#!/usr/bin/env bash

# spaceranger_count v0.3.0
# 
# 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:
#  * Jakub Majercik (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="spaceranger_count"
VIASH_META_FUNCTIONALITY_NAME="spaceranger_count"
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 ghcr.io/data-intuitive/spaceranger:3.1
ENTRYPOINT []
RUN DEBIAN_FRONTEND=noninteractive apt update && \
apt upgrade -y && apt install -y procps && rm -rf /var/lib/apt/lists/*

LABEL org.opencontainers.image.authors="Jakub Majercik"
LABEL org.opencontainers.image.description="Companion container for running component mapping spaceranger_count"
LABEL org.opencontainers.image.created="2026-02-18T10:46:05Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="84e2b7cc63aa97671f5df15385e35180aad6d7df"
LABEL org.opencontainers.image.version="v0.3.0"

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 "spaceranger_count v0.3.0"
  echo ""
  echo "Count gene expression and protein expression reads from a single capture area."
  echo ""
  echo "Inputs:"
  echo "    --gex_reference"
  echo "        type: file, required parameter, file must exist"
  echo "        example: /path/to/refdata-gex-GRCh38-2020-A"
  echo "        Path of folder containing 10x-compatible reference"
  echo ""
  echo "    --input"
  echo "        type: file, required parameter, multiple values allowed, file must exist"
  echo "        example: sample_S1_L001_R1_001.fastq.gz;sample_S1_L001_R2_001.fastq.gz"
  echo "        The fastq.gz files to align. Can also be a single directory containing"
  echo "        fastq.gz files."
  echo "        Individual FASTQ files should follow the naming convention of 10x"
  echo "        Genomics:"
  echo "        [Sample Name]_S[Sample Number]_L[Lane Number]_[Read Type]_001.fastq.gz"
  echo "        Where:"
  echo "        [Sample Name] is the name assigned during sample preparation/sequencing"
  echo "        S[Sample Number] is the sample index (usually S1, S2, etc.)"
  echo "        L[Lane Number] identifies the sequencing lane (L001, L002, etc.)"
  echo "        [Read Type] will be one of:"
  echo "        R1 - Read 1 (contains the spatial barcode and UMI)"
  echo "        R2 - Read 2 (contains the actual cDNA sequence)"
  echo ""
  echo "    --probe_set"
  echo "        type: file, required parameter, file must exist"
  echo "        example: Visium_Human_Transcriptome_Probe_Set_v2.0_GRCh38-2020-A.csv"
  echo "        CSV file specifying the probe set used"
  echo ""
  echo "    --cytaimage"
  echo "        type: file, file must exist"
  echo "        example: cyta_image.tif"
  echo "        Brightfield image generated by the CytAssist instrument."
  echo "        When using CytAssist workflow, either this or --image must be provided."
  echo ""
  echo "    --image"
  echo "        type: file, file must exist"
  echo "        example: brightfield.tif"
  echo "        H&E or fluorescence microscope image in TIFF or JPG format."
  echo "        Required for standard Visium workflow, optional when using --cytaimage"
  echo "        for CytAssist workflow."
  echo ""
  echo "Outputs:"
  echo "    --output"
  echo "        type: file, required parameter, output, file must exist"
  echo "        example: /path/to/output"
  echo "        The folder to store the alignment results"
  echo ""
  echo "Slide Information:"
  echo "    --slide"
  echo "        type: string"
  echo "        example: V10J25-015"
  echo "        Visium slide serial number (e.g., 'V10J25-015')"
  echo ""
  echo "    --area"
  echo "        type: string"
  echo "        example: A1"
  echo "        Visium capture area identifier (e.g., 'A1')"
  echo ""
  echo "    --unknown_slide"
  echo "        type: string"
  echo "        choices: [ visium-1, visium-2, visium-2-large, visium-hd ]"
  echo "        Use this option if the slide serial number and area were entered"
  echo "        incorrectly on the CytAssist"
  echo "        instrument and the correct values are unknown. Not compatible with"
  echo "        --slide, --area, or"
  echo "        --slide-file options"
  echo ""
  echo "    --slidefile"
  echo "        type: file, file must exist"
  echo "        example: slide_design.gpr"
  echo "        Slide design file for offline use"
  echo ""
  echo "    --override_id"
  echo "        type: boolean_true"
  echo "        Overrides the slide serial number and capture area provided in the"
  echo "        Cytassist image metadata"
  echo ""
  echo "Image Options:"
  echo "    --darkimage"
  echo "        type: file, file must exist"
  echo "        example: fluorescence.tif"
  echo "        Multi-channel, dark-background fluorescence image"
  echo ""
  echo "    --colorizedimage"
  echo "        type: file, file must exist"
  echo "        example: colored_fluorescence.tif"
  echo "        Color image representing pre-colored dark-background fluorescence images"
  echo ""
  echo "    --dapi_index"
  echo "        type: integer"
  echo "        example: 1"
  echo "        min: 1"
  echo "        Index of DAPI channel (1-indexed) of fluorescence image"
  echo ""
  echo "    --image_scale"
  echo "        type: double"
  echo "        example: 0.65"
  echo "        min: 0.01"
  echo "        max: 10.0"
  echo "        Microns per microscope image pixel"
  echo ""
  echo "    --reorient_images"
  echo "        type: boolean"
  echo "        default: true"
  echo "        Whether to rotate and mirror image to align fiducial pattern"
  echo ""
  echo "Processing Options:"
  echo "    --create_bam"
  echo "        type: boolean, required parameter"
  echo "        default: true"
  echo "        Enable or disable BAM file generation"
  echo ""
  echo "    --nosecondary"
  echo "        type: boolean_true"
  echo "        Disable secondary analysis (e.g., clustering)"
  echo ""
  echo "    --r1_length"
  echo "        type: integer"
  echo "        min: 1"
  echo "        Hard trim the input Read 1 to this length before analysis"
  echo ""
  echo "    --r2_length"
  echo "        type: integer"
  echo "        min: 1"
  echo "        Hard trim the input Read 2 to this length before analysis"
  echo ""
  echo "    --filter_probes"
  echo "        type: boolean"
  echo "        default: true"
  echo "        Whether to filter the probe set using the \"included\" column"
  echo ""
  echo "    --custom_bin_size"
  echo "        type: integer"
  echo "        min: 4"
  echo "        max: 100"
  echo "        Bin Visium HD data to specified size in microns (4-100, even values"
  echo "        only) in addition to the standard binning size (2 µm, 8 µm, 16 µm)"
  echo ""
  echo "Input Selection:"
  echo "    --project"
  echo "        type: string"
  echo "        Project folder name within mkfastq output"
  echo ""
  echo "    --sample"
