#!/usr/bin/env bash

# create_eset v0.8.3
# 
# This wrapper script is auto-generated by viash 0.9.4 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:
#  * Dries Schaumont (maintainer)
#  * Marijke Van Moerbeke (author)

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="create_eset"
VIASH_META_FUNCTIONALITY_NAME="create_eset"
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"



# 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 rocker/r2u:24.04
ENTRYPOINT []
RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes")' && \
  Rscript -e 'options(warn = 2); if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")' && \
  Rscript -e 'options(warn = 2); if (!requireNamespace("Seurat", quietly = TRUE)) BiocManager::install("Seurat")' && \
  Rscript -e 'options(warn = 2); remotes::install_cran(c("data.table", "nlcv"), repos = "https://cran.rstudio.com")'

LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
LABEL org.opencontainers.image.description="Companion container for running component eset create_eset"
LABEL org.opencontainers.image.created="2025-07-29T10:38:57Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="a62d4e3c959cf3cf7b46806acbaafed2526cc5ac"
LABEL org.opencontainers.image.version="v0.8.3"

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)


# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
  echo "create_eset v0.8.3"
  echo ""
  echo "Arguments:"
  echo "    --pDataFile"
  echo "        type: file, required parameter, file must exist"
  echo ""
  echo "    --fDataFile"
  echo "        type: file, required parameter, file must exist"
  echo ""
  echo "    --mappingDir"
  echo "        type: file, required parameter, multiple values allowed, file must exist"
  echo ""
  echo "    --poolName"
  echo "        type: string, required parameter"
  echo ""
  echo "    --output"
  echo "        type: file, required parameter, output, file must exist"
  echo "        default: eset.\$id.rds"
  echo ""
  echo "Viash built in Computational Requirements:"
  echo "    ---cpus=INT"
  echo "        Number of CPUs to use"
  echo "    ---memory=STRING"
  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
  echo ""
  echo "Viash built in Docker:"
  echo "    ---setup=STRATEGY"
  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
  echo "        Default: ifneedbepullelsecachedbuild"
  echo "    ---dockerfile"
  echo "        Print the dockerfile to stdout."
  echo "    ---docker_run_args=ARG"
  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
  echo "    ---docker_image_id"
  echo "        Print the docker image id to stdout."
  echo "    ---debug"
  echo "        Enter the docker container for debugging purposes."
  echo ""
  echo "Viash built in Engines:"
  echo "    ---engine=ENGINE_ID"
  echo "        Specify the engine to use. Options are: docker, native."
  echo "        Default: docker"
}

# 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 "$1")"
            shift 1
            ;;
        --version)
            echo "create_eset v0.8.3"
            exit
            ;;
        --pDataFile)
            [ -n "$VIASH_PAR_PDATAFILE" ] && ViashError Bad arguments for option \'--pDataFile\': \'$VIASH_PAR_PDATAFILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PDATAFILE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --pDataFile. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --pDataFile=*)
            [ -n "$VIASH_PAR_PDATAFILE" ] && ViashError Bad arguments for option \'--pDataFile=*\': \'$VIASH_PAR_PDATAFILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PDATAFILE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --fDataFile)
            [ -n "$VIASH_PAR_FDATAFILE" ] && ViashError Bad arguments for option \'--fDataFile\': \'$VIASH_PAR_FDATAFILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FDATAFILE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --fDataFile. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --fDataFile=*)
            [ -n "$VIASH_PAR_FDATAFILE" ] && ViashError Bad arguments for option \'--fDataFile=*\': \'$VIASH_PAR_FDATAFILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FDATAFILE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --mappingDir)
            if [ -z "$VIASH_PAR_MAPPINGDIR" ]; then
              VIASH_PAR_MAPPINGDIR="$2"
            else
              VIASH_PAR_MAPPINGDIR="$VIASH_PAR_MAPPINGDIR;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --mappingDir. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --mappingDir=*)
            if [ -z "$VIASH_PAR_MAPPINGDIR" ]; then
              VIASH_PAR_MAPPINGDIR=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_MAPPINGDIR="$VIASH_PAR_MAPPINGDIR;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --poolName)
            [ -n "$VIASH_PAR_POOLNAME" ] && ViashError Bad arguments for option \'--poolName\': \'$VIASH_PAR_POOLNAME\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_POOLNAME="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --poolName. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --poolName=*)
            [ -n "$VIASH_PAR_POOLNAME" ] && ViashError Bad arguments for option \'--poolName=*\': \'$VIASH_PAR_POOLNAME\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_POOLNAME=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --output)
            [ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --output. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --output=*)
            [ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output=*\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        ---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/htrnaseq/eset/create_eset:v0.8.3'
  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_PDATAFILE+x} ]; then
  ViashError '--pDataFile' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_PAR_FDATAFILE+x} ]; then
  ViashError '--fDataFile' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_PAR_MAPPINGDIR+x} ]; then
  ViashError '--mappingDir' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_PAR_POOLNAME+x} ]; then
  ViashError '--poolName' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_PAR_OUTPUT+x} ]; then
  ViashError '--output' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_NAME+x} ]; then
  ViashError 'name' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then
  ViashError 'functionality_name' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_RESOURCES_DIR+x} ]; then
  ViashError 'resources_dir' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_EXECUTABLE+x} ]; then
  ViashError 'executable' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_CONFIG+x} ]; then
  ViashError 'config' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_TEMP_DIR+x} ]; then
  ViashError 'temp_dir' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi

