#!/usr/bin/env bash

# sortmerna 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.

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="sortmerna"
VIASH_META_FUNCTIONALITY_NAME="sortmerna"
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 "sortmerna add_sgdemux"
  echo ""
  echo "Local sequence alignment tool for filtering, mapping and clustering. The main"
  echo "application of SortMeRNA is filtering rRNA from metatranscriptomic data."
  echo ""
  echo "Input:"
  echo "    --paired"
  echo "        type: boolean_true"
  echo "        Reads are paired-end. If a single reads file is provided, use this"
  echo "        option"
  echo "        to indicate the file contains interleaved paired reads when neither"
  echo "        'paired_in' | 'paired_out' | 'out2' | 'sout' are specified."
  echo ""
  echo "    --input"
  echo "        type: file, multiple values allowed, file must exist"
  echo "        Input fastq"
  echo ""
  echo "    --ref"
  echo "        type: file, multiple values allowed, file must exist"
  echo "        Reference fasta file(s) for rRNA database."
  echo ""
  echo "    --ribo_database_manifest"
  echo "        type: file, file must exist"
  echo "        Text file containing paths to fasta files (one per line) that will be"
  echo "        used to create the database for SortMeRNA."
  echo ""
  echo "Output:"
  echo "    --log"
  echo "        type: file, output"
  echo "        example: \$id.sortmerna.log"
  echo "        Sortmerna log file."
  echo ""
  echo "    --aligned, --output"
  echo "        type: file, output, file must exist"
  echo "        Directory and file prefix for aligned output. The appropriate extension:"
  echo "        (fasta|fastq|blast|sam|etc) is automatically added."
  echo "        If 'dir' is not specified, the output is created in the WORKDIR/out/."
  echo "        If 'pfx' is not specified, the prefix 'aligned' is used."
  echo ""
  echo "    --other"
  echo "        type: file, output, file must exist"
  echo "        Create Non-aligned reads output file with this path/prefix. Must be used"
  echo "        with fastx."
  echo ""
  echo "Options:"
  echo "    --kvdb"
  echo "        type: string"
  echo "        Path to directory of the key-value database file, used for storing the"
  echo "        alignment results."
  echo ""
  echo "    --idx_dir"
  echo "        type: string"
  echo "        Path to the directory for storing the reference index files."
  echo ""
  echo "    --readb"
  echo "        type: string"
  echo "        Path to the directory for storing pre-processed reads."
  echo ""
  echo "    --fastx"
  echo "        type: boolean_true"
  echo "        Output aligned reads into FASTA/FASTQ file"
  echo ""
  echo "    --sam"
  echo "        type: boolean_true"
  echo "        Output SAM alignment for aligned reads."
  echo ""
  echo "    --sq"
  echo "        type: boolean_true"
  echo "        Add SQ tags to the SAM file"
  echo ""
  echo "    --blast"
  echo "        type: string"
  echo "        choices: [ 0, 1, 1 cigar, 1 cigar qcov, 1 cigar qcov qstrand ]"
  echo "        Blast options:"
  echo "        * '0'                    - pairwise"
  echo "        * '1'                    - tabular(Blast - m 8 format)"
  echo "        * '1 cigar'              - tabular + column for CIGAR"
  echo "        * '1 cigar qcov'         - tabular + columns for CIGAR and query"
  echo "        coverage"
  echo "        * '1 cigar qcov qstrand' - tabular + columns for CIGAR, query coverage"
  echo "        and strand"
  echo ""
  echo "    --num_alignments"
  echo "        type: integer"
  echo "        example: 0"
  echo "        Report first INT alignments per read reaching E-value. If Int = 0, all"
  echo "        alignments will be output. Default: '0'"
  echo ""
  echo "    --min_lis"
  echo "        type: integer"
  echo "        example: 2"
  echo "        search all alignments having the first INT longest LIS. LIS stands for"
  echo "        Longest Increasing Subsequence, it is"
  echo "        computed using seeds' positions to expand hits into longer matches prior"
  echo "        to Smith-Waterman alignment. Default: '2'."
  echo ""
  echo "    --print_all_reads"
  echo "        type: boolean_true"
  echo "        output null alignment strings for non-aligned reads to SAM and/or BLAST"
  echo "        tabular files."
  echo ""
  echo "    --paired_in"
  echo "        type: boolean_true"
  echo "        In the case where a pair of reads is aligned with a score above the"
  echo "        threshold, the output of the reads is controlled"
  echo "        by the following options:"
  echo "        * --paired_in and --paired_out are both false: Only one read per pair is"
  echo "        output to the aligned fasta file."
  echo "        * --paired_in is true and --paired_out is false: Both reads of the pair"
  echo "        are output to the aligned fasta file."
  echo "        * --paired_in is false and --paired_out is true: Both reads are output"
  echo "        the the other fasta file (if it is specified)."
  echo ""
  echo "    --paired_out"
  echo "        type: boolean_true"
  echo "        See description of --paired_in."
  echo ""
  echo "    --out2"
  echo "        type: boolean_true"
  echo "        Output paired reads into separate files. Must be used with '--fastx'. If"
  echo "        a single reads file is provided, this options"
  echo "        implies interleaved paired reads. When used with 'sout', four (4) output"
  echo "        files for aligned reads will be generated:"
  echo "        'aligned-paired-fwd, aligned-paired-rev, aligned-singleton-fwd,"
  echo "        aligned-singleton-rev'. If 'other' option is also used,"
  echo "        eight (8) output files will be generated."
  echo ""
  echo "    --sout"
  echo "        type: boolean_true"
  echo "        Separate paired and singleton aligned reads. Must be used with"
  echo "        '--fastx'. If a single reads file is provided,"
  echo "        this options implies interleaved paired reads. Cannot be used with"
  echo "        '--paired_in' or '--paired_out'."
  echo ""
  echo "    --zip_out"
  echo "        type: string"
  echo "        example: -1"
  echo "        choices: [ 1, true, t, yes, y, 0, false, f, no, n, -1 ]"
  echo "        Compress the output files. The possible values are:"
  echo "        * '1/true/t/yes/y'"
  echo "        * '0/false/f/no/n'"
  echo "        *'-1' (the same format as input - default)"
  echo "        The values are Not case sensitive."
  echo ""
  echo "    --match"
  echo "        type: integer"
  echo "        example: 2"
  echo "        Smith-Waterman score for a match (positive integer). Default: '2'."
  echo ""
  echo "    --mismatch"
  echo "        type: integer"
  echo "        example: -3"
  echo "        Smith-Waterman penalty for a mismatch (negative integer). Default: '-3'."
  echo ""
  echo "    --gap_open"
  echo "        type: integer"
  echo "        example: 5"
  echo "        Smith-Waterman penalty for introducing a gap (positive integer)."
  echo "        Default: '5'."
  echo ""
  echo "    --gap_ext"
  echo "        type: integer"
  echo "        example: 2"
  echo "        Smith-Waterman penalty for extending a gap (positive integer). Default:"
  echo "        '2'."
  echo ""
  echo "    --N"
  echo "        type: integer"
  echo "        example: -1"
  echo "        Smith-Waterman penalty for ambiguous letters (N's) scored as --mismatch."
  echo "        Default: '-1'."
  echo ""
  echo "    --a"
  echo "        type: integer"
  echo "        example: 1"
  echo "        Number of threads to use. Default: '1'."
  echo ""
  echo "    --e"
  echo "        type: double"
  echo "        example: 1.0"
  echo "        E-value threshold. Default: '1'."
  echo ""
  echo "    --F"
  echo "        type: boolean_true"
  echo "        Search only the forward strand."
  echo ""
  echo "    --R"
  echo "        type: boolean_true"
  echo "        Search only the reverse-complementary strand."
  echo ""
  echo "    --num_alignment"
  echo "        type: integer"
  echo "        example: -1"
  echo "        Report first INT alignments per read reaching E-value (--num_alignments"
  echo "        0 signifies all alignments will be output)."
  echo "        Default: '-1'"
  echo ""
  echo "    --best"
  echo "        type: integer"
  echo "        example: 1"
  echo "        Report INT best alignments per read reaching E-value by searching"
  echo "        --min_lis INT candidate alignments (--best 0"
  echo "        signifies all candidate alignments will be searched) Default: '1'."
  echo ""
  echo "    -v, --verbose"
  echo "        type: boolean_true"
  echo "        Verbose output."
  echo ""
  echo "OTU picking options:"
  echo "    --id"
  echo "        type: double"
  echo "        example: 0.97"
  echo "        %id similarity threshold (the alignment must still pass the E-value"
  echo "        threshold). Default: '0.97'."
  echo ""
  echo "    --coverage"
  echo "        type: double"
  echo "        example: 0.97"
  echo "        %query coverage threshold (the alignment must still pass the E-value"
  echo "        threshold). Default: '0.97'."
  echo ""
  echo "    --de_novo"
  echo "        type: boolean_true"
  echo "        FASTA/FASTQ file for reads matching database < %id off (set using --id)"
  echo "        and < %cov (set using --coverage)"
  echo "        (alignment must still pass the E-value threshold)."
  echo ""
  echo "    --otu_map"
  echo "        type: boolean_true"
  echo "        Output OTU map (input to QIIME's make_otu_table.py)."
  echo ""
  echo "Advanced options:"
  echo "    --num_seed"
  echo "        type: integer"
  echo "        example: 2"
  echo "        Number of seeds matched before searching for candidate LIS. Default:"
  echo "        '2'."
  echo ""
  echo "    --passes"
  echo "        type: integer, multiple values allowed"
  echo "        Three intervals at which to place the seed on the read L,L/2,3 (L is the"
  echo "        seed length set in ./indexdb_rna)."
  echo ""
  echo "    --edge"
  echo "        type: string"
  echo "        example: 4"
  echo "        The number (or percentage if followed by %) of nucleotides to add to"
  echo "        each edge of the alignment region on the"
  echo "        reference sequence before performing Smith-Waterman alignment. Default:"
  echo "        '4'."
  echo ""
  echo "    --full_search"
  echo "        type: boolean_true"
  echo "        Search for all 0-error and 1-error seed off matches in the index rather"
  echo "        than stopping after finding a 0-error match"
  echo "        (<1% gain in sensitivity with up four-fold decrease in speed)."
  echo ""
  echo "Indexing Options:"
  echo "    --index"
  echo "        type: integer"
  echo "        example: 2"
  echo "        choices: [ 0, 1, 2 ]"
  echo "        Create index files for the reference database. By default when this"
  echo "        option is not used, the program checks the"
  echo "        reference index and builds it if not already existing."
  echo "        This can be changed by using '-index' as follows:"
  echo "        * '-index 0' - skip indexing. If the index does not exist, the program"
  echo "        will terminate"
  echo "                                and warn to build the index prior performing the"
  echo "        alignment"
  echo "        * '-index 1' - only perform the indexing and terminate"
  echo "        * '-index 2' - the default behaviour, the same as when not using this"
  echo "        option at all"
  echo ""
  echo "    -L"
  echo "        type: double"
  echo "        example: 18.0"
  echo "        Indexing seed length. Default: '18'"
  echo ""
  echo "    --interval"
  echo "        type: integer"
  echo "        example: 1"
  echo "        Index every Nth L-mer in the reference database. Default: '1'"
  echo ""
  echo "    --max_pos"
  echo "        type: integer"
  echo "        example: 1000"
  echo "        Maximum number of positions to store for each unique L-mer. Set to 0 to"
  echo "        store all positions. Default: '1000'"
}

