#!/usr/bin/env bash

# bases2fastq main
# 
# 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 (author, maintainer)

set -e

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

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

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

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

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

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

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

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

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

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

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

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

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

# define meta fields
VIASH_META_NAME="bases2fastq"
VIASH_META_FUNCTIONALITY_NAME="bases2fastq"
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 elembio/bases2fastq:2.2.1
ENTRYPOINT []
RUN bases2fastq --version 2>&1 | head -1 | sed 's/.*version \([0-9\\.]*\).*/bases2fastq: \1/' > /var/software_versions.txt

LABEL org.opencontainers.image.authors="Dries Schaumont"
LABEL org.opencontainers.image.description="Companion container for running component bases2fastq"
LABEL org.opencontainers.image.created="2025-10-03T08:11:10Z"
LABEL org.opencontainers.image.source="https://github.com/Illumina/bases2fastq"
LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b"
LABEL org.opencontainers.image.version="main"

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 "bases2fastq main"
  echo ""
  echo "Bases2Fastq demultiplexes sequencing data generated by Element Biosciences"
  echo "instruments and converts base calls into FASTQ files."
  echo ""
  echo "Input:"
  echo "    --analysis_directory"
  echo "        type: file, required parameter, file must exist"
  echo "        example: input"
  echo "        Location of analysis directory"
  echo ""
  echo "    -r, --run_manifest"
  echo "        type: file, file must exist"
  echo "        Location of run manifest to use instead of default RunManifest.csv found"
  echo "        in analysis directory"
  echo ""
  echo "Output:"
  echo "    -o, --output_directory"
  echo "        type: file, required parameter, output, file must exist"
  echo "        example: fastq_dir"
  echo "        Location to save output fastqs"
  echo ""
  echo "    --report"
  echo "        type: file, output, file must exist"
  echo "        Output location for the HTML report"
  echo ""
  echo "    --logs"
  echo "        type: file, output, file must exist"
  echo "        example: logs_dir"
  echo "        Directory containing log files"
  echo ""
  echo "Arguments:"
  echo "    --chemistry_version"
  echo "        type: string"
  echo "        Run parameters override, chemistry version."
  echo ""
  echo "    -d, --demux_only"
  echo "        type: boolean_true"
  echo "        Generate demux files and indexing stats without generating FASTQ"
  echo ""
  echo "    --detect_adapters"
  echo "        type: boolean_true"
  echo "        Detect adapters sequences, overriding any sequences present in run"
  echo "        manifest."
  echo ""
  echo "    --error_on_missing"
  echo "        type: boolean_true"
  echo "        Terminate execution for a missing file (by default, missing files are"
  echo "        skipped and execution continues). Also set by --strict."
  echo ""
  echo "    -e, --exclude_tile"
  echo "        type: string, multiple values allowed"
  echo "        Regex matching tile names to exclude. This flag can be specified"
  echo "        multiple times. (e.g. L1.*C0[23]S.)"
  echo ""
  echo "    --filter_mask"
  echo "        type: string"
  echo "        Run parameters override, custom pass filter mask."
  echo ""
  echo "    --flowcell_id"
  echo "        type: string"
  echo "        Run parameters override, flowcell ID."
  echo ""
  echo "    --force_index_orientation"
  echo "        type: boolean_true"
  echo "        Do not attempt to find orientation for I1/I2 reads (reverse complement)."
  echo "        Use orientation given in run manifest."
  echo ""
  echo "    --group_fastq"
  echo "        type: boolean_true"
  echo "        Group all FASTQ/stats/metrics for a project are in the project folder."
  echo ""
  echo "    --i1_cycles"
  echo "        type: integer"
  echo "        min: 1"
  echo "        Run parameters override, I1 cycles."
  echo ""
  echo "    --i2_cycles"
  echo "        type: integer"
  echo "        min: 1"
  echo "        Run parameters override, I2 cycles"
  echo ""
  echo "    -i, --include_tile"
  echo "        type: string, multiple values allowed"
  echo "        Regex matching tile names to include. This flag"
  echo "        can be specified multiple times. (e.g. L1.*C0[23]S.)"
  echo ""
  echo "    --kit_configuration"
  echo "        type: string"
