$VIASH_PAR_QUALITY_CUTOFF_R2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_QUALITY_CUTOFF_R2="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --quality_cutoff_r2. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --quality_cutoff_r2=*)
            [ -n "$VIASH_PAR_QUALITY_CUTOFF_R2" ] && ViashError Bad arguments for option \'--quality_cutoff_r2=*\': \'$VIASH_PAR_QUALITY_CUTOFF_R2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_QUALITY_CUTOFF_R2=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -Q)
            [ -n "$VIASH_PAR_QUALITY_CUTOFF_R2" ] && ViashError Bad arguments for option \'-Q\': \'$VIASH_PAR_QUALITY_CUTOFF_R2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_QUALITY_CUTOFF_R2="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -Q. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --quality_base)
            [ -n "$VIASH_PAR_QUALITY_BASE" ] && ViashError Bad arguments for option \'--quality_base\': \'$VIASH_PAR_QUALITY_BASE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_QUALITY_BASE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --quality_base. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --quality_base=*)
            [ -n "$VIASH_PAR_QUALITY_BASE" ] && ViashError Bad arguments for option \'--quality_base=*\': \'$VIASH_PAR_QUALITY_BASE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_QUALITY_BASE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --poly_a)
            [ -n "$VIASH_PAR_POLY_A" ] && ViashError Bad arguments for option \'--poly_a\': \'$VIASH_PAR_POLY_A\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_POLY_A=true
            shift 1
            ;;
        --length)
            [ -n "$VIASH_PAR_LENGTH" ] && ViashError Bad arguments for option \'--length\': \'$VIASH_PAR_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LENGTH="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --length. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --length=*)
            [ -n "$VIASH_PAR_LENGTH" ] && ViashError Bad arguments for option \'--length=*\': \'$VIASH_PAR_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LENGTH=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -l)
            [ -n "$VIASH_PAR_LENGTH" ] && ViashError Bad arguments for option \'-l\': \'$VIASH_PAR_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LENGTH="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -l. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --trim_n)
            [ -n "$VIASH_PAR_TRIM_N" ] && ViashError Bad arguments for option \'--trim_n\': \'$VIASH_PAR_TRIM_N\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_TRIM_N=true
            shift 1
            ;;
        --length_tag)
            [ -n "$VIASH_PAR_LENGTH_TAG" ] && ViashError Bad arguments for option \'--length_tag\': \'$VIASH_PAR_LENGTH_TAG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LENGTH_TAG="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --length_tag. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --length_tag=*)
            [ -n "$VIASH_PAR_LENGTH_TAG" ] && ViashError Bad arguments for option \'--length_tag=*\': \'$VIASH_PAR_LENGTH_TAG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LENGTH_TAG=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --strip_suffix)
            [ -n "$VIASH_PAR_STRIP_SUFFIX" ] && ViashError Bad arguments for option \'--strip_suffix\': \'$VIASH_PAR_STRIP_SUFFIX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_STRIP_SUFFIX="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --strip_suffix. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --strip_suffix=*)
            [ -n "$VIASH_PAR_STRIP_SUFFIX" ] && ViashError Bad arguments for option \'--strip_suffix=*\': \'$VIASH_PAR_STRIP_SUFFIX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_STRIP_SUFFIX=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --prefix)
            [ -n "$VIASH_PAR_PREFIX" ] && ViashError Bad arguments for option \'--prefix\': \'$VIASH_PAR_PREFIX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PREFIX="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --prefix. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --prefix=*)
            [ -n "$VIASH_PAR_PREFIX" ] && ViashError Bad arguments for option \'--prefix=*\': \'$VIASH_PAR_PREFIX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PREFIX=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -x)
            [ -n "$VIASH_PAR_PREFIX" ] && ViashError Bad arguments for option \'-x\': \'$VIASH_PAR_PREFIX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PREFIX="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -x. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --suffix)
            [ -n "$VIASH_PAR_SUFFIX" ] && ViashError Bad arguments for option \'--suffix\': \'$VIASH_PAR_SUFFIX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SUFFIX="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --suffix. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --suffix=*)
            [ -n "$VIASH_PAR_SUFFIX" ] && ViashError Bad arguments for option \'--suffix=*\': \'$VIASH_PAR_SUFFIX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SUFFIX=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -y)
            [ -n "$VIASH_PAR_SUFFIX" ] && ViashError Bad arguments for option \'-y\': \'$VIASH_PAR_SUFFIX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SUFFIX="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -y. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --rename)
            [ -n "$VIASH_PAR_RENAME" ] && ViashError Bad arguments for option \'--rename\': \'$VIASH_PAR_RENAME\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_RENAME="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --rename. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --rename=*)
            [ -n "$VIASH_PAR_RENAME" ] && ViashError Bad arguments for option \'--rename=*\': \'$VIASH_PAR_RENAME\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_RENAME=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --zero_cap)
            [ -n "$VIASH_PAR_ZERO_CAP" ] && ViashError Bad arguments for option \'--zero_cap\': \'$VIASH_PAR_ZERO_CAP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ZERO_CAP=true
            shift 1
            ;;
        -z)
            [ -n "$VIASH_PAR_ZERO_CAP" ] && ViashError Bad arguments for option \'-z\': \'$VIASH_PAR_ZERO_CAP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ZERO_CAP=true
            shift 1
            ;;
        --minimum_length)
            [ -n "$VIASH_PAR_MINIMUM_LENGTH" ] && ViashError Bad arguments for option \'--minimum_length\': \'$VIASH_PAR_MINIMUM_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MINIMUM_LENGTH="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --minimum_length. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --minimum_length=*)
            [ -n "$VIASH_PAR_MINIMUM_LENGTH" ] && ViashError Bad arguments for option \'--minimum_length=*\': \'$VIASH_PAR_MINIMUM_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MINIMUM_LENGTH=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -m)
            [ -n "$VIASH_PAR_MINIMUM_LENGTH" ] && ViashError Bad arguments for option \'-m\': \'$VIASH_PAR_MINIMUM_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MINIMUM_LENGTH="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -m. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --maximum_length)
            [ -n "$VIASH_PAR_MAXIMUM_LENGTH" ] && ViashError Bad arguments for option \'--maximum_length\': \'$VIASH_PAR_MAXIMUM_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAXIMUM_LENGTH="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --maximum_length. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --maximum_length=*)
            [ -n "$VIASH_PAR_MAXIMUM_LENGTH" ] && ViashError Bad arguments for option \'--maximum_length=*\': \'$VIASH_PAR_MAXIMUM_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAXIMUM_LENGTH=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -M)
            [ -n "$VIASH_PAR_MAXIMUM_LENGTH" ] && ViashError Bad arguments for option \'-M\': \'$VIASH_PAR_MAXIMUM_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAXIMUM_LENGTH="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -M. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --max_n)
            [ -n "$VIASH_PAR_MAX_N" ] && ViashError Bad arguments for option \'--max_n\': \'$VIASH_PAR_MAX_N\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_N="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --max_n. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --max_n=*)
            [ -n "$VIASH_PAR_MAX_N" ] && ViashError Bad arguments for option \'--max_n=*\': \'$VIASH_PAR_MAX_N\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_N=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --max_expected_errors)
            [ -n "$VIASH_PAR_MAX_EXPECTED_ERRORS" ] && ViashError Bad arguments for option \'--max_expected_errors\': \'$VIASH_PAR_MAX_EXPECTED_ERRORS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_EXPECTED_ERRORS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --max_expected_errors. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --max_expected_errors=*)
            [ -n "$VIASH_PAR_MAX_EXPECTED_ERRORS" ] && ViashError Bad arguments for option \'--max_expected_errors=*\': \'$VIASH_PAR_MAX_EXPECTED_ERRORS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_EXPECTED_ERRORS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --max_ee)
            [ -n "$VIASH_PAR_MAX_EXPECTED_ERRORS" ] && ViashError Bad arguments for option \'--max_ee\': \'$VIASH_PAR_MAX_EXPECTED_ERRORS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_EXPECTED_ERRORS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --max_ee. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --max_average_error_rate)
            [ -n "$VIASH_PAR_MAX_AVERAGE_ERROR_RATE" ] && ViashError Bad arguments for option \'--max_average_error_rate\': \'$VIASH_PAR_MAX_AVERAGE_ERROR_RATE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_AVERAGE_ERROR_RATE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --max_average_error_rate. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --max_average_error_rate=*)
            [ -n "$VIASH_PAR_MAX_AVERAGE_ERROR_RATE" ] && ViashError Bad arguments for option \'--max_average_error_rate=*\': \'$VIASH_PAR_MAX_AVERAGE_ERROR_RATE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_AVERAGE_ERROR_RATE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --max_aer)
            [ -n "$VIASH_PAR_MAX_AVERAGE_ERROR_RATE" ] && ViashError Bad arguments for option \'--max_aer\': \'$VIASH_PAR_MAX_AVERAGE_ERROR_RATE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_AVERAGE_ERROR_RATE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --max_aer. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --discard_trimmed)
            [ -n "$VIASH_PAR_DISCARD_TRIMMED" ] && ViashError Bad arguments for option \'--discard_trimmed\': \'$VIASH_PAR_DISCARD_TRIMMED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_DISCARD_TRIMMED=true
            shift 1
            ;;
        --discard)
            [ -n "$VIASH_PAR_DISCARD_TRIMMED" ] && ViashError Bad arguments for option \'--discard\': \'$VIASH_PAR_DISCARD_TRIMMED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_DISCARD_TRIMMED=true
            shift 1
            ;;
        --discard_untrimmed)
            [ -n "$VIASH_PAR_DISCARD_UNTRIMMED" ] && ViashError Bad arguments for option \'--discard_untrimmed\': \'$VIASH_PAR_DISCARD_UNTRIMMED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_DISCARD_UNTRIMMED=true
            shift 1
            ;;
        --trimmed_only)
            [ -n "$VIASH_PAR_DISCARD_UNTRIMMED" ] && ViashError Bad arguments for option \'--trimmed_only\': \'$VIASH_PAR_DISCARD_UNTRIMMED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_DISCARD_UNTRIMMED=true
            shift 1
            ;;
        --discard_casava)
            [ -n "$VIASH_PAR_DISCARD_CASAVA" ] && ViashError Bad arguments for option \'--discard_casava\': \'$VIASH_PAR_DISCARD_CASAVA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_DISCARD_CASAVA=true
            shift 1
            ;;
        --report)
            [ -n "$VIASH_PAR_REPORT" ] && ViashError Bad arguments for option \'--report\': \'$VIASH_PAR_REPORT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_REPORT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --report. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --report=*)
            [ -n "$VIASH_PAR_REPORT" ] && ViashError Bad arguments for option \'--report=*\': \'$VIASH_PAR_REPORT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_REPORT=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --json)
            [ -n "$VIASH_PAR_JSON" ] && ViashError Bad arguments for option \'--json\': \'$VIASH_PAR_JSON\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_JSON=true
            shift 1
            ;;
        --output)
            [ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --output. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --output=*)
            [ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output=*\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --fasta)
            [ -n "$VIASH_PAR_FASTA" ] && ViashError Bad arguments for option \'--fasta\': \'$VIASH_PAR_FASTA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FASTA=true
            shift 1
            ;;
        --info_file)
            [ -n "$VIASH_PAR_INFO_FILE" ] && ViashError Bad arguments for option \'--info_file\': \'$VIASH_PAR_INFO_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INFO_FILE=true
            shift 1
            ;;
        --debug)
            [ -n "$VIASH_PAR_DEBUG" ] && ViashError Bad arguments for option \'--debug\': \'$VIASH_PAR_DEBUG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_DEBUG=true
            shift 1
            ;;
        ---engine)
            VIASH_ENGINE_ID="$2"
            shift 2
            ;;
        ---engine=*)
            VIASH_ENGINE_ID="$(ViashRemoveFlags "$1")"
            shift 1
            ;;
        ---setup)
            VIASH_MODE='setup'
            VIASH_SETUP_STRATEGY="$2"
            shift 2
            ;;
        ---setup=*)
            VIASH_MODE='setup'
            VIASH_SETUP_STRATEGY="$(ViashRemoveFlags "$1")"
            shift 1
            ;;
        ---dockerfile)
            VIASH_MODE='dockerfile'
            shift 1
            ;;
        ---docker_run_args)
            VIASH_DOCKER_RUN_ARGS+=("$2")
            shift 2
            ;;
        ---docker_run_args=*)
            VIASH_DOCKER_RUN_ARGS+=("$(ViashRemoveFlags "$1")")
            shift 1
            ;;
        ---docker_image_id)
            VIASH_MODE='docker_image_id'
            shift 1
            ;;
        ---debug)
            VIASH_MODE='debug'
            shift 1
            ;;
        ---cpus)
            [ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_CPUS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to ---cpus. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        ---cpus=*)
            [ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus=*\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_CPUS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        ---memory)
            [ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_MEMORY="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to ---memory. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        ---memory=*)
            [ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory=*\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_MEMORY=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        *)  # positional arg or unknown option
            # since the positional args will be eval'd, can we always quote, instead of using ViashQuote
            VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'"
            [[ $1 == -* ]] && ViashWarning $1 looks like a parameter but is not a defined parameter and will instead be treated as a positional argument. Use "--help" to get more information on the parameters.
            shift # past argument
            ;;
    esac
done