# 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 quay.io/biocontainers/sortmerna:4.3.6--h9ee0642_0
ENTRYPOINT []
RUN echo SortMeRNA: `sortmerna --version | sed -n 's/.*version \([0-9]\+\.[0-9]\+\.[0-9]\+\).*/\1/p'`

LABEL org.opencontainers.image.description="Companion container for running component sortmerna"
LABEL org.opencontainers.image.created="2024-11-14T12:50:41Z"
LABEL org.opencontainers.image.source="https://github.com/sortmerna/sortmerna"
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 "$1")"
            shift 1
            ;;
        --version)
            echo "sortmerna add_sgdemux"
            exit
            ;;
        --paired)
            [ -n "$VIASH_PAR_PAIRED" ] && ViashError Bad arguments for option \'--paired\': \'$VIASH_PAR_PAIRED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PAIRED=true
            shift 1
            ;;
        --input)
            if [ -z "$VIASH_PAR_INPUT" ]; then
              VIASH_PAR_INPUT="$2"
            else
              VIASH_PAR_INPUT="$VIASH_PAR_INPUT;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --input. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --input=*)
            if [ -z "$VIASH_PAR_INPUT" ]; then
              VIASH_PAR_INPUT=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_INPUT="$VIASH_PAR_INPUT;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --ref)
            if [ -z "$VIASH_PAR_REF" ]; then
              VIASH_PAR_REF="$2"
            else
              VIASH_PAR_REF="$VIASH_PAR_REF;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --ref. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --ref=*)
            if [ -z "$VIASH_PAR_REF" ]; then
              VIASH_PAR_REF=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_REF="$VIASH_PAR_REF;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --ribo_database_manifest)
            [ -n "$VIASH_PAR_RIBO_DATABASE_MANIFEST" ] && ViashError Bad arguments for option \'--ribo_database_manifest\': \'$VIASH_PAR_RIBO_DATABASE_MANIFEST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_RIBO_DATABASE_MANIFEST="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --ribo_database_manifest. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --ribo_database_manifest=*)
            [ -n "$VIASH_PAR_RIBO_DATABASE_MANIFEST" ] && ViashError Bad arguments for option \'--ribo_database_manifest=*\': \'$VIASH_PAR_RIBO_DATABASE_MANIFEST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_RIBO_DATABASE_MANIFEST=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --log)
            [ -n "$VIASH_PAR_LOG" ] && ViashError Bad arguments for option \'--log\': \'$VIASH_PAR_LOG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LOG="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --log. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --log=*)
            [ -n "$VIASH_PAR_LOG" ] && ViashError Bad arguments for option \'--log=*\': \'$VIASH_PAR_LOG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LOG=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --output)
            [ -n "$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 "$1")
            shift 1
            ;;
        --aligned)
            [ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--aligned\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --aligned. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --other)
            [ -n "$VIASH_PAR_OTHER" ] && ViashError Bad arguments for option \'--other\': \'$VIASH_PAR_OTHER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OTHER="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --other. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --other=*)
            [ -n "$VIASH_PAR_OTHER" ] && ViashError Bad arguments for option \'--other=*\': \'$VIASH_PAR_OTHER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OTHER=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --kvdb)
            [ -n "$VIASH_PAR_KVDB" ] && ViashError Bad arguments for option \'--kvdb\': \'$VIASH_PAR_KVDB\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_KVDB="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --kvdb. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --kvdb=*)
            [ -n "$VIASH_PAR_KVDB" ] && ViashError Bad arguments for option \'--kvdb=*\': \'$VIASH_PAR_KVDB\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_KVDB=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --idx_dir)
            [ -n "$VIASH_PAR_IDX_DIR" ] && ViashError Bad arguments for option \'--idx_dir\': \'$VIASH_PAR_IDX_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_IDX_DIR="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --idx_dir. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --idx_dir=*)
            [ -n "$VIASH_PAR_IDX_DIR" ] && ViashError Bad arguments for option \'--idx_dir=*\': \'$VIASH_PAR_IDX_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_IDX_DIR=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --readb)
            [ -n "$VIASH_PAR_READB" ] && ViashError Bad arguments for option \'--readb\': \'$VIASH_PAR_READB\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_READB="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --readb. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --readb=*)
            [ -n "$VIASH_PAR_READB" ] && ViashError Bad arguments for option \'--readb=*\': \'$VIASH_PAR_READB\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_READB=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --fastx)
            [ -n "$VIASH_PAR_FASTX" ] && ViashError Bad arguments for option \'--fastx\': \'$VIASH_PAR_FASTX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FASTX=true
            shift 1
            ;;
        --sam)
            [ -n "$VIASH_PAR_SAM" ] && ViashError Bad arguments for option \'--sam\': \'$VIASH_PAR_SAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SAM=true
            shift 1
            ;;
        --sq)
            [ -n "$VIASH_PAR_SQ" ] && ViashError Bad arguments for option \'--sq\': \'$VIASH_PAR_SQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SQ=true
            shift 1
            ;;
        --blast)
            [ -n "$VIASH_PAR_BLAST" ] && ViashError Bad arguments for option \'--blast\': \'$VIASH_PAR_BLAST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_BLAST="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --blast. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --blast=*)
            [ -n "$VIASH_PAR_BLAST" ] && ViashError Bad arguments for option \'--blast=*\': \'$VIASH_PAR_BLAST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_BLAST=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --num_alignments)
            [ -n "$VIASH_PAR_NUM_ALIGNMENTS" ] && ViashError Bad arguments for option \'--num_alignments\': \'$VIASH_PAR_NUM_ALIGNMENTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_NUM_ALIGNMENTS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --num_alignments. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --num_alignments=*)
            [ -n "$VIASH_PAR_NUM_ALIGNMENTS" ] && ViashError Bad arguments for option \'--num_alignments=*\': \'$VIASH_PAR_NUM_ALIGNMENTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_NUM_ALIGNMENTS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --min_lis)