  echo "        type: string"
  echo "        Prefix of FASTQ filenames to select"
  echo ""
  echo "    --lanes"
  echo "        type: integer, multiple values allowed"
  echo "        example: 1;2;3"
  echo "        Only use FASTQs from selected lanes"
  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 "$1")"
            shift 1
            ;;
        --version)
            echo "spaceranger_count v0.3.0"
            exit
            ;;
        --gex_reference)
            [ -n "$VIASH_PAR_GEX_REFERENCE" ] && ViashError Bad arguments for option \'--gex_reference\': \'$VIASH_PAR_GEX_REFERENCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_GEX_REFERENCE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --gex_reference. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --gex_reference=*)
            [ -n "$VIASH_PAR_GEX_REFERENCE" ] && ViashError Bad arguments for option \'--gex_reference=*\': \'$VIASH_PAR_GEX_REFERENCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_GEX_REFERENCE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --input)
            if [ -z "$VIASH_PAR_INPUT" ]; then
              VIASH_PAR_INPUT="$2"
            else
              VIASH_PAR_INPUT="$VIASH_PAR_INPUT;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --input. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --input=*)
            if [ -z "$VIASH_PAR_INPUT" ]; then
              VIASH_PAR_INPUT=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_INPUT="$VIASH_PAR_INPUT;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --probe_set)
            [ -n "$VIASH_PAR_PROBE_SET" ] && ViashError Bad arguments for option \'--probe_set\': \'$VIASH_PAR_PROBE_SET\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PROBE_SET="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --probe_set. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --probe_set=*)
            [ -n "$VIASH_PAR_PROBE_SET" ] && ViashError Bad arguments for option \'--probe_set=*\': \'$VIASH_PAR_PROBE_SET\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PROBE_SET=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --cytaimage)
            [ -n "$VIASH_PAR_CYTAIMAGE" ] && ViashError Bad arguments for option \'--cytaimage\': \'$VIASH_PAR_CYTAIMAGE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CYTAIMAGE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --cytaimage. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --cytaimage=*)
            [ -n "$VIASH_PAR_CYTAIMAGE" ] && ViashError Bad arguments for option \'--cytaimage=*\': \'$VIASH_PAR_CYTAIMAGE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CYTAIMAGE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --image)
            [ -n "$VIASH_PAR_IMAGE" ] && ViashError Bad arguments for option \'--image\': \'$VIASH_PAR_IMAGE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_IMAGE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --image. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --image=*)
            [ -n "$VIASH_PAR_IMAGE" ] && ViashError Bad arguments for option \'--image=*\': \'$VIASH_PAR_IMAGE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_IMAGE=$(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 "$1")
            shift 1
            ;;
        --slide)
            [ -n "$VIASH_PAR_SLIDE" ] && ViashError Bad arguments for option \'--slide\': \'$VIASH_PAR_SLIDE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SLIDE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --slide. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --slide=*)
            [ -n "$VIASH_PAR_SLIDE" ] && ViashError Bad arguments for option \'--slide=*\': \'$VIASH_PAR_SLIDE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SLIDE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --area)
            [ -n "$VIASH_PAR_AREA" ] && ViashError Bad arguments for option \'--area\': \'$VIASH_PAR_AREA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_AREA="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --area. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --area=*)
            [ -n "$VIASH_PAR_AREA" ] && ViashError Bad arguments for option \'--area=*\': \'$VIASH_PAR_AREA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_AREA=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --unknown_slide)
            [ -n "$VIASH_PAR_UNKNOWN_SLIDE" ] && ViashError Bad arguments for option \'--unknown_slide\': \'$VIASH_PAR_UNKNOWN_SLIDE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_UNKNOWN_SLIDE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --unknown_slide. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --unknown_slide=*)
            [ -n "$VIASH_PAR_UNKNOWN_SLIDE" ] && ViashError Bad arguments for option \'--unknown_slide=*\': \'$VIASH_PAR_UNKNOWN_SLIDE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_UNKNOWN_SLIDE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --slidefile)
            [ -n "$VIASH_PAR_SLIDEFILE" ] && ViashError Bad arguments for option \'--slidefile\': \'$VIASH_PAR_SLIDEFILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SLIDEFILE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --slidefile. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --slidefile=*)
            [ -n "$VIASH_PAR_SLIDEFILE" ] && ViashError Bad arguments for option \'--slidefile=*\': \'$VIASH_PAR_SLIDEFILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SLIDEFILE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --override_id)
            [ -n "$VIASH_PAR_OVERRIDE_ID" ] && ViashError Bad arguments for option \'--override_id\': \'$VIASH_PAR_OVERRIDE_ID\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OVERRIDE_ID=true
            shift 1
            ;;
        --darkimage)
            [ -n "$VIASH_PAR_DARKIMAGE" ] && ViashError Bad arguments for option \'--darkimage\': \'$VIASH_PAR_DARKIMAGE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_DARKIMAGE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --darkimage. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --darkimage=*)
            [ -n "$VIASH_PAR_DARKIMAGE" ] && ViashError Bad arguments for option \'--darkimage=*\': \'$VIASH_PAR_DARKIMAGE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_DARKIMAGE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --colorizedimage)
            [ -n "$VIASH_PAR_COLORIZEDIMAGE" ] && ViashError Bad arguments for option \'--colorizedimage\': \'$VIASH_PAR_COLORIZEDIMAGE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_COLORIZEDIMAGE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --colorizedimage. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --colorizedimage=*)
            [ -n "$VIASH_PAR_COLORIZEDIMAGE" ] && ViashError Bad arguments for option \'--colorizedimage=*\': \'$VIASH_PAR_COLORIZEDIMAGE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_COLORIZEDIMAGE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --dapi_index)