# check whether required files exist
if [ ! -z "$VIASH_PAR_PDATAFILE" ] && [ ! -e "$VIASH_PAR_PDATAFILE" ]; then
  ViashError "Input file '$VIASH_PAR_PDATAFILE' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_FDATAFILE" ] && [ ! -e "$VIASH_PAR_FDATAFILE" ]; then
  ViashError "Input file '$VIASH_PAR_FDATAFILE' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_MAPPINGDIR" ]; then
  IFS=';'
  set -f
  for file in $VIASH_PAR_MAPPINGDIR; do
    unset IFS
    if [ ! -e "$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 "$VIASH_META_CPUS" ]]; then
  if ! [[ "$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 "$VIASH_PAR_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_OUTPUT")"
fi

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

if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  # detect volumes from file arguments
  VIASH_CHOWN_VARS=()
if [ ! -z "$VIASH_PAR_PDATAFILE" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_PDATAFILE")" )
  VIASH_PAR_PDATAFILE=$(ViashDockerAutodetectMount "$VIASH_PAR_PDATAFILE")
fi
if [ ! -z "$VIASH_PAR_FDATAFILE" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_FDATAFILE")" )
  VIASH_PAR_FDATAFILE=$(ViashDockerAutodetectMount "$VIASH_PAR_FDATAFILE")
fi
if [ ! -z "$VIASH_PAR_MAPPINGDIR" ]; then
  VIASH_TEST_MAPPINGDIR=()
  IFS=';'
  for var in $VIASH_PAR_MAPPINGDIR; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_MAPPINGDIR+=( "$var" )
  done
  VIASH_PAR_MAPPINGDIR=$(IFS=';' ; echo "${VIASH_TEST_MAPPINGDIR[*]}")
fi
if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT")" )
  VIASH_PAR_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT" )
fi
if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(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-create_eset-XXXXXX").R
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'
library(Biobase)
library(data.table)
library(nlcv)
library(Matrix)
library(Seurat)

### VIASH START
# The following code has been auto-generated by Viash.
# treat warnings as errors
.viash_orig_warn <- options(warn = 2)