            [ -n "$VIASH_PAR_MIN_LIS" ] && ViashError Bad arguments for option \'--min_lis\': \'$VIASH_PAR_MIN_LIS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MIN_LIS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --min_lis. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --min_lis=*)
            [ -n "$VIASH_PAR_MIN_LIS" ] && ViashError Bad arguments for option \'--min_lis=*\': \'$VIASH_PAR_MIN_LIS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MIN_LIS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --print_all_reads)
            [ -n "$VIASH_PAR_PRINT_ALL_READS" ] && ViashError Bad arguments for option \'--print_all_reads\': \'$VIASH_PAR_PRINT_ALL_READS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PRINT_ALL_READS=true
            shift 1
            ;;
        --paired_in)
            [ -n "$VIASH_PAR_PAIRED_IN" ] && ViashError Bad arguments for option \'--paired_in\': \'$VIASH_PAR_PAIRED_IN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PAIRED_IN=true
            shift 1
            ;;
        --paired_out)
            [ -n "$VIASH_PAR_PAIRED_OUT" ] && ViashError Bad arguments for option \'--paired_out\': \'$VIASH_PAR_PAIRED_OUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PAIRED_OUT=true
            shift 1
            ;;
        --out2)
            [ -n "$VIASH_PAR_OUT2" ] && ViashError Bad arguments for option \'--out2\': \'$VIASH_PAR_OUT2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUT2=true
            shift 1
            ;;
        --sout)
            [ -n "$VIASH_PAR_SOUT" ] && ViashError Bad arguments for option \'--sout\': \'$VIASH_PAR_SOUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SOUT=true
            shift 1
            ;;
        --zip_out)
            [ -n "$VIASH_PAR_ZIP_OUT" ] && ViashError Bad arguments for option \'--zip_out\': \'$VIASH_PAR_ZIP_OUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ZIP_OUT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --zip_out. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --zip_out=*)
            [ -n "$VIASH_PAR_ZIP_OUT" ] && ViashError Bad arguments for option \'--zip_out=*\': \'$VIASH_PAR_ZIP_OUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ZIP_OUT=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --match)
            [ -n "$VIASH_PAR_MATCH" ] && ViashError Bad arguments for option \'--match\': \'$VIASH_PAR_MATCH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MATCH="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --match. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --match=*)
            [ -n "$VIASH_PAR_MATCH" ] && ViashError Bad arguments for option \'--match=*\': \'$VIASH_PAR_MATCH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MATCH=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --mismatch)
            [ -n "$VIASH_PAR_MISMATCH" ] && ViashError Bad arguments for option \'--mismatch\': \'$VIASH_PAR_MISMATCH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MISMATCH="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --mismatch. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --mismatch=*)
            [ -n "$VIASH_PAR_MISMATCH" ] && ViashError Bad arguments for option \'--mismatch=*\': \'$VIASH_PAR_MISMATCH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MISMATCH=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --gap_open)
            [ -n "$VIASH_PAR_GAP_OPEN" ] && ViashError Bad arguments for option \'--gap_open\': \'$VIASH_PAR_GAP_OPEN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_GAP_OPEN="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --gap_open. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --gap_open=*)
            [ -n "$VIASH_PAR_GAP_OPEN" ] && ViashError Bad arguments for option \'--gap_open=*\': \'$VIASH_PAR_GAP_OPEN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_GAP_OPEN=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --gap_ext)
            [ -n "$VIASH_PAR_GAP_EXT" ] && ViashError Bad arguments for option \'--gap_ext\': \'$VIASH_PAR_GAP_EXT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_GAP_EXT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --gap_ext. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --gap_ext=*)
            [ -n "$VIASH_PAR_GAP_EXT" ] && ViashError Bad arguments for option \'--gap_ext=*\': \'$VIASH_PAR_GAP_EXT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_GAP_EXT=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --N)
            [ -n "$VIASH_PAR_N" ] && ViashError Bad arguments for option \'--N\': \'$VIASH_PAR_N\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_N="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --N. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --N=*)
            [ -n "$VIASH_PAR_N" ] && ViashError Bad arguments for option \'--N=*\': \'$VIASH_PAR_N\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_N=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --a)
            [ -n "$VIASH_PAR_A" ] && ViashError Bad arguments for option \'--a\': \'$VIASH_PAR_A\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_A="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --a. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --a=*)
            [ -n "$VIASH_PAR_A" ] && ViashError Bad arguments for option \'--a=*\': \'$VIASH_PAR_A\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_A=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --e)
            [ -n "$VIASH_PAR_E" ] && ViashError Bad arguments for option \'--e\': \'$VIASH_PAR_E\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_E="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --e. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --e=*)
            [ -n "$VIASH_PAR_E" ] && ViashError Bad arguments for option \'--e=*\': \'$VIASH_PAR_E\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_E=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --F)
            [ -n "$VIASH_PAR_F" ] && ViashError Bad arguments for option \'--F\': \'$VIASH_PAR_F\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_F=true
            shift 1
            ;;
        --R)
            [ -n "$VIASH_PAR_R" ] && ViashError Bad arguments for option \'--R\': \'$VIASH_PAR_R\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_R=true
            shift 1
            ;;
        --num_alignment)
            [ -n "$VIASH_PAR_NUM_ALIGNMENT" ] && ViashError Bad arguments for option \'--num_alignment\': \'$VIASH_PAR_NUM_ALIGNMENT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_NUM_ALIGNMENT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --num_alignment. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --num_alignment=*)
            [ -n "$VIASH_PAR_NUM_ALIGNMENT" ] && ViashError Bad arguments for option \'--num_alignment=*\': \'$VIASH_PAR_NUM_ALIGNMENT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_NUM_ALIGNMENT=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --best)
            [ -n "$VIASH_PAR_BEST" ] && ViashError Bad arguments for option \'--best\': \'$VIASH_PAR_BEST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_BEST="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --best. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --best=*)
