#!/usr/bin/env bash

# nanoplot 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="nanoplot"
VIASH_META_FUNCTIONALITY_NAME="nanoplot"
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 "nanoplot add_sgdemux"
  echo ""
  echo "Run NanoPlot on nanopore-sequenced reads."
  echo "NanoPlot is a plotting tool for long read sequencing data and alignments."
  echo ""
  echo "Inputs:"
  echo "    --fastq"
  echo "        type: file, multiple values allowed, file must exist"
  echo "        example: read.fq"
  echo "        Input fastq file(s), separated by \";\"."
  echo ""
  echo "    --fasta"
  echo "        type: file, multiple values allowed, file must exist"
  echo "        example: read.fa"
  echo "        Input fasta file(s), separated by \";\"."
  echo ""
  echo "    --fastq_rich"
  echo "        type: file, multiple values allowed, file must exist"
  echo "        example: read.fq"
  echo "        Input fastq file(s) generated by albacore or"
  echo "        MinKNOW with additional information concerning channel and time,"
  echo "        separated by \";\"."
  echo ""
  echo "    --fastq_minimal"
  echo "        type: file, multiple values allowed, file must exist"
  echo "        example: read.fq"
  echo "        Input fastq file(s) generated by albacore or MinKNOW with"
  echo "        additional information concerning channel and time. Minimal data is"
  echo "        extracted"
  echo "        swiftly without elaborate checks. Separated by \";\"."
  echo ""
  echo "    --summary"
  echo "        type: file, multiple values allowed, file must exist"
  echo "        example: read.txt"
  echo "        Input summary file(s) generated by albacore or guppy, separated by \";\"."
  echo ""
  echo "    --bam"
  echo "        type: file, multiple values allowed, file must exist"
  echo "        example: read.bam"
  echo "        Input sorted bam file(s), separated by \";\"."
  echo ""
  echo "    --ubam"
  echo "        type: file, multiple values allowed, file must exist"
  echo "        example: read.ubam"
  echo "        Input unmapped bam file(s), separated by \";\"."
  echo ""
  echo "    --cram"
  echo "        type: file, multiple values allowed, file must exist"
  echo "        example: read.cram"
  echo "        Input sorted cram file(s), separated by \";\"."
  echo ""
  echo "    --pickle"
  echo "        type: file, multiple values allowed, file must exist"
  echo "        example: read.pkl"
  echo "        Input pickle file stored earlier, separated by \";\"."
  echo ""
  echo "    --arrow, --feather"
  echo "        type: file, multiple values allowed, file must exist"
  echo "        example: read.arrow"
  echo "        Input feather file(s), separated by \";\"."
  echo ""
  echo "Outputs:"
  echo "    -o, --outdir"
  echo "        type: file, required parameter, output, file must exist"
  echo "        Specify directory in which output has to be created."
  echo ""
  echo "Options:"
  echo "    --verbose"
  echo "        type: boolean_true"
  echo "        Write log messages also to terminal"
  echo ""
  echo "    --store"
  echo "        type: boolean_true"
  echo "        Store the extracted data in a pickle file for future plotting."
  echo ""
  echo "    --raw"
  echo "        type: boolean_true"
  echo "        Store the extracted data in tab separated file."
  echo ""
  echo "    --huge"
  echo "        type: boolean_true"
  echo "        Input data is one very large file."
  echo ""
  echo "    --no_static"
  echo "        type: boolean_false"
  echo "        Do not make static (png) plots."
  echo ""
  echo "    -p, --prefix"
  echo "        type: string"
  echo "        Specify an optional prefix to be used for the output files."
  echo ""
  echo "    --tsv_stats"
  echo "        type: boolean_true"
  echo "        Output the stats file as a properly formatted TSV."
  echo ""
  echo "    --only_report"
  echo "        type: boolean_true"
  echo "        Output only the report."
  echo ""
  echo "    --info_in_report"
  echo "        type: boolean_true"
  echo "        Add NanoPlot run info in the report."
  echo ""
  echo "Filtering or transforming input:"
  echo "    --maxlength"
  echo "        type: integer"
  echo "        Drop reads longer than length specified."
  echo ""
  echo "    --minlength"
  echo "        type: integer"
  echo "        Drop reads shorter than length specified."
  echo ""
  echo "    --drop_outliers"
  echo "        type: boolean_false"
  echo "        Drop outlier reads with extreme long length."
  echo ""
  echo "    --downsample"
  echo "        type: integer"
  echo "        Reduce dataset to N reads by random sampling."
  echo ""
  echo "    --loglength"
  echo "        type: boolean_true"
  echo "        Logarithmic scaling of lengths in plots."
  echo ""
  echo "    --percentqual"
  echo "        type: boolean_true"
  echo "        Use qualities as theoretical percent identities."
  echo ""
  echo "    --alength"
  echo "        type: boolean_true"
  echo "        Use aligned read lengths rather than sequenced length (bam mode)."
  echo ""
  echo "    --minqual"
  echo "        type: integer"
  echo "        Drop reads with an average quality lower than specified."
  echo ""
  echo "    --runtime_until"
  echo "        type: integer"
  echo "        Only take the N first hours of a run."
  echo ""
  echo "    --readtype"
  echo "        type: string"
  echo "        Which read type to extract information about from summary."
  echo "        Options are 1D, 2D, 1D2"
  echo ""
  echo "    --barcoded"
  echo "        type: boolean_true"
  echo "        Use if you want to split the summary file by barcode."
  echo ""
  echo "    --no_supplementary"
  echo "        type: boolean_false"
  echo "        Use if you want to remove supplementary alignments."
  echo ""
  echo "Customizing plots:"
  echo "    -c, --color"
  echo "        type: string"
  echo "        Specify a color for the plots, must be a valid matplotlib color."
  echo ""
  echo "    -cm, --colormap"
  echo "        type: string"
  echo "        Specify a valid matplotlib colormap for the heatmap."
  echo ""
  echo "    -f, --format"
  echo "        type: string"
  echo "        default: png"
  echo "        Specify the output format of the plots."
  echo "        {eps,jpeg,jpg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff}"
  echo ""
  echo "    --plots"
  echo "        type: string"
  echo "        Specify which bivariate plots have to be made."
  echo "        [{kde,hex,dot} ...]"
  echo ""
  echo "    --legacy"
  echo "        type: string"
  echo "        Specify which bivariate plots have to be made (legacy mode)."
  echo "        [{kde,dot,hex} ...]"
  echo ""
  echo "    --listcolors"
  echo "        type: boolean_true"
  echo "        List the colors which are available for plotting and exit."
  echo ""
  echo "    --listcolormaps"
  echo "        type: boolean_true"
  echo "        List the colormaps which are available for plotting and exit."
  echo ""
  echo "    --no_N50"
  echo "        type: boolean_false"
  echo "        Hide the N50 mark in the read length histogram."
  echo ""
  echo "    --N50"
  echo "        type: boolean_true"
  echo "        Show the N50 mark in the read length histogram."
  echo ""
  echo "    --title"
  echo "        type: string"
  echo "        Add a title to all plots, requires quoting if using spaces."
  echo ""
  echo "    --font_scale"
  echo "        type: double"
  echo "        Scale the font of the plots by a factor."
  echo ""
  echo "    --dpi"
  echo "        type: integer"
  echo "        Set the dpi for saving images."
  echo ""
  echo "    --hide_stats"
  echo "        type: boolean_false"
  echo "        Not adding Pearson R stats in some bivariate plots."
}