par <- list(
  "pDataFile" = $( if [ ! -z ${VIASH_PAR_PDATAFILE+x} ]; then echo -n "'"; echo -n "$VIASH_PAR_PDATAFILE" | sed "s#['\\]#\\\\&#g"; echo "'"; else echo NULL; fi ),
  "fDataFile" = $( if [ ! -z ${VIASH_PAR_FDATAFILE+x} ]; then echo -n "'"; echo -n "$VIASH_PAR_FDATAFILE" | sed "s#['\\]#\\\\&#g"; echo "'"; else echo NULL; fi ),
  "mappingDir" = $( if [ ! -z ${VIASH_PAR_MAPPINGDIR+x} ]; then echo -n "strsplit('"; echo -n "$VIASH_PAR_MAPPINGDIR" | sed "s#['\\]#\\\\&#g"; echo "', split = ';')[[1]]"; else echo NULL; fi ),
  "poolName" = $( if [ ! -z ${VIASH_PAR_POOLNAME+x} ]; then echo -n "'"; echo -n "$VIASH_PAR_POOLNAME" | sed "s#['\\]#\\\\&#g"; echo "'"; else echo NULL; fi ),
  "output" = $( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo -n "'"; echo -n "$VIASH_PAR_OUTPUT" | sed "s#['\\]#\\\\&#g"; echo "'"; else echo NULL; fi )
)
meta <- list(
  "name" = $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo -n "'"; echo -n "$VIASH_META_NAME" | sed "s#['\\]#\\\\&#g"; echo "'"; else echo NULL; fi ),
  "functionality_name" = $( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo -n "'"; echo -n "$VIASH_META_FUNCTIONALITY_NAME" | sed "s#['\\]#\\\\&#g"; echo "'"; else echo NULL; fi ),
  "resources_dir" = $( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo -n "'"; echo -n "$VIASH_META_RESOURCES_DIR" | sed "s#['\\]#\\\\&#g"; echo "'"; else echo NULL; fi ),
  "executable" = $( if [ ! -z ${VIASH_META_EXECUTABLE+x} ]; then echo -n "'"; echo -n "$VIASH_META_EXECUTABLE" | sed "s#['\\]#\\\\&#g"; echo "'"; else echo NULL; fi ),
  "config" = $( if [ ! -z ${VIASH_META_CONFIG+x} ]; then echo -n "'"; echo -n "$VIASH_META_CONFIG" | sed "s#['\\]#\\\\&#g"; echo "'"; else echo NULL; fi ),
  "temp_dir" = $( if [ ! -z ${VIASH_META_TEMP_DIR+x} ]; then echo -n "'"; echo -n "$VIASH_META_TEMP_DIR" | sed "s#['\\]#\\\\&#g"; echo "'"; else echo NULL; fi ),
  "cpus" = $( if [ ! -z ${VIASH_META_CPUS+x} ]; then echo -n "as.integer('"; echo -n "$VIASH_META_CPUS" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi ),
  "memory_b" = $( if [ ! -z ${VIASH_META_MEMORY_B+x} ]; then echo -n "bit64::as.integer64('"; echo -n "$VIASH_META_MEMORY_B" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi ),
  "memory_kb" = $( if [ ! -z ${VIASH_META_MEMORY_KB+x} ]; then echo -n "bit64::as.integer64('"; echo -n "$VIASH_META_MEMORY_KB" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi ),
  "memory_mb" = $( if [ ! -z ${VIASH_META_MEMORY_MB+x} ]; then echo -n "bit64::as.integer64('"; echo -n "$VIASH_META_MEMORY_MB" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi ),
  "memory_gb" = $( if [ ! -z ${VIASH_META_MEMORY_GB+x} ]; then echo -n "bit64::as.integer64('"; echo -n "$VIASH_META_MEMORY_GB" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi ),
  "memory_tb" = $( if [ ! -z ${VIASH_META_MEMORY_TB+x} ]; then echo -n "bit64::as.integer64('"; echo -n "$VIASH_META_MEMORY_TB" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi ),
  "memory_pb" = $( if [ ! -z ${VIASH_META_MEMORY_PB+x} ]; then echo -n "bit64::as.integer64('"; echo -n "$VIASH_META_MEMORY_PB" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi ),
  "memory_kib" = $( if [ ! -z ${VIASH_META_MEMORY_KIB+x} ]; then echo -n "bit64::as.integer64('"; echo -n "$VIASH_META_MEMORY_KIB" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi ),
  "memory_mib" = $( if [ ! -z ${VIASH_META_MEMORY_MIB+x} ]; then echo -n "bit64::as.integer64('"; echo -n "$VIASH_META_MEMORY_MIB" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi ),
  "memory_gib" = $( if [ ! -z ${VIASH_META_MEMORY_GIB+x} ]; then echo -n "bit64::as.integer64('"; echo -n "$VIASH_META_MEMORY_GIB" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi ),
  "memory_tib" = $( if [ ! -z ${VIASH_META_MEMORY_TIB+x} ]; then echo -n "bit64::as.integer64('"; echo -n "$VIASH_META_MEMORY_TIB" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi ),
  "memory_pib" = $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo -n "bit64::as.integer64('"; echo -n "$VIASH_META_MEMORY_PIB" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi )
)
dep <- list(
  
)