            [ -n "$VIASH_PAR_BEST" ] && ViashError Bad arguments for option \'--best=*\': \'$VIASH_PAR_BEST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_BEST=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --verbose)
            [ -n "$VIASH_PAR_VERBOSE" ] && ViashError Bad arguments for option \'--verbose\': \'$VIASH_PAR_VERBOSE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_VERBOSE=true
            shift 1
            ;;
        -v)
            [ -n "$VIASH_PAR_VERBOSE" ] && ViashError Bad arguments for option \'-v\': \'$VIASH_PAR_VERBOSE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_VERBOSE=true
            shift 1
            ;;
        --id)
            [ -n "$VIASH_PAR_ID" ] && ViashError Bad arguments for option \'--id\': \'$VIASH_PAR_ID\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ID="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --id. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --id=*)
            [ -n "$VIASH_PAR_ID" ] && ViashError Bad arguments for option \'--id=*\': \'$VIASH_PAR_ID\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ID=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --coverage)
            [ -n "$VIASH_PAR_COVERAGE" ] && ViashError Bad arguments for option \'--coverage\': \'$VIASH_PAR_COVERAGE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_COVERAGE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --coverage. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --coverage=*)
            [ -n "$VIASH_PAR_COVERAGE" ] && ViashError Bad arguments for option \'--coverage=*\': \'$VIASH_PAR_COVERAGE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_COVERAGE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --de_novo)
            [ -n "$VIASH_PAR_DE_NOVO" ] && ViashError Bad arguments for option \'--de_novo\': \'$VIASH_PAR_DE_NOVO\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_DE_NOVO=true
            shift 1
            ;;
        --otu_map)
            [ -n "$VIASH_PAR_OTU_MAP" ] && ViashError Bad arguments for option \'--otu_map\': \'$VIASH_PAR_OTU_MAP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OTU_MAP=true
            shift 1
            ;;
        --num_seed)
            [ -n "$VIASH_PAR_NUM_SEED" ] && ViashError Bad arguments for option \'--num_seed\': \'$VIASH_PAR_NUM_SEED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_NUM_SEED="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --num_seed. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --num_seed=*)
            [ -n "$VIASH_PAR_NUM_SEED" ] && ViashError Bad arguments for option \'--num_seed=*\': \'$VIASH_PAR_NUM_SEED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_NUM_SEED=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --passes)
            if [ -z "$VIASH_PAR_PASSES" ]; then
              VIASH_PAR_PASSES="$2"
            else
              VIASH_PAR_PASSES="$VIASH_PAR_PASSES;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --passes. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --passes=*)
            if [ -z "$VIASH_PAR_PASSES" ]; then
              VIASH_PAR_PASSES=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_PASSES="$VIASH_PAR_PASSES;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --edge)
            [ -n "$VIASH_PAR_EDGE" ] && ViashError Bad arguments for option \'--edge\': \'$VIASH_PAR_EDGE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_EDGE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --edge. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --edge=*)
            [ -n "$VIASH_PAR_EDGE" ] && ViashError Bad arguments for option \'--edge=*\': \'$VIASH_PAR_EDGE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_EDGE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --full_search)
            [ -n "$VIASH_PAR_FULL_SEARCH" ] && ViashError Bad arguments for option \'--full_search\': \'$VIASH_PAR_FULL_SEARCH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FULL_SEARCH=true
            shift 1
            ;;
        --index)
            [ -n "$VIASH_PAR_INDEX" ] && ViashError Bad arguments for option \'--index\': \'$VIASH_PAR_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INDEX="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --index. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --index=*)
            [ -n "$VIASH_PAR_INDEX" ] && ViashError Bad arguments for option \'--index=*\': \'$VIASH_PAR_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INDEX=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -L)
            [ -n "$VIASH_PAR_L" ] && ViashError Bad arguments for option \'-L\': \'$VIASH_PAR_L\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_L="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -L. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --interval)
            [ -n "$VIASH_PAR_INTERVAL" ] && ViashError Bad arguments for option \'--interval\': \'$VIASH_PAR_INTERVAL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INTERVAL="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --interval. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --interval=*)
            [ -n "$VIASH_PAR_INTERVAL" ] && ViashError Bad arguments for option \'--interval=*\': \'$VIASH_PAR_INTERVAL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INTERVAL=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --max_pos)
            [ -n "$VIASH_PAR_MAX_POS" ] && ViashError Bad arguments for option \'--max_pos\': \'$VIASH_PAR_MAX_POS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_POS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --max_pos. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --max_pos=*)
            [ -n "$VIASH_PAR_MAX_POS" ] && ViashError Bad arguments for option \'--max_pos=*\': \'$VIASH_PAR_MAX_POS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_POS=$(ViashRemoveFlags "$1")
            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/sortmerna: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_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_PAIRED+x} ]; then
  VIASH_PAR_PAIRED="false"
fi
if [ -z ${VIASH_PAR_FASTX+x} ]; then
  VIASH_PAR_FASTX="false"
fi
if [ -z ${VIASH_PAR_SAM+x} ]; then
  VIASH_PAR_SAM="false"
fi
if [ -z ${VIASH_PAR_SQ+x} ]; then
  VIASH_PAR_SQ="false"
fi
if [ -z ${VIASH_PAR_PRINT_ALL_READS+x} ]; then
  VIASH_PAR_PRINT_ALL_READS="false"
fi
if [ -z ${VIASH_PAR_PAIRED_IN+x} ]; then
  VIASH_PAR_PAIRED_IN="false"
fi
if [ -z ${VIASH_PAR_PAIRED_OUT+x} ]; then
  VIASH_PAR_PAIRED_OUT="false"
fi
if [ -z ${VIASH_PAR_OUT2+x} ]; then
  VIASH_PAR_OUT2="false"
fi
if [ -z ${VIASH_PAR_SOUT+x} ]; then
  VIASH_PAR_SOUT="false"
fi
if [ -z ${VIASH_PAR_F+x} ]; then
  VIASH_PAR_F="false"
fi
if [ -z ${VIASH_PAR_R+x} ]; then
  VIASH_PAR_R="false"
fi
if [ -z ${VIASH_PAR_VERBOSE+x} ]; then
  VIASH_PAR_VERBOSE="false"
fi
if [ -z ${VIASH_PAR_DE_NOVO+x} ]; then
  VIASH_PAR_DE_NOVO="false"
fi
if [ -z ${VIASH_PAR_OTU_MAP+x} ]; then
  VIASH_PAR_OTU_MAP="false"
fi
if [ -z ${VIASH_PAR_FULL_SEARCH+x} ]; then
  VIASH_PAR_FULL_SEARCH="false"
fi

