#!/usr/bin/env bash

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

set -e

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

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

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

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

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

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

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

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

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

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

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

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

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

# define meta fields
VIASH_META_NAME="multiqc"
VIASH_META_FUNCTIONALITY_NAME="multiqc"
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 "multiqc add_sgdemux"
  echo ""
  echo "MultiQC aggregates results from bioinformatics analyses across many samples into"
  echo "a single report."
  echo "It searches a given directory for analysis logs and compiles a HTML report. It's"
  echo "a general use tool, perfect for summarising the output from numerous"
  echo "bioinformatics tools."
  echo ""
  echo "Input:"
  echo "    --input"
  echo "        type: file, required parameter, multiple values allowed, file must exist"
  echo "        example: data/results"
  echo "        File paths to be searched for analysis results to be included in the"
  echo "        report."
  echo ""
  echo "Ouput:"
  echo "    --output_report"
  echo "        type: file, output"
  echo "        example: multiqc_report.html"
  echo "        Filepath of the generated report."
  echo ""
  echo "    --output_data"
  echo "        type: file, output"
  echo "        example: multiqc_data"
  echo "        Output directory for parsed data files. If not provided, parsed data"
  echo "        will not be published."
  echo ""
  echo "    --output_plots"
  echo "        type: file, output"
  echo "        example: multiqc_plots"
  echo "        Output directory for generated plots. If not provided, plots will not be"
  echo "        published."
  echo ""
  echo "Modules and analyses to run:"
  echo "    --include_modules"
  echo "        type: string, multiple values allowed"
  echo "        example: fastqc;cutadapt"
  echo "        Use only these module"
  echo ""
  echo "    --exclude_modules"
  echo "        type: string, multiple values allowed"
  echo "        example: fastqc;cutadapt"
  echo "        Do not use only these modules"
  echo ""
  echo "    --ignore_analysis"
  echo "        type: string, multiple values allowed"
  echo "        example: run_one/*;run_two/*"
  echo ""
  echo "    --ignore_samples"
  echo "        type: string, multiple values allowed"
  echo "        example: sample_1*;sample_3*"
  echo ""
  echo "    --ignore_symlinks"
  echo "        type: boolean_true"
  echo "        Ignore symlinked directories and files"
  echo ""
  echo "Sample name handling:"
  echo "    --dirs"
  echo "        type: boolean_true"
  echo "        Prepend directory to sample names to avoid clashing filenames"
  echo ""
  echo "    --dirs_depth"
  echo "        type: integer"
  echo "        Prepend n directories to sample names. Negative number to take from"
  echo "        start of path."
  echo ""
  echo "    --full_names"
  echo "        type: boolean_true"
  echo "        Do not clean the sample names (leave as full file name)"
  echo ""
  echo "    --fn_as_s_name"
  echo "        type: boolean_true"
  echo "        Use the log filename as the sample name"
  echo ""
  echo "    --replace_names"
  echo "        type: file, file must exist"
  echo "        example: replace_names.tsv"
  echo "        TSV file to rename sample names during report generation"
  echo ""
  echo "Report Customisation:"
  echo "    --title"
  echo "        type: string"
  echo "        Report title. Printed as page header, used for filename if not otherwise"
  echo "        specified."
  echo ""
  echo "    --comment"
  echo "        type: string"
  echo "        Custom comment, will be printed at the top of the report."
  echo ""
  echo "    --template"
  echo "        type: string"
  echo "        choices: [ default, gathered, geo, highcharts, sections, simple ]"
  echo "        Report template to use."
  echo ""
  echo "    --sample_names"
  echo "        type: file, file must exist"
  echo "        example: sample_names.tsv"
  echo "        TSV file containing alternative sample names for renaming buttons in the"
  echo "        report."
  echo ""
  echo "    --sample_filters"
  echo "        type: file, file must exist"
  echo "        example: sample_filters.tsv"
  echo "        TSV file containing show/hide patterns for the report"
  echo ""
  echo "    --custom_css_file"
  echo "        type: file, file must exist"
  echo "        example: custom_style_sheet.css"
  echo "        Custom CSS file to add to the final report"
  echo ""
  echo "    --profile_runtime"
  echo "        type: boolean_true"
  echo "        Add analysis of how long MultiQC takes to run to the report"
  echo ""
  echo "MultiQC behaviour:"
  echo "    --verbose"
  echo "        type: boolean_true"
  echo "        Increase output verbosity."
  echo ""
  echo "    --quiet"
  echo "        type: boolean_true"
  echo "        Only show log warnings"
  echo ""
  echo "    --strict"
  echo "        type: boolean_true"
  echo "        Don't catch exceptions, run additional code checks to help development."
  echo ""
  echo "    --development"
  echo "        type: boolean_true"
  echo "        Development mode. Do not compress and minimise JS, export uncompressed"
  echo "        plot data."
  echo ""
  echo "    --require_logs"
  echo "        type: boolean_true"
  echo "        Require all explicitly requested modules to have log files. If not,"
  echo "        MultiQC will exit with an error."
  echo ""
  echo "    --no_megaqc_upload"
  echo "        type: boolean_true"
  echo "        Don't upload generated report to MegaQC, even if MegaQC options are"
  echo "        found."
  echo ""
  echo "    --no_ansi"
  echo "        type: boolean_true"
  echo "        Disable coloured log output."
  echo ""
  echo "    --cl_config"
  echo "        type: string"
  echo "        example: qualimap_config: { general_stats_coverage: [20,40,200] }"
  echo "        YAML formatted string that allows to customize MultiQC behaviour like"
  echo "        input file detection."
  echo ""
  echo "Output format:"
  echo "    --flat"
  echo "        type: boolean_true"
  echo "        Use only flat plots (static images)."
  echo ""
  echo "    --interactive"
  echo "        type: boolean_true"
  echo "        Use only interactive plots (in-browser Javascript)."
  echo ""
  echo "    --data_dir"
  echo "        type: boolean_true"
  echo "        Force the parsed data directory to be created."
  echo ""
  echo "    --no_data_dir"
  echo "        type: boolean_true"
  echo "        Prevent the parsed data directory from being created."
  echo ""
  echo "    --zip_data_dir"
  echo "        type: boolean_true"
  echo "        Compress the data directory."
  echo ""
  echo "    --data_format"
  echo "        type: string"
  echo "        choices: [ tsv, csv, json, yaml ]"
  echo "        Output parsed data in a different format than the default 'txt'."
  echo ""
  echo "    --pdf"
  echo "        type: boolean_true"
  echo "        Creates PDF report with the 'simple' template. Requires Pandoc to be"
  echo "        installed."
}