  echo "        Run parameters override, kit configuration."
  echo ""
  echo "    --legacy_fastq"
  echo "        type: boolean_true"
  echo "        Legacy naming for FASTQ files (e.g. SampleName_S1_L001_R1_001.fastq.gz)"
  echo ""
  echo "    -l, --log_level"
  echo "        type: string"
  echo "        example: INFO"
  echo "        choices: [ DEBUG, INFO, WARNING, ERROR ]"
  echo "        Severity level for logging."
  echo ""
  echo "    --no_error_on_invalid"
  echo "        type: boolean_true"
  echo "        Skip invalid files and continue execution. Overridden by --strict"
  echo "        options"
  echo ""
  echo "    --no_projects"
  echo "        type: boolean_true"
  echo "        Disable project directories"
  echo ""
  echo "    --num_unassigned"
  echo "        type: integer"
  echo "        example: 30"
  echo "        min: 0"
  echo "        max: 1000"
  echo "        Max Number of unassigned sequences to report."
  echo ""
  echo "    --preparation_workflow"
  echo "        type: string"
  echo "        Run parameters override, preparation workflow."
  echo ""
  echo "    --qc_only"
  echo "        type: boolean_true"
  echo "        Quickly generate run stats for single tile without generating FASTQ."
  echo "        Use --include_tile/--exclude_tile to define custom tile set."
  echo ""
  echo "    --r1_cycles"
  echo "        type: integer"
  echo "        min: 1"
  echo "        Run parameters override, R1 cycles."
  echo ""
  echo "    --r2_cycles"
  echo "        type: integer"
  echo "        min: 1"
  echo "        Run parameters override, R2 cycles."
  echo ""
  echo "    --split_lanes"
  echo "        type: boolean_true"
  echo "        Split FASTQ files by lane."
  echo ""
  echo "    --skip_qc_report"
  echo "        type: boolean_true"
  echo "        Do not generate HTML QC report."
  echo ""
  echo "    --skip_multi_qc"
  echo "        type: boolean_true"
  echo "        Do not generate MultiQC HTML report."
  echo ""
  echo "    --settings"
  echo "        type: string, multiple values allowed"
  echo "        Run manifest settings override. This option may be specified multiple"
  echo "        times."
  echo ""
  echo "Cyto-fastq Arguments:"
  echo "    --batch"
  echo "        type: string"
  echo "        Restrict cyto-fastq generation to batch(es) that match comma delimited"
  echo "        list (e.g. --batch B01,B02,B03)."
  echo ""
  echo "    --cyto_fastq_mask"
  echo "        type: string, multiple values allowed"
  echo "        Cycle mask for cyto fastq generation. This flag can be specified"
  echo "        multiple times."
  echo ""
  echo "    --panel"
  echo "        type: file, file must exist"
  echo "        Local or remote path to panel JSON"
  echo ""
  echo "    --per_target_fastq"
  echo "        type: boolean_true"
  echo "        Create per-target fastq for each cell assignment target site in each"
  echo "        DISS batch according to FastqMasks in TargetCellAssignmentManifest."
  echo ""
  echo "    --tca_manifest"
  echo "        type: file, file must exist"
  echo "        Location of TargetCellAssignmentManifest to use instead of default csv"
  echo "        found in analysis directory"
  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 "$1")"
            shift 1
            ;;
        --version)
            echo "bases2fastq main"
            exit
            ;;
        --analysis_directory)
            [ -n "$VIASH_PAR_ANALYSIS_DIRECTORY" ] && ViashError Bad arguments for option \'--analysis_directory\': \'$VIASH_PAR_ANALYSIS_DIRECTORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ANALYSIS_DIRECTORY="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --analysis_directory. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --analysis_directory=*)
            [ -n "$VIASH_PAR_ANALYSIS_DIRECTORY" ] && ViashError Bad arguments for option \'--analysis_directory=*\': \'$VIASH_PAR_ANALYSIS_DIRECTORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ANALYSIS_DIRECTORY=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --run_manifest)
            [ -n "$VIASH_PAR_RUN_MANIFEST" ] && ViashError Bad arguments for option \'--run_manifest\': \'$VIASH_PAR_RUN_MANIFEST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_RUN_MANIFEST="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --run_manifest. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --run_manifest=*)
            [ -n "$VIASH_PAR_RUN_MANIFEST" ] && ViashError Bad arguments for option \'--run_manifest=*\': \'$VIASH_PAR_RUN_MANIFEST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_RUN_MANIFEST=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -r)
            [ -n "$VIASH_PAR_RUN_MANIFEST" ] && ViashError Bad arguments for option \'-r\': \'$VIASH_PAR_RUN_MANIFEST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_RUN_MANIFEST="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -r. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --output_directory)