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

# check whether parameters values are of the right type
if [[ -n "$VIASH_PAR_PAIRED" ]]; then
  if ! [[ "$VIASH_PAR_PAIRED" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--paired' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_FASTX" ]]; then
  if ! [[ "$VIASH_PAR_FASTX" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--fastx' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SAM" ]]; then
  if ! [[ "$VIASH_PAR_SAM" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--sam' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SQ" ]]; then
  if ! [[ "$VIASH_PAR_SQ" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--sq' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_NUM_ALIGNMENTS" ]]; then
  if ! [[ "$VIASH_PAR_NUM_ALIGNMENTS" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--num_alignments' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_MIN_LIS" ]]; then
  if ! [[ "$VIASH_PAR_MIN_LIS" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--min_lis' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_PRINT_ALL_READS" ]]; then
  if ! [[ "$VIASH_PAR_PRINT_ALL_READS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--print_all_reads' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_PAIRED_IN" ]]; then
  if ! [[ "$VIASH_PAR_PAIRED_IN" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--paired_in' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_PAIRED_OUT" ]]; then
  if ! [[ "$VIASH_PAR_PAIRED_OUT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--paired_out' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_OUT2" ]]; then
  if ! [[ "$VIASH_PAR_OUT2" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--out2' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SOUT" ]]; then
  if ! [[ "$VIASH_PAR_SOUT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--sout' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_MATCH" ]]; then
  if ! [[ "$VIASH_PAR_MATCH" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--match' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_MISMATCH" ]]; then
  if ! [[ "$VIASH_PAR_MISMATCH" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--mismatch' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_GAP_OPEN" ]]; then
  if ! [[ "$VIASH_PAR_GAP_OPEN" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--gap_open' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_GAP_EXT" ]]; then
  if ! [[ "$VIASH_PAR_GAP_EXT" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--gap_ext' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_N" ]]; then
  if ! [[ "$VIASH_PAR_N" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--N' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_A" ]]; then
  if ! [[ "$VIASH_PAR_A" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--a' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_E" ]]; then
  if ! [[ "$VIASH_PAR_E" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--e' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_F" ]]; then
  if ! [[ "$VIASH_PAR_F" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--F' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_R" ]]; then
  if ! [[ "$VIASH_PAR_R" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--R' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_NUM_ALIGNMENT" ]]; then
  if ! [[ "$VIASH_PAR_NUM_ALIGNMENT" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--num_alignment' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_BEST" ]]; then
  if ! [[ "$VIASH_PAR_BEST" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--best' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_VERBOSE" ]]; then
  if ! [[ "$VIASH_PAR_VERBOSE" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--verbose' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_ID" ]]; then
  if ! [[ "$VIASH_PAR_ID" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--id' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_COVERAGE" ]]; then
  if ! [[ "$VIASH_PAR_COVERAGE" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--coverage' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_DE_NOVO" ]]; then
  if ! [[ "$VIASH_PAR_DE_NOVO" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--de_novo' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_OTU_MAP" ]]; then
  if ! [[ "$VIASH_PAR_OTU_MAP" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--otu_map' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_NUM_SEED" ]]; then
  if ! [[ "$VIASH_PAR_NUM_SEED" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--num_seed' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [ -n "$VIASH_PAR_PASSES" ]; then
  IFS=';'
  set -f
  for val in $VIASH_PAR_PASSES; do
    if ! [[ "${val}" =~ ^[-+]?[0-9]+$ ]]; then
      ViashError '--passes' 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 "$VIASH_PAR_FULL_SEARCH" ]]; then
  if ! [[ "$VIASH_PAR_FULL_SEARCH" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--full_search' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_INDEX" ]]; then