# 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/multiqc:1.21--pyhdfd78af_0
ENTRYPOINT []
RUN multiqc --version | sed 's/multiqc, version\s\(.*\)/multiqc: "\1"/' > /var/software_versions.txt

LABEL org.opencontainers.image.authors="Dorien Roosen"
LABEL org.opencontainers.image.description="Companion container for running component multiqc"
LABEL org.opencontainers.image.created="2024-11-14T12:50:40Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
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 "$1")"
            shift 1
            ;;
        --version)
            echo "multiqc add_sgdemux"
            exit
            ;;
        --input)
            if [ -z "$VIASH_PAR_INPUT" ]; then
              VIASH_PAR_INPUT="$2"
            else
              VIASH_PAR_INPUT="$VIASH_PAR_INPUT;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --input. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --input=*)
            if [ -z "$VIASH_PAR_INPUT" ]; then
              VIASH_PAR_INPUT=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_INPUT="$VIASH_PAR_INPUT;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --output_report)
            [ -n "$VIASH_PAR_OUTPUT_REPORT" ] && ViashError Bad arguments for option \'--output_report\': \'$VIASH_PAR_OUTPUT_REPORT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_REPORT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --output_report. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --output_report=*)
            [ -n "$VIASH_PAR_OUTPUT_REPORT" ] && ViashError Bad arguments for option \'--output_report=*\': \'$VIASH_PAR_OUTPUT_REPORT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_REPORT=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --output_data)
            [ -n "$VIASH_PAR_OUTPUT_DATA" ] && ViashError Bad arguments for option \'--output_data\': \'$VIASH_PAR_OUTPUT_DATA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_DATA="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --output_data. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --output_data=*)
            [ -n "$VIASH_PAR_OUTPUT_DATA" ] && ViashError Bad arguments for option \'--output_data=*\': \'$VIASH_PAR_OUTPUT_DATA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_DATA=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --output_plots)
            [ -n "$VIASH_PAR_OUTPUT_PLOTS" ] && ViashError Bad arguments for option \'--output_plots\': \'$VIASH_PAR_OUTPUT_PLOTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_PLOTS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --output_plots. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --output_plots=*)
            [ -n "$VIASH_PAR_OUTPUT_PLOTS" ] && ViashError Bad arguments for option \'--output_plots=*\': \'$VIASH_PAR_OUTPUT_PLOTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_PLOTS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --include_modules)
            if [ -z "$VIASH_PAR_INCLUDE_MODULES" ]; then
              VIASH_PAR_INCLUDE_MODULES="$2"
            else
              VIASH_PAR_INCLUDE_MODULES="$VIASH_PAR_INCLUDE_MODULES;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --include_modules. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --include_modules=*)
            if [ -z "$VIASH_PAR_INCLUDE_MODULES" ]; then
              VIASH_PAR_INCLUDE_MODULES=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_INCLUDE_MODULES="$VIASH_PAR_INCLUDE_MODULES;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --exclude_modules)
            if [ -z "$VIASH_PAR_EXCLUDE_MODULES" ]; then
              VIASH_PAR_EXCLUDE_MODULES="$2"
            else
              VIASH_PAR_EXCLUDE_MODULES="$VIASH_PAR_EXCLUDE_MODULES;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --exclude_modules. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --exclude_modules=*)
            if [ -z "$VIASH_PAR_EXCLUDE_MODULES" ]; then
              VIASH_PAR_EXCLUDE_MODULES=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_EXCLUDE_MODULES="$VIASH_PAR_EXCLUDE_MODULES;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --ignore_analysis)
            if [ -z "$VIASH_PAR_IGNORE_ANALYSIS" ]; then
              VIASH_PAR_IGNORE_ANALYSIS="$2"
            else
              VIASH_PAR_IGNORE_ANALYSIS="$VIASH_PAR_IGNORE_ANALYSIS;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --ignore_analysis. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --ignore_analysis=*)
            if [ -z "$VIASH_PAR_IGNORE_ANALYSIS" ]; then
              VIASH_PAR_IGNORE_ANALYSIS=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_IGNORE_ANALYSIS="$VIASH_PAR_IGNORE_ANALYSIS;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --ignore_samples)
            if [ -z "$VIASH_PAR_IGNORE_SAMPLES" ]; then
              VIASH_PAR_IGNORE_SAMPLES="$2"
            else
              VIASH_PAR_IGNORE_SAMPLES="$VIASH_PAR_IGNORE_SAMPLES;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --ignore_samples. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --ignore_samples=*)
            if [ -z "$VIASH_PAR_IGNORE_SAMPLES" ]; then
              VIASH_PAR_IGNORE_SAMPLES=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_IGNORE_SAMPLES="$VIASH_PAR_IGNORE_SAMPLES;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --ignore_symlinks)
            [ -n "$VIASH_PAR_IGNORE_SYMLINKS" ] && ViashError Bad arguments for option \'--ignore_symlinks\': \'$VIASH_PAR_IGNORE_SYMLINKS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_IGNORE_SYMLINKS=true
            shift 1
            ;;
        --dirs)
            [ -n "$VIASH_PAR_DIRS" ] && ViashError Bad arguments for option \'--dirs\': \'$VIASH_PAR_DIRS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_DIRS=true
            shift 1
            ;;
        --dirs_depth)
            [ -n "$VIASH_PAR_DIRS_DEPTH" ] && ViashError Bad arguments for option \'--dirs_depth\': \'$VIASH_PAR_DIRS_DEPTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_DIRS_DEPTH="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --dirs_depth. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --dirs_depth=*)
            [ -n "$VIASH_PAR_DIRS_DEPTH" ] && ViashError Bad arguments for option \'--dirs_depth=*\': \'$VIASH_PAR_DIRS_DEPTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_DIRS_DEPTH=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --full_names)
            [ -n "$VIASH_PAR_FULL_NAMES" ] && ViashError Bad arguments for option \'--full_names\': \'$VIASH_PAR_FULL_NAMES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FULL_NAMES=true
            shift 1
            ;;
        --fn_as_s_name)
            [ -n "$VIASH_PAR_FN_AS_S_NAME" ] && ViashError Bad arguments for option \'--fn_as_s_name\': \'$VIASH_PAR_FN_AS_S_NAME\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FN_AS_S_NAME=true
            shift 1
            ;;
        --replace_names)
            [ -n "$VIASH_PAR_REPLACE_NAMES" ] && ViashError Bad arguments for option \'--replace_names\': \'$VIASH_PAR_REPLACE_NAMES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_REPLACE_NAMES="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --replace_names. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --replace_names=*)
            [ -n "$VIASH_PAR_REPLACE_NAMES" ] && ViashError Bad arguments for option \'--replace_names=*\': \'$VIASH_PAR_REPLACE_NAMES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_REPLACE_NAMES=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --title)
            [ -n "$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 "$1")
            shift 1
            ;;
        --comment)
            [ -n "$VIASH_PAR_COMMENT" ] && ViashError Bad arguments for option \'--comment\': \'$VIASH_PAR_COMMENT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_COMMENT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --comment. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --comment=*)
            [ -n "$VIASH_PAR_COMMENT" ] && ViashError Bad arguments for option \'--comment=*\': \'$VIASH_PAR_COMMENT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_COMMENT=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --template)
            [ -n "$VIASH_PAR_TEMPLATE" ] && ViashError Bad arguments for option \'--template\': \'$VIASH_PAR_TEMPLATE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_TEMPLATE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --template. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --template=*)
            [ -n "$VIASH_PAR_TEMPLATE" ] && ViashError Bad arguments for option \'--template=*\': \'$VIASH_PAR_TEMPLATE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_TEMPLATE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --sample_names)