            [ -n "$VIASH_PAR_OUTPUT_DIRECTORY" ] && ViashError Bad arguments for option \'--output_directory\': \'$VIASH_PAR_OUTPUT_DIRECTORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_DIRECTORY="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --output_directory. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --output_directory=*)
            [ -n "$VIASH_PAR_OUTPUT_DIRECTORY" ] && ViashError Bad arguments for option \'--output_directory=*\': \'$VIASH_PAR_OUTPUT_DIRECTORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_DIRECTORY=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -o)
            [ -n "$VIASH_PAR_OUTPUT_DIRECTORY" ] && ViashError Bad arguments for option \'-o\': \'$VIASH_PAR_OUTPUT_DIRECTORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_DIRECTORY="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -o. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --report)
            [ -n "$VIASH_PAR_REPORT" ] && ViashError Bad arguments for option \'--report\': \'$VIASH_PAR_REPORT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_REPORT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --report. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --report=*)
            [ -n "$VIASH_PAR_REPORT" ] && ViashError Bad arguments for option \'--report=*\': \'$VIASH_PAR_REPORT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_REPORT=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --logs)
            [ -n "$VIASH_PAR_LOGS" ] && ViashError Bad arguments for option \'--logs\': \'$VIASH_PAR_LOGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LOGS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --logs. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --logs=*)
            [ -n "$VIASH_PAR_LOGS" ] && ViashError Bad arguments for option \'--logs=*\': \'$VIASH_PAR_LOGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LOGS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --chemistry_version)
            [ -n "$VIASH_PAR_CHEMISTRY_VERSION" ] && ViashError Bad arguments for option \'--chemistry_version\': \'$VIASH_PAR_CHEMISTRY_VERSION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CHEMISTRY_VERSION="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --chemistry_version. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --chemistry_version=*)
            [ -n "$VIASH_PAR_CHEMISTRY_VERSION" ] && ViashError Bad arguments for option \'--chemistry_version=*\': \'$VIASH_PAR_CHEMISTRY_VERSION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CHEMISTRY_VERSION=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --demux_only)
            [ -n "$VIASH_PAR_DEMUX_ONLY" ] && ViashError Bad arguments for option \'--demux_only\': \'$VIASH_PAR_DEMUX_ONLY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_DEMUX_ONLY=true
            shift 1
            ;;
        -d)
            [ -n "$VIASH_PAR_DEMUX_ONLY" ] && ViashError Bad arguments for option \'-d\': \'$VIASH_PAR_DEMUX_ONLY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_DEMUX_ONLY=true
            shift 1
            ;;
        --detect_adapters)
            [ -n "$VIASH_PAR_DETECT_ADAPTERS" ] && ViashError Bad arguments for option \'--detect_adapters\': \'$VIASH_PAR_DETECT_ADAPTERS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_DETECT_ADAPTERS=true
            shift 1
            ;;
        --error_on_missing)
            [ -n "$VIASH_PAR_ERROR_ON_MISSING" ] && ViashError Bad arguments for option \'--error_on_missing\': \'$VIASH_PAR_ERROR_ON_MISSING\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ERROR_ON_MISSING=true
            shift 1
            ;;
        --exclude_tile)
            if [ -z "$VIASH_PAR_EXCLUDE_TILE" ]; then
              VIASH_PAR_EXCLUDE_TILE="$2"
            else
              VIASH_PAR_EXCLUDE_TILE="$VIASH_PAR_EXCLUDE_TILE;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --exclude_tile. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --exclude_tile=*)
            if [ -z "$VIASH_PAR_EXCLUDE_TILE" ]; then
              VIASH_PAR_EXCLUDE_TILE=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_EXCLUDE_TILE="$VIASH_PAR_EXCLUDE_TILE;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        -e)
            if [ -z "$VIASH_PAR_EXCLUDE_TILE" ]; then
              VIASH_PAR_EXCLUDE_TILE="$2"
            else
              VIASH_PAR_EXCLUDE_TILE="$VIASH_PAR_EXCLUDE_TILE;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -e. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --filter_mask)
            [ -n "$VIASH_PAR_FILTER_MASK" ] && ViashError Bad arguments for option \'--filter_mask\': \'$VIASH_PAR_FILTER_MASK\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FILTER_MASK="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --filter_mask. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --filter_mask=*)