# parse positional parameters
eval set -- $VIASH_POSITIONAL_ARGS


if   [ "$VIASH_ENGINE_ID" == "native" ]  ; then
  VIASH_ENGINE_TYPE='native'
elif   [ "$VIASH_ENGINE_ID" == "docker" ]  ; then
  VIASH_ENGINE_TYPE='docker'
else
  ViashError "Engine '$VIASH_ENGINE_ID' is not recognized. Options are: docker, native."
  exit 1
fi

if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  # check if docker is installed properly
  ViashDockerInstallationCheck

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/cutadapt:add_sgdemux'
  fi

  # print dockerfile
  if [ "$VIASH_MODE" == "dockerfile" ]; then
    ViashDockerfile "$VIASH_ENGINE_ID"
    exit 0

  elif [ "$VIASH_MODE" == "docker_image_id" ]; then
    echo "$VIASH_DOCKER_IMAGE_ID"
    exit 0
  
  # enter docker container
  elif [[ "$VIASH_MODE" == "debug" ]]; then
    VIASH_CMD="docker run --entrypoint=bash ${VIASH_DOCKER_RUN_ARGS[@]} -v '$(pwd)':/pwd --workdir /pwd -t $VIASH_DOCKER_IMAGE_ID"
    ViashNotice "+ $VIASH_CMD"
    eval $VIASH_CMD
    exit 

  # build docker image
  elif [ "$VIASH_MODE" == "setup" ]; then
    ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY"
    ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash'
    exit 0
  fi

  # check if docker image exists
  ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild
  ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash'
fi

# setting computational defaults

# helper function for parsing memory strings
function ViashMemoryAsBytes {
  local memory=`echo "$1" | tr '[:upper:]' '[:lower:]' | tr -d '[:space:]'`
  local memory_regex='^([0-9]+)([kmgtp]i?b?|b)$'
  if [[ $memory =~ $memory_regex ]]; then
    local number=${memory/[^0-9]*/}
    local symbol=${memory/*[0-9]/}
    