# 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 [[ "$engine_id" == "docker" ]]; then
    cat << 'VIASHDOCKER'
FROM quay.io/biocontainers/nanoplot:1.43.0--pyhdfd78af_1
ENTRYPOINT []
RUN version=$(NanoPlot --version) && \
echo "$version" > /var/software_versions.txt

LABEL org.opencontainers.image.description="Companion container for running component nanoplot"
LABEL org.opencontainers.image.created="2024-11-14T12:50:40Z"
LABEL org.opencontainers.image.source="https://github.com/wdecoster/NanoPlot"
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 "$1")"
            shift 1
            ;;
        --version)
            echo "nanoplot add_sgdemux"
            exit
            ;;
        --fastq)
            if [ -z "$VIASH_PAR_FASTQ" ]; then
              VIASH_PAR_FASTQ="$2"
            else
              VIASH_PAR_FASTQ="$VIASH_PAR_FASTQ;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --fastq. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --fastq=*)
            if [ -z "$VIASH_PAR_FASTQ" ]; then
              VIASH_PAR_FASTQ=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_FASTQ="$VIASH_PAR_FASTQ;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --fasta)
            if [ -z "$VIASH_PAR_FASTA" ]; then
              VIASH_PAR_FASTA="$2"
            else
              VIASH_PAR_FASTA="$VIASH_PAR_FASTA;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --fasta. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --fasta=*)
            if [ -z "$VIASH_PAR_FASTA" ]; then
              VIASH_PAR_FASTA=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_FASTA="$VIASH_PAR_FASTA;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --fastq_rich)
            if [ -z "$VIASH_PAR_FASTQ_RICH" ]; then
              VIASH_PAR_FASTQ_RICH="$2"
            else
              VIASH_PAR_FASTQ_RICH="$VIASH_PAR_FASTQ_RICH;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --fastq_rich. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --fastq_rich=*)
            if [ -z "$VIASH_PAR_FASTQ_RICH" ]; then
              VIASH_PAR_FASTQ_RICH=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_FASTQ_RICH="$VIASH_PAR_FASTQ_RICH;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --fastq_minimal)
            if [ -z "$VIASH_PAR_FASTQ_MINIMAL" ]; then
              VIASH_PAR_FASTQ_MINIMAL="$2"
            else
              VIASH_PAR_FASTQ_MINIMAL="$VIASH_PAR_FASTQ_MINIMAL;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --fastq_minimal. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --fastq_minimal=*)
            if [ -z "$VIASH_PAR_FASTQ_MINIMAL" ]; then
              VIASH_PAR_FASTQ_MINIMAL=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_FASTQ_MINIMAL="$VIASH_PAR_FASTQ_MINIMAL;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --summary)
            if [ -z "$VIASH_PAR_SUMMARY" ]; then
              VIASH_PAR_SUMMARY="$2"
            else
              VIASH_PAR_SUMMARY="$VIASH_PAR_SUMMARY;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --summary. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --summary=*)
            if [ -z "$VIASH_PAR_SUMMARY" ]; then
              VIASH_PAR_SUMMARY=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_SUMMARY="$VIASH_PAR_SUMMARY;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --bam)
            if [ -z "$VIASH_PAR_BAM" ]; then
              VIASH_PAR_BAM="$2"
            else
              VIASH_PAR_BAM="$VIASH_PAR_BAM;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --bam. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --bam=*)
            if [ -z "$VIASH_PAR_BAM" ]; then
              VIASH_PAR_BAM=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_BAM="$VIASH_PAR_BAM;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --ubam)
            if [ -z "$VIASH_PAR_UBAM" ]; then
              VIASH_PAR_UBAM="$2"
            else
              VIASH_PAR_UBAM="$VIASH_PAR_UBAM;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --ubam. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --ubam=*)
            if [ -z "$VIASH_PAR_UBAM" ]; then
              VIASH_PAR_UBAM=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_UBAM="$VIASH_PAR_UBAM;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --cram)
            if [ -z "$VIASH_PAR_CRAM" ]; then
              VIASH_PAR_CRAM="$2"
            else
              VIASH_PAR_CRAM="$VIASH_PAR_CRAM;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --cram. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --cram=*)
            if [ -z "$VIASH_PAR_CRAM" ]; then
              VIASH_PAR_CRAM=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_CRAM="$VIASH_PAR_CRAM;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --pickle)
            if [ -z "$VIASH_PAR_PICKLE" ]; then
              VIASH_PAR_PICKLE="$2"
            else
              VIASH_PAR_PICKLE="$VIASH_PAR_PICKLE;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --pickle. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --pickle=*)
            if [ -z "$VIASH_PAR_PICKLE" ]; then
              VIASH_PAR_PICKLE=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_PICKLE="$VIASH_PAR_PICKLE;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --feather)
            if [ -z "$VIASH_PAR_FEATHER" ]; then
              VIASH_PAR_FEATHER="$2"
            else
              VIASH_PAR_FEATHER="$VIASH_PAR_FEATHER;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --feather. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --feather=*)
            if [ -z "$VIASH_PAR_FEATHER" ]; then
              VIASH_PAR_FEATHER=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_FEATHER="$VIASH_PAR_FEATHER;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --arrow)
            if [ -z "$VIASH_PAR_FEATHER" ]; then
              VIASH_PAR_FEATHER="$2"
            else
              VIASH_PAR_FEATHER="$VIASH_PAR_FEATHER;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --arrow. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outdir)
            [ -n "$VIASH_PAR_OUTDIR" ] && ViashError Bad arguments for option \'--outdir\': \'$VIASH_PAR_OUTDIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTDIR="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outdir. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outdir=*)
            [ -n "$VIASH_PAR_OUTDIR" ] && ViashError Bad arguments for option \'--outdir=*\': \'$VIASH_PAR_OUTDIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTDIR=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -o)
            [ -n "$VIASH_PAR_OUTDIR" ] && ViashError Bad arguments for option \'-o\': \'$VIASH_PAR_OUTDIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTDIR="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -o. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --verbose)
            [ -n "$VIASH_PAR_VERBOSE" ] && ViashError Bad arguments for option \'--verbose\': \'$VIASH_PAR_VERBOSE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_VERBOSE=true
            shift 1
            ;;
        --store)
            [ -n "$VIASH_PAR_STORE" ] && ViashError Bad arguments for option \'--store\': \'$VIASH_PAR_STORE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_STORE=true
            shift 1
            ;;
        --raw)
            [ -n "$VIASH_PAR_RAW" ] && ViashError Bad arguments for option \'--raw\': \'$VIASH_PAR_RAW\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_RAW=true
            shift 1
            ;;
        --huge)
            [ -n "$VIASH_PAR_HUGE" ] && ViashError Bad arguments for option \'--huge\': \'$VIASH_PAR_HUGE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_HUGE=true
            shift 1
            ;;
        --no_static)
            [ -n "$VIASH_PAR_NO_STATIC" ] && ViashError Bad arguments for option \'--no_static\': \'$VIASH_PAR_NO_STATIC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_NO_STATIC=false
            shift 1
            ;;
        --prefix)
            [ -n "$VIASH_PAR_PREFIX" ] && ViashError Bad arguments for option \'--prefix\': \'$VIASH_PAR_PREFIX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PREFIX="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --prefix. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --prefix=*)
            [ -n "$VIASH_PAR_PREFIX" ] && ViashError Bad arguments for option \'--prefix=*\': \'$VIASH_PAR_PREFIX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PREFIX=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -p)
            [ -n "$VIASH_PAR_PREFIX" ] && ViashError Bad arguments for option \'-p\': \'$VIASH_PAR_PREFIX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PREFIX="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -p. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --tsv_stats)
            [ -n "$VIASH_PAR_TSV_STATS" ] && ViashError Bad arguments for option \'--tsv_stats\': \'$VIASH_PAR_TSV_STATS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_TSV_STATS=true
            shift 1
            ;;
        --only_report)
            [ -n "$VIASH_PAR_ONLY_REPORT" ] && ViashError Bad arguments for option \'--only_report\': \'$VIASH_PAR_ONLY_REPORT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ONLY_REPORT=true
            shift 1
            ;;
        --info_in_report)
            [ -n "$VIASH_PAR_INFO_IN_REPORT" ] && ViashError Bad arguments for option \'--info_in_report\': \'$VIASH_PAR_INFO_IN_REPORT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INFO_IN_REPORT=true
            shift 1
            ;;
        --maxlength)
            [ -n "$VIASH_PAR_MAXLENGTH" ] && ViashError Bad arguments for option \'--maxlength\': \'$VIASH_PAR_MAXLENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAXLENGTH="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --maxlength. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --maxlength=*)
            [ -n "$VIASH_PAR_MAXLENGTH" ] && ViashError Bad arguments for option \'--maxlength=*\': \'$VIASH_PAR_MAXLENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAXLENGTH=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --minlength)
            [ -n "$VIASH_PAR_MINLENGTH" ] && ViashError Bad arguments for option \'--minlength\': \'$VIASH_PAR_MINLENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MINLENGTH="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --minlength. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --minlength=*)