            [ -n "$VIASH_PAR_FILTER_MASK" ] && ViashError Bad arguments for option \'--filter_mask=*\': \'$VIASH_PAR_FILTER_MASK\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FILTER_MASK=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --flowcell_id)
            [ -n "$VIASH_PAR_FLOWCELL_ID" ] && ViashError Bad arguments for option \'--flowcell_id\': \'$VIASH_PAR_FLOWCELL_ID\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FLOWCELL_ID="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --flowcell_id. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --flowcell_id=*)
            [ -n "$VIASH_PAR_FLOWCELL_ID" ] && ViashError Bad arguments for option \'--flowcell_id=*\': \'$VIASH_PAR_FLOWCELL_ID\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FLOWCELL_ID=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --force_index_orientation)
            [ -n "$VIASH_PAR_FORCE_INDEX_ORIENTATION" ] && ViashError Bad arguments for option \'--force_index_orientation\': \'$VIASH_PAR_FORCE_INDEX_ORIENTATION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FORCE_INDEX_ORIENTATION=true
            shift 1
            ;;
        --group_fastq)
            [ -n "$VIASH_PAR_GROUP_FASTQ" ] && ViashError Bad arguments for option \'--group_fastq\': \'$VIASH_PAR_GROUP_FASTQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_GROUP_FASTQ=true
            shift 1
            ;;
        --i1_cycles)
            [ -n "$VIASH_PAR_I1_CYCLES" ] && ViashError Bad arguments for option \'--i1_cycles\': \'$VIASH_PAR_I1_CYCLES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_I1_CYCLES="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --i1_cycles. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --i1_cycles=*)
            [ -n "$VIASH_PAR_I1_CYCLES" ] && ViashError Bad arguments for option \'--i1_cycles=*\': \'$VIASH_PAR_I1_CYCLES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_I1_CYCLES=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --i2_cycles)
            [ -n "$VIASH_PAR_I2_CYCLES" ] && ViashError Bad arguments for option \'--i2_cycles\': \'$VIASH_PAR_I2_CYCLES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_I2_CYCLES="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --i2_cycles. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --i2_cycles=*)
            [ -n "$VIASH_PAR_I2_CYCLES" ] && ViashError Bad arguments for option \'--i2_cycles=*\': \'$VIASH_PAR_I2_CYCLES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_I2_CYCLES=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --include_tile)
            if [ -z "$VIASH_PAR_INCLUDE_TILE" ]; then
              VIASH_PAR_INCLUDE_TILE="$2"
            else
              VIASH_PAR_INCLUDE_TILE="$VIASH_PAR_INCLUDE_TILE;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --include_tile. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --include_tile=*)
            if [ -z "$VIASH_PAR_INCLUDE_TILE" ]; then
              VIASH_PAR_INCLUDE_TILE=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_INCLUDE_TILE="$VIASH_PAR_INCLUDE_TILE;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        -i)
            if [ -z "$VIASH_PAR_INCLUDE_TILE" ]; then
              VIASH_PAR_INCLUDE_TILE="$2"
            else
              VIASH_PAR_INCLUDE_TILE="$VIASH_PAR_INCLUDE_TILE;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -i. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --kit_configuration)
            [ -n "$VIASH_PAR_KIT_CONFIGURATION" ] && ViashError Bad arguments for option \'--kit_configuration\': \'$VIASH_PAR_KIT_CONFIGURATION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_KIT_CONFIGURATION="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --kit_configuration. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --kit_configuration=*)
            [ -n "$VIASH_PAR_KIT_CONFIGURATION" ] && ViashError Bad arguments for option \'--kit_configuration=*\': \'$VIASH_PAR_KIT_CONFIGURATION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_KIT_CONFIGURATION=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --legacy_fastq)
            [ -n "$VIASH_PAR_LEGACY_FASTQ" ] && ViashError Bad arguments for option \'--legacy_fastq\': \'$VIASH_PAR_LEGACY_FASTQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LEGACY_FASTQ=true
            shift 1
            ;;
        --log_level)
            [ -n "$VIASH_PAR_LOG_LEVEL" ] && ViashError Bad arguments for option \'--log_level\': \'$VIASH_PAR_LOG_LEVEL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LOG_LEVEL="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --log_level. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --log_level=*)
            [ -n "$VIASH_PAR_LOG_LEVEL" ] && ViashError Bad arguments for option \'--log_level=*\': \'$VIASH_PAR_LOG_LEVEL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LOG_LEVEL=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -l)