    case $symbol in
      b)      memory_b=$number ;;
      kb|k)   memory_b=$(( $number * 1000 )) ;;
      mb|m)   memory_b=$(( $number * 1000 * 1000 )) ;;
      gb|g)   memory_b=$(( $number * 1000 * 1000 * 1000 )) ;;
      tb|t)   memory_b=$(( $number * 1000 * 1000 * 1000 * 1000 )) ;;
      pb|p)   memory_b=$(( $number * 1000 * 1000 * 1000 * 1000 * 1000 )) ;;
      kib|ki)   memory_b=$(( $number * 1024 )) ;;
      mib|mi)   memory_b=$(( $number * 1024 * 1024 )) ;;
      gib|gi)   memory_b=$(( $number * 1024 * 1024 * 1024 )) ;;
      tib|ti)   memory_b=$(( $number * 1024 * 1024 * 1024 * 1024 )) ;;
      pib|pi)   memory_b=$(( $number * 1024 * 1024 * 1024 * 1024 * 1024 )) ;;
    esac
    echo "$memory_b"
  fi
}
# compute memory in different units
if [ ! -z ${VIASH_META_MEMORY+x} ]; then
  VIASH_META_MEMORY_B=`ViashMemoryAsBytes $VIASH_META_MEMORY`
  # do not define other variables if memory_b is an empty string
  if [ ! -z "$VIASH_META_MEMORY_B" ]; then
    VIASH_META_MEMORY_KB=$(( ($VIASH_META_MEMORY_B+999) / 1000 ))
    VIASH_META_MEMORY_MB=$(( ($VIASH_META_MEMORY_KB+999) / 1000 ))
    VIASH_META_MEMORY_GB=$(( ($VIASH_META_MEMORY_MB+999) / 1000 ))
    VIASH_META_MEMORY_TB=$(( ($VIASH_META_MEMORY_GB+999) / 1000 ))
    VIASH_META_MEMORY_PB=$(( ($VIASH_META_MEMORY_TB+999) / 1000 ))
    VIASH_META_MEMORY_KIB=$(( ($VIASH_META_MEMORY_B+1023) / 1024 ))
    VIASH_META_MEMORY_MIB=$(( ($VIASH_META_MEMORY_KIB+1023) / 1024 ))
    VIASH_META_MEMORY_GIB=$(( ($VIASH_META_MEMORY_MIB+1023) / 1024 ))
    VIASH_META_MEMORY_TIB=$(( ($VIASH_META_MEMORY_GIB+1023) / 1024 ))
    VIASH_META_MEMORY_PIB=$(( ($VIASH_META_MEMORY_TIB+1023) / 1024 ))
  else
    # unset memory if string is empty
    unset $VIASH_META_MEMORY_B
  fi
fi
# unset nproc if string is empty
if [ -z "$VIASH_META_CPUS" ]; then
  unset $VIASH_META_CPUS
fi


# check whether required parameters exist
if [ -z ${VIASH_PAR_INPUT+x} ]; then
  ViashError '--input' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_PAR_OUTPUT+x} ]; then
  ViashError '--output' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_NAME+x} ]; then
  ViashError 'name' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then
  ViashError 'functionality_name' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_RESOURCES_DIR+x} ]; then
  ViashError 'resources_dir' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_EXECUTABLE+x} ]; then
  ViashError 'executable' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_CONFIG+x} ]; then
  ViashError 'config' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_TEMP_DIR+x} ]; then
  ViashError 'temp_dir' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi

# filling in defaults
if [ -z ${VIASH_PAR_PAIR_ADAPTERS+x} ]; then
  VIASH_PAR_PAIR_ADAPTERS="false"
fi
if [ -z ${VIASH_PAR_INTERLEAVED+x} ]; then
  VIASH_PAR_INTERLEAVED="false"
fi
if [ -z ${VIASH_PAR_NO_INDELS+x} ]; then
  VIASH_PAR_NO_INDELS="false"
fi
if [ -z ${VIASH_PAR_MATCH_READ_WILDCARDS+x} ]; then
  VIASH_PAR_MATCH_READ_WILDCARDS="false"
fi
if [ -z ${VIASH_PAR_NO_MATCH_ADAPTER_WILDCARDS+x} ]; then
  VIASH_PAR_NO_MATCH_ADAPTER_WILDCARDS="false"
fi
if [ -z ${VIASH_PAR_REVCOMP+x} ]; then
  VIASH_PAR_REVCOMP="false"
fi
if [ -z ${VIASH_PAR_POLY_A+x} ]; then
  VIASH_PAR_POLY_A="false"
fi
if [ -z ${VIASH_PAR_TRIM_N+x} ]; then
  VIASH_PAR_TRIM_N="false"
fi
if [ -z ${VIASH_PAR_ZERO_CAP+x} ]; then
  VIASH_PAR_ZERO_CAP="false"
fi
if [ -z ${VIASH_PAR_DISCARD_TRIMMED+x} ]; then
  VIASH_PAR_DISCARD_TRIMMED="false"
fi
if [ -z ${VIASH_PAR_DISCARD_UNTRIMMED+x} ]; then
  VIASH_PAR_DISCARD_UNTRIMMED="false"
fi
if [ -z ${VIASH_PAR_DISCARD_CASAVA+x} ]; then
  VIASH_PAR_DISCARD_CASAVA="false"
fi
if [ -z ${VIASH_PAR_JSON+x} ]; then
  VIASH_PAR_JSON="false"
fi
if [ -z ${VIASH_PAR_FASTA+x} ]; then
  VIASH_PAR_FASTA="false"
fi
if [ -z ${VIASH_PAR_INFO_FILE+x} ]; then
  VIASH_PAR_INFO_FILE="false"
fi
if [ -z ${VIASH_PAR_DEBUG+x} ]; then
  VIASH_PAR_DEBUG="false"
fi

# check whether required files exist
if [ ! -z "$VIASH_PAR_ADAPTER_FASTA" ]; then
  IFS=';'
  set -f
  for file in $VIASH_PAR_ADAPTER_FASTA; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_FRONT_FASTA" ] && [ ! -e "$VIASH_PAR_FRONT_FASTA" ]; then
  ViashError "Input file '$VIASH_PAR_FRONT_FASTA' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_ANYWHERE_FASTA" ] && [ ! -e "$VIASH_PAR_ANYWHERE_FASTA" ]; then
  ViashError "Input file '$VIASH_PAR_ANYWHERE_FASTA' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_ADAPTER_R2_FASTA" ] && [ ! -e "$VIASH_PAR_ADAPTER_R2_FASTA" ]; then
  ViashError "Input file '$VIASH_PAR_ADAPTER_R2_FASTA' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_FRONT_R2_FASTA" ] && [ ! -e "$VIASH_PAR_FRONT_R2_FASTA" ]; then
  ViashError "Input file '$VIASH_PAR_FRONT_R2_FASTA' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_ANYWHERE_R2_FASTA" ] && [ ! -e "$VIASH_PAR_ANYWHERE_R2_FASTA" ]; then
  ViashError "Input file '$VIASH_PAR_ANYWHERE_R2_FASTA' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_INPUT" ] && [ ! -e "$VIASH_PAR_INPUT" ]; then
  ViashError "Input file '$VIASH_PAR_INPUT' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_INPUT_R2" ] && [ ! -e "$VIASH_PAR_INPUT_R2" ]; then
  ViashError "Input file '$VIASH_PAR_INPUT_R2' does not exist."
  exit 1
fi

# check whether parameters values are of the right type
if [[ -n "$VIASH_PAR_PAIR_ADAPTERS" ]]; then
  if ! [[ "$VIASH_PAR_PAIR_ADAPTERS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--pair_adapters' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_INTERLEAVED" ]]; then
  if ! [[ "$VIASH_PAR_INTERLEAVED" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--interleaved' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_ERROR_RATE" ]]; then
  if ! [[ "$VIASH_PAR_ERROR_RATE" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--error_rate' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_NO_INDELS" ]]; then
  if ! [[ "$VIASH_PAR_NO_INDELS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--no_indels' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_TIMES" ]]; then
  if ! [[ "$VIASH_PAR_TIMES" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--times' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_OVERLAP" ]]; then
  if ! [[ "$VIASH_PAR_OVERLAP" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--overlap' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_MATCH_READ_WILDCARDS" ]]; then
  if ! [[ "$VIASH_PAR_MATCH_READ_WILDCARDS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--match_read_wildcards' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_NO_MATCH_ADAPTER_WILDCARDS" ]]; then
  if ! [[ "$VIASH_PAR_NO_MATCH_ADAPTER_WILDCARDS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--no_match_adapter_wildcards' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_REVCOMP" ]]; then
  if ! [[ "$VIASH_PAR_REVCOMP" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--revcomp' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [ -n "$VIASH_PAR_CUT" ]; then
  IFS=';'
  set -f
  for val in $VIASH_PAR_CUT; do
    if ! [[ "${val}" =~ ^[-+]?[0-9]+$ ]]; then
      ViashError '--cut' has to be an integer. Use "--help" to get more information on the parameters.
      exit 1
    fi
  done
  set +f
  unset IFS
fi

if [ -n "$VIASH_PAR_CUT_R2" ]; then
  IFS=';'
  set -f
  for val in $VIASH_PAR_CUT_R2; do
    if ! [[ "${val}" =~ ^[-+]?[0-9]+$ ]]; then
      ViashError '--cut_r2' has to be an integer. Use "--help" to get more information on the parameters.
      exit 1
    fi
  done
  set +f
  unset IFS
fi