            [ -n "$VIASH_PAR_DAPI_INDEX" ] && ViashError Bad arguments for option \'--dapi_index\': \'$VIASH_PAR_DAPI_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_DAPI_INDEX="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --dapi_index. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --dapi_index=*)
            [ -n "$VIASH_PAR_DAPI_INDEX" ] && ViashError Bad arguments for option \'--dapi_index=*\': \'$VIASH_PAR_DAPI_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_DAPI_INDEX=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --image_scale)
            [ -n "$VIASH_PAR_IMAGE_SCALE" ] && ViashError Bad arguments for option \'--image_scale\': \'$VIASH_PAR_IMAGE_SCALE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_IMAGE_SCALE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --image_scale. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --image_scale=*)
            [ -n "$VIASH_PAR_IMAGE_SCALE" ] && ViashError Bad arguments for option \'--image_scale=*\': \'$VIASH_PAR_IMAGE_SCALE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_IMAGE_SCALE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --reorient_images)
            [ -n "$VIASH_PAR_REORIENT_IMAGES" ] && ViashError Bad arguments for option \'--reorient_images\': \'$VIASH_PAR_REORIENT_IMAGES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_REORIENT_IMAGES="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --reorient_images. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --reorient_images=*)
            [ -n "$VIASH_PAR_REORIENT_IMAGES" ] && ViashError Bad arguments for option \'--reorient_images=*\': \'$VIASH_PAR_REORIENT_IMAGES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_REORIENT_IMAGES=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --create_bam)
            [ -n "$VIASH_PAR_CREATE_BAM" ] && ViashError Bad arguments for option \'--create_bam\': \'$VIASH_PAR_CREATE_BAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CREATE_BAM="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --create_bam. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --create_bam=*)
            [ -n "$VIASH_PAR_CREATE_BAM" ] && ViashError Bad arguments for option \'--create_bam=*\': \'$VIASH_PAR_CREATE_BAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CREATE_BAM=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --nosecondary)
            [ -n "$VIASH_PAR_NOSECONDARY" ] && ViashError Bad arguments for option \'--nosecondary\': \'$VIASH_PAR_NOSECONDARY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_NOSECONDARY=true
            shift 1
            ;;
        --r1_length)
            [ -n "$VIASH_PAR_R1_LENGTH" ] && ViashError Bad arguments for option \'--r1_length\': \'$VIASH_PAR_R1_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_R1_LENGTH="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --r1_length. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --r1_length=*)
            [ -n "$VIASH_PAR_R1_LENGTH" ] && ViashError Bad arguments for option \'--r1_length=*\': \'$VIASH_PAR_R1_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_R1_LENGTH=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --r2_length)
            [ -n "$VIASH_PAR_R2_LENGTH" ] && ViashError Bad arguments for option \'--r2_length\': \'$VIASH_PAR_R2_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_R2_LENGTH="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --r2_length. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --r2_length=*)
            [ -n "$VIASH_PAR_R2_LENGTH" ] && ViashError Bad arguments for option \'--r2_length=*\': \'$VIASH_PAR_R2_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_R2_LENGTH=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --filter_probes)
            [ -n "$VIASH_PAR_FILTER_PROBES" ] && ViashError Bad arguments for option \'--filter_probes\': \'$VIASH_PAR_FILTER_PROBES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FILTER_PROBES="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --filter_probes. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --filter_probes=*)
            [ -n "$VIASH_PAR_FILTER_PROBES" ] && ViashError Bad arguments for option \'--filter_probes=*\': \'$VIASH_PAR_FILTER_PROBES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FILTER_PROBES=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --custom_bin_size)
            [ -n "$VIASH_PAR_CUSTOM_BIN_SIZE" ] && ViashError Bad arguments for option \'--custom_bin_size\': \'$VIASH_PAR_CUSTOM_BIN_SIZE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CUSTOM_BIN_SIZE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --custom_bin_size. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --custom_bin_size=*)
            [ -n "$VIASH_PAR_CUSTOM_BIN_SIZE" ] && ViashError Bad arguments for option \'--custom_bin_size=*\': \'$VIASH_PAR_CUSTOM_BIN_SIZE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CUSTOM_BIN_SIZE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --project)
            [ -n "$VIASH_PAR_PROJECT" ] && ViashError Bad arguments for option \'--project\': \'$VIASH_PAR_PROJECT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PROJECT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --project. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --project=*)
            [ -n "$VIASH_PAR_PROJECT" ] && ViashError Bad arguments for option \'--project=*\': \'$VIASH_PAR_PROJECT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PROJECT=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --sample)
            [ -n "$VIASH_PAR_SAMPLE" ] && ViashError Bad arguments for option \'--sample\': \'$VIASH_PAR_SAMPLE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SAMPLE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --sample. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --sample=*)
            [ -n "$VIASH_PAR_SAMPLE" ] && ViashError Bad arguments for option \'--sample=*\': \'$VIASH_PAR_SAMPLE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SAMPLE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --lanes)
            if [ -z "$VIASH_PAR_LANES" ]; then
              VIASH_PAR_LANES="$2"
            else
              VIASH_PAR_LANES="$VIASH_PAR_LANES;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --lanes. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --lanes=*)
            if [ -z "$VIASH_PAR_LANES" ]; then
              VIASH_PAR_LANES=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_LANES="$VIASH_PAR_LANES;"$(ViashRemoveFlags "$1")
            fi
            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/openpipeline_spatial/mapping/spaceranger_count:v0.3.0'
  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" 'bash'
    exit 0
  fi