            [ -n "$VIASH_PAR_LOG_LEVEL" ] && ViashError Bad arguments for option \'-l\': \'$VIASH_PAR_LOG_LEVEL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LOG_LEVEL="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -l. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --no_error_on_invalid)
            [ -n "$VIASH_PAR_NO_ERROR_ON_INVALID" ] && ViashError Bad arguments for option \'--no_error_on_invalid\': \'$VIASH_PAR_NO_ERROR_ON_INVALID\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_NO_ERROR_ON_INVALID=true
            shift 1
            ;;
        --no_projects)
            [ -n "$VIASH_PAR_NO_PROJECTS" ] && ViashError Bad arguments for option \'--no_projects\': \'$VIASH_PAR_NO_PROJECTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_NO_PROJECTS=true
            shift 1
            ;;
        --num_unassigned)
            [ -n "$VIASH_PAR_NUM_UNASSIGNED" ] && ViashError Bad arguments for option \'--num_unassigned\': \'$VIASH_PAR_NUM_UNASSIGNED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_NUM_UNASSIGNED="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --num_unassigned. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --num_unassigned=*)
            [ -n "$VIASH_PAR_NUM_UNASSIGNED" ] && ViashError Bad arguments for option \'--num_unassigned=*\': \'$VIASH_PAR_NUM_UNASSIGNED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_NUM_UNASSIGNED=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --preparation_workflow)
            [ -n "$VIASH_PAR_PREPARATION_WORKFLOW" ] && ViashError Bad arguments for option \'--preparation_workflow\': \'$VIASH_PAR_PREPARATION_WORKFLOW\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PREPARATION_WORKFLOW="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --preparation_workflow. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --preparation_workflow=*)
            [ -n "$VIASH_PAR_PREPARATION_WORKFLOW" ] && ViashError Bad arguments for option \'--preparation_workflow=*\': \'$VIASH_PAR_PREPARATION_WORKFLOW\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PREPARATION_WORKFLOW=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --qc_only)
            [ -n "$VIASH_PAR_QC_ONLY" ] && ViashError Bad arguments for option \'--qc_only\': \'$VIASH_PAR_QC_ONLY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_QC_ONLY=true
            shift 1
            ;;
        --r1_cycles)
            [ -n "$VIASH_PAR_R1_CYCLES" ] && ViashError Bad arguments for option \'--r1_cycles\': \'$VIASH_PAR_R1_CYCLES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_R1_CYCLES="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --r1_cycles. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --r1_cycles=*)
            [ -n "$VIASH_PAR_R1_CYCLES" ] && ViashError Bad arguments for option \'--r1_cycles=*\': \'$VIASH_PAR_R1_CYCLES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_R1_CYCLES=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --r2_cycles)
            [ -n "$VIASH_PAR_R2_CYCLES" ] && ViashError Bad arguments for option \'--r2_cycles\': \'$VIASH_PAR_R2_CYCLES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_R2_CYCLES="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --r2_cycles. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --r2_cycles=*)
            [ -n "$VIASH_PAR_R2_CYCLES" ] && ViashError Bad arguments for option \'--r2_cycles=*\': \'$VIASH_PAR_R2_CYCLES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_R2_CYCLES=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --split_lanes)
            [ -n "$VIASH_PAR_SPLIT_LANES" ] && ViashError Bad arguments for option \'--split_lanes\': \'$VIASH_PAR_SPLIT_LANES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SPLIT_LANES=true
            shift 1
            ;;
        --skip_qc_report)
            [ -n "$VIASH_PAR_SKIP_QC_REPORT" ] && ViashError Bad arguments for option \'--skip_qc_report\': \'$VIASH_PAR_SKIP_QC_REPORT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SKIP_QC_REPORT=true
            shift 1
            ;;
        --skip_multi_qc)
            [ -n "$VIASH_PAR_SKIP_MULTI_QC" ] && ViashError Bad arguments for option \'--skip_multi_qc\': \'$VIASH_PAR_SKIP_MULTI_QC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SKIP_MULTI_QC=true
            shift 1
            ;;
        --settings)
            if [ -z "$VIASH_PAR_SETTINGS" ]; then
              VIASH_PAR_SETTINGS="$2"
            else
              VIASH_PAR_SETTINGS="$VIASH_PAR_SETTINGS;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --settings. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --settings=*)
            if [ -z "$VIASH_PAR_SETTINGS" ]; then
              VIASH_PAR_SETTINGS=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_SETTINGS="$VIASH_PAR_SETTINGS;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --batch)
            [ -n "$VIASH_PAR_BATCH" ] && ViashError Bad arguments for option \'--batch\': \'$VIASH_PAR_BATCH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_BATCH="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --batch. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --batch=*)