# restore original warn setting
options(.viash_orig_warn)
rm(.viash_orig_warn)

### VIASH END


Read10X <- function(data_dir = NULL, gene_column = 2, unique_features = TRUE) {
  full.data <- list()
  for (i in seq_along(along.with = data_dir)) {
    run <- data_dir[i]
    if (!dir.exists(paths = run)) {
      stop("Directory provided does not exist")
    }
    barcode.loc <- file.path(run, "barcodes.tsv")
    gene.loc <- file.path(run, "features.tsv")
    features.loc <- file.path(run, "features.tsv.gz")
    matrix.loc <- file.path(run, "matrix.mtx")
    pre_ver_3 <- file.exists(gene.loc)
    if (!pre_ver_3) {
      addgz <- function(s) {
        return(paste0(s, ".gz"))
      }
      barcode.loc <- addgz(s = barcode.loc)
      matrix.loc <- addgz(s = matrix.loc)
    }
    if (!file.exists(barcode.loc)) {
      stop("Barcode file missing")
    }
    if (!pre_ver_3 && !file.exists(features.loc)) {
      stop("Gene name or features file missing")
    }
    if (!file.exists(matrix.loc)) {
      stop("Expression matrix file missing")
    }
    data <- readMM(file = matrix.loc)
    cell.names <- readLines(barcode.loc)
    if (all(grepl(pattern = "\\\\-1\$", x = cell.names))) {
      cell.names <- as.vector(x = as.character(x = sapply(X = cell.names, 
                                                          FUN = ExtractField, field = 1, delim = "-")))
    }
    if (is.null(x = names(x = data_dir))) {
      if (i < 2) {
        colnames(x = data) <- cell.names
      }
      else {
        colnames(x = data) <- paste0(i, "_", cell.names)
      }
    }
    else {
      colnames(x = data) <- paste0(names(x = data_dir)[i], 
                                   "_", cell.names)
    }
    feature.names <- read.delim(file = ifelse(test = pre_ver_3, 
                                              yes = gene.loc, no = features.loc), header = FALSE, 
                                stringsAsFactors = FALSE)
    if (any(is.na(x = feature.names[, gene_column]))) {
      warning("Some features names are NA. Replacing NA names with ID from the opposite column requested", 
              call. = FALSE, immediate. = TRUE)
      na.features <- which(x = is.na(x = feature.names[, 
                                                       gene_column]))
      replacement.column <- ifelse(test = gene_column == 
                                     2, yes = 1, no = 2)
      feature.names[na.features, gene_column] <- feature.names[na.features, 
                                                               replacement.column]
    }
    if (unique_features) {
      fcols = ncol(x = feature.names)
      if (fcols < gene_column) {
        stop(paste0("gene_column was set to ", gene_column,
                    " but feature.tsv.gz (or genes.tsv) only has ",
                    fcols, " columns.", " Try setting the gene_column ",
                    "argument to a value <= to ", 
                    fcols, "."))
      }
      rownames(x = data) <- make.unique(names = feature.names[, 
                                                              gene_column])
    }
    if (ncol(x = feature.names) > 2) {
      data_types <- factor(x = feature.names\$V3)
      lvls <- levels(x = data_types)
      if (length(x = lvls) > 1 && length(x = full.data) == 0) {
        message(paste0("10X data contains more than one type and is ",
                       "being returned as a list containing matrices ",
                       "of each type."))
      }
      expr_name <- "Gene Expression"
      if (expr_name %in% lvls) {
        lvls <- c(expr_name, lvls[-which(x = lvls == 
                                           expr_name)])
      }
      data <- lapply(X = lvls, FUN = function(l) {
        return(data[data_types == l, , drop = FALSE])
      })
      names(x = data) <- lvls
    } else {
      data <- list(data)
    }
    full.data[[length(x = full.data) + 1]] <- data
  }
  list_of_data <- list()
  for (j in 1:length(x = full.data[[1]])) {
    list_of_data[[j]] <- do.call(cbind, lapply(X = full.data, 
                                               FUN = \`[[\`, j))
    list_of_data[[j]] <- as(object = list_of_data[[j]], Class = "CsparseMatrix")
  }
  names(x = list_of_data) <- names(x = full.data[[1]])
  if (length(x = list_of_data) == 1) {
    return(list_of_data[[1]])
  } else {
    return(list_of_data)
  }
}

match_features <- function(exprs_matrix, fdata) {

  identical_features <- all(rownames(exprs_matrix) == rownames(fdata))

  if (nrow(exprs_matrix) != nrow(fdata) || !identical_features) {
    message(paste0("Features in 'fData' and expression matrix differ. ",
                   "Only matching features are returned."))
  }

  features <- intersect(rownames(exprs_matrix), rownames(fdata))
  exprs_matrix <- exprs_matrix[which(rownames(exprs_matrix) %in% features), ]
  fdata <- fdata[which(rownames(fdata) %in% features), ]

  fdata[, seq_len(ncol(fdata))] <- lapply(fdata[, seq_len(ncol(fdata)), drop = FALSE], as.character)
  # order features in exprs mat according to fdata
  exprs_matrix <- exprs_matrix[match(rownames(fdata), rownames(exprs_matrix)), ]

  list(exprs_matrix = exprs_matrix, fdata = fdata)