            [ -n "$VIASH_PAR_SAMPLE_NAMES" ] && ViashError Bad arguments for option \'--sample_names\': \'$VIASH_PAR_SAMPLE_NAMES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SAMPLE_NAMES="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --sample_names. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --sample_names=*)
            [ -n "$VIASH_PAR_SAMPLE_NAMES" ] && ViashError Bad arguments for option \'--sample_names=*\': \'$VIASH_PAR_SAMPLE_NAMES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SAMPLE_NAMES=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --sample_filters)
            [ -n "$VIASH_PAR_SAMPLE_FILTERS" ] && ViashError Bad arguments for option \'--sample_filters\': \'$VIASH_PAR_SAMPLE_FILTERS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SAMPLE_FILTERS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --sample_filters. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --sample_filters=*)
            [ -n "$VIASH_PAR_SAMPLE_FILTERS" ] && ViashError Bad arguments for option \'--sample_filters=*\': \'$VIASH_PAR_SAMPLE_FILTERS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SAMPLE_FILTERS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --custom_css_file)
            [ -n "$VIASH_PAR_CUSTOM_CSS_FILE" ] && ViashError Bad arguments for option \'--custom_css_file\': \'$VIASH_PAR_CUSTOM_CSS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CUSTOM_CSS_FILE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --custom_css_file. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --custom_css_file=*)
            [ -n "$VIASH_PAR_CUSTOM_CSS_FILE" ] && ViashError Bad arguments for option \'--custom_css_file=*\': \'$VIASH_PAR_CUSTOM_CSS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CUSTOM_CSS_FILE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --profile_runtime)
            [ -n "$VIASH_PAR_PROFILE_RUNTIME" ] && ViashError Bad arguments for option \'--profile_runtime\': \'$VIASH_PAR_PROFILE_RUNTIME\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PROFILE_RUNTIME=true
            shift 1
            ;;
        --verbose)
            [ -n "$VIASH_PAR_VERBOSE" ] && ViashError Bad arguments for option \'--verbose\': \'$VIASH_PAR_VERBOSE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_VERBOSE=true
            shift 1
            ;;
        --quiet)
            [ -n "$VIASH_PAR_QUIET" ] && ViashError Bad arguments for option \'--quiet\': \'$VIASH_PAR_QUIET\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_QUIET=true
            shift 1
            ;;
        --strict)
            [ -n "$VIASH_PAR_STRICT" ] && ViashError Bad arguments for option \'--strict\': \'$VIASH_PAR_STRICT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_STRICT=true
            shift 1
            ;;
        --development)
            [ -n "$VIASH_PAR_DEVELOPMENT" ] && ViashError Bad arguments for option \'--development\': \'$VIASH_PAR_DEVELOPMENT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_DEVELOPMENT=true
            shift 1
            ;;
        --require_logs)
            [ -n "$VIASH_PAR_REQUIRE_LOGS" ] && ViashError Bad arguments for option \'--require_logs\': \'$VIASH_PAR_REQUIRE_LOGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_REQUIRE_LOGS=true
            shift 1
            ;;
        --no_megaqc_upload)
            [ -n "$VIASH_PAR_NO_MEGAQC_UPLOAD" ] && ViashError Bad arguments for option \'--no_megaqc_upload\': \'$VIASH_PAR_NO_MEGAQC_UPLOAD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_NO_MEGAQC_UPLOAD=true
            shift 1
            ;;
        --no_ansi)
            [ -n "$VIASH_PAR_NO_ANSI" ] && ViashError Bad arguments for option \'--no_ansi\': \'$VIASH_PAR_NO_ANSI\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_NO_ANSI=true
            shift 1
            ;;
        --cl_config)
            [ -n "$VIASH_PAR_CL_CONFIG" ] && ViashError Bad arguments for option \'--cl_config\': \'$VIASH_PAR_CL_CONFIG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CL_CONFIG="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --cl_config. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --cl_config=*)
            [ -n "$VIASH_PAR_CL_CONFIG" ] && ViashError Bad arguments for option \'--cl_config=*\': \'$VIASH_PAR_CL_CONFIG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CL_CONFIG=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --flat)
            [ -n "$VIASH_PAR_FLAT" ] && ViashError Bad arguments for option \'--flat\': \'$VIASH_PAR_FLAT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FLAT=true
            shift 1
            ;;
        --interactive)
            [ -n "$VIASH_PAR_INTERACTIVE" ] && ViashError Bad arguments for option \'--interactive\': \'$VIASH_PAR_INTERACTIVE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INTERACTIVE=true
            shift 1
            ;;
        --data_dir)
            [ -n "$VIASH_PAR_DATA_DIR" ] && ViashError Bad arguments for option \'--data_dir\': \'$VIASH_PAR_DATA_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_DATA_DIR=true
            shift 1
            ;;
        --no_data_dir)
            [ -n "$VIASH_PAR_NO_DATA_DIR" ] && ViashError Bad arguments for option \'--no_data_dir\': \'$VIASH_PAR_NO_DATA_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_NO_DATA_DIR=true
            shift 1
            ;;
        --zip_data_dir)
            [ -n "$VIASH_PAR_ZIP_DATA_DIR" ] && ViashError Bad arguments for option \'--zip_data_dir\': \'$VIASH_PAR_ZIP_DATA_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ZIP_DATA_DIR=true
            shift 1
            ;;
        --data_format)
            [ -n "$VIASH_PAR_DATA_FORMAT" ] && ViashError Bad arguments for option \'--data_format\': \'$VIASH_PAR_DATA_FORMAT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_DATA_FORMAT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --data_format. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --data_format=*)
            [ -n "$VIASH_PAR_DATA_FORMAT" ] && ViashError Bad arguments for option \'--data_format=*\': \'$VIASH_PAR_DATA_FORMAT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_DATA_FORMAT=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --pdf)
            [ -n "$VIASH_PAR_PDF" ] && ViashError Bad arguments for option \'--pdf\': \'$VIASH_PAR_PDF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PDF=true
            shift 1
            ;;
        ---engine)
            VIASH_ENGINE_ID="$2"
            shift 2
            ;;
        ---engine=*)
            VIASH_ENGINE_ID="$(ViashRemoveFlags "$1")"
            shift 1
            ;;
        ---setup)
            VIASH_MODE='setup'
            VIASH_SETUP_STRATEGY="$2"
            shift 2
            ;;
        ---setup=*)
            VIASH_MODE='setup'
            VIASH_SETUP_STRATEGY="$(ViashRemoveFlags "$1")"
            shift 1
            ;;
        ---dockerfile)
            VIASH_MODE='dockerfile'
            shift 1
            ;;
        ---docker_run_args)
            VIASH_DOCKER_RUN_ARGS+=("$2")
            shift 2
            ;;
        ---docker_run_args=*)
            VIASH_DOCKER_RUN_ARGS+=("$(ViashRemoveFlags "$1")")
            shift 1
            ;;
        ---docker_image_id)
            VIASH_MODE='docker_image_id'
            shift 1
            ;;
        ---debug)
            VIASH_MODE='debug'
            shift 1
            ;;
        ---cpus)
            [ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_CPUS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to ---cpus. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        ---cpus=*)
            [ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus=*\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_CPUS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        ---memory)
            [ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_MEMORY="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to ---memory. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        ---memory=*)
            [ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory=*\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_MEMORY=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        *)  # positional arg or unknown option
            # since the positional args will be eval'd, can we always quote, instead of using ViashQuote
            VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'"
            [[ $1 == -* ]] && ViashWarning $1 looks like a parameter but is not a defined parameter and will instead be treated as a positional argument. Use "--help" to get more information on the parameters.
            shift # past argument
            ;;
    esac
done