  # check if docker image exists
  ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild
  ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" '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_GEX_REFERENCE+x} ]; then
  ViashError '--gex_reference' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_PAR_INPUT+x} ]; then
  ViashError '--input' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_PAR_PROBE_SET+x} ]; then
  ViashError '--probe_set' 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_PAR_CREATE_BAM+x} ]; then
  ViashError '--create_bam' 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_OVERRIDE_ID+x} ]; then
  VIASH_PAR_OVERRIDE_ID="false"
fi
if [ -z ${VIASH_PAR_REORIENT_IMAGES+x} ]; then
  VIASH_PAR_REORIENT_IMAGES="true"
fi
if [ -z ${VIASH_PAR_NOSECONDARY+x} ]; then
  VIASH_PAR_NOSECONDARY="false"
fi
if [ -z ${VIASH_PAR_FILTER_PROBES+x} ]; then
  VIASH_PAR_FILTER_PROBES="true"
fi

# check whether required files exist
if [ ! -z "$VIASH_PAR_GEX_REFERENCE" ] && [ ! -e "$VIASH_PAR_GEX_REFERENCE" ]; then
  ViashError "Input file '$VIASH_PAR_GEX_REFERENCE' does not exist."
  exit 1
fi
if [ ! -z "$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_PROBE_SET" ] && [ ! -e "$VIASH_PAR_PROBE_SET" ]; then
  ViashError "Input file '$VIASH_PAR_PROBE_SET' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_CYTAIMAGE" ] && [ ! -e "$VIASH_PAR_CYTAIMAGE" ]; then
  ViashError "Input file '$VIASH_PAR_CYTAIMAGE' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_IMAGE" ] && [ ! -e "$VIASH_PAR_IMAGE" ]; then
  ViashError "Input file '$VIASH_PAR_IMAGE' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_SLIDEFILE" ] && [ ! -e "$VIASH_PAR_SLIDEFILE" ]; then
  ViashError "Input file '$VIASH_PAR_SLIDEFILE' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_DARKIMAGE" ] && [ ! -e "$VIASH_PAR_DARKIMAGE" ]; then
  ViashError "Input file '$VIASH_PAR_DARKIMAGE' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_COLORIZEDIMAGE" ] && [ ! -e "$VIASH_PAR_COLORIZEDIMAGE" ]; then
  ViashError "Input file '$VIASH_PAR_COLORIZEDIMAGE' does not exist."
  exit 1
fi