}


create_pdata <- function(sample_file, pool_name, barcodes) {
  cols_to_remove <- c("SampleFileName", "Output", "Measure", "Strandedness")
  pData <- sample_file[, !colnames(sample_file) %in% cols_to_remove,
                       drop = FALSE]
  rownames(pData) <- lapply(sample_file\$WellBC,
                            \\(x) paste(pool_name, x, sep = "_"))
  # pData[, ] <- lapply(pData, as.factor)
  pData\$PoolName <- pool_name
  pData <- pData[match(barcodes, pData\$WellBC), ]
  return(pData)
}

check_sample_file <- function(mapping_dir, sample_file){

  message("Checking sample annotation:")

  requireNamespace("tools")
  mapping_dir <- unlist(lapply(mapping_dir, function(x) {
    if (!dir.exists(x)) {
      stop(sprintf(paste0("Could not find directory ",
                          "provided in 'mappingDir' argument (%s)."), x))
    }
    tools::file_path_as_absolute(x)
  }))


  # additional check for STARsolo
  check_STARsolo_output <- function(x) {
    files <- c("barcodes.tsv", "features.tsv", "matrix.mtx")
    test <- list.files(x) %in% c(files, paste0(files, ".gz"))
    length(test) != 0 && all(test)
  }


  if (!"WellBC" %in% colnames(sample_file)) {
    stop(paste0("STARsolo output is used. The sample annotation must ",
                "contain 'WellBC' column providing cell barcodes."))
  }

  mapping_dir <- unique(mapping_dir)
  all_STARsolo_files_present <- all(
    unlist(
      lapply(mapping_dir, function(x) {
        check_STARsolo_output(x)
      })
    )
  )
  if (!all_STARsolo_files_present) {
    stop(paste0("Could not find files: 'barcodes', 'features' and 'matrix'",
                " for STARsolo output. Please check 'mappingDir' argument."))
  }

  message("- 'SampleFileName' column - OK")



  list(sample_expression_files = mapping_dir)
}

create_exprs_matrix <- function(exprs_matrix_path, exprs_file_paths,
                                output, measure, col_names, cell_barcodes) {

  read_matrix <- Read10X(data_dir = exprs_file_paths, gene_column = 1)
  # keep index of feature names containing "_" because Seurat
  #changes them to "-" and they no longer match with fdata[, "gene_id"]
  idx <- grep("_", rownames(read_matrix))

  requireNamespace("Seurat")
  seurat_object <- Seurat::CreateSeuratObject(counts = read_matrix)

  exprs_matrix <- as.matrix(seurat_object[['RNA']]\$counts)
  # replace "-" with "_" for features with "_" 
  # before converting to Seurat object
  rownames(exprs_matrix)[idx] <- gsub("-", "_", rownames(exprs_matrix)[idx])
  requireNamespace("stringr")
  exprs_matrix <- exprs_matrix[, stringr::str_detect(colnames(exprs_matrix),
                                  paste(cell_barcodes, collapse = "|"))]


  # check if rownames are ENSEMBL and remove version suffix
  isENSEMBL <- all(grepl("ENS", rownames(exprs_matrix)))
  if (isENSEMBL) {
    # do not use gsub("(.+)[.]\\\\d+", "\\\\1", rownames(exprs_matrix)),
    # so that ENS000000.1_PAR_Y can be kept
    rownames(exprs_matrix) <- gsub("\\\\.\\\\d+\$", "", rownames(exprs_matrix))
  }


  colnames(exprs_matrix) <- col_names

  exprs_matrix
}

create_eset <- function(feature_annotation_path,
                        sample_annotation_path,
                        mapping_dir,
                        barcodes,
                        output_path,
                        pool_name,
                        exprs_matrix_path = NULL,
                        path = NULL,
                        add_eset_annotation = NULL) {
  if (!file.exists(feature_annotation_path)) {
    stop("Could not find feature annotation at '", feature_annotation_path, "'")
  }