if [[ -n "$VIASH_PAR_QUALITY_BASE" ]]; then
  if ! [[ "$VIASH_PAR_QUALITY_BASE" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--quality_base' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_POLY_A" ]]; then
  if ! [[ "$VIASH_PAR_POLY_A" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--poly_a' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_LENGTH" ]]; then
  if ! [[ "$VIASH_PAR_LENGTH" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--length' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_TRIM_N" ]]; then
  if ! [[ "$VIASH_PAR_TRIM_N" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--trim_n' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_ZERO_CAP" ]]; then
  if ! [[ "$VIASH_PAR_ZERO_CAP" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--zero_cap' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_MAX_EXPECTED_ERRORS" ]]; then
  if ! [[ "$VIASH_PAR_MAX_EXPECTED_ERRORS" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--max_expected_errors' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_MAX_AVERAGE_ERROR_RATE" ]]; then
  if ! [[ "$VIASH_PAR_MAX_AVERAGE_ERROR_RATE" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--max_average_error_rate' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_DISCARD_TRIMMED" ]]; then
  if ! [[ "$VIASH_PAR_DISCARD_TRIMMED" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--discard_trimmed' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_DISCARD_UNTRIMMED" ]]; then
  if ! [[ "$VIASH_PAR_DISCARD_UNTRIMMED" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--discard_untrimmed' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_DISCARD_CASAVA" ]]; then
  if ! [[ "$VIASH_PAR_DISCARD_CASAVA" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--discard_casava' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_JSON" ]]; then
  if ! [[ "$VIASH_PAR_JSON" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--json' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_OUTPUT" ]]; then
  if ! [[ "$VIASH_PAR_OUTPUT" =~ \* ]]; then
    ViashError '--output' has to be a path containing a wildcard, e.g. 'output_*.txt'. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_FASTA" ]]; then
  if ! [[ "$VIASH_PAR_FASTA" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--fasta' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_INFO_FILE" ]]; then
  if ! [[ "$VIASH_PAR_INFO_FILE" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--info_file' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_DEBUG" ]]; then
  if ! [[ "$VIASH_PAR_DEBUG" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--debug' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_CPUS" ]]; then
  if ! [[ "$VIASH_META_CPUS" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'cpus' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_B" ]]; then
  if ! [[ "$VIASH_META_MEMORY_B" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_b' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_KB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_KB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_kb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_MB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_MB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_mb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_GB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_GB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_gb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_TB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_TB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_tb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_PB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_PB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_pb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_KIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_KIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_kib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_MIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_MIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_mib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_GIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_GIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_gib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_TIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_TIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_tib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_PIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_PIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_pib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi

# check whether value is belongs to a set of choices
if [ ! -z "$VIASH_PAR_PAIR_FILTER" ]; then
  VIASH_PAR_PAIR_FILTER_CHOICES=("any;both;first")
  IFS=';'
  set -f
  if ! [[ ";${VIASH_PAR_PAIR_FILTER_CHOICES[*]};" =~ ";$VIASH_PAR_PAIR_FILTER;" ]]; then
    ViashError '--pair_filter' specified value of \'$VIASH_PAR_PAIR_FILTER\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
    exit 1
  fi
  set +f
  unset IFS
fi

if [ ! -z "$VIASH_PAR_ACTION" ]; then
  VIASH_PAR_ACTION_CHOICES=("trim;retain;mask;lowercase;none")
  IFS=';'
  set -f
  if ! [[ ";${VIASH_PAR_ACTION_CHOICES[*]};" =~ ";$VIASH_PAR_ACTION;" ]]; then
    ViashError '--action' specified value of \'$VIASH_PAR_ACTION\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
    exit 1
  fi
  set +f
  unset IFS
fi

if [ ! -z "$VIASH_PAR_DEMULTIPLEX_MODE" ]; then
  VIASH_PAR_DEMULTIPLEX_MODE_CHOICES=("single;unique_dual;combinatorial_dual")
  IFS=';'
  set -f
  if ! [[ ";${VIASH_PAR_DEMULTIPLEX_MODE_CHOICES[*]};" =~ ";$VIASH_PAR_DEMULTIPLEX_MODE;" ]]; then
    ViashError '--demultiplex_mode' specified value of \'$VIASH_PAR_DEMULTIPLEX_MODE\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
    exit 1
  fi
  set +f
  unset IFS
fi

if [ ! -z "$VIASH_PAR_REPORT" ]; then
  VIASH_PAR_REPORT_CHOICES=("full;minimal")
  IFS=';'
  set -f
  if ! [[ ";${VIASH_PAR_REPORT_CHOICES[*]};" =~ ";$VIASH_PAR_REPORT;" ]]; then
    ViashError '--report' specified value of \'$VIASH_PAR_REPORT\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
    exit 1
  fi
  set +f
  unset IFS
fi

# create parent directories of output files, if so desired
if [ ! -z "$VIASH_PAR_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_OUTPUT")"
fi

if  [ "$VIASH_ENGINE_ID" == "native" ]  ; then
  if [ "$VIASH_MODE" == "run" ]; then
    VIASH_CMD="bash"
  else
    ViashError "Engine '$VIASH_ENGINE_ID' does not support mode '$VIASH_MODE'."
    exit 1
  fi
fi

if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  # detect volumes from file arguments
  VIASH_CHOWN_VARS=()
if [ ! -z "$VIASH_PAR_ADAPTER_FASTA" ]; then
  VIASH_TEST_ADAPTER_FASTA=()
  IFS=';'
  for var in $VIASH_PAR_ADAPTER_FASTA; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_ADAPTER_FASTA+=( "$var" )
  done
  VIASH_PAR_ADAPTER_FASTA=$(IFS=';' ; echo "${VIASH_TEST_ADAPTER_FASTA[*]}")
fi
if [ ! -z "$VIASH_PAR_FRONT_FASTA" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_FRONT_FASTA")" )
  VIASH_PAR_FRONT_FASTA=$(ViashDockerAutodetectMount "$VIASH_PAR_FRONT_FASTA")
fi
if [ ! -z "$VIASH_PAR_ANYWHERE_FASTA" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_ANYWHERE_FASTA")" )
  VIASH_PAR_ANYWHERE_FASTA=$(ViashDockerAutodetectMount "$VIASH_PAR_ANYWHERE_FASTA")
fi
if [ ! -z "$VIASH_PAR_ADAPTER_R2_FASTA" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_ADAPTER_R2_FASTA")" )
  VIASH_PAR_ADAPTER_R2_FASTA=$(ViashDockerAutodetectMount "$VIASH_PAR_ADAPTER_R2_FASTA")
fi
if [ ! -z "$VIASH_PAR_FRONT_R2_FASTA" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_FRONT_R2_FASTA")" )
  VIASH_PAR_FRONT_R2_FASTA=$(ViashDockerAutodetectMount "$VIASH_PAR_FRONT_R2_FASTA")
fi
if [ ! -z "$VIASH_PAR_ANYWHERE_R2_FASTA" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_ANYWHERE_R2_FASTA")" )
  VIASH_PAR_ANYWHERE_R2_FASTA=$(ViashDockerAutodetectMount "$VIASH_PAR_ANYWHERE_R2_FASTA")
fi
if [ ! -z "$VIASH_PAR_INPUT" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INPUT")" )
  VIASH_PAR_INPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_INPUT")
fi
if [ ! -z "$VIASH_PAR_INPUT_R2" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INPUT_R2")" )
  VIASH_PAR_INPUT_R2=$(ViashDockerAutodetectMount "$VIASH_PAR_INPUT_R2")
fi
if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
  VIASH_TEST_OUTPUT=()
  IFS=';'
  for var in $VIASH_PAR_OUTPUT; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_OUTPUT+=( "$var" )
    VIASH_CHOWN_VARS+=( "$var" )
  done
  VIASH_PAR_OUTPUT=$(IFS=';' ; echo "${VIASH_TEST_OUTPUT[*]}")
fi
if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_RESOURCES_DIR")" )
  VIASH_META_RESOURCES_DIR=$(ViashDockerAutodetectMount "$VIASH_META_RESOURCES_DIR")
fi
if [ ! -z "$VIASH_META_EXECUTABLE" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_EXECUTABLE")" )
  VIASH_META_EXECUTABLE=$(ViashDockerAutodetectMount "$VIASH_META_EXECUTABLE")
fi
if [ ! -z "$VIASH_META_CONFIG" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_CONFIG")" )
  VIASH_META_CONFIG=$(ViashDockerAutodetectMount "$VIASH_META_CONFIG")
fi
if [ ! -z "$VIASH_META_TEMP_DIR" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_TEMP_DIR")" )
  VIASH_META_TEMP_DIR=$(ViashDockerAutodetectMount "$VIASH_META_TEMP_DIR")
fi
  