# check whether parameters values are of the right type
if [[ -n "$VIASH_PAR_OVERRIDE_ID" ]]; then
  if ! [[ "$VIASH_PAR_OVERRIDE_ID" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--override_id' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_DAPI_INDEX" ]]; then
  if ! [[ "$VIASH_PAR_DAPI_INDEX" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--dapi_index' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
  if [[ $VIASH_PAR_DAPI_INDEX -lt 1 ]]; then
    ViashError '--dapi_index' has be more than or equal to 1. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_IMAGE_SCALE" ]]; then
  if ! [[ "$VIASH_PAR_IMAGE_SCALE" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--image_scale' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
  if command -v bc &> /dev/null; then
    if ! [[ `echo $VIASH_PAR_IMAGE_SCALE '>=' 0.01 | bc` -eq 1 ]]; then
      ViashError '--image_scale' has be more than or equal to 0.01. Use "--help" to get more information on the parameters.
      exit 1
    fi
  elif command -v awk &> /dev/null; then
    if ! [[ `awk -v n1=$VIASH_PAR_IMAGE_SCALE -v n2=0.01 'BEGIN { print (n1 >= n2) ? "1" : "0" }'` -eq 1 ]]; then
      ViashError '--image_scale' has be more than or equal to 0.01. Use "--help" to get more information on the parameters.
      exit 1
    fi
  else
    ViashWarning '--image_scale' specifies a minimum value but the value was not verified as neither \'bc\' or \`awk\` are present on the system.
  fi
  if command -v bc &> /dev/null; then
    if ! [[ `echo $VIASH_PAR_IMAGE_SCALE '<=' 10.0 | bc` -eq 1 ]]; then
      ViashError '--image_scale' has to be less than or equal to 10.0. Use "--help" to get more information on the parameters.
      exit 1
    fi
  elif command -v awk &> /dev/null; then
    if ! [[ `awk -v n1=$VIASH_PAR_IMAGE_SCALE -v n2=10.0 'BEGIN { print (n1 <= n2) ? "1" : "0" }'` -eq 1 ]]; then
      ViashError '--image_scale' has be less than or equal to 10.0. Use "--help" to get more information on the parameters.
      exit 1
    fi
  else
    ViashWarning '--image_scale' specifies a maximum value but the value was not verified as neither \'bc\' or \'awk\' are present on the system.
  fi
fi
if [[ -n "$VIASH_PAR_REORIENT_IMAGES" ]]; then
  if ! [[ "$VIASH_PAR_REORIENT_IMAGES" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--reorient_images' has to be a boolean. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_CREATE_BAM" ]]; then
  if ! [[ "$VIASH_PAR_CREATE_BAM" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--create_bam' has to be a boolean. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_NOSECONDARY" ]]; then
  if ! [[ "$VIASH_PAR_NOSECONDARY" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--nosecondary' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_R1_LENGTH" ]]; then
  if ! [[ "$VIASH_PAR_R1_LENGTH" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--r1_length' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
  if [[ $VIASH_PAR_R1_LENGTH -lt 1 ]]; then
    ViashError '--r1_length' has be more than or equal to 1. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_R2_LENGTH" ]]; then
  if ! [[ "$VIASH_PAR_R2_LENGTH" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--r2_length' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
  if [[ $VIASH_PAR_R2_LENGTH -lt 1 ]]; then
    ViashError '--r2_length' has be more than or equal to 1. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_FILTER_PROBES" ]]; then
  if ! [[ "$VIASH_PAR_FILTER_PROBES" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--filter_probes' has to be a boolean. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_CUSTOM_BIN_SIZE" ]]; then
  if ! [[ "$VIASH_PAR_CUSTOM_BIN_SIZE" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--custom_bin_size' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
  if [[ $VIASH_PAR_CUSTOM_BIN_SIZE -lt 4 ]]; then
    ViashError '--custom_bin_size' has be more than or equal to 4. Use "--help" to get more information on the parameters.
    exit 1
  fi
  if [[ $VIASH_PAR_CUSTOM_BIN_SIZE -gt 100 ]]; then
    ViashError '--custom_bin_size' has be less than or equal to 100. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [ -n "$VIASH_PAR_LANES" ]; then
  IFS=';'
  set -f
  for val in $VIASH_PAR_LANES; do
    if ! [[ "${val}" =~ ^[-+]?[0-9]+$ ]]; then
      ViashError '--lanes' has to be an integer. Use "--help" to get more information on the parameters.
      exit 1
    fi
  done
  set +f
  unset IFS
fi

if [[ -n "$VIASH_META_CPUS" ]]; then
  if ! [[ "$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 "$VIASH_PAR_UNKNOWN_SLIDE" ]; then
  VIASH_PAR_UNKNOWN_SLIDE_CHOICES=("visium-1;visium-2;visium-2-large;visium-hd")
  IFS=';'
  set -f
  if ! [[ ";${VIASH_PAR_UNKNOWN_SLIDE_CHOICES[*]};" =~ ";$VIASH_PAR_UNKNOWN_SLIDE;" ]]; then
    ViashError '--unknown_slide' specified value of \'$VIASH_PAR_UNKNOWN_SLIDE\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
    exit 1
  fi
  set +f
  unset IFS
fi