  if (!file.exists(sample_annotation_path)) {
    stop("Could not find sample annotation at '", sample_annotation_path, "'")
  }

  if(!is.null(exprs_matrix_path)) {
    if(!file.exists(exprs_matrix_path)) {
      stop("Could not find expression matrix at '", exprs_matrix_path, "'")
    }
  }

  if(!is.null(path)) {
    if(!dir.exists(path)) {
      stop("Provided 'path': '", path, "' does not exist.")
    }
  }

  ##### Import annotation files #####
  message("Importing feature annotation")
  fdata_file <- read.table(feature_annotation_path, header = TRUE,
                           sep = "\\t", quote = "\\"",
                           comment.char = "", stringsAsFactors = FALSE)

  # for backwards compatibility
  if("ENSEMBL" %in% colnames(fdata_file) && !all(grepl("ENS", fdata_file[, "ENSEMBL"])) & !"gene_id" %in% colnames(fdata_file)) {
    colnames(fdata_file)[which(colnames(fdata_file) == "ENSEMBL")] <- "gene_id"
  }

  # Check gene annotation
  if(!"gene_id" %in% colnames(fdata_file))
    stop("'gene_id' column with unique feature identifiers must be present in 'feature_annotation_path'.")

  # check if duplicated ids are present
  if(any(duplicated(fdata_file\$gene_id)))
    stop("Duplicated features ids are not allowed. Please check the 'gene_id' column in 'feature_annotation_path'.")

  message("Importing sample annotation")
  sample_file <- read.table(sample_annotation_path, header = TRUE,
                            sep = "\\t", quote = "\\"",
                            comment.char = "", stringsAsFactors = FALSE)
  # Check sample annotation
  check_sample_file_list <- check_sample_file(mapping_dir = mapping_dir,
                                              sample_file = sample_file)
  output <- "STARsolo"
  measure <- "counts"
  sample_expression_files <- check_sample_file_list\$sample_expression_files

  ##### Create phenodata #####
  pdata_eset <- create_pdata(sample_file = sample_file, pool_name = pool_name,
                             barcodes = barcodes)

  ##### Create expression matrix #####
  message("Creating expression matrix")

  exprs_matrix_eset <- create_exprs_matrix(
    exprs_matrix_path = exprs_matrix_path,
    exprs_file_paths = sample_expression_files,
    output = output,
    measure = measure,
    col_names = rownames(pdata_eset),
    cell_barcodes = barcodes
  )


  ##### Create featuredata #####
  message("Creating feature data")

  fdata_eset <- fdata_file
  rownames(fdata_eset) <- fdata_eset[, "gene_id"]

  # intersect features between exprs matrix and fdata
  feature_files <- match_features(exprs_matrix = exprs_matrix_eset,
                                  fdata = fdata_eset)

  fdata_eset <- feature_files\$fdata
  exprs_matrix_eset <- feature_files\$exprs_matrix

  ##### Create eSet #####
  message("Creating eset")

  if (nrow(pdata_eset) != ncol(exprs_matrix_eset)) {
    stop("nrow(pData) and ncol(exprsMatrix) differ")
  }

  if (nrow(fdata_eset) != nrow(exprs_matrix_eset)) {
    stop("nrow(fData) and nrow(exprsMatrix) differ")
  }

  if (!all(rownames(pdata_eset) == colnames(exprs_matrix_eset))) {
    stop("rownames(pData) and colnames(exprsMatrix) differ")
  }

  if (!all(rownames(fdata_eset) == rownames(exprs_matrix_eset))) {
    stop("rownames(fData) and rownames(exprsMatrix) differ")
  }

  if (!inherits(exprs_matrix_eset, "matrix")) {
    stop("exprsMatrix must be of class 'matrix'")
  }



  additional_info <- paste0("Additional information about eSet \\n",
                            "  Expression matrix created from ",
                            output, " output. \\n",
                            "  Expression matrix contains non-transformed ",
                            ifelse(output %in% c("STAR", "STARsolo"),
                                   "counts",
                                   ifelse(measure == "expected_count",
                                          "counts", measure)), ".")