# parse positional parameters
eval set -- $VIASH_POSITIONAL_ARGS


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

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

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

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

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

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

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

# setting computational defaults

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


# check whether required parameters exist
if [ -z ${VIASH_PAR_INPUT+x} ]; then
  ViashError '--input' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_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_IGNORE_SYMLINKS+x} ]; then
  VIASH_PAR_IGNORE_SYMLINKS="false"
fi
if [ -z ${VIASH_PAR_DIRS+x} ]; then
  VIASH_PAR_DIRS="false"
fi
if [ -z ${VIASH_PAR_FULL_NAMES+x} ]; then
  VIASH_PAR_FULL_NAMES="false"
fi
if [ -z ${VIASH_PAR_FN_AS_S_NAME+x} ]; then
  VIASH_PAR_FN_AS_S_NAME="false"
fi
if [ -z ${VIASH_PAR_PROFILE_RUNTIME+x} ]; then
  VIASH_PAR_PROFILE_RUNTIME="false"
fi
if [ -z ${VIASH_PAR_VERBOSE+x} ]; then
  VIASH_PAR_VERBOSE="false"
fi
if [ -z ${VIASH_PAR_QUIET+x} ]; then
  VIASH_PAR_QUIET="false"
fi
if [ -z ${VIASH_PAR_STRICT+x} ]; then
  VIASH_PAR_STRICT="false"
fi
if [ -z ${VIASH_PAR_DEVELOPMENT+x} ]; then
  VIASH_PAR_DEVELOPMENT="false"
fi
if [ -z ${VIASH_PAR_REQUIRE_LOGS+x} ]; then
  VIASH_PAR_REQUIRE_LOGS="false"
fi
if [ -z ${VIASH_PAR_NO_MEGAQC_UPLOAD+x} ]; then
  VIASH_PAR_NO_MEGAQC_UPLOAD="false"
fi
if [ -z ${VIASH_PAR_NO_ANSI+x} ]; then
  VIASH_PAR_NO_ANSI="false"
fi
if [ -z ${VIASH_PAR_FLAT+x} ]; then
  VIASH_PAR_FLAT="false"
fi
if [ -z ${VIASH_PAR_INTERACTIVE+x} ]; then
  VIASH_PAR_INTERACTIVE="false"
fi
if [ -z ${VIASH_PAR_DATA_DIR+x} ]; then
  VIASH_PAR_DATA_DIR="false"
fi
if [ -z ${VIASH_PAR_NO_DATA_DIR+x} ]; then
  VIASH_PAR_NO_DATA_DIR="false"
fi
if [ -z ${VIASH_PAR_ZIP_DATA_DIR+x} ]; then
  VIASH_PAR_ZIP_DATA_DIR="false"
fi
if [ -z ${VIASH_PAR_PDF+x} ]; then
  VIASH_PAR_PDF="false"
fi