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

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

if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  # detect volumes from file arguments
  VIASH_CHOWN_VARS=()
if [ ! -z "$VIASH_PAR_GEX_REFERENCE" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_GEX_REFERENCE")" )
  VIASH_PAR_GEX_REFERENCE=$(ViashDockerAutodetectMount "$VIASH_PAR_GEX_REFERENCE")
fi
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 "$VIASH_PAR_PROBE_SET" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_PROBE_SET")" )
  VIASH_PAR_PROBE_SET=$(ViashDockerAutodetectMount "$VIASH_PAR_PROBE_SET")
fi
if [ ! -z "$VIASH_PAR_CYTAIMAGE" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_CYTAIMAGE")" )
  VIASH_PAR_CYTAIMAGE=$(ViashDockerAutodetectMount "$VIASH_PAR_CYTAIMAGE")
fi
if [ ! -z "$VIASH_PAR_IMAGE" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_IMAGE")" )
  VIASH_PAR_IMAGE=$(ViashDockerAutodetectMount "$VIASH_PAR_IMAGE")
fi
if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT")" )
  VIASH_PAR_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT" )
fi
if [ ! -z "$VIASH_PAR_SLIDEFILE" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_SLIDEFILE")" )
  VIASH_PAR_SLIDEFILE=$(ViashDockerAutodetectMount "$VIASH_PAR_SLIDEFILE")
fi
if [ ! -z "$VIASH_PAR_DARKIMAGE" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_DARKIMAGE")" )
  VIASH_PAR_DARKIMAGE=$(ViashDockerAutodetectMount "$VIASH_PAR_DARKIMAGE")
fi
if [ ! -z "$VIASH_PAR_COLORIZEDIMAGE" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_COLORIZEDIMAGE")" )
  VIASH_PAR_COLORIZEDIMAGE=$(ViashDockerAutodetectMount "$VIASH_PAR_COLORIZEDIMAGE")
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-spaceranger_count-XXXXXX").sh
function clean_up {
  rm "\$tempscript"
}
function interrupt {
  echo -e "\nCTRL-C Pressed..."
  exit 1
}
trap clean_up EXIT
trap interrupt INT SIGINT
cat > "\$tempscript" << 'VIASHMAIN'
#!/bin/bash