            [ -n "$VIASH_PAR_MINLENGTH" ] && ViashError Bad arguments for option \'--minlength=*\': \'$VIASH_PAR_MINLENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MINLENGTH=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --drop_outliers)
            [ -n "$VIASH_PAR_DROP_OUTLIERS" ] && ViashError Bad arguments for option \'--drop_outliers\': \'$VIASH_PAR_DROP_OUTLIERS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_DROP_OUTLIERS=false
            shift 1
            ;;
        --downsample)
            [ -n "$VIASH_PAR_DOWNSAMPLE" ] && ViashError Bad arguments for option \'--downsample\': \'$VIASH_PAR_DOWNSAMPLE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_DOWNSAMPLE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --downsample. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --downsample=*)
            [ -n "$VIASH_PAR_DOWNSAMPLE" ] && ViashError Bad arguments for option \'--downsample=*\': \'$VIASH_PAR_DOWNSAMPLE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_DOWNSAMPLE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --loglength)
            [ -n "$VIASH_PAR_LOGLENGTH" ] && ViashError Bad arguments for option \'--loglength\': \'$VIASH_PAR_LOGLENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LOGLENGTH=true
            shift 1
            ;;
        --percentqual)
            [ -n "$VIASH_PAR_PERCENTQUAL" ] && ViashError Bad arguments for option \'--percentqual\': \'$VIASH_PAR_PERCENTQUAL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PERCENTQUAL=true
            shift 1
            ;;
        --alength)
            [ -n "$VIASH_PAR_ALENGTH" ] && ViashError Bad arguments for option \'--alength\': \'$VIASH_PAR_ALENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALENGTH=true
            shift 1
            ;;
        --minqual)
            [ -n "$VIASH_PAR_MINQUAL" ] && ViashError Bad arguments for option \'--minqual\': \'$VIASH_PAR_MINQUAL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MINQUAL="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --minqual. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --minqual=*)
            [ -n "$VIASH_PAR_MINQUAL" ] && ViashError Bad arguments for option \'--minqual=*\': \'$VIASH_PAR_MINQUAL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MINQUAL=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --runtime_until)
            [ -n "$VIASH_PAR_RUNTIME_UNTIL" ] && ViashError Bad arguments for option \'--runtime_until\': \'$VIASH_PAR_RUNTIME_UNTIL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_RUNTIME_UNTIL="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --runtime_until. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --runtime_until=*)
            [ -n "$VIASH_PAR_RUNTIME_UNTIL" ] && ViashError Bad arguments for option \'--runtime_until=*\': \'$VIASH_PAR_RUNTIME_UNTIL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_RUNTIME_UNTIL=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --readtype)
            [ -n "$VIASH_PAR_READTYPE" ] && ViashError Bad arguments for option \'--readtype\': \'$VIASH_PAR_READTYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_READTYPE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --readtype. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --readtype=*)
            [ -n "$VIASH_PAR_READTYPE" ] && ViashError Bad arguments for option \'--readtype=*\': \'$VIASH_PAR_READTYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_READTYPE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --barcoded)
            [ -n "$VIASH_PAR_BARCODED" ] && ViashError Bad arguments for option \'--barcoded\': \'$VIASH_PAR_BARCODED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_BARCODED=true
            shift 1
            ;;
        --no_supplementary)
            [ -n "$VIASH_PAR_NO_SUPPLEMENTARY" ] && ViashError Bad arguments for option \'--no_supplementary\': \'$VIASH_PAR_NO_SUPPLEMENTARY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_NO_SUPPLEMENTARY=false
            shift 1
            ;;
        --color)
            [ -n "$VIASH_PAR_COLOR" ] && ViashError Bad arguments for option \'--color\': \'$VIASH_PAR_COLOR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_COLOR="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --color. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --color=*)
            [ -n "$VIASH_PAR_COLOR" ] && ViashError Bad arguments for option \'--color=*\': \'$VIASH_PAR_COLOR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_COLOR=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -c)
            [ -n "$VIASH_PAR_COLOR" ] && ViashError Bad arguments for option \'-c\': \'$VIASH_PAR_COLOR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_COLOR="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -c. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --colormap)
            [ -n "$VIASH_PAR_COLORMAP" ] && ViashError Bad arguments for option \'--colormap\': \'$VIASH_PAR_COLORMAP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_COLORMAP="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --colormap. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --colormap=*)
            [ -n "$VIASH_PAR_COLORMAP" ] && ViashError Bad arguments for option \'--colormap=*\': \'$VIASH_PAR_COLORMAP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_COLORMAP=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -cm)
            [ -n "$VIASH_PAR_COLORMAP" ] && ViashError Bad arguments for option \'-cm\': \'$VIASH_PAR_COLORMAP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_COLORMAP="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -cm. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --format)
            [ -n "$VIASH_PAR_FORMAT" ] && ViashError Bad arguments for option \'--format\': \'$VIASH_PAR_FORMAT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FORMAT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --format. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --format=*)
            [ -n "$VIASH_PAR_FORMAT" ] && ViashError Bad arguments for option \'--format=*\': \'$VIASH_PAR_FORMAT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FORMAT=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -f)
            [ -n "$VIASH_PAR_FORMAT" ] && ViashError Bad arguments for option \'-f\': \'$VIASH_PAR_FORMAT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FORMAT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -f. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --plots)
            [ -n "$VIASH_PAR_PLOTS" ] && ViashError Bad arguments for option \'--plots\': \'$VIASH_PAR_PLOTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PLOTS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --plots. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --plots=*)
            [ -n "$VIASH_PAR_PLOTS" ] && ViashError Bad arguments for option \'--plots=*\': \'$VIASH_PAR_PLOTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PLOTS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --legacy)
            [ -n "$VIASH_PAR_LEGACY" ] && ViashError Bad arguments for option \'--legacy\': \'$VIASH_PAR_LEGACY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LEGACY="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --legacy. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --legacy=*)
            [ -n "$VIASH_PAR_LEGACY" ] && ViashError Bad arguments for option \'--legacy=*\': \'$VIASH_PAR_LEGACY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LEGACY=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --listcolors)
            [ -n "$VIASH_PAR_LISTCOLORS" ] && ViashError Bad arguments for option \'--listcolors\': \'$VIASH_PAR_LISTCOLORS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LISTCOLORS=true
            shift 1
            ;;
        --listcolormaps)
            [ -n "$VIASH_PAR_LISTCOLORMAPS" ] && ViashError Bad arguments for option \'--listcolormaps\': \'$VIASH_PAR_LISTCOLORMAPS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LISTCOLORMAPS=true
            shift 1
            ;;
        --no_N50)
            [ -n "$VIASH_PAR_NO_N50" ] && ViashError Bad arguments for option \'--no_N50\': \'$VIASH_PAR_NO_N50\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_NO_N50=false
            shift 1
            ;;
        --N50)
            [ -n "$VIASH_PAR_N50" ] && ViashError Bad arguments for option \'--N50\': \'$VIASH_PAR_N50\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_N50=true
            shift 1
            ;;
        --title)
            [ -n "$VIASH_PAR_TITLE" ] && ViashError Bad arguments for option \'--title\': \'$VIASH_PAR_TITLE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_TITLE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --title. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --title=*)
            [ -n "$VIASH_PAR_TITLE" ] && ViashError Bad arguments for option \'--title=*\': \'$VIASH_PAR_TITLE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_TITLE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --font_scale)
            [ -n "$VIASH_PAR_FONT_SCALE" ] && ViashError Bad arguments for option \'--font_scale\': \'$VIASH_PAR_FONT_SCALE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FONT_SCALE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --font_scale. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --font_scale=*)
            [ -n "$VIASH_PAR_FONT_SCALE" ] && ViashError Bad arguments for option \'--font_scale=*\': \'$VIASH_PAR_FONT_SCALE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FONT_SCALE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --dpi)
            [ -n "$VIASH_PAR_DPI" ] && ViashError Bad arguments for option \'--dpi\': \'$VIASH_PAR_DPI\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_DPI="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --dpi. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --dpi=*)
            [ -n "$VIASH_PAR_DPI" ] && ViashError Bad arguments for option \'--dpi=*\': \'$VIASH_PAR_DPI\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_DPI=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --hide_stats)
            [ -n "$VIASH_PAR_HIDE_STATS" ] && ViashError Bad arguments for option \'--hide_stats\': \'$VIASH_PAR_HIDE_STATS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_HIDE_STATS=false
            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/nanoplot:add_sgdemux'
  fi