  if ! [[ "$VIASH_PAR_INDEX" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--index' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_L" ]]; then
  if ! [[ "$VIASH_PAR_L" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '-L' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_INTERVAL" ]]; then
  if ! [[ "$VIASH_PAR_INTERVAL" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--interval' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_MAX_POS" ]]; then
  if ! [[ "$VIASH_PAR_MAX_POS" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--max_pos' has to be an integer. 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 "$VIASH_PAR_BLAST" ]; then
  VIASH_PAR_BLAST_CHOICES=("0;1;1 cigar;1 cigar qcov;1 cigar qcov qstrand")
  IFS=';'
  set -f
  if ! [[ ";${VIASH_PAR_BLAST_CHOICES[*]};" =~ ";$VIASH_PAR_BLAST;" ]]; then
    ViashError '--blast' specified value of \'$VIASH_PAR_BLAST\' 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 "$VIASH_PAR_ZIP_OUT" ]; then
  VIASH_PAR_ZIP_OUT_CHOICES=("1;true;t;yes;y;0;false;f;no;n;-1")
  IFS=';'
  set -f
  if ! [[ ";${VIASH_PAR_ZIP_OUT_CHOICES[*]};" =~ ";$VIASH_PAR_ZIP_OUT;" ]]; then
    ViashError '--zip_out' specified value of \'$VIASH_PAR_ZIP_OUT\' 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 "$VIASH_PAR_INDEX" ]; then
  VIASH_PAR_INDEX_CHOICES=("0;1;2")
  IFS=';'
  set -f
  if ! [[ ";${VIASH_PAR_INDEX_CHOICES[*]};" =~ ";$VIASH_PAR_INDEX;" ]]; then
    ViashError '--index' specified value of \'$VIASH_PAR_INDEX\' 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 "$VIASH_PAR_LOG" ] && [ ! -d "$(dirname "$VIASH_PAR_LOG")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_LOG")"
fi
if [ ! -z "$VIASH_PAR_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_OUTPUT")"
fi
if [ ! -z "$VIASH_PAR_OTHER" ] && [ ! -d "$(dirname "$VIASH_PAR_OTHER")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_OTHER")"
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_INPUT" ]; then
  VIASH_TEST_INPUT=()
  IFS=';'
  for var in $VIASH_PAR_INPUT; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_INPUT+=( "$var" )
  done
  VIASH_PAR_INPUT=$(IFS=';' ; echo "${VIASH_TEST_INPUT[*]}")
fi
if [ ! -z "$VIASH_PAR_REF" ]; then
  VIASH_TEST_REF=()
  IFS=';'
  for var in $VIASH_PAR_REF; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_REF+=( "$var" )
  done
  VIASH_PAR_REF=$(IFS=';' ; echo "${VIASH_TEST_REF[*]}")
fi
if [ ! -z "$VIASH_PAR_RIBO_DATABASE_MANIFEST" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_RIBO_DATABASE_MANIFEST")" )
  VIASH_PAR_RIBO_DATABASE_MANIFEST=$(ViashDockerAutodetectMount "$VIASH_PAR_RIBO_DATABASE_MANIFEST")
fi
if [ ! -z "$VIASH_PAR_LOG" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_LOG")" )
  VIASH_PAR_LOG=$(ViashDockerAutodetectMount "$VIASH_PAR_LOG")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_LOG" )
fi
if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT")" )
  VIASH_PAR_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT" )
fi
if [ ! -z "$VIASH_PAR_OTHER" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OTHER")" )
  VIASH_PAR_OTHER=$(ViashDockerAutodetectMount "$VIASH_PAR_OTHER")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_OTHER" )
fi
if [ ! -z "$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-sortmerna-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 ${VIASH_PAR_PAIRED+x} ]; then echo "${VIASH_PAR_PAIRED}" | sed "s#'#'\"'\"'#g;s#.*#par_paired='&'#" ; else echo "# par_paired="; 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 ${VIASH_PAR_REF+x} ]; then echo "${VIASH_PAR_REF}" | sed "s#'#'\"'\"'#g;s#.*#par_ref='&'#" ; else echo "# par_ref="; fi )
$( if [ ! -z ${VIASH_PAR_RIBO_DATABASE_MANIFEST+x} ]; then echo "${VIASH_PAR_RIBO_DATABASE_MANIFEST}" | sed "s#'#'\"'\"'#g;s#.*#par_ribo_database_manifest='&'#" ; else echo "# par_ribo_database_manifest="; fi )
$( if [ ! -z ${VIASH_PAR_LOG+x} ]; then echo "${VIASH_PAR_LOG}" | sed "s#'#'\"'\"'#g;s#.*#par_log='&'#" ; else echo "# par_log="; 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 ${VIASH_PAR_OTHER+x} ]; then echo "${VIASH_PAR_OTHER}" | sed "s#'#'\"'\"'#g;s#.*#par_other='&'#" ; else echo "# par_other="; fi )
$( if [ ! -z ${VIASH_PAR_KVDB+x} ]; then echo "${VIASH_PAR_KVDB}" | sed "s#'#'\"'\"'#g;s#.*#par_kvdb='&'#" ; else echo "# par_kvdb="; fi )
$( if [ ! -z ${VIASH_PAR_IDX_DIR+x} ]; then echo "${VIASH_PAR_IDX_DIR}" | sed "s#'#'\"'\"'#g;s#.*#par_idx_dir='&'#" ; else echo "# par_idx_dir="; fi )
$( if [ ! -z ${VIASH_PAR_READB+x} ]; then echo "${VIASH_PAR_READB}" | sed "s#'#'\"'\"'#g;s#.*#par_readb='&'#" ; else echo "# par_readb="; fi )
$( if [ ! -z ${VIASH_PAR_FASTX+x} ]; then echo "${VIASH_PAR_FASTX}" | sed "s#'#'\"'\"'#g;s#.*#par_fastx='&'#" ; else echo "# par_fastx="; fi )
$( if [ ! -z ${VIASH_PAR_SAM+x} ]; then echo "${VIASH_PAR_SAM}" | sed "s#'#'\"'\"'#g;s#.*#par_sam='&'#" ; else echo "# par_sam="; fi )