  # get unique mounts
  VIASH_UNIQUE_MOUNTS=($(for val in "${VIASH_DIRECTORY_MOUNTS[@]}"; do echo "$val"; done | sort -u))
fi

if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  # change file ownership
  function ViashPerformChown {
    if (( ${#VIASH_CHOWN_VARS[@]} )); then
      set +e
      VIASH_CMD="docker run --entrypoint=bash --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_DOCKER_IMAGE_ID -c 'chown $(id -u):$(id -g) --silent --recursive ${VIASH_CHOWN_VARS[@]}'"
      ViashDebug "+ $VIASH_CMD"
      eval $VIASH_CMD
      set -e
    fi
  }
  trap ViashPerformChown EXIT
fi

if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  # helper function for filling in extra docker args
  if [ ! -z "$VIASH_META_MEMORY_B" ]; then
    VIASH_DOCKER_RUN_ARGS+=("--memory=${VIASH_META_MEMORY_B}")
  fi
  if [ ! -z "$VIASH_META_CPUS" ]; then
    VIASH_DOCKER_RUN_ARGS+=("--cpus=${VIASH_META_CPUS}")
  fi
fi

if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  VIASH_CMD="docker run --entrypoint=bash ${VIASH_DOCKER_RUN_ARGS[@]} ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_DOCKER_IMAGE_ID"
fi


# set dependency paths


ViashDebug "Running command: $(echo $VIASH_CMD)"
cat << VIASHEOF | eval $VIASH_CMD
set -e
tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-cutadapt-XXXXXX").sh
function clean_up {
  rm "\$tempscript"
}
function interrupt {
  echo -e "\nCTRL-C Pressed..."
  exit 1
}
trap clean_up EXIT
trap interrupt INT SIGINT
cat > "\$tempscript" << 'VIASHMAIN'
#!/bin/bash