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

# check whether parameters values are of the right type
if [[ -n "$VIASH_PAR_IGNORE_SYMLINKS" ]]; then
  if ! [[ "$VIASH_PAR_IGNORE_SYMLINKS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--ignore_symlinks' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_DIRS" ]]; then
  if ! [[ "$VIASH_PAR_DIRS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--dirs' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_DIRS_DEPTH" ]]; then
  if ! [[ "$VIASH_PAR_DIRS_DEPTH" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--dirs_depth' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_FULL_NAMES" ]]; then
  if ! [[ "$VIASH_PAR_FULL_NAMES" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--full_names' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_FN_AS_S_NAME" ]]; then
  if ! [[ "$VIASH_PAR_FN_AS_S_NAME" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--fn_as_s_name' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_PROFILE_RUNTIME" ]]; then
  if ! [[ "$VIASH_PAR_PROFILE_RUNTIME" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--profile_runtime' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_VERBOSE" ]]; then
  if ! [[ "$VIASH_PAR_VERBOSE" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--verbose' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_QUIET" ]]; then
  if ! [[ "$VIASH_PAR_QUIET" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--quiet' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_STRICT" ]]; then
  if ! [[ "$VIASH_PAR_STRICT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--strict' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_DEVELOPMENT" ]]; then
  if ! [[ "$VIASH_PAR_DEVELOPMENT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--development' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_REQUIRE_LOGS" ]]; then
  if ! [[ "$VIASH_PAR_REQUIRE_LOGS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--require_logs' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_NO_MEGAQC_UPLOAD" ]]; then
  if ! [[ "$VIASH_PAR_NO_MEGAQC_UPLOAD" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--no_megaqc_upload' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_NO_ANSI" ]]; then
  if ! [[ "$VIASH_PAR_NO_ANSI" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--no_ansi' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_FLAT" ]]; then
  if ! [[ "$VIASH_PAR_FLAT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--flat' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_INTERACTIVE" ]]; then
  if ! [[ "$VIASH_PAR_INTERACTIVE" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--interactive' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_DATA_DIR" ]]; then
  if ! [[ "$VIASH_PAR_DATA_DIR" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--data_dir' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_NO_DATA_DIR" ]]; then
  if ! [[ "$VIASH_PAR_NO_DATA_DIR" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--no_data_dir' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_ZIP_DATA_DIR" ]]; then
  if ! [[ "$VIASH_PAR_ZIP_DATA_DIR" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--zip_data_dir' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_PDF" ]]; then
  if ! [[ "$VIASH_PAR_PDF" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--pdf' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_CPUS" ]]; then
  if ! [[ "$VIASH_META_CPUS" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'cpus' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_B" ]]; then
  if ! [[ "$VIASH_META_MEMORY_B" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_b' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_KB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_KB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_kb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_MB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_MB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_mb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_GB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_GB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_gb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_TB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_TB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_tb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_PB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_PB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_pb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_KIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_KIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_kib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_MIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_MIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_mib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_GIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_GIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_gib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_TIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_TIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_tib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_PIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_PIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_pib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi

# check whether value is belongs to a set of choices
if [ ! -z "$VIASH_PAR_TEMPLATE" ]; then
  VIASH_PAR_TEMPLATE_CHOICES=("default;gathered;geo;highcharts;sections;simple")
  IFS=';'
  set -f
  if ! [[ ";${VIASH_PAR_TEMPLATE_CHOICES[*]};" =~ ";$VIASH_PAR_TEMPLATE;" ]]; then
    ViashError '--template' specified value of \'$VIASH_PAR_TEMPLATE\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
    exit 1
  fi
  set +f
  unset IFS
fi

if [ ! -z "$VIASH_PAR_DATA_FORMAT" ]; then
  VIASH_PAR_DATA_FORMAT_CHOICES=("tsv;csv;json;yaml")
  IFS=';'
  set -f
  if ! [[ ";${VIASH_PAR_DATA_FORMAT_CHOICES[*]};" =~ ";$VIASH_PAR_DATA_FORMAT;" ]]; then
    ViashError '--data_format' specified value of \'$VIASH_PAR_DATA_FORMAT\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
    exit 1
  fi
  set +f
  unset IFS
fi