$( if [ ! -z ${VIASH_PAR_SQ+x} ]; then echo "${VIASH_PAR_SQ}" | sed "s#'#'\"'\"'#g;s#.*#par_sq='&'#" ; else echo "# par_sq="; fi )
$( if [ ! -z ${VIASH_PAR_BLAST+x} ]; then echo "${VIASH_PAR_BLAST}" | sed "s#'#'\"'\"'#g;s#.*#par_blast='&'#" ; else echo "# par_blast="; fi )
$( if [ ! -z ${VIASH_PAR_NUM_ALIGNMENTS+x} ]; then echo "${VIASH_PAR_NUM_ALIGNMENTS}" | sed "s#'#'\"'\"'#g;s#.*#par_num_alignments='&'#" ; else echo "# par_num_alignments="; fi )
$( if [ ! -z ${VIASH_PAR_MIN_LIS+x} ]; then echo "${VIASH_PAR_MIN_LIS}" | sed "s#'#'\"'\"'#g;s#.*#par_min_lis='&'#" ; else echo "# par_min_lis="; fi )
$( if [ ! -z ${VIASH_PAR_PRINT_ALL_READS+x} ]; then echo "${VIASH_PAR_PRINT_ALL_READS}" | sed "s#'#'\"'\"'#g;s#.*#par_print_all_reads='&'#" ; else echo "# par_print_all_reads="; fi )
$( if [ ! -z ${VIASH_PAR_PAIRED_IN+x} ]; then echo "${VIASH_PAR_PAIRED_IN}" | sed "s#'#'\"'\"'#g;s#.*#par_paired_in='&'#" ; else echo "# par_paired_in="; fi )
$( if [ ! -z ${VIASH_PAR_PAIRED_OUT+x} ]; then echo "${VIASH_PAR_PAIRED_OUT}" | sed "s#'#'\"'\"'#g;s#.*#par_paired_out='&'#" ; else echo "# par_paired_out="; fi )
$( if [ ! -z ${VIASH_PAR_OUT2+x} ]; then echo "${VIASH_PAR_OUT2}" | sed "s#'#'\"'\"'#g;s#.*#par_out2='&'#" ; else echo "# par_out2="; fi )
$( if [ ! -z ${VIASH_PAR_SOUT+x} ]; then echo "${VIASH_PAR_SOUT}" | sed "s#'#'\"'\"'#g;s#.*#par_sout='&'#" ; else echo "# par_sout="; fi )
$( if [ ! -z ${VIASH_PAR_ZIP_OUT+x} ]; then echo "${VIASH_PAR_ZIP_OUT}" | sed "s#'#'\"'\"'#g;s#.*#par_zip_out='&'#" ; else echo "# par_zip_out="; fi )
$( if [ ! -z ${VIASH_PAR_MATCH+x} ]; then echo "${VIASH_PAR_MATCH}" | sed "s#'#'\"'\"'#g;s#.*#par_match='&'#" ; else echo "# par_match="; fi )
$( if [ ! -z ${VIASH_PAR_MISMATCH+x} ]; then echo "${VIASH_PAR_MISMATCH}" | sed "s#'#'\"'\"'#g;s#.*#par_mismatch='&'#" ; else echo "# par_mismatch="; fi )
$( if [ ! -z ${VIASH_PAR_GAP_OPEN+x} ]; then echo "${VIASH_PAR_GAP_OPEN}" | sed "s#'#'\"'\"'#g;s#.*#par_gap_open='&'#" ; else echo "# par_gap_open="; fi )
$( if [ ! -z ${VIASH_PAR_GAP_EXT+x} ]; then echo "${VIASH_PAR_GAP_EXT}" | sed "s#'#'\"'\"'#g;s#.*#par_gap_ext='&'#" ; else echo "# par_gap_ext="; fi )
$( if [ ! -z ${VIASH_PAR_N+x} ]; then echo "${VIASH_PAR_N}" | sed "s#'#'\"'\"'#g;s#.*#par_N='&'#" ; else echo "# par_N="; fi )
$( if [ ! -z ${VIASH_PAR_A+x} ]; then echo "${VIASH_PAR_A}" | sed "s#'#'\"'\"'#g;s#.*#par_a='&'#" ; else echo "# par_a="; fi )
$( if [ ! -z ${VIASH_PAR_E+x} ]; then echo "${VIASH_PAR_E}" | sed "s#'#'\"'\"'#g;s#.*#par_e='&'#" ; else echo "# par_e="; fi )
$( if [ ! -z ${VIASH_PAR_F+x} ]; then echo "${VIASH_PAR_F}" | sed "s#'#'\"'\"'#g;s#.*#par_F='&'#" ; else echo "# par_F="; fi )
$( if [ ! -z ${VIASH_PAR_R+x} ]; then echo "${VIASH_PAR_R}" | sed "s#'#'\"'\"'#g;s#.*#par_R='&'#" ; else echo "# par_R="; fi )
$( if [ ! -z ${VIASH_PAR_NUM_ALIGNMENT+x} ]; then echo "${VIASH_PAR_NUM_ALIGNMENT}" | sed "s#'#'\"'\"'#g;s#.*#par_num_alignment='&'#" ; else echo "# par_num_alignment="; fi )
$( if [ ! -z ${VIASH_PAR_BEST+x} ]; then echo "${VIASH_PAR_BEST}" | sed "s#'#'\"'\"'#g;s#.*#par_best='&'#" ; else echo "# par_best="; fi )
$( if [ ! -z ${VIASH_PAR_VERBOSE+x} ]; then echo "${VIASH_PAR_VERBOSE}" | sed "s#'#'\"'\"'#g;s#.*#par_verbose='&'#" ; else echo "# par_verbose="; fi )
$( if [ ! -z ${VIASH_PAR_ID+x} ]; then echo "${VIASH_PAR_ID}" | sed "s#'#'\"'\"'#g;s#.*#par_id='&'#" ; else echo "# par_id="; fi )
$( if [ ! -z ${VIASH_PAR_COVERAGE+x} ]; then echo "${VIASH_PAR_COVERAGE}" | sed "s#'#'\"'\"'#g;s#.*#par_coverage='&'#" ; else echo "# par_coverage="; fi )
$( if [ ! -z ${VIASH_PAR_DE_NOVO+x} ]; then echo "${VIASH_PAR_DE_NOVO}" | sed "s#'#'\"'\"'#g;s#.*#par_de_novo='&'#" ; else echo "# par_de_novo="; fi )
$( if [ ! -z ${VIASH_PAR_OTU_MAP+x} ]; then echo "${VIASH_PAR_OTU_MAP}" | sed "s#'#'\"'\"'#g;s#.*#par_otu_map='&'#" ; else echo "# par_otu_map="; fi )
$( if [ ! -z ${VIASH_PAR_NUM_SEED+x} ]; then echo "${VIASH_PAR_NUM_SEED}" | sed "s#'#'\"'\"'#g;s#.*#par_num_seed='&'#" ; else echo "# par_num_seed="; fi )
$( if [ ! -z ${VIASH_PAR_PASSES+x} ]; then echo "${VIASH_PAR_PASSES}" | sed "s#'#'\"'\"'#g;s#.*#par_passes='&'#" ; else echo "# par_passes="; fi )
$( if [ ! -z ${VIASH_PAR_EDGE+x} ]; then echo "${VIASH_PAR_EDGE}" | sed "s#'#'\"'\"'#g;s#.*#par_edge='&'#" ; else echo "# par_edge="; fi )
$( if [ ! -z ${VIASH_PAR_FULL_SEARCH+x} ]; then echo "${VIASH_PAR_FULL_SEARCH}" | sed "s#'#'\"'\"'#g;s#.*#par_full_search='&'#" ; else echo "# par_full_search="; fi )
$( if [ ! -z ${VIASH_PAR_INDEX+x} ]; then echo "${VIASH_PAR_INDEX}" | sed "s#'#'\"'\"'#g;s#.*#par_index='&'#" ; else echo "# par_index="; fi )
$( if [ ! -z ${VIASH_PAR_L+x} ]; then echo "${VIASH_PAR_L}" | sed "s#'#'\"'\"'#g;s#.*#par_L='&'#" ; else echo "# par_L="; fi )
$( if [ ! -z ${VIASH_PAR_INTERVAL+x} ]; then echo "${VIASH_PAR_INTERVAL}" | sed "s#'#'\"'\"'#g;s#.*#par_interval='&'#" ; else echo "# par_interval="; fi )
$( if [ ! -z ${VIASH_PAR_MAX_POS+x} ]; then echo "${VIASH_PAR_MAX_POS}" | sed "s#'#'\"'\"'#g;s#.*#par_max_pos='&'#" ; else echo "# par_max_pos="; 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