## VIASH START
# The following code has been auto-generated by Viash.
$( if [ ! -z ${VIASH_PAR_ADAPTER+x} ]; then echo "${VIASH_PAR_ADAPTER}" | sed "s#'#'\"'\"'#g;s#.*#par_adapter='&'#" ; else echo "# par_adapter="; fi )
$( if [ ! -z ${VIASH_PAR_FRONT+x} ]; then echo "${VIASH_PAR_FRONT}" | sed "s#'#'\"'\"'#g;s#.*#par_front='&'#" ; else echo "# par_front="; fi )
$( if [ ! -z ${VIASH_PAR_ANYWHERE+x} ]; then echo "${VIASH_PAR_ANYWHERE}" | sed "s#'#'\"'\"'#g;s#.*#par_anywhere='&'#" ; else echo "# par_anywhere="; fi )
$( if [ ! -z ${VIASH_PAR_ADAPTER_FASTA+x} ]; then echo "${VIASH_PAR_ADAPTER_FASTA}" | sed "s#'#'\"'\"'#g;s#.*#par_adapter_fasta='&'#" ; else echo "# par_adapter_fasta="; fi )
$( if [ ! -z ${VIASH_PAR_FRONT_FASTA+x} ]; then echo "${VIASH_PAR_FRONT_FASTA}" | sed "s#'#'\"'\"'#g;s#.*#par_front_fasta='&'#" ; else echo "# par_front_fasta="; fi )
$( if [ ! -z ${VIASH_PAR_ANYWHERE_FASTA+x} ]; then echo "${VIASH_PAR_ANYWHERE_FASTA}" | sed "s#'#'\"'\"'#g;s#.*#par_anywhere_fasta='&'#" ; else echo "# par_anywhere_fasta="; fi )
$( if [ ! -z ${VIASH_PAR_ADAPTER_R2+x} ]; then echo "${VIASH_PAR_ADAPTER_R2}" | sed "s#'#'\"'\"'#g;s#.*#par_adapter_r2='&'#" ; else echo "# par_adapter_r2="; fi )
$( if [ ! -z ${VIASH_PAR_FRONT_R2+x} ]; then echo "${VIASH_PAR_FRONT_R2}" | sed "s#'#'\"'\"'#g;s#.*#par_front_r2='&'#" ; else echo "# par_front_r2="; fi )
$( if [ ! -z ${VIASH_PAR_ANYWHERE_R2+x} ]; then echo "${VIASH_PAR_ANYWHERE_R2}" | sed "s#'#'\"'\"'#g;s#.*#par_anywhere_r2='&'#" ; else echo "# par_anywhere_r2="; fi )
$( if [ ! -z ${VIASH_PAR_ADAPTER_R2_FASTA+x} ]; then echo "${VIASH_PAR_ADAPTER_R2_FASTA}" | sed "s#'#'\"'\"'#g;s#.*#par_adapter_r2_fasta='&'#" ; else echo "# par_adapter_r2_fasta="; fi )
$( if [ ! -z ${VIASH_PAR_FRONT_R2_FASTA+x} ]; then echo "${VIASH_PAR_FRONT_R2_FASTA}" | sed "s#'#'\"'\"'#g;s#.*#par_front_r2_fasta='&'#" ; else echo "# par_front_r2_fasta="; fi )
$( if [ ! -z ${VIASH_PAR_ANYWHERE_R2_FASTA+x} ]; then echo "${VIASH_PAR_ANYWHERE_R2_FASTA}" | sed "s#'#'\"'\"'#g;s#.*#par_anywhere_r2_fasta='&'#" ; else echo "# par_anywhere_r2_fasta="; fi )
$( if [ ! -z ${VIASH_PAR_PAIR_ADAPTERS+x} ]; then echo "${VIASH_PAR_PAIR_ADAPTERS}" | sed "s#'#'\"'\"'#g;s#.*#par_pair_adapters='&'#" ; else echo "# par_pair_adapters="; fi )
$( if [ ! -z ${VIASH_PAR_PAIR_FILTER+x} ]; then echo "${VIASH_PAR_PAIR_FILTER}" | sed "s#'#'\"'\"'#g;s#.*#par_pair_filter='&'#" ; else echo "# par_pair_filter="; fi )
$( if [ ! -z ${VIASH_PAR_INTERLEAVED+x} ]; then echo "${VIASH_PAR_INTERLEAVED}" | sed "s#'#'\"'\"'#g;s#.*#par_interleaved='&'#" ; else echo "# par_interleaved="; fi )
$( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_input='&'#" ; else echo "# par_input="; fi )
$( if [ ! -z ${VIASH_PAR_INPUT_R2+x} ]; then echo "${VIASH_PAR_INPUT_R2}" | sed "s#'#'\"'\"'#g;s#.*#par_input_r2='&'#" ; else echo "# par_input_r2="; fi )
$( if [ ! -z ${VIASH_PAR_ERROR_RATE+x} ]; then echo "${VIASH_PAR_ERROR_RATE}" | sed "s#'#'\"'\"'#g;s#.*#par_error_rate='&'#" ; else echo "# par_error_rate="; fi )
$( if [ ! -z ${VIASH_PAR_NO_INDELS+x} ]; then echo "${VIASH_PAR_NO_INDELS}" | sed "s#'#'\"'\"'#g;s#.*#par_no_indels='&'#" ; else echo "# par_no_indels="; fi )
$( if [ ! -z ${VIASH_PAR_TIMES+x} ]; then echo "${VIASH_PAR_TIMES}" | sed "s#'#'\"'\"'#g;s#.*#par_times='&'#" ; else echo "# par_times="; fi )
$( if [ ! -z ${VIASH_PAR_OVERLAP+x} ]; then echo "${VIASH_PAR_OVERLAP}" | sed "s#'#'\"'\"'#g;s#.*#par_overlap='&'#" ; else echo "# par_overlap="; fi )
$( if [ ! -z ${VIASH_PAR_MATCH_READ_WILDCARDS+x} ]; then echo "${VIASH_PAR_MATCH_READ_WILDCARDS}" | sed "s#'#'\"'\"'#g;s#.*#par_match_read_wildcards='&'#" ; else echo "# par_match_read_wildcards="; fi )
$( if [ ! -z ${VIASH_PAR_NO_MATCH_ADAPTER_WILDCARDS+x} ]; then echo "${VIASH_PAR_NO_MATCH_ADAPTER_WILDCARDS}" | sed "s#'#'\"'\"'#g;s#.*#par_no_match_adapter_wildcards='&'#" ; else echo "# par_no_match_adapter_wildcards="; fi )
$( if [ ! -z ${VIASH_PAR_ACTION+x} ]; then echo "${VIASH_PAR_ACTION}" | sed "s#'#'\"'\"'#g;s#.*#par_action='&'#" ; else echo "# par_action="; fi )
$( if [ ! -z ${VIASH_PAR_REVCOMP+x} ]; then echo "${VIASH_PAR_REVCOMP}" | sed "s#'#'\"'\"'#g;s#.*#par_revcomp='&'#" ; else echo "# par_revcomp="; fi )
$( if [ ! -z ${VIASH_PAR_DEMULTIPLEX_MODE+x} ]; then echo "${VIASH_PAR_DEMULTIPLEX_MODE}" | sed "s#'#'\"'\"'#g;s#.*#par_demultiplex_mode='&'#" ; else echo "# par_demultiplex_mode="; fi )
$( if [ ! -z ${VIASH_PAR_CUT+x} ]; then echo "${VIASH_PAR_CUT}" | sed "s#'#'\"'\"'#g;s#.*#par_cut='&'#" ; else echo "# par_cut="; fi )
$( if [ ! -z ${VIASH_PAR_CUT_R2+x} ]; then echo "${VIASH_PAR_CUT_R2}" | sed "s#'#'\"'\"'#g;s#.*#par_cut_r2='&'#" ; else echo "# par_cut_r2="; fi )
$( if [ ! -z ${VIASH_PAR_NEXTSEQ_TRIM+x} ]; then echo "${VIASH_PAR_NEXTSEQ_TRIM}" | sed "s#'#'\"'\"'#g;s#.*#par_nextseq_trim='&'#" ; else echo "# par_nextseq_trim="; fi )
$( if [ ! -z ${VIASH_PAR_QUALITY_CUTOFF+x} ]; then echo "${VIASH_PAR_QUALITY_CUTOFF}" | sed "s#'#'\"'\"'#g;s#.*#par_quality_cutoff='&'#" ; else echo "# par_quality_cutoff="; fi )
$( if [ ! -z ${VIASH_PAR_QUALITY_CUTOFF_R2+x} ]; then echo "${VIASH_PAR_QUALITY_CUTOFF_R2}" | sed "s#'#'\"'\"'#g;s#.*#par_quality_cutoff_r2='&'#" ; else echo "# par_quality_cutoff_r2="; fi )
$( if [ ! -z ${VIASH_PAR_QUALITY_BASE+x} ]; then echo "${VIASH_PAR_QUALITY_BASE}" | sed "s#'#'\"'\"'#g;s#.*#par_quality_base='&'#" ; else echo "# par_quality_base="; fi )
$( if [ ! -z ${VIASH_PAR_POLY_A+x} ]; then echo "${VIASH_PAR_POLY_A}" | sed "s#'#'\"'\"'#g;s#.*#par_poly_a='&'#" ; else echo "# par_poly_a="; fi )
$( if [ ! -z ${VIASH_PAR_LENGTH+x} ]; then echo "${VIASH_PAR_LENGTH}" | sed "s#'#'\"'\"'#g;s#.*#par_length='&'#" ; else echo "# par_length="; fi )
$( if [ ! -z ${VIASH_PAR_TRIM_N+x} ]; then echo "${VIASH_PAR_TRIM_N}" | sed "s#'#'\"'\"'#g;s#.*#par_trim_n='&'#" ; else echo "# par_trim_n="; fi )
$( if [ ! -z ${VIASH_PAR_LENGTH_TAG+x} ]; then echo "${VIASH_PAR_LENGTH_TAG}" | sed "s#'#'\"'\"'#g;s#.*#par_length_tag='&'#" ; else echo "# par_length_tag="; fi )
$( if [ ! -z ${VIASH_PAR_STRIP_SUFFIX+x} ]; then echo "${VIASH_PAR_STRIP_SUFFIX}" | sed "s#'#'\"'\"'#g;s#.*#par_strip_suffix='&'#" ; else echo "# par_strip_suffix="; fi )
$( if [ ! -z ${VIASH_PAR_PREFIX+x} ]; then echo "${VIASH_PAR_PREFIX}" | sed "s#'#'\"'\"'#g;s#.*#par_prefix='&'#" ; else echo "# par_prefix="; fi )
$( if [ ! -z ${VIASH_PAR_SUFFIX+x} ]; then echo "${VIASH_PAR_SUFFIX}" | sed "s#'#'\"'\"'#g;s#.*#par_suffix='&'#" ; else echo "# par_suffix="; fi )
$( if [ ! -z ${VIASH_PAR_RENAME+x} ]; then echo "${VIASH_PAR_RENAME}" | sed "s#'#'\"'\"'#g;s#.*#par_rename='&'#" ; else echo "# par_rename="; fi )
$( if [ ! -z ${VIASH_PAR_ZERO_CAP+x} ]; then echo "${VIASH_PAR_ZERO_CAP}" | sed "s#'#'\"'\"'#g;s#.*#par_zero_cap='&'#" ; else echo "# par_zero_cap="; fi )
$( if [ ! -z ${VIASH_PAR_MINIMUM_LENGTH+x} ]; then echo "${VIASH_PAR_MINIMUM_LENGTH}" | sed "s#'#'\"'\"'#g;s#.*#par_minimum_length='&'#" ; else echo "# par_minimum_length="; fi )
$( if [ ! -z ${VIASH_PAR_MAXIMUM_LENGTH+x} ]; then echo "${VIASH_PAR_MAXIMUM_LENGTH}" | sed "s#'#'\"'\"'#g;s#.*#par_maximum_length='&'#" ; else echo "# par_maximum_length="; fi )
$( if [ ! -z ${VIASH_PAR_MAX_N+x} ]; then echo "${VIASH_PAR_MAX_N}" | sed "s#'#'\"'\"'#g;s#.*#par_max_n='&'#" ; else echo "# par_max_n="; fi )
$( if [ ! -z ${VIASH_PAR_MAX_EXPECTED_ERRORS+x} ]; then echo "${VIASH_PAR_MAX_EXPECTED_ERRORS}" | sed "s#'#'\"'\"'#g;s#.*#par_max_expected_errors='&'#" ; else echo "# par_max_expected_errors="; fi )
$( if [ ! -z ${VIASH_PAR_MAX_AVERAGE_ERROR_RATE+x} ]; then echo "${VIASH_PAR_MAX_AVERAGE_ERROR_RATE}" | sed "s#'#'\"'\"'#g;s#.*#par_max_average_error_rate='&'#" ; else echo "# par_max_average_error_rate="; fi )
$( if [ ! -z ${VIASH_PAR_DISCARD_TRIMMED+x} ]; then echo "${VIASH_PAR_DISCARD_TRIMMED}" | sed "s#'#'\"'\"'#g;s#.*#par_discard_trimmed='&'#" ; else echo "# par_discard_trimmed="; fi )
$( if [ ! -z ${VIASH_PAR_DISCARD_UNTRIMMED+x} ]; then echo "${VIASH_PAR_DISCARD_UNTRIMMED}" | sed "s#'#'\"'\"'#g;s#.*#par_discard_untrimmed='&'#" ; else echo "# par_discard_untrimmed="; fi )
$( if [ ! -z ${VIASH_PAR_DISCARD_CASAVA+x} ]; then echo "${VIASH_PAR_DISCARD_CASAVA}" | sed "s#'#'\"'\"'#g;s#.*#par_discard_casava='&'#" ; else echo "# par_discard_casava="; fi )
$( if [ ! -z ${VIASH_PAR_REPORT+x} ]; then echo "${VIASH_PAR_REPORT}" | sed "s#'#'\"'\"'#g;s#.*#par_report='&'#" ; else echo "# par_report="; fi )
$( if [ ! -z ${VIASH_PAR_JSON+x} ]; then echo "${VIASH_PAR_JSON}" | sed "s#'#'\"'\"'#g;s#.*#par_json='&'#" ; else echo "# par_json="; fi )
$( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "${VIASH_PAR_OUTPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_output='&'#" ; else echo "# par_output="; fi )
$( if [ ! -z ${VIASH_PAR_FASTA+x} ]; then echo "${VIASH_PAR_FASTA}" | sed "s#'#'\"'\"'#g;s#.*#par_fasta='&'#" ; else echo "# par_fasta="; fi )
$( if [ ! -z ${VIASH_PAR_INFO_FILE+x} ]; then echo "${VIASH_PAR_INFO_FILE}" | sed "s#'#'\"'\"'#g;s#.*#par_info_file='&'#" ; else echo "# par_info_file="; fi )
$( if [ ! -z ${VIASH_PAR_DEBUG+x} ]; then echo "${VIASH_PAR_DEBUG}" | sed "s#'#'\"'\"'#g;s#.*#par_debug='&'#" ; else echo "# par_debug="; fi )
$( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi )
$( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi )
$( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "${VIASH_META_RESOURCES_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_resources_dir='&'#" ; else echo "# meta_resources_dir="; fi )
$( if [ ! -z ${VIASH_META_EXECUTABLE+x} ]; then echo "${VIASH_META_EXECUTABLE}" | sed "s#'#'\"'\"'#g;s#.*#meta_executable='&'#" ; else echo "# meta_executable="; fi )
$( if [ ! -z ${VIASH_META_CONFIG+x} ]; then echo "${VIASH_META_CONFIG}" | sed "s#'#'\"'\"'#g;s#.*#meta_config='&'#" ; else echo "# meta_config="; fi )
$( if [ ! -z ${VIASH_META_TEMP_DIR+x} ]; then echo "${VIASH_META_TEMP_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_temp_dir='&'#" ; else echo "# meta_temp_dir="; fi )
$( if [ ! -z ${VIASH_META_CPUS+x} ]; then echo "${VIASH_META_CPUS}" | sed "s#'#'\"'\"'#g;s#.*#meta_cpus='&'#" ; else echo "# meta_cpus="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_B+x} ]; then echo "${VIASH_META_MEMORY_B}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_b='&'#" ; else echo "# meta_memory_b="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_KB+x} ]; then echo "${VIASH_META_MEMORY_KB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_kb='&'#" ; else echo "# meta_memory_kb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_MB+x} ]; then echo "${VIASH_META_MEMORY_MB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_mb='&'#" ; else echo "# meta_memory_mb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_GB+x} ]; then echo "${VIASH_META_MEMORY_GB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_gb='&'#" ; else echo "# meta_memory_gb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_TB+x} ]; then echo "${VIASH_META_MEMORY_TB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_tb='&'#" ; else echo "# meta_memory_tb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_PB+x} ]; then echo "${VIASH_META_MEMORY_PB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_pb='&'#" ; else echo "# meta_memory_pb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_KIB+x} ]; then echo "${VIASH_META_MEMORY_KIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_kib='&'#" ; else echo "# meta_memory_kib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_MIB+x} ]; then echo "${VIASH_META_MEMORY_MIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_mib='&'#" ; else echo "# meta_memory_mib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_GIB+x} ]; then echo "${VIASH_META_MEMORY_GIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_gib='&'#" ; else echo "# meta_memory_gib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_TIB+x} ]; then echo "${VIASH_META_MEMORY_TIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_tib='&'#" ; else echo "# meta_memory_tib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_pib='&'#" ; else echo "# meta_memory_pib="; fi )