set -eo pipefail

## VIASH START
# The following code has been auto-generated by Viash.
$( if [ ! -z ${VIASH_PAR_GEX_REFERENCE+x} ]; then echo "${VIASH_PAR_GEX_REFERENCE}" | sed "s#'#'\"'\"'#g;s#.*#par_gex_reference='&'#" ; else echo "# par_gex_reference="; fi )
$( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_input='&'#" ; else echo "# par_input="; fi )
$( if [ ! -z ${VIASH_PAR_PROBE_SET+x} ]; then echo "${VIASH_PAR_PROBE_SET}" | sed "s#'#'\"'\"'#g;s#.*#par_probe_set='&'#" ; else echo "# par_probe_set="; fi )
$( if [ ! -z ${VIASH_PAR_CYTAIMAGE+x} ]; then echo "${VIASH_PAR_CYTAIMAGE}" | sed "s#'#'\"'\"'#g;s#.*#par_cytaimage='&'#" ; else echo "# par_cytaimage="; fi )
$( if [ ! -z ${VIASH_PAR_IMAGE+x} ]; then echo "${VIASH_PAR_IMAGE}" | sed "s#'#'\"'\"'#g;s#.*#par_image='&'#" ; else echo "# par_image="; fi )
$( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "${VIASH_PAR_OUTPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_output='&'#" ; else echo "# par_output="; fi )
$( if [ ! -z ${VIASH_PAR_SLIDE+x} ]; then echo "${VIASH_PAR_SLIDE}" | sed "s#'#'\"'\"'#g;s#.*#par_slide='&'#" ; else echo "# par_slide="; fi )
$( if [ ! -z ${VIASH_PAR_AREA+x} ]; then echo "${VIASH_PAR_AREA}" | sed "s#'#'\"'\"'#g;s#.*#par_area='&'#" ; else echo "# par_area="; fi )
$( if [ ! -z ${VIASH_PAR_UNKNOWN_SLIDE+x} ]; then echo "${VIASH_PAR_UNKNOWN_SLIDE}" | sed "s#'#'\"'\"'#g;s#.*#par_unknown_slide='&'#" ; else echo "# par_unknown_slide="; fi )
$( if [ ! -z ${VIASH_PAR_SLIDEFILE+x} ]; then echo "${VIASH_PAR_SLIDEFILE}" | sed "s#'#'\"'\"'#g;s#.*#par_slidefile='&'#" ; else echo "# par_slidefile="; fi )
$( if [ ! -z ${VIASH_PAR_OVERRIDE_ID+x} ]; then echo "${VIASH_PAR_OVERRIDE_ID}" | sed "s#'#'\"'\"'#g;s#.*#par_override_id='&'#" ; else echo "# par_override_id="; fi )
$( if [ ! -z ${VIASH_PAR_DARKIMAGE+x} ]; then echo "${VIASH_PAR_DARKIMAGE}" | sed "s#'#'\"'\"'#g;s#.*#par_darkimage='&'#" ; else echo "# par_darkimage="; fi )
$( if [ ! -z ${VIASH_PAR_COLORIZEDIMAGE+x} ]; then echo "${VIASH_PAR_COLORIZEDIMAGE}" | sed "s#'#'\"'\"'#g;s#.*#par_colorizedimage='&'#" ; else echo "# par_colorizedimage="; fi )
$( if [ ! -z ${VIASH_PAR_DAPI_INDEX+x} ]; then echo "${VIASH_PAR_DAPI_INDEX}" | sed "s#'#'\"'\"'#g;s#.*#par_dapi_index='&'#" ; else echo "# par_dapi_index="; fi )
$( if [ ! -z ${VIASH_PAR_IMAGE_SCALE+x} ]; then echo "${VIASH_PAR_IMAGE_SCALE}" | sed "s#'#'\"'\"'#g;s#.*#par_image_scale='&'#" ; else echo "# par_image_scale="; fi )
$( if [ ! -z ${VIASH_PAR_REORIENT_IMAGES+x} ]; then echo "${VIASH_PAR_REORIENT_IMAGES}" | sed "s#'#'\"'\"'#g;s#.*#par_reorient_images='&'#" ; else echo "# par_reorient_images="; fi )
$( if [ ! -z ${VIASH_PAR_CREATE_BAM+x} ]; then echo "${VIASH_PAR_CREATE_BAM}" | sed "s#'#'\"'\"'#g;s#.*#par_create_bam='&'#" ; else echo "# par_create_bam="; fi )
$( if [ ! -z ${VIASH_PAR_NOSECONDARY+x} ]; then echo "${VIASH_PAR_NOSECONDARY}" | sed "s#'#'\"'\"'#g;s#.*#par_nosecondary='&'#" ; else echo "# par_nosecondary="; fi )
$( if [ ! -z ${VIASH_PAR_R1_LENGTH+x} ]; then echo "${VIASH_PAR_R1_LENGTH}" | sed "s#'#'\"'\"'#g;s#.*#par_r1_length='&'#" ; else echo "# par_r1_length="; fi )
$( if [ ! -z ${VIASH_PAR_R2_LENGTH+x} ]; then echo "${VIASH_PAR_R2_LENGTH}" | sed "s#'#'\"'\"'#g;s#.*#par_r2_length='&'#" ; else echo "# par_r2_length="; fi )
$( if [ ! -z ${VIASH_PAR_FILTER_PROBES+x} ]; then echo "${VIASH_PAR_FILTER_PROBES}" | sed "s#'#'\"'\"'#g;s#.*#par_filter_probes='&'#" ; else echo "# par_filter_probes="; fi )
$( if [ ! -z ${VIASH_PAR_CUSTOM_BIN_SIZE+x} ]; then echo "${VIASH_PAR_CUSTOM_BIN_SIZE}" | sed "s#'#'\"'\"'#g;s#.*#par_custom_bin_size='&'#" ; else echo "# par_custom_bin_size="; fi )
$( if [ ! -z ${VIASH_PAR_PROJECT+x} ]; then echo "${VIASH_PAR_PROJECT}" | sed "s#'#'\"'\"'#g;s#.*#par_project='&'#" ; else echo "# par_project="; fi )
$( if [ ! -z ${VIASH_PAR_SAMPLE+x} ]; then echo "${VIASH_PAR_SAMPLE}" | sed "s#'#'\"'\"'#g;s#.*#par_sample='&'#" ; else echo "# par_sample="; fi )
$( if [ ! -z ${VIASH_PAR_LANES+x} ]; then echo "${VIASH_PAR_LANES}" | sed "s#'#'\"'\"'#g;s#.*#par_lanes='&'#" ; else echo "# par_lanes="; fi )
$( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi )
$( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi )
$( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "${VIASH_META_RESOURCES_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_resources_dir='&'#" ; else echo "# meta_resources_dir="; fi )
$( if [ ! -z ${VIASH_META_EXECUTABLE+x} ]; then echo "${VIASH_META_EXECUTABLE}" | sed "s#'#'\"'\"'#g;s#.*#meta_executable='&'#" ; else echo "# meta_executable="; fi )
$( if [ ! -z ${VIASH_META_CONFIG+x} ]; then echo "${VIASH_META_CONFIG}" | sed "s#'#'\"'\"'#g;s#.*#meta_config='&'#" ; else echo "# meta_config="; fi )
$( if [ ! -z ${VIASH_META_TEMP_DIR+x} ]; then echo "${VIASH_META_TEMP_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_temp_dir='&'#" ; else echo "# meta_temp_dir="; fi )
$( if [ ! -z ${VIASH_META_CPUS+x} ]; then echo "${VIASH_META_CPUS}" | sed "s#'#'\"'\"'#g;s#.*#meta_cpus='&'#" ; else echo "# meta_cpus="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_B+x} ]; then echo "${VIASH_META_MEMORY_B}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_b='&'#" ; else echo "# meta_memory_b="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_KB+x} ]; then echo "${VIASH_META_MEMORY_KB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_kb='&'#" ; else echo "# meta_memory_kb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_MB+x} ]; then echo "${VIASH_META_MEMORY_MB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_mb='&'#" ; else echo "# meta_memory_mb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_GB+x} ]; then echo "${VIASH_META_MEMORY_GB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_gb='&'#" ; else echo "# meta_memory_gb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_TB+x} ]; then echo "${VIASH_META_MEMORY_TB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_tb='&'#" ; else echo "# meta_memory_tb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_PB+x} ]; then echo "${VIASH_META_MEMORY_PB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_pb='&'#" ; else echo "# meta_memory_pb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_KIB+x} ]; then echo "${VIASH_META_MEMORY_KIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_kib='&'#" ; else echo "# meta_memory_kib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_MIB+x} ]; then echo "${VIASH_META_MEMORY_MIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_mib='&'#" ; else echo "# meta_memory_mib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_GIB+x} ]; then echo "${VIASH_META_MEMORY_GIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_gib='&'#" ; else echo "# meta_memory_gib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_TIB+x} ]; then echo "${VIASH_META_MEMORY_TIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_tib='&'#" ; else echo "# meta_memory_tib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_pib='&'#" ; else echo "# meta_memory_pib="; fi )

## VIASH END

unset_if_false=(
    par_override_id
    par_nosecondary
)