set -eo pipefail

unset_if_false=( par_fastx par_sq par_fastx par_print_all_reads par_paired_in par_paired_out
                 par_F par_R par_verbose par_de_novo par_otu_map par_full_search par_out2
                 par_sout par_sam par_paired )


for var in "\${unset_if_false[@]}"; do
    if [ "\${!var}" == "false" ]; then
        unset \$var
    fi
done

reads=()
IFS=";" read -ra input <<< "\$par_input"
if [ "\${#input[@]}" -eq 2 ]; then
    reads="--reads \${input[0]} --reads \${input[1]}"
    # set paired to true in case it's not
    par_paired=true
else
    reads="--reads \${input[0]}"
    par_paired=false
fi

refs=()

# check if references are input normally or through a manifest file
if [[ ! -z "\$par_ribo_database_manifest" ]]; then
    while IFS= read -r path || [[ -n \$path ]]; do
        refs=\$refs" --ref \$path"
    done < \$par_ribo_database_manifest

elif [[ ! -z "\$par_ref" ]]; then
    IFS=";" read -ra ref <<< "\$par_ref"
    for i in "\${ref[@]}"
    do
        refs+="-ref \$i "
    done

else 
    echo "No reference fasta file(s) provided"
    exit 1
fi


sortmerna \\
    \$refs \\
    \$reads \\
    --workdir . \\
    \${par_output:+--aligned "\${par_output}"} \\
    \${par_fastx:+--fastx} \\
    \${par_other:+--other "\${par_other}"} \\
    \${par_kvdb:+--kvdb "\${par_kvdb}"} \\
    \${par_idx_dir:+--idx-dir "\${par_idx_dir}"} \\
    \${par_readb:+--readb "\${par_readb}"} \\
    \${par_sam:+--sam} \\
    \${par_sq:+--sq} \\
    \${par_blast:+--blast "\${par_blast}"} \\
    \${par_num_alignments:+--num_alignments "\${par_num_alignments}"} \\
    \${par_min_lis:+--min_lis "\${par_min_lis}"} \\
    \${par_print_all_reads:+--print_all_reads} \\
    \${par_paired_in:+--paired_in} \\
    \${par_paired_out:+--paired_out} \\
    \${par_out2:+--out2} \\
    \${par_sout:+--sout} \\
    \${par_zip_out:+--zip-out "\${par_zip_out}"} \\
    \${par_match:+--match "\${par_match}"} \\
    \${par_mismatch:+--mismatch "\${par_mismatch}"} \\
    \${par_gap_open:+--gap_open "\${par_gap_open}"} \\
    \${par_gap_ext:+--gap_ext "\${par_gap_ext}"} \\
    \${par_N:+-N "\${par_N}"} \\
    \${par_a:+-a "\${par_a}"} \\
    \${par_e:+-e "\${par_e}"} \\
    \${par_F:+-F} \\
    \${par_R:+-R} \\
    \${par_num_alignment:+--num_alignment "\${par_num_alignment}"} \\
    \${par_best:+--best "\${par_best}"} \\
    \${par_verbose:+--verbose} \\
    \${par_id:+--id "\${par_id}"} \\
    \${par_coverage:+--coverage "\${par_coverage}"} \\
    \${par_de_novo:+--de_novo} \\
    \${par_otu_map:+--otu_map} \\
    \${par_num_seed:+--num_seed "\${par_num_seed}"} \\
    \${par_passes:+--passes "\${par_passes}"} \\
    \${par_edge:+--edge "\${par_edge}"} \\
    \${par_full_search:+--full_search} \\
    \${par_index:+--index "\${par_index}"} \\
    \${par_L:+-L \$par_L} \\
    \${par_interval:+--interval "\${par_interval}"} \\
    \${par_max_pos:+--max_pos "\${par_max_pos}"}


if [ ! -z \$par_log ]; then
    mv "\${par_output}.log" \$par_log
fi

exit 0
VIASHMAIN
bash "\$tempscript" &
wait "\$!"

VIASHEOF


if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  # strip viash automount from file paths
  
  if [ ! -z "$VIASH_PAR_INPUT" ]; then
    unset VIASH_TEST_INPUT
    IFS=';'
    for var in $VIASH_PAR_INPUT; do
      unset IFS
      if [ -z "$VIASH_TEST_INPUT" ]; then
      VIASH_TEST_INPUT="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_INPUT="$VIASH_TEST_INPUT;""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_INPUT="$VIASH_TEST_INPUT"
  fi
  if [ ! -z "$VIASH_PAR_REF" ]; then
    unset VIASH_TEST_REF
    IFS=';'
    for var in $VIASH_PAR_REF; do
      unset IFS
      if [ -z "$VIASH_TEST_REF" ]; then
      VIASH_TEST_REF="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_REF="$VIASH_TEST_REF;""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_REF="$VIASH_TEST_REF"
  fi
  if [ ! -z "$VIASH_PAR_RIBO_DATABASE_MANIFEST" ]; then
    VIASH_PAR_RIBO_DATABASE_MANIFEST=$(ViashDockerStripAutomount "$VIASH_PAR_RIBO_DATABASE_MANIFEST")
  fi
  if [ ! -z "$VIASH_PAR_LOG" ]; then
    VIASH_PAR_LOG=$(ViashDockerStripAutomount "$VIASH_PAR_LOG")
  fi
  if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
    VIASH_PAR_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT")
  fi
  if [ ! -z "$VIASH_PAR_OTHER" ]; then
    VIASH_PAR_OTHER=$(ViashDockerStripAutomount "$VIASH_PAR_OTHER")
  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 "$VIASH_PAR_OUTPUT" ] && [ ! -e "$VIASH_PAR_OUTPUT" ]; then
  ViashError "Output file '$VIASH_PAR_OUTPUT' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_OTHER" ] && [ ! -e "$VIASH_PAR_OTHER" ]; then
  ViashError "Output file '$VIASH_PAR_OTHER' does not exist."
  exit 1
fi


exit 0