## VIASH END

function debug {
  [[ "\$par_debug" == "true" ]] && echo "DEBUG: \$@"
}

output_dir=\$(dirname \$par_output)
[[ ! -d \$output_dir ]] && mkdir -p \$output_dir

# Init
###########################################################

echo ">> Paired-end data or not?"

mode=""
if [[ -z \$par_input_r2 ]]; then
  mode="se"
  echo "  Single end"
  input="\$par_input"
else
  echo "  Paired end"
  mode="pe"
  input="\$par_input \$par_input_r2"
fi

# Adapter arguments
#   - paired and single-end
#   - string and fasta
###########################################################

function add_flags {
  local arg=\$1
  local flag=\$2
  local prefix=\$3
  [[ -z \$prefix ]] && prefix=""

  # This function should not be called if the input is empty
  # but check for it just in case
  if [[ -z \$arg ]]; then
    return
  fi

  local output=""
  IFS=';' read -r -a array <<< "\$arg"
  for a in "\${array[@]}"; do
    output="\$output \$flag \$prefix\$a"
  done
  echo \$output
}

debug ">> Parsing arguments dealing with adapters"
adapter_args=\$(echo \\
  \${par_adapter:+\$(add_flags "\$par_adapter" "--adapter")} \\
  \${par_adapter_fasta:+\$(add_flags "\$par_adapter_fasta" "--adapter" "file:")} \\
  \${par_front:+\$(add_flags "\$par_front" "--front")} \\
  \${par_front_fasta:+\$(add_flags "\$par_front_fasta" "--front" "file:")} \\
  \${par_anywhere:+\$(add_flags "\$par_anywhere" "--anywhere")} \\
  \${par_anywhere_fasta:+\$(add_flags "\$par_anywhere_fasta" "--anywhere" "file:")} \\
  \${par_adapter_r2:+\$(add_flags "\$par_adapter_r2" "-A")} \\
  \${par_adapter_fasta_r2:+\$(add_flags "\$par_adapter_fasta_r2" "-A" "file:")} \\
  \${par_front_r2:+\$(add_flags "\$par_front_r2" "-G")} \\
  \${par_front_fasta_r2:+\$(add_flags "\$par_front_fasta_r2" "-G" "file:")} \\
  \${par_anywhere_r2:+\$(add_flags "\$par_anywhere_r2" "-B")} \\
  \${par_anywhere_fasta_r2:+\$(add_flags "\$par_anywhere_fasta_r2" "-B" "file:")} \\
)

debug "Arguments to cutadapt:"
debug "\$adapter_args"
debug

# Paired-end options
###########################################################
echo ">> Parsing arguments for paired-end reads"
[[ "\$par_pair_adapters" == "false" ]] && unset par_pair_adapters
[[ "\$par_interleaved" == "false" ]] && unset par_interleaved

paired_args=\$(echo \\
  \${par_pair_adapters:+--pair-adapters} \\
  \${par_pair_filter:+--pair-filter "\${par_pair_filter}"} \\
  \${par_interleaved:+--interleaved}
)
debug "Arguments to cutadapt:"
debug \$paired_args
debug

# Input arguments 
###########################################################
echo ">> Parsing input arguments"
[[ "\$par_no_indels" == "false" ]] && unset par_no_indels
[[ "\$par_match_read_wildcards" == "false" ]] && unset par_match_read_wildcards
[[ "\$par_no_match_adapter_wildcards" == "false" ]] && unset par_no_match_adapter_wildcards
[[ "\$par_revcomp" == "false" ]] && unset par_revcomp

input_args=\$(echo \\
  \${par_error_rate:+--error-rate "\${par_error_rate}"} \\
  \${par_no_indels:+--no-indels} \\
  \${par_times:+--times "\${par_times}"} \\
  \${par_overlap:+--overlap "\${par_overlap}"} \\
  \${par_match_read_wildcards:+--match-read-wildcards} \\
  \${par_no_match_adapter_wildcards:+--no-match-adapter-wildcards} \\
  \${par_action:+--action="\${par_action}"} \\
  \${par_revcomp:+--revcomp} \\
)
debug "Arguments to cutadapt:"
debug \$input_args
debug

# Read modifications
###########################################################
echo ">> Parsing read modification arguments"
[[ "\$par_poly_a" == "false" ]] && unset par_poly_a
[[ "\$par_trim_n" == "false" ]] && unset par_trim_n
[[ "\$par_zero_cap" == "false" ]] && unset par_zero_cap

mod_args=\$(echo \\
  \${par_cut:+--cut "\${par_cut}"} \\
  \${par_cut_r2:+--cut_r2 "\${par_cut_r2}"} \\
  \${par_nextseq_trim:+--nextseq-trim "\${par_nextseq_trim}"} \\
  \${par_quality_cutoff:+--quality-cutoff "\${par_quality_cutoff}"} \\
  \${par_quality_cutoff_r2:+-Q "\${par_quality_cutoff_r2}"} \\
  \${par_quality_base:+--quality-base "\${par_quality_base}"} \\
  \${par_poly_a:+--poly-a} \\
  \${par_length:+--length "\${par_length}"} \\
  \${par_trim_n:+--trim-n} \\
  \${par_length_tag:+--length-tag "\${par_length_tag}"} \\
  \${par_strip_suffix:+--strip-suffix "\${par_strip_suffix}"} \\
  \${par_prefix:+--prefix "\${par_prefix}"} \\
  \${par_suffix:+--suffix "\${par_suffix}"} \\
  \${par_rename:+--rename "\${par_rename}"} \\
  \${par_zero_cap:+--zero-cap} \\
)
debug "Arguments to cutadapt:"
debug \$mod_args
debug