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

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

if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  # detect volumes from file arguments
  VIASH_CHOWN_VARS=()
if [ ! -z "$VIASH_PAR_INPUT" ]; then
  VIASH_TEST_INPUT=()
  IFS=';'
  for var in $VIASH_PAR_INPUT; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_INPUT+=( "$var" )
  done
  VIASH_PAR_INPUT=$(IFS=';' ; echo "${VIASH_TEST_INPUT[*]}")
fi
if [ ! -z "$VIASH_PAR_OUTPUT_REPORT" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT_REPORT")" )
  VIASH_PAR_OUTPUT_REPORT=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT_REPORT")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT_REPORT" )
fi
if [ ! -z "$VIASH_PAR_OUTPUT_DATA" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT_DATA")" )
  VIASH_PAR_OUTPUT_DATA=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT_DATA")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT_DATA" )
fi
if [ ! -z "$VIASH_PAR_OUTPUT_PLOTS" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT_PLOTS")" )
  VIASH_PAR_OUTPUT_PLOTS=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT_PLOTS")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT_PLOTS" )
fi
if [ ! -z "$VIASH_PAR_REPLACE_NAMES" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_REPLACE_NAMES")" )
  VIASH_PAR_REPLACE_NAMES=$(ViashDockerAutodetectMount "$VIASH_PAR_REPLACE_NAMES")
fi
if [ ! -z "$VIASH_PAR_SAMPLE_NAMES" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_SAMPLE_NAMES")" )
  VIASH_PAR_SAMPLE_NAMES=$(ViashDockerAutodetectMount "$VIASH_PAR_SAMPLE_NAMES")
fi
if [ ! -z "$VIASH_PAR_SAMPLE_FILTERS" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_SAMPLE_FILTERS")" )
  VIASH_PAR_SAMPLE_FILTERS=$(ViashDockerAutodetectMount "$VIASH_PAR_SAMPLE_FILTERS")
fi
if [ ! -z "$VIASH_PAR_CUSTOM_CSS_FILE" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_CUSTOM_CSS_FILE")" )
  VIASH_PAR_CUSTOM_CSS_FILE=$(ViashDockerAutodetectMount "$VIASH_PAR_CUSTOM_CSS_FILE")
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-multiqc-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'
## VIASH START
# The following code has been auto-generated by Viash.
$( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_input='&'#" ; else echo "# par_input="; fi )
$( if [ ! -z ${VIASH_PAR_OUTPUT_REPORT+x} ]; then echo "${VIASH_PAR_OUTPUT_REPORT}" | sed "s#'#'\"'\"'#g;s#.*#par_output_report='&'#" ; else echo "# par_output_report="; fi )
$( if [ ! -z ${VIASH_PAR_OUTPUT_DATA+x} ]; then echo "${VIASH_PAR_OUTPUT_DATA}" | sed "s#'#'\"'\"'#g;s#.*#par_output_data='&'#" ; else echo "# par_output_data="; fi )
$( if [ ! -z ${VIASH_PAR_OUTPUT_PLOTS+x} ]; then echo "${VIASH_PAR_OUTPUT_PLOTS}" | sed "s#'#'\"'\"'#g;s#.*#par_output_plots='&'#" ; else echo "# par_output_plots="; fi )
$( if [ ! -z ${VIASH_PAR_INCLUDE_MODULES+x} ]; then echo "${VIASH_PAR_INCLUDE_MODULES}" | sed "s#'#'\"'\"'#g;s#.*#par_include_modules='&'#" ; else echo "# par_include_modules="; fi )
$( if [ ! -z ${VIASH_PAR_EXCLUDE_MODULES+x} ]; then echo "${VIASH_PAR_EXCLUDE_MODULES}" | sed "s#'#'\"'\"'#g;s#.*#par_exclude_modules='&'#" ; else echo "# par_exclude_modules="; fi )
$( if [ ! -z ${VIASH_PAR_IGNORE_ANALYSIS+x} ]; then echo "${VIASH_PAR_IGNORE_ANALYSIS}" | sed "s#'#'\"'\"'#g;s#.*#par_ignore_analysis='&'#" ; else echo "# par_ignore_analysis="; fi )
$( if [ ! -z ${VIASH_PAR_IGNORE_SAMPLES+x} ]; then echo "${VIASH_PAR_IGNORE_SAMPLES}" | sed "s#'#'\"'\"'#g;s#.*#par_ignore_samples='&'#" ; else echo "# par_ignore_samples="; fi )
$( if [ ! -z ${VIASH_PAR_IGNORE_SYMLINKS+x} ]; then echo "${VIASH_PAR_IGNORE_SYMLINKS}" | sed "s#'#'\"'\"'#g;s#.*#par_ignore_symlinks='&'#" ; else echo "# par_ignore_symlinks="; fi )
$( if [ ! -z ${VIASH_PAR_DIRS+x} ]; then echo "${VIASH_PAR_DIRS}" | sed "s#'#'\"'\"'#g;s#.*#par_dirs='&'#" ; else echo "# par_dirs="; fi )
$( if [ ! -z ${VIASH_PAR_DIRS_DEPTH+x} ]; then echo "${VIASH_PAR_DIRS_DEPTH}" | sed "s#'#'\"'\"'#g;s#.*#par_dirs_depth='&'#" ; else echo "# par_dirs_depth="; fi )