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

# Make sure paths are absolute
par_gex_reference=\`realpath \$par_gex_reference\`
par_output=\`realpath \$par_output\`
par_probe_set=\`realpath \$par_probe_set\`
[[ -n "\${par_image:-}" ]] && par_image=\$(realpath "\$par_image")
[[ -n "\${par_cytaimage:-}" ]] && par_cytaimage=\$(realpath "\$par_cytaimage")

# create temporary directory
tmpdir=\$(mktemp -d "\$meta_temp_dir/\$meta_name-XXXXXXXX")
function clean_up {
    rm -rf "\$tmpdir"
}
trap clean_up EXIT

# process inputs
# for every fastq file found, make a symlink into the tempdir
fastq_dir="\$tmpdir/fastqs"
mkdir -p "\$fastq_dir"
IFS=";"
for var in \$par_input; do
  unset IFS
  abs_path=\`realpath \$var\`
  if [ -d "\$abs_path" ]; then
    find "\$abs_path" -name *.fastq.gz -exec ln -s {} "\$fastq_dir" \\;
  else
    ln -s "\$abs_path" "\$fastq_dir"
  fi
done

# process reference
if file \$par_gex_reference | grep -q 'gzip compressed data'; then
  echo "Untarring genome"
  reference_dir="\$tmpdir/fastqs"
  mkdir -p "\$reference_dir"
  tar -xvf "\$par_gex_reference" -C "\$reference_dir" --strip-components=1
  par_gex_reference="\$reference_dir"
fi

# cd into tempdir
cd "\$tmpdir"

temp_id="spaceranger_run"

spaceranger count \\
  --id="\$temp_id" \\
  --fastqs="\$fastq_dir" \\
  --transcriptome="\$par_gex_reference" \\
  \${par_probe_set:+--probe-set="\$par_probe_set"} \\
  \${par_cytaimage:+--cytaimage="\$par_cytaimage"} \\
  \${par_image:+--image="\$par_image"} \\
  \${par_slide:+--slide="\$par_slide"} \\
  \${par_area:+--area="\$par_area"} \\
  \${par_unknown_slide:+--unknown-slide="\$par_unknown_slide"} \\
  \${par_slidefile:+--slidefile="\$par_slidefile"} \\
  \${par_override_id:+--override-id} \\
  \${par_darkimage:+--darkimage="\$par_darkimage"} \\
  \${par_colorizedimage:+--colorizedimage="\$par_colorizedimage"} \\
  \${par_dapi_index:+--dapi-index="\$par_dapi_index"} \\
  \${par_image_scale:+--image-scale="\$par_image_scale"} \\
  \${par_reorient_images:+--reorient-images="\$par_reorient_images"} \\
  \${par_create_bam:+--create-bam="\$par_create_bam"} \\
  \${par_nosecondary:+--nosecondary} \\
  \${par_r1_length:+--r1-length="\$par_r1_length"} \\
  \${par_r2_length:+--r2-length="\$par_r2_length"} \\
  \${par_filter_probes:+--filter-probes="\$par_filter_probes"} \\
  \${par_custom_bin_size:+--custom-bin-size="\$par_custom_bin_size"} \\
  \${par_project:+--project="\$par_project"} \\
  \${par_sample:+--sample="\$par_sample"} \\
  \${par_lanes:+--lanes="\$par_lanes"} \\
  \${meta_cpus:+--localcores="\$meta_cpus"} \\
  \${meta_memory_gb:+--localmem=\$((\$meta_memory_gb-2))}

mkdir -p "\$par_output"
mv -f "\$temp_id"/outs/* "\$par_output"/
rm -rf "\$temp_id"/outs
VIASHMAIN
bash "\$tempscript" &
wait "\$!"

VIASHEOF


if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  # strip viash automount from file paths
  
  if [ ! -z "$VIASH_PAR_GEX_REFERENCE" ]; then
    VIASH_PAR_GEX_REFERENCE=$(ViashDockerStripAutomount "$VIASH_PAR_GEX_REFERENCE")
  fi
  if [ ! -z "$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 "$VIASH_PAR_PROBE_SET" ]; then
    VIASH_PAR_PROBE_SET=$(ViashDockerStripAutomount "$VIASH_PAR_PROBE_SET")
  fi
  if [ ! -z "$VIASH_PAR_CYTAIMAGE" ]; then
    VIASH_PAR_CYTAIMAGE=$(ViashDockerStripAutomount "$VIASH_PAR_CYTAIMAGE")
  fi
  if [ ! -z "$VIASH_PAR_IMAGE" ]; then
    VIASH_PAR_IMAGE=$(ViashDockerStripAutomount "$VIASH_PAR_IMAGE")
  fi
  if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
    VIASH_PAR_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT")
  fi
  if [ ! -z "$VIASH_PAR_SLIDEFILE" ]; then
    VIASH_PAR_SLIDEFILE=$(ViashDockerStripAutomount "$VIASH_PAR_SLIDEFILE")
  fi
  if [ ! -z "$VIASH_PAR_DARKIMAGE" ]; then
    VIASH_PAR_DARKIMAGE=$(ViashDockerStripAutomount "$VIASH_PAR_DARKIMAGE")
  fi
  if [ ! -z "$VIASH_PAR_COLORIZEDIMAGE" ]; then
    VIASH_PAR_COLORIZEDIMAGE=$(ViashDockerStripAutomount "$VIASH_PAR_COLORIZEDIMAGE")
  fi
  if [ ! -z "$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