  if (isTRUE(!is.null(add_eset_annotation) &
               is.character(add_eset_annotation))) {
    additional_info <- paste0(additional_info, "\\n", "  ", add_eset_annotation)
  }

  fdata_eset <- new("AnnotatedDataFrame", data = fdata_eset)
  pdata_eset <- new("AnnotatedDataFrame", data = pdata_eset)

  requireNamespace("Biobase")
  eset <- Biobase::ExpressionSet(assayData = exprs_matrix_eset,
                                  phenoData = pdata_eset,
                                  featureData = fdata_eset,
                                  annotation = additional_info)

  eset <- eset[, colSums(exprs(eset)) != 0]
  saveRDS(eset, file = output_path)

  message(paste0("eset created succesfully for ", ncol(eset),
                 " samples and ", nrow(eset),
                 " genes and saved at ", output_path, ".")) 

  eset
}


p_data_file <- par\$pDataFile
f_data_file <- par\$fDataFile
pool_name <- par\$poolName
mapping_dir <- lapply(par\$mappingDir,
                      \\(x) file.path(x, "Solo.out", "Gene", "raw"))

get_barcode_from_mapping_dir <- function(raw_dir) {
  barcodes_file <- file.path(raw_dir, "barcodes.tsv")
  if (!file.exists(barcodes_file)) {
    stop(paste0("Expected the 'Solo.out/Gene/raw' directory at ",
                raw_dir, " to contain a 'barcodes.tsv' file."))
  }
  barcodes <- readLines(barcodes_file)
  if (length(barcodes) != 1) {
    stop(paste0("A single STAR Solo folder should only have ",
                "mapped one (1) barcode, but found '",
                length(barcodes), "'for mapping directory ", raw_dir))
  }
  return(barcodes)
}

barcodes <- lapply(mapping_dir, get_barcode_from_mapping_dir)

print(paste0("mappingDir: ", mapping_dir))
print(paste0("pDataFile: ", p_data_file))
print(paste0("fDataFile: ", f_data_file))
print(paste0("poolName: ", pool_name))
print(paste0("barcodes: ", barcodes))



# CREATE ESET WITH RAW UMI COUNTS

eset <- create_eset(feature_annotation_path = f_data_file,
                    sample_annotation_path = p_data_file,
                    mapping_dir = mapping_dir,
                    barcodes = barcodes,
                    output_path = par\$output,
                    pool_name = pool_name,
                    path = NULL,
                    exprs_matrix_path = NULL)
VIASHMAIN
Rscript "\$tempscript" &
wait "\$!"

VIASHEOF


if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  # strip viash automount from file paths
  
  if [ ! -z "$VIASH_PAR_PDATAFILE" ]; then
    VIASH_PAR_PDATAFILE=$(ViashDockerStripAutomount "$VIASH_PAR_PDATAFILE")
  fi
  if [ ! -z "$VIASH_PAR_FDATAFILE" ]; then
    VIASH_PAR_FDATAFILE=$(ViashDockerStripAutomount "$VIASH_PAR_FDATAFILE")
  fi
  if [ ! -z "$VIASH_PAR_MAPPINGDIR" ]; then
    unset VIASH_TEST_MAPPINGDIR
    IFS=';'
    for var in $VIASH_PAR_MAPPINGDIR; do
      unset IFS
      if [ -z "$VIASH_TEST_MAPPINGDIR" ]; then
      VIASH_TEST_MAPPINGDIR="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_MAPPINGDIR="$VIASH_TEST_MAPPINGDIR;""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_MAPPINGDIR="$VIASH_TEST_MAPPINGDIR"
  fi
  if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
    VIASH_PAR_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT")
  fi
  if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
    VIASH_META_RESOURCES_DIR=$(ViashDockerStripAutomount "$VIASH_META_RESOURCES_DIR")
  fi
  if [ ! -z "$VIASH_META_EXECUTABLE" ]; then
    VIASH_META_EXECUTABLE=$(ViashDockerStripAutomount "$VIASH_META_EXECUTABLE")
  fi
  if [ ! -z "$VIASH_META_CONFIG" ]; then
    VIASH_META_CONFIG=$(ViashDockerStripAutomount "$VIASH_META_CONFIG")
  fi
  if [ ! -z "$VIASH_META_TEMP_DIR" ]; then
    VIASH_META_TEMP_DIR=$(ViashDockerStripAutomount "$VIASH_META_TEMP_DIR")
  fi
fi


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


exit 0