# Filtering of processed reads arguments
###########################################################
echo ">> Filtering of processed reads arguments"
[[ "\$par_discard_trimmed" == "false" ]] && unset par_discard_trimmed
[[ "\$par_discard_untrimmed" == "false" ]] && unset par_discard_untrimmed
[[ "\$par_discard_casava" == "false" ]] && unset par_discard_casava

# Parse and transform the minimum and maximum length arguments
[[ -z \$par_minimum_length   ]]

filter_args=\$(echo \\
  \${par_minimum_length:+--minimum-length "\${par_minimum_length}"} \\
  \${par_maximum_length:+--maximum-length "\${par_maximum_length}"} \\
  \${par_max_n:+--max-n "\${par_max_n}"} \\
  \${par_max_expected_errors:+--max-expected-errors "\${par_max_expected_errors}"} \\
  \${par_max_average_error_rate:+--max-average-error-rate "\${par_max_average_error_rate}"} \\
  \${par_discard_trimmed:+--discard-trimmed} \\
  \${par_discard_untrimmed:+--discard-untrimmed} \\
  \${par_discard_casava:+--discard-casava} \\
)
debug "Arguments to cutadapt:"
debug \$filter_args
debug

# Optional output arguments
###########################################################
echo ">> Optional arguments"
[[ "\$par_json" == "false" ]] && unset par_json
[[ "\$par_fasta" == "false" ]] && unset par_fasta
[[ "\$par_info_file" == "false" ]] && unset par_info_file

optional_output_args=\$(echo \\
  \${par_report:+--report "\${par_report}"} \\
  \${par_json:+--json "report.json"} \\
  \${par_fasta:+--fasta} \\
  \${par_info_file:+--info-file "info.txt"} \\
)

debug "Arguments to cutadapt:"
debug \$optional_output_args
debug

# Output arguments
# We write the output to a directory rather than
# individual files.
###########################################################

if [[ -z \$par_fasta ]]; then
  ext="fastq"
else
  ext="fasta"
fi

demultiplex_mode="\$par_demultiplex_mode"
if [[ \$mode == "se" ]]; then
  if [[ "\$demultiplex_mode" == "unique_dual" ]] || [[ "\$demultiplex_mode" == "combinatorial_dual" ]]; then
    echo "Demultiplexing dual indexes is not possible with single-end data."
    exit 1
  fi
  prefix="trimmed_"
  if [[ ! -z "\$demultiplex_mode" ]]; then
    prefix="{name}_"
  fi
  output_args=\$(echo \\
    --output "\$output_dir/\${prefix}001.\$ext" \\
  )
else
  demultiplex_indicator_r1='{name}_'
  demultiplex_indicator_r2=\$demultiplex_indicator_r1
  if [[ "\$demultiplex_mode" == "combinatorial_dual" ]]; then
    demultiplex_indicator_r1='{name1}_{name2}_'
    demultiplex_indicator_r2='{name1}_{name2}_'
  fi
  prefix_r1="trimmed_"
  prefix_r2="trimmed_"
  if [[ ! -z "\$demultiplex_mode" ]]; then
    prefix_r1=\$demultiplex_indicator_r1
    prefix_r2=\$demultiplex_indicator_r2
  fi
  output_args=\$(echo \\
    --output "\$output_dir/\${prefix_r1}R1_001.\$ext" \\
    --paired-output "\$output_dir/\${prefix_r2}R2_001.\$ext" \\
  )
fi

debug "Arguments to cutadapt:"
debug \$output_args
debug

# Full CLI
# Set the --cores argument to 0 unless meta_cpus is set
###########################################################
echo ">> Running cutadapt"
par_cpus=0
[[ ! -z \$meta_cpus ]] && par_cpus=\$meta_cpus

cli=\$(echo \\
  \$input \\
  \$adapter_args \\
  \$paired_args \\
  \$input_args \\
  \$mod_args \\
  \$filter_args \\
  \$optional_output_args \\
  \$output_args \\
  --cores \$par_cpus
)

debug ">> Full CLI to be run:"
debug cutadapt \$cli | sed -e 's/--/\\r\\n  --/g'
debug

cutadapt \$cli
VIASHMAIN
bash "\$tempscript" &
wait "\$!"

VIASHEOF


if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  # strip viash automount from file paths
  
  if [ ! -z "$VIASH_PAR_ADAPTER_FASTA" ]; then
    unset VIASH_TEST_ADAPTER_FASTA
    IFS=';'
    for var in $VIASH_PAR_ADAPTER_FASTA; do
      unset IFS
      if [ -z "$VIASH_TEST_ADAPTER_FASTA" ]; then
      VIASH_TEST_ADAPTER_FASTA="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_ADAPTER_FASTA="$VIASH_TEST_ADAPTER_FASTA;""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_ADAPTER_FASTA="$VIASH_TEST_ADAPTER_FASTA"
  fi
  if [ ! -z "$VIASH_PAR_FRONT_FASTA" ]; then
    VIASH_PAR_FRONT_FASTA=$(ViashDockerStripAutomount "$VIASH_PAR_FRONT_FASTA")
  fi
  if [ ! -z "$VIASH_PAR_ANYWHERE_FASTA" ]; then
    VIASH_PAR_ANYWHERE_FASTA=$(ViashDockerStripAutomount "$VIASH_PAR_ANYWHERE_FASTA")
  fi
  if [ ! -z "$VIASH_PAR_ADAPTER_R2_FASTA" ]; then
    VIASH_PAR_ADAPTER_R2_FASTA=$(ViashDockerStripAutomount "$VIASH_PAR_ADAPTER_R2_FASTA")
  fi
  if [ ! -z "$VIASH_PAR_FRONT_R2_FASTA" ]; then
    VIASH_PAR_FRONT_R2_FASTA=$(ViashDockerStripAutomount "$VIASH_PAR_FRONT_R2_FASTA")
  fi
  if [ ! -z "$VIASH_PAR_ANYWHERE_R2_FASTA" ]; then
    VIASH_PAR_ANYWHERE_R2_FASTA=$(ViashDockerStripAutomount "$VIASH_PAR_ANYWHERE_R2_FASTA")
  fi
  if [ ! -z "$VIASH_PAR_INPUT" ]; then
    VIASH_PAR_INPUT=$(ViashDockerStripAutomount "$VIASH_PAR_INPUT")
  fi
  if [ ! -z "$VIASH_PAR_INPUT_R2" ]; then
    VIASH_PAR_INPUT_R2=$(ViashDockerStripAutomount "$VIASH_PAR_INPUT_R2")
  fi
  if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
    VIASH_PAR_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT")
  fi
  if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
    VIASH_META_RESOURCES_DIR=$(ViashDockerStripAutomount "$VIASH_META_RESOURCES_DIR")
  fi
  if [ ! -z "$VIASH_META_EXECUTABLE" ]; then
    VIASH_META_EXECUTABLE=$(ViashDockerStripAutomount "$VIASH_META_EXECUTABLE")
  fi
  if [ ! -z "$VIASH_META_CONFIG" ]; then
    VIASH_META_CONFIG=$(ViashDockerStripAutomount "$VIASH_META_CONFIG")
  fi
  if [ ! -z "$VIASH_META_TEMP_DIR" ]; then
    VIASH_META_TEMP_DIR=$(ViashDockerStripAutomount "$VIASH_META_TEMP_DIR")
  fi
fi


# check whether required files exist
if [ ! -z "$VIASH_PAR_OUTPUT" ] && ! compgen -G "$VIASH_PAR_OUTPUT" > /dev/null; then
  ViashError "Output file '$VIASH_PAR_OUTPUT' does not exist."
  exit 1
fi


exit 0