$( if [ ! -z ${VIASH_PAR_FULL_NAMES+x} ]; then echo "${VIASH_PAR_FULL_NAMES}" | sed "s#'#'\"'\"'#g;s#.*#par_full_names='&'#" ; else echo "# par_full_names="; fi )
$( if [ ! -z ${VIASH_PAR_FN_AS_S_NAME+x} ]; then echo "${VIASH_PAR_FN_AS_S_NAME}" | sed "s#'#'\"'\"'#g;s#.*#par_fn_as_s_name='&'#" ; else echo "# par_fn_as_s_name="; fi )
$( if [ ! -z ${VIASH_PAR_REPLACE_NAMES+x} ]; then echo "${VIASH_PAR_REPLACE_NAMES}" | sed "s#'#'\"'\"'#g;s#.*#par_replace_names='&'#" ; else echo "# par_replace_names="; 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 ${VIASH_PAR_COMMENT+x} ]; then echo "${VIASH_PAR_COMMENT}" | sed "s#'#'\"'\"'#g;s#.*#par_comment='&'#" ; else echo "# par_comment="; fi )
$( if [ ! -z ${VIASH_PAR_TEMPLATE+x} ]; then echo "${VIASH_PAR_TEMPLATE}" | sed "s#'#'\"'\"'#g;s#.*#par_template='&'#" ; else echo "# par_template="; fi )
$( if [ ! -z ${VIASH_PAR_SAMPLE_NAMES+x} ]; then echo "${VIASH_PAR_SAMPLE_NAMES}" | sed "s#'#'\"'\"'#g;s#.*#par_sample_names='&'#" ; else echo "# par_sample_names="; fi )
$( if [ ! -z ${VIASH_PAR_SAMPLE_FILTERS+x} ]; then echo "${VIASH_PAR_SAMPLE_FILTERS}" | sed "s#'#'\"'\"'#g;s#.*#par_sample_filters='&'#" ; else echo "# par_sample_filters="; fi )
$( if [ ! -z ${VIASH_PAR_CUSTOM_CSS_FILE+x} ]; then echo "${VIASH_PAR_CUSTOM_CSS_FILE}" | sed "s#'#'\"'\"'#g;s#.*#par_custom_css_file='&'#" ; else echo "# par_custom_css_file="; fi )
$( if [ ! -z ${VIASH_PAR_PROFILE_RUNTIME+x} ]; then echo "${VIASH_PAR_PROFILE_RUNTIME}" | sed "s#'#'\"'\"'#g;s#.*#par_profile_runtime='&'#" ; else echo "# par_profile_runtime="; 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 ${VIASH_PAR_QUIET+x} ]; then echo "${VIASH_PAR_QUIET}" | sed "s#'#'\"'\"'#g;s#.*#par_quiet='&'#" ; else echo "# par_quiet="; fi )
$( if [ ! -z ${VIASH_PAR_STRICT+x} ]; then echo "${VIASH_PAR_STRICT}" | sed "s#'#'\"'\"'#g;s#.*#par_strict='&'#" ; else echo "# par_strict="; fi )
$( if [ ! -z ${VIASH_PAR_DEVELOPMENT+x} ]; then echo "${VIASH_PAR_DEVELOPMENT}" | sed "s#'#'\"'\"'#g;s#.*#par_development='&'#" ; else echo "# par_development="; fi )
$( if [ ! -z ${VIASH_PAR_REQUIRE_LOGS+x} ]; then echo "${VIASH_PAR_REQUIRE_LOGS}" | sed "s#'#'\"'\"'#g;s#.*#par_require_logs='&'#" ; else echo "# par_require_logs="; fi )
$( if [ ! -z ${VIASH_PAR_NO_MEGAQC_UPLOAD+x} ]; then echo "${VIASH_PAR_NO_MEGAQC_UPLOAD}" | sed "s#'#'\"'\"'#g;s#.*#par_no_megaqc_upload='&'#" ; else echo "# par_no_megaqc_upload="; fi )
$( if [ ! -z ${VIASH_PAR_NO_ANSI+x} ]; then echo "${VIASH_PAR_NO_ANSI}" | sed "s#'#'\"'\"'#g;s#.*#par_no_ansi='&'#" ; else echo "# par_no_ansi="; fi )
$( if [ ! -z ${VIASH_PAR_CL_CONFIG+x} ]; then echo "${VIASH_PAR_CL_CONFIG}" | sed "s#'#'\"'\"'#g;s#.*#par_cl_config='&'#" ; else echo "# par_cl_config="; fi )
$( if [ ! -z ${VIASH_PAR_FLAT+x} ]; then echo "${VIASH_PAR_FLAT}" | sed "s#'#'\"'\"'#g;s#.*#par_flat='&'#" ; else echo "# par_flat="; fi )
$( if [ ! -z ${VIASH_PAR_INTERACTIVE+x} ]; then echo "${VIASH_PAR_INTERACTIVE}" | sed "s#'#'\"'\"'#g;s#.*#par_interactive='&'#" ; else echo "# par_interactive="; fi )
$( if [ ! -z ${VIASH_PAR_DATA_DIR+x} ]; then echo "${VIASH_PAR_DATA_DIR}" | sed "s#'#'\"'\"'#g;s#.*#par_data_dir='&'#" ; else echo "# par_data_dir="; fi )
$( if [ ! -z ${VIASH_PAR_NO_DATA_DIR+x} ]; then echo "${VIASH_PAR_NO_DATA_DIR}" | sed "s#'#'\"'\"'#g;s#.*#par_no_data_dir='&'#" ; else echo "# par_no_data_dir="; fi )
$( if [ ! -z ${VIASH_PAR_ZIP_DATA_DIR+x} ]; then echo "${VIASH_PAR_ZIP_DATA_DIR}" | sed "s#'#'\"'\"'#g;s#.*#par_zip_data_dir='&'#" ; else echo "# par_zip_data_dir="; fi )
$( if [ ! -z ${VIASH_PAR_DATA_FORMAT+x} ]; then echo "${VIASH_PAR_DATA_FORMAT}" | sed "s#'#'\"'\"'#g;s#.*#par_data_format='&'#" ; else echo "# par_data_format="; fi )
$( if [ ! -z ${VIASH_PAR_PDF+x} ]; then echo "${VIASH_PAR_PDF}" | sed "s#'#'\"'\"'#g;s#.*#par_pdf='&'#" ; else echo "# par_pdf="; 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
#!/bin/bash