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

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

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

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

# setting computational defaults

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


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

# filling in defaults
if [ -z ${VIASH_PAR_VERBOSE+x} ]; then
  VIASH_PAR_VERBOSE="false"
fi
if [ -z ${VIASH_PAR_STORE+x} ]; then
  VIASH_PAR_STORE="false"
fi
if [ -z ${VIASH_PAR_RAW+x} ]; then
  VIASH_PAR_RAW="false"
fi
if [ -z ${VIASH_PAR_HUGE+x} ]; then
  VIASH_PAR_HUGE="false"
fi
if [ -z ${VIASH_PAR_NO_STATIC+x} ]; then
  VIASH_PAR_NO_STATIC="true"
fi
if [ -z ${VIASH_PAR_TSV_STATS+x} ]; then
  VIASH_PAR_TSV_STATS="false"
fi
if [ -z ${VIASH_PAR_ONLY_REPORT+x} ]; then
  VIASH_PAR_ONLY_REPORT="false"
fi
if [ -z ${VIASH_PAR_INFO_IN_REPORT+x} ]; then
  VIASH_PAR_INFO_IN_REPORT="false"
fi
if [ -z ${VIASH_PAR_DROP_OUTLIERS+x} ]; then
  VIASH_PAR_DROP_OUTLIERS="true"
fi
if [ -z ${VIASH_PAR_LOGLENGTH+x} ]; then
  VIASH_PAR_LOGLENGTH="false"
fi
if [ -z ${VIASH_PAR_PERCENTQUAL+x} ]; then
  VIASH_PAR_PERCENTQUAL="false"
fi
if [ -z ${VIASH_PAR_ALENGTH+x} ]; then
  VIASH_PAR_ALENGTH="false"
fi
if [ -z ${VIASH_PAR_BARCODED+x} ]; then
  VIASH_PAR_BARCODED="false"
fi
if [ -z ${VIASH_PAR_NO_SUPPLEMENTARY+x} ]; then
  VIASH_PAR_NO_SUPPLEMENTARY="true"
fi
if [ -z ${VIASH_PAR_FORMAT+x} ]; then
  VIASH_PAR_FORMAT="png"
fi
if [ -z ${VIASH_PAR_LISTCOLORS+x} ]; then
  VIASH_PAR_LISTCOLORS="false"
fi
if [ -z ${VIASH_PAR_LISTCOLORMAPS+x} ]; then
  VIASH_PAR_LISTCOLORMAPS="false"
fi
if [ -z ${VIASH_PAR_NO_N50+x} ]; then
  VIASH_PAR_NO_N50="true"
fi
if [ -z ${VIASH_PAR_N50+x} ]; then
  VIASH_PAR_N50="false"
fi
if [ -z ${VIASH_PAR_HIDE_STATS+x} ]; then
  VIASH_PAR_HIDE_STATS="true"
fi

# check whether required files exist
if [ ! -z "$VIASH_PAR_FASTQ" ]; then
  IFS=';'
  set -f
  for file in $VIASH_PAR_FASTQ; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_FASTA" ]; then
  IFS=';'
  set -f
  for file in $VIASH_PAR_FASTA; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_FASTQ_RICH" ]; then
  IFS=';'
  set -f
  for file in $VIASH_PAR_FASTQ_RICH; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_FASTQ_MINIMAL" ]; then
  IFS=';'
  set -f
  for file in $VIASH_PAR_FASTQ_MINIMAL; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_SUMMARY" ]; then
  IFS=';'
  set -f
  for file in $VIASH_PAR_SUMMARY; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_BAM" ]; then
  IFS=';'
  set -f
  for file in $VIASH_PAR_BAM; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_UBAM" ]; then
  IFS=';'
  set -f
  for file in $VIASH_PAR_UBAM; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_CRAM" ]; then
  IFS=';'
  set -f
  for file in $VIASH_PAR_CRAM; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_PICKLE" ]; then
  IFS=';'
  set -f
  for file in $VIASH_PAR_PICKLE; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_FEATHER" ]; then
  IFS=';'
  set -f
  for file in $VIASH_PAR_FEATHER; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi

# check whether parameters values are of the right type
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 "$VIASH_PAR_STORE" ]]; then
  if ! [[ "$VIASH_PAR_STORE" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--store' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_RAW" ]]; then
  if ! [[ "$VIASH_PAR_RAW" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--raw' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_HUGE" ]]; then
  if ! [[ "$VIASH_PAR_HUGE" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--huge' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_NO_STATIC" ]]; then
  if ! [[ "$VIASH_PAR_NO_STATIC" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--no_static' has to be a boolean_false. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_TSV_STATS" ]]; then
  if ! [[ "$VIASH_PAR_TSV_STATS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--tsv_stats' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_ONLY_REPORT" ]]; then
  if ! [[ "$VIASH_PAR_ONLY_REPORT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--only_report' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_INFO_IN_REPORT" ]]; then
  if ! [[ "$VIASH_PAR_INFO_IN_REPORT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--info_in_report' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_MAXLENGTH" ]]; then
  if ! [[ "$VIASH_PAR_MAXLENGTH" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--maxlength' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_MINLENGTH" ]]; then
  if ! [[ "$VIASH_PAR_MINLENGTH" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--minlength' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_DROP_OUTLIERS" ]]; then
  if ! [[ "$VIASH_PAR_DROP_OUTLIERS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--drop_outliers' has to be a boolean_false. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_DOWNSAMPLE" ]]; then
  if ! [[ "$VIASH_PAR_DOWNSAMPLE" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--downsample' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_LOGLENGTH" ]]; then
  if ! [[ "$VIASH_PAR_LOGLENGTH" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--loglength' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_PERCENTQUAL" ]]; then
  if ! [[ "$VIASH_PAR_PERCENTQUAL" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--percentqual' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_ALENGTH" ]]; then
  if ! [[ "$VIASH_PAR_ALENGTH" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--alength' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_MINQUAL" ]]; then
  if ! [[ "$VIASH_PAR_MINQUAL" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--minqual' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_RUNTIME_UNTIL" ]]; then
  if ! [[ "$VIASH_PAR_RUNTIME_UNTIL" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--runtime_until' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_BARCODED" ]]; then
  if ! [[ "$VIASH_PAR_BARCODED" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--barcoded' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_NO_SUPPLEMENTARY" ]]; then
  if ! [[ "$VIASH_PAR_NO_SUPPLEMENTARY" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--no_supplementary' has to be a boolean_false. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_LISTCOLORS" ]]; then
  if ! [[ "$VIASH_PAR_LISTCOLORS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--listcolors' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_LISTCOLORMAPS" ]]; then
  if ! [[ "$VIASH_PAR_LISTCOLORMAPS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--listcolormaps' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_NO_N50" ]]; then
  if ! [[ "$VIASH_PAR_NO_N50" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--no_N50' has to be a boolean_false. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_N50" ]]; then
  if ! [[ "$VIASH_PAR_N50" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--N50' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_FONT_SCALE" ]]; then
  if ! [[ "$VIASH_PAR_FONT_SCALE" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--font_scale' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_DPI" ]]; then
  if ! [[ "$VIASH_PAR_DPI" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--dpi' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_HIDE_STATS" ]]; then
  if ! [[ "$VIASH_PAR_HIDE_STATS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--hide_stats' has to be a boolean_false. 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

# create parent directories of output files, if so desired
if [ ! -z "$VIASH_PAR_OUTDIR" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTDIR")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_OUTDIR")"
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_FASTQ" ]; then
  VIASH_TEST_FASTQ=()
  IFS=';'
  for var in $VIASH_PAR_FASTQ; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_FASTQ+=( "$var" )
  done
  VIASH_PAR_FASTQ=$(IFS=';' ; echo "${VIASH_TEST_FASTQ[*]}")
fi
if [ ! -z "$VIASH_PAR_FASTA" ]; then
  VIASH_TEST_FASTA=()
  IFS=';'
  for var in $VIASH_PAR_FASTA; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_FASTA+=( "$var" )
  done
  VIASH_PAR_FASTA=$(IFS=';' ; echo "${VIASH_TEST_FASTA[*]}")
fi
if [ ! -z "$VIASH_PAR_FASTQ_RICH" ]; then
  VIASH_TEST_FASTQ_RICH=()
  IFS=';'
  for var in $VIASH_PAR_FASTQ_RICH; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_FASTQ_RICH+=( "$var" )
  done
  VIASH_PAR_FASTQ_RICH=$(IFS=';' ; echo "${VIASH_TEST_FASTQ_RICH[*]}")
fi
if [ ! -z "$VIASH_PAR_FASTQ_MINIMAL" ]; then
  VIASH_TEST_FASTQ_MINIMAL=()
  IFS=';'
  for var in $VIASH_PAR_FASTQ_MINIMAL; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_FASTQ_MINIMAL+=( "$var" )
  done
  VIASH_PAR_FASTQ_MINIMAL=$(IFS=';' ; echo "${VIASH_TEST_FASTQ_MINIMAL[*]}")
fi
if [ ! -z "$VIASH_PAR_SUMMARY" ]; then
  VIASH_TEST_SUMMARY=()
  IFS=';'
  for var in $VIASH_PAR_SUMMARY; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_SUMMARY+=( "$var" )
  done
  VIASH_PAR_SUMMARY=$(IFS=';' ; echo "${VIASH_TEST_SUMMARY[*]}")
fi
if [ ! -z "$VIASH_PAR_BAM" ]; then
  VIASH_TEST_BAM=()
  IFS=';'
  for var in $VIASH_PAR_BAM; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_BAM+=( "$var" )
  done
  VIASH_PAR_BAM=$(IFS=';' ; echo "${VIASH_TEST_BAM[*]}")
fi
if [ ! -z "$VIASH_PAR_UBAM" ]; then
  VIASH_TEST_UBAM=()
  IFS=';'
  for var in $VIASH_PAR_UBAM; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_UBAM+=( "$var" )
  done
  VIASH_PAR_UBAM=$(IFS=';' ; echo "${VIASH_TEST_UBAM[*]}")
fi
if [ ! -z "$VIASH_PAR_CRAM" ]; then
  VIASH_TEST_CRAM=()
  IFS=';'
  for var in $VIASH_PAR_CRAM; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_CRAM+=( "$var" )
  done
  VIASH_PAR_CRAM=$(IFS=';' ; echo "${VIASH_TEST_CRAM[*]}")
fi
if [ ! -z "$VIASH_PAR_PICKLE" ]; then
  VIASH_TEST_PICKLE=()
  IFS=';'
  for var in $VIASH_PAR_PICKLE; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_PICKLE+=( "$var" )
  done
  VIASH_PAR_PICKLE=$(IFS=';' ; echo "${VIASH_TEST_PICKLE[*]}")
fi
if [ ! -z "$VIASH_PAR_FEATHER" ]; then
  VIASH_TEST_FEATHER=()
  IFS=';'
  for var in $VIASH_PAR_FEATHER; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_FEATHER+=( "$var" )
  done
  VIASH_PAR_FEATHER=$(IFS=';' ; echo "${VIASH_TEST_FEATHER[*]}")
fi
if [ ! -z "$VIASH_PAR_OUTDIR" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTDIR")" )
  VIASH_PAR_OUTDIR=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTDIR")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTDIR" )
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-nanoplot-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