# disable flags
unset_if_false=(
    par_ignore_symlinks
    par_dirs
    par_full_names
    par_fn_as_s_name
    par_profile_runtime
    par_verbose
    par_quiet
    par_strict
    par_development
    par_require_logs
    par_no_megaqc_upload
    par_no_ansi
    par_flat
    par_interactive
    par_static_plot_export
    par_data_dir
    par_no_data_dir
    par_zip_data_dir
    par_pdf
)

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

# handle inputs
out_dir=\$(dirname "\$par_output_report")
output_report_file=\$(basename "\$par_output_report")
report_name="\${output_report_file%.*}"

# handle outputs
[[ -z "\$par_output_report" ]] && no_report=true
[[ -z "\$par_output_data" ]] && no_data_dir=true
[[ ! -z "\$par_output_data" ]] && data_dir=true
[[ ! -z "\$par_output_plots" ]] && export=true

# handle multiples
IFS=";" read -ra inputs <<< \$par_input

if [[ -n "\$par_include_modules" ]]; then
    include_modules=""
    IFS=";" read -ra incl_modules <<< \$par_include_modules
    for i in "\${incl_modules[@]}"; do
        include_modules+="--include \$i "
    done
    unset IFS
fi

if [[ -n "\$par_exclude_modules" ]]; then
    exclude_modules=""
    IFS=";" read -ra excl_modules <<< \$par_exclude_modules
    for i in "\${excl_modules[@]}"; do
        exclude_modules+="--exclude \$i"
    done
    unset IFS
fi

if [[ -n "\$par_ignore_analysis" ]]; then
    ignore=""
    IFS=";" read -ra ignore_analysis <<< \$par_ignore_analysis
    for i in "\${ignore_analysis[@]}"; do
        ignore+="--ignore \$i "
    done
    unset IFS
fi

if [[ -n "\$par_ignore_samples" ]]; then
    ignore_samples=""
    IFS=";" read -ra ign_samples <<< \$par_ignore_samples
    for i in "\${ign_samples[@]}"; do
        ignore_samples+="--ignore-samples \$i"
    done
    unset IFS
fi

# run multiqc
multiqc \\
    \${par_output_report:+--filename "\$report_name"} \\
    \${out_dir:+--outdir "\$out_dir"} \\
    \${no_report:+--no-report} \\
    \${no_data_dir:+--no-data-dir} \\
    \${data_dir:+--data-dir} \\
    \${export:+--export} \\
    \${par_title:+--title "\$par_title"} \\
    \${par_comment:+--comment "\$par_comment"} \\
    \${par_template:+--template "\$par_template"} \\
    \${par_sample_names:+--sample-names "\$par_sample_names"} \\
    \${par_sample_filters:+--sample-filters "\$par_sample_filters"} \\
    \${par_custom_css_file:+--custom-css-file "\$par_custom_css_file"} \\
    \${par_profile_runtime:+--profile-runtime} \\
    \${par_dirs:+--dirs} \\
    \${par_dirs_depth:+--dirs-depth "\$par_dirs_depth"} \\
    \${par_full_names:+--full-names} \\
    \${par_fn_as_s_name:+--fn-as-s-name} \\
    \${par_ignore_names:+--ignore-names "\$par_ignore_names"} \\
    \${par_ignore_symlinks:+--ignore-symlinks} \\
    \${ignore_samples} \\
    \${ignore} \\
    \${exclude_modules} \\
    \${include_modules} \\
    \${par_include_modules:+--include-modules "\$par_include_modules"} \\
    \${par_data_format:+--data-format "\$par_data_format"} \\
    \${par_cl_config:+--cl-config "\$par_cl_config"} \\
    \${par_zip_data_dir:+--zip-data-dir} \\
    \${par_pdf:+--pdf} \\
    \${par_interactive:+--interactive} \\
    \${par_flat:+--flat} \\
    \${par_verbose:+--verbose} \\
    \${par_quiet:+--quiet} \\
    \${par_strict:+--strict} \\
    \${par_no_megaqc_upload:+--no-megaqc-upload} \\
    \${par_no_ansi:+--no-ansi} \\
    \${par_profile_runtime:+--profile-runtime} \\
    \${par_require_logs:+--require-logs} \\
    \${par_development:+--development} \\
    --force \\
    "\${inputs[@]}" 

# Move outputs

if [[ -n "\$par_output_data" ]] && [[ -d "\${out_dir}/\${report_name}_data" ]]; then
    mv "\${out_dir}/\${report_name}_data" "\$par_output_data"
elif [[ -n "\$par_output_data" ]] && [[ ! -d "\${out_dir}/\${report_name}_data" ]]; then
    echo "WARNING: Data could not be saved because data folder was not generated by multiqc. This could be due to filtering out of modules or samples."
fi

if [[ -n "\$par_output_plots" ]] && [[ -d "\${out_dir}/\${report_name}_plots" ]]; then
    mv "\${out_dir}/\${report_name}_plots" "\$par_output_plots"
elif [[ -n "\$par_output_plots" ]] && [[ ! -d "\${out_dir}/\${report_name}_plots" ]]; then
    echo "WARNING: Plots could not be saved because plots folder was not generated by multiqc. This could be due to filtering out of modules or samples."
fi
VIASHMAIN
bash "\$tempscript" &
wait "\$!"

VIASHEOF


if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  # strip viash automount from file paths
  
  if [ ! -z "$VIASH_PAR_INPUT" ]; then
    unset VIASH_TEST_INPUT
    IFS=';'
    for var in $VIASH_PAR_INPUT; do
      unset IFS
      if [ -z "$VIASH_TEST_INPUT" ]; then
      VIASH_TEST_INPUT="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_INPUT="$VIASH_TEST_INPUT;""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_INPUT="$VIASH_TEST_INPUT"
  fi
  if [ ! -z "$VIASH_PAR_OUTPUT_REPORT" ]; then
    VIASH_PAR_OUTPUT_REPORT=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT_REPORT")
  fi
  if [ ! -z "$VIASH_PAR_OUTPUT_DATA" ]; then
    VIASH_PAR_OUTPUT_DATA=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT_DATA")
  fi
  if [ ! -z "$VIASH_PAR_OUTPUT_PLOTS" ]; then
    VIASH_PAR_OUTPUT_PLOTS=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT_PLOTS")
  fi
  if [ ! -z "$VIASH_PAR_REPLACE_NAMES" ]; then
    VIASH_PAR_REPLACE_NAMES=$(ViashDockerStripAutomount "$VIASH_PAR_REPLACE_NAMES")
  fi
  if [ ! -z "$VIASH_PAR_SAMPLE_NAMES" ]; then
    VIASH_PAR_SAMPLE_NAMES=$(ViashDockerStripAutomount "$VIASH_PAR_SAMPLE_NAMES")
  fi
  if [ ! -z "$VIASH_PAR_SAMPLE_FILTERS" ]; then
    VIASH_PAR_SAMPLE_FILTERS=$(ViashDockerStripAutomount "$VIASH_PAR_SAMPLE_FILTERS")
  fi
  if [ ! -z "$VIASH_PAR_CUSTOM_CSS_FILE" ]; then
    VIASH_PAR_CUSTOM_CSS_FILE=$(ViashDockerStripAutomount "$VIASH_PAR_CUSTOM_CSS_FILE")
  fi
  if [ ! -z "$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


exit 0