set -eo pipefail

## VIASH START
# The following code has been auto-generated by Viash.
$( if [ ! -z ${VIASH_PAR_FASTQ+x} ]; then echo "${VIASH_PAR_FASTQ}" | sed "s#'#'\"'\"'#g;s#.*#par_fastq='&'#" ; else echo "# par_fastq="; fi )
$( if [ ! -z ${VIASH_PAR_FASTA+x} ]; then echo "${VIASH_PAR_FASTA}" | sed "s#'#'\"'\"'#g;s#.*#par_fasta='&'#" ; else echo "# par_fasta="; fi )
$( if [ ! -z ${VIASH_PAR_FASTQ_RICH+x} ]; then echo "${VIASH_PAR_FASTQ_RICH}" | sed "s#'#'\"'\"'#g;s#.*#par_fastq_rich='&'#" ; else echo "# par_fastq_rich="; fi )
$( if [ ! -z ${VIASH_PAR_FASTQ_MINIMAL+x} ]; then echo "${VIASH_PAR_FASTQ_MINIMAL}" | sed "s#'#'\"'\"'#g;s#.*#par_fastq_minimal='&'#" ; else echo "# par_fastq_minimal="; fi )
$( if [ ! -z ${VIASH_PAR_SUMMARY+x} ]; then echo "${VIASH_PAR_SUMMARY}" | sed "s#'#'\"'\"'#g;s#.*#par_summary='&'#" ; else echo "# par_summary="; fi )
$( if [ ! -z ${VIASH_PAR_BAM+x} ]; then echo "${VIASH_PAR_BAM}" | sed "s#'#'\"'\"'#g;s#.*#par_bam='&'#" ; else echo "# par_bam="; fi )
$( if [ ! -z ${VIASH_PAR_UBAM+x} ]; then echo "${VIASH_PAR_UBAM}" | sed "s#'#'\"'\"'#g;s#.*#par_ubam='&'#" ; else echo "# par_ubam="; fi )
$( if [ ! -z ${VIASH_PAR_CRAM+x} ]; then echo "${VIASH_PAR_CRAM}" | sed "s#'#'\"'\"'#g;s#.*#par_cram='&'#" ; else echo "# par_cram="; fi )
$( if [ ! -z ${VIASH_PAR_PICKLE+x} ]; then echo "${VIASH_PAR_PICKLE}" | sed "s#'#'\"'\"'#g;s#.*#par_pickle='&'#" ; else echo "# par_pickle="; fi )
$( if [ ! -z ${VIASH_PAR_FEATHER+x} ]; then echo "${VIASH_PAR_FEATHER}" | sed "s#'#'\"'\"'#g;s#.*#par_feather='&'#" ; else echo "# par_feather="; fi )
$( if [ ! -z ${VIASH_PAR_OUTDIR+x} ]; then echo "${VIASH_PAR_OUTDIR}" | sed "s#'#'\"'\"'#g;s#.*#par_outdir='&'#" ; else echo "# par_outdir="; 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 ${VIASH_PAR_STORE+x} ]; then echo "${VIASH_PAR_STORE}" | sed "s#'#'\"'\"'#g;s#.*#par_store='&'#" ; else echo "# par_store="; fi )
$( if [ ! -z ${VIASH_PAR_RAW+x} ]; then echo "${VIASH_PAR_RAW}" | sed "s#'#'\"'\"'#g;s#.*#par_raw='&'#" ; else echo "# par_raw="; fi )
$( if [ ! -z ${VIASH_PAR_HUGE+x} ]; then echo "${VIASH_PAR_HUGE}" | sed "s#'#'\"'\"'#g;s#.*#par_huge='&'#" ; else echo "# par_huge="; fi )
$( if [ ! -z ${VIASH_PAR_NO_STATIC+x} ]; then echo "${VIASH_PAR_NO_STATIC}" | sed "s#'#'\"'\"'#g;s#.*#par_no_static='&'#" ; else echo "# par_no_static="; fi )
$( if [ ! -z ${VIASH_PAR_PREFIX+x} ]; then echo "${VIASH_PAR_PREFIX}" | sed "s#'#'\"'\"'#g;s#.*#par_prefix='&'#" ; else echo "# par_prefix="; fi )
$( if [ ! -z ${VIASH_PAR_TSV_STATS+x} ]; then echo "${VIASH_PAR_TSV_STATS}" | sed "s#'#'\"'\"'#g;s#.*#par_tsv_stats='&'#" ; else echo "# par_tsv_stats="; fi )
$( if [ ! -z ${VIASH_PAR_ONLY_REPORT+x} ]; then echo "${VIASH_PAR_ONLY_REPORT}" | sed "s#'#'\"'\"'#g;s#.*#par_only_report='&'#" ; else echo "# par_only_report="; fi )
$( if [ ! -z ${VIASH_PAR_INFO_IN_REPORT+x} ]; then echo "${VIASH_PAR_INFO_IN_REPORT}" | sed "s#'#'\"'\"'#g;s#.*#par_info_in_report='&'#" ; else echo "# par_info_in_report="; fi )
$( if [ ! -z ${VIASH_PAR_MAXLENGTH+x} ]; then echo "${VIASH_PAR_MAXLENGTH}" | sed "s#'#'\"'\"'#g;s#.*#par_maxlength='&'#" ; else echo "# par_maxlength="; fi )
$( if [ ! -z ${VIASH_PAR_MINLENGTH+x} ]; then echo "${VIASH_PAR_MINLENGTH}" | sed "s#'#'\"'\"'#g;s#.*#par_minlength='&'#" ; else echo "# par_minlength="; fi )
$( if [ ! -z ${VIASH_PAR_DROP_OUTLIERS+x} ]; then echo "${VIASH_PAR_DROP_OUTLIERS}" | sed "s#'#'\"'\"'#g;s#.*#par_drop_outliers='&'#" ; else echo "# par_drop_outliers="; fi )
$( if [ ! -z ${VIASH_PAR_DOWNSAMPLE+x} ]; then echo "${VIASH_PAR_DOWNSAMPLE}" | sed "s#'#'\"'\"'#g;s#.*#par_downsample='&'#" ; else echo "# par_downsample="; fi )
$( if [ ! -z ${VIASH_PAR_LOGLENGTH+x} ]; then echo "${VIASH_PAR_LOGLENGTH}" | sed "s#'#'\"'\"'#g;s#.*#par_loglength='&'#" ; else echo "# par_loglength="; fi )
$( if [ ! -z ${VIASH_PAR_PERCENTQUAL+x} ]; then echo "${VIASH_PAR_PERCENTQUAL}" | sed "s#'#'\"'\"'#g;s#.*#par_percentqual='&'#" ; else echo "# par_percentqual="; fi )
$( if [ ! -z ${VIASH_PAR_ALENGTH+x} ]; then echo "${VIASH_PAR_ALENGTH}" | sed "s#'#'\"'\"'#g;s#.*#par_alength='&'#" ; else echo "# par_alength="; fi )
$( if [ ! -z ${VIASH_PAR_MINQUAL+x} ]; then echo "${VIASH_PAR_MINQUAL}" | sed "s#'#'\"'\"'#g;s#.*#par_minqual='&'#" ; else echo "# par_minqual="; fi )
$( if [ ! -z ${VIASH_PAR_RUNTIME_UNTIL+x} ]; then echo "${VIASH_PAR_RUNTIME_UNTIL}" | sed "s#'#'\"'\"'#g;s#.*#par_runtime_until='&'#" ; else echo "# par_runtime_until="; fi )
$( if [ ! -z ${VIASH_PAR_READTYPE+x} ]; then echo "${VIASH_PAR_READTYPE}" | sed "s#'#'\"'\"'#g;s#.*#par_readtype='&'#" ; else echo "# par_readtype="; fi )
$( if [ ! -z ${VIASH_PAR_BARCODED+x} ]; then echo "${VIASH_PAR_BARCODED}" | sed "s#'#'\"'\"'#g;s#.*#par_barcoded='&'#" ; else echo "# par_barcoded="; fi )
$( if [ ! -z ${VIASH_PAR_NO_SUPPLEMENTARY+x} ]; then echo "${VIASH_PAR_NO_SUPPLEMENTARY}" | sed "s#'#'\"'\"'#g;s#.*#par_no_supplementary='&'#" ; else echo "# par_no_supplementary="; fi )
$( if [ ! -z ${VIASH_PAR_COLOR+x} ]; then echo "${VIASH_PAR_COLOR}" | sed "s#'#'\"'\"'#g;s#.*#par_color='&'#" ; else echo "# par_color="; fi )
$( if [ ! -z ${VIASH_PAR_COLORMAP+x} ]; then echo "${VIASH_PAR_COLORMAP}" | sed "s#'#'\"'\"'#g;s#.*#par_colormap='&'#" ; else echo "# par_colormap="; fi )
$( if [ ! -z ${VIASH_PAR_FORMAT+x} ]; then echo "${VIASH_PAR_FORMAT}" | sed "s#'#'\"'\"'#g;s#.*#par_format='&'#" ; else echo "# par_format="; fi )
$( if [ ! -z ${VIASH_PAR_PLOTS+x} ]; then echo "${VIASH_PAR_PLOTS}" | sed "s#'#'\"'\"'#g;s#.*#par_plots='&'#" ; else echo "# par_plots="; fi )
$( if [ ! -z ${VIASH_PAR_LEGACY+x} ]; then echo "${VIASH_PAR_LEGACY}" | sed "s#'#'\"'\"'#g;s#.*#par_legacy='&'#" ; else echo "# par_legacy="; fi )
$( if [ ! -z ${VIASH_PAR_LISTCOLORS+x} ]; then echo "${VIASH_PAR_LISTCOLORS}" | sed "s#'#'\"'\"'#g;s#.*#par_listcolors='&'#" ; else echo "# par_listcolors="; fi )
$( if [ ! -z ${VIASH_PAR_LISTCOLORMAPS+x} ]; then echo "${VIASH_PAR_LISTCOLORMAPS}" | sed "s#'#'\"'\"'#g;s#.*#par_listcolormaps='&'#" ; else echo "# par_listcolormaps="; fi )
$( if [ ! -z ${VIASH_PAR_NO_N50+x} ]; then echo "${VIASH_PAR_NO_N50}" | sed "s#'#'\"'\"'#g;s#.*#par_no_N50='&'#" ; else echo "# par_no_N50="; fi )
$( if [ ! -z ${VIASH_PAR_N50+x} ]; then echo "${VIASH_PAR_N50}" | sed "s#'#'\"'\"'#g;s#.*#par_N50='&'#" ; else echo "# par_N50="; fi )
$( if [ ! -z ${VIASH_PAR_TITLE+x} ]; then echo "${VIASH_PAR_TITLE}" | sed "s#'#'\"'\"'#g;s#.*#par_title='&'#" ; else echo "# par_title="; fi )
$( if [ ! -z ${VIASH_PAR_FONT_SCALE+x} ]; then echo "${VIASH_PAR_FONT_SCALE}" | sed "s#'#'\"'\"'#g;s#.*#par_font_scale='&'#" ; else echo "# par_font_scale="; fi )
$( if [ ! -z ${VIASH_PAR_DPI+x} ]; then echo "${VIASH_PAR_DPI}" | sed "s#'#'\"'\"'#g;s#.*#par_dpi='&'#" ; else echo "# par_dpi="; fi )
$( if [ ! -z ${VIASH_PAR_HIDE_STATS+x} ]; then echo "${VIASH_PAR_HIDE_STATS}" | sed "s#'#'\"'\"'#g;s#.*#par_hide_stats='&'#" ; else echo "# par_hide_stats="; 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

# Unset flags
unset_if_false=( 
    par_verbose
    par_store
    par_raw
    par_huge
    par_no_static
    par_tsv_stats
    par_only_report
    par_info_in_report
    par_drop_outliers
    par_loglength
    par_percentqual
    par_alength
    par_barcoded
    par_no_supplementary
    par_listcolors
    par_listcolormaps
    par_no_N50
    par_N50
    par_hide_stats
)

for var in "\${unset_if_false[@]}"; do
    test_val="\${!var}"
    [[ "\$test_val" == "false" ]] && unset \$var
done

par_fastq="\${par_fastq//;/ }"
par_fasta="\${par_fasta//;/ }"
par_fastq_rich="\${par_fastq_rich//;/ }"
par_fastq_minimal="\${par_fastq_minimal//;/ }"
par_summary="\${par_summary//;/ }"
par_bam="\${par_bam//;/ }"
par_ubam="\${par_ubam//;/ }"
par_cram="\${par_cram//;/ }"
par_pickle="\${par_pickle//;/ }"
par_feather="\${par_feather//;/ }"


inputs=( 
    "\$par_fastq" 
    "\$par_fasta"
    "\$par_fastq_rich"
    "\$par_fastq_minimal"
    "\$par_summary"
    "\$par_bam"
    "\$par_ubam"
    "\$par_cram"
    "\$par_pickle"
    "\$par_feather"
)

one_input=false
for var in "\${inputs[@]}"; do
    if [ -n "\$var" ]; then # if the parameter is not empty
        if [ "\$one_input" = "false" ]; then
            one_input=true
        else # Multiple input file types specified
            echo "Error: Multiple input file types specified."
            exit 1
        fi
    fi
done

if [ ! "\$one_input" ]; then
    echo "Error: No input file type specified."
    exit 1
fi



# Run NanoPlot
NanoPlot \\
    \${par_fastq:+--fastq \$par_fastq} \\
    \${par_fasta:+--fasta \$par_fasta} \\
    \${par_fastq_rich:+--fastq_rich \$par_fastq_rich} \\
    \${par_fastq_minimal:+--fastq_minimal \$par_fastq_minimal} \\
    \${par_summary:+--summary \$par_summary} \\
    \${par_bam:+--bam \$par_bam} \\
    \${par_ubam:+--ubam \$par_ubam} \\
    \${par_cram:+--cram \$par_cram} \\
    \${par_pickle:+--pickle \$par_pickle} \\
    \${par_feather:+--feather \$par_feather} \\
    \${par_verbose:+--verbose} \\
    \${par_store:+--store} \\
    \${par_raw:+--raw} \\
    \${par_huge:+--huge} \\
    \${par_no_static:+--no_static} \\
    \${par_prefix:+--prefix "\$par_prefix"} \\
    \${par_tsv_stats:+--tsv_stats} \\
    \${par_only_report:+--only-report} \\
    \${par_info_in_report:+--info_in_report} \\
    \${par_maxlength:+--maxlength "\$par_maxlength"} \\
    \${par_minlength:+--minlength "\$par_minlength"} \\
    \${par_drop_outliers:+--drop_outliers} \\
    \${par_downsample:+--downsample "\$par_downsample"} \\
    \${par_loglength:+--loglength} \\
    \${par_percentqual:+--percentqual} \\
    \${par_alength:+--alength} \\
    \${par_minqual:+--minqual "\$par_minqual"} \\
    \${par_runtime_until:+--runtime_until "\$par_runtime_until"} \\
    \${par_readtype:+--readtype "\$par_readtype"} \\
    \${par_barcoded:+--barcoded} \\
    \${par_no_supplementary:+--no_supplementary} \\
    \${par_color:+--color "\$par_color"} \\
    \${par_colormap:+--colormap "\$par_colormap"} \\
    \${par_format:+--format "\$par_format"} \\
    \${par_plots:+--plots "\$par_plots"} \\
    \${par_legacy:+--legacy "\$par_legacy"} \\
    \${par_listcolors:+--listcolors} \\
    \${par_listcolormaps:+--listcolormaps} \\
    \${par_no_N50:+--no-N50} \\
    \${par_N50:+--N50} \\
    \${par_title:+--title "\$par_title"} \\
    \${par_font_scale:+--font_scale "\$par_font_scale"} \\
    \${par_dpi:+--dpi "\$par_dpi"} \\
    \${par_hide_stats:+--hide_stats} \\
    \${meta_cpus:+--threads "\$meta_cpus"} \\
    --outdir "\$par_outdir"

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

VIASHEOF


if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  # strip viash automount from file paths
  
  if [ ! -z "$VIASH_PAR_FASTQ" ]; then
    unset VIASH_TEST_FASTQ
    IFS=';'
    for var in $VIASH_PAR_FASTQ; do
      unset IFS
      if [ -z "$VIASH_TEST_FASTQ" ]; then
      VIASH_TEST_FASTQ="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_FASTQ="$VIASH_TEST_FASTQ;""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_FASTQ="$VIASH_TEST_FASTQ"
  fi
  if [ ! -z "$VIASH_PAR_FASTA" ]; then
    unset VIASH_TEST_FASTA
    IFS=';'
    for var in $VIASH_PAR_FASTA; do
      unset IFS
      if [ -z "$VIASH_TEST_FASTA" ]; then
      VIASH_TEST_FASTA="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_FASTA="$VIASH_TEST_FASTA;""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_FASTA="$VIASH_TEST_FASTA"
  fi
  if [ ! -z "$VIASH_PAR_FASTQ_RICH" ]; then
    unset VIASH_TEST_FASTQ_RICH
    IFS=';'
    for var in $VIASH_PAR_FASTQ_RICH; do
      unset IFS
      if [ -z "$VIASH_TEST_FASTQ_RICH" ]; then
      VIASH_TEST_FASTQ_RICH="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_FASTQ_RICH="$VIASH_TEST_FASTQ_RICH;""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_FASTQ_RICH="$VIASH_TEST_FASTQ_RICH"
  fi
  if [ ! -z "$VIASH_PAR_FASTQ_MINIMAL" ]; then
    unset VIASH_TEST_FASTQ_MINIMAL
    IFS=';'
    for var in $VIASH_PAR_FASTQ_MINIMAL; do
      unset IFS
      if [ -z "$VIASH_TEST_FASTQ_MINIMAL" ]; then
      VIASH_TEST_FASTQ_MINIMAL="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_FASTQ_MINIMAL="$VIASH_TEST_FASTQ_MINIMAL;""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_FASTQ_MINIMAL="$VIASH_TEST_FASTQ_MINIMAL"
  fi
  if [ ! -z "$VIASH_PAR_SUMMARY" ]; then
    unset VIASH_TEST_SUMMARY
    IFS=';'
    for var in $VIASH_PAR_SUMMARY; do
      unset IFS
      if [ -z "$VIASH_TEST_SUMMARY" ]; then
      VIASH_TEST_SUMMARY="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_SUMMARY="$VIASH_TEST_SUMMARY;""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_SUMMARY="$VIASH_TEST_SUMMARY"
  fi
  if [ ! -z "$VIASH_PAR_BAM" ]; then
    unset VIASH_TEST_BAM
    IFS=';'
    for var in $VIASH_PAR_BAM; do
      unset IFS
      if [ -z "$VIASH_TEST_BAM" ]; then
      VIASH_TEST_BAM="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_BAM="$VIASH_TEST_BAM;""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_BAM="$VIASH_TEST_BAM"
  fi
  if [ ! -z "$VIASH_PAR_UBAM" ]; then
    unset VIASH_TEST_UBAM
    IFS=';'
    for var in $VIASH_PAR_UBAM; do
      unset IFS
      if [ -z "$VIASH_TEST_UBAM" ]; then
      VIASH_TEST_UBAM="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_UBAM="$VIASH_TEST_UBAM;""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_UBAM="$VIASH_TEST_UBAM"
  fi
  if [ ! -z "$VIASH_PAR_CRAM" ]; then
    unset VIASH_TEST_CRAM
    IFS=';'
    for var in $VIASH_PAR_CRAM; do
      unset IFS
      if [ -z "$VIASH_TEST_CRAM" ]; then
      VIASH_TEST_CRAM="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_CRAM="$VIASH_TEST_CRAM;""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_CRAM="$VIASH_TEST_CRAM"
  fi
  if [ ! -z "$VIASH_PAR_PICKLE" ]; then
    unset VIASH_TEST_PICKLE
    IFS=';'
    for var in $VIASH_PAR_PICKLE; do
      unset IFS
      if [ -z "$VIASH_TEST_PICKLE" ]; then
      VIASH_TEST_PICKLE="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_PICKLE="$VIASH_TEST_PICKLE;""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_PICKLE="$VIASH_TEST_PICKLE"
  fi
  if [ ! -z "$VIASH_PAR_FEATHER" ]; then
    unset VIASH_TEST_FEATHER
    IFS=';'
    for var in $VIASH_PAR_FEATHER; do
      unset IFS
      if [ -z "$VIASH_TEST_FEATHER" ]; then
      VIASH_TEST_FEATHER="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_FEATHER="$VIASH_TEST_FEATHER;""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_FEATHER="$VIASH_TEST_FEATHER"
  fi
  if [ ! -z "$VIASH_PAR_OUTDIR" ]; then
    VIASH_PAR_OUTDIR=$(ViashDockerStripAutomount "$VIASH_PAR_OUTDIR")
  fi
  if [ ! -z "$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 "$VIASH_PAR_OUTDIR" ] && [ ! -e "$VIASH_PAR_OUTDIR" ]; then
  ViashError "Output file '$VIASH_PAR_OUTDIR' does not exist."
  exit 1
fi


exit 0