            [ -n "$VIASH_PAR_BATCH" ] && ViashError Bad arguments for option \'--batch=*\': \'$VIASH_PAR_BATCH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_BATCH=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --cyto_fastq_mask)
            if [ -z "$VIASH_PAR_CYTO_FASTQ_MASK" ]; then
              VIASH_PAR_CYTO_FASTQ_MASK="$2"
            else
              VIASH_PAR_CYTO_FASTQ_MASK="$VIASH_PAR_CYTO_FASTQ_MASK;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --cyto_fastq_mask. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --cyto_fastq_mask=*)
            if [ -z "$VIASH_PAR_CYTO_FASTQ_MASK" ]; then
              VIASH_PAR_CYTO_FASTQ_MASK=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_CYTO_FASTQ_MASK="$VIASH_PAR_CYTO_FASTQ_MASK;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --panel)
            [ -n "$VIASH_PAR_PANEL" ] && ViashError Bad arguments for option \'--panel\': \'$VIASH_PAR_PANEL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PANEL="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --panel. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --panel=*)
            [ -n "$VIASH_PAR_PANEL" ] && ViashError Bad arguments for option \'--panel=*\': \'$VIASH_PAR_PANEL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PANEL=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --per_target_fastq)
            [ -n "$VIASH_PAR_PER_TARGET_FASTQ" ] && ViashError Bad arguments for option \'--per_target_fastq\': \'$VIASH_PAR_PER_TARGET_FASTQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PER_TARGET_FASTQ=true
            shift 1
            ;;
        --tca_manifest)
            [ -n "$VIASH_PAR_TCA_MANIFEST" ] && ViashError Bad arguments for option \'--tca_manifest\': \'$VIASH_PAR_TCA_MANIFEST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_TCA_MANIFEST="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --tca_manifest. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --tca_manifest=*)
            [ -n "$VIASH_PAR_TCA_MANIFEST" ] && ViashError Bad arguments for option \'--tca_manifest=*\': \'$VIASH_PAR_TCA_MANIFEST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_TCA_MANIFEST=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        ---engine)
            VIASH_ENGINE_ID="$2"
            shift 2
            ;;
        ---engine=*)
            VIASH_ENGINE_ID="$(ViashRemoveFlags "$1")"
            shift 1
            ;;
        ---setup)
            VIASH_MODE='setup'
            VIASH_SETUP_STRATEGY="$2"
            shift 2
            ;;
        ---setup=*)
            VIASH_MODE='setup'
            VIASH_SETUP_STRATEGY="$(ViashRemoveFlags "$1")"
            shift 1
            ;;
        ---dockerfile)
            VIASH_MODE='dockerfile'
            shift 1
            ;;
        ---docker_run_args)
            VIASH_DOCKER_RUN_ARGS+=("$2")
            shift 2
            ;;
        ---docker_run_args=*)
            VIASH_DOCKER_RUN_ARGS+=("$(ViashRemoveFlags "$1")")
            shift 1
            ;;
        ---docker_image_id)
            VIASH_MODE='docker_image_id'
            shift 1
            ;;
        ---debug)
            VIASH_MODE='debug'
            shift 1
            ;;
        ---cpus)
            [ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_CPUS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to ---cpus. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        ---cpus=*)
            [ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus=*\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_CPUS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        ---memory)
            [ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_MEMORY="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to ---memory. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        ---memory=*)
            [ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory=*\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_MEMORY=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        *)  # positional arg or unknown option
            # since the positional args will be eval'd, can we always quote, instead of using ViashQuote
            VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'"
            [[ $1 == -* ]] && ViashWarning $1 looks like a parameter but is not a defined parameter and will instead be treated as a positional argument. Use "--help" to get more information on the parameters.
            shift # past argument
            ;;
    esac
done

# parse positional parameters
eval set -- $VIASH_POSITIONAL_ARGS


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

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

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bases2fastq:main'
  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" 'bases2fastq' 'ps' 'bash'
    exit 0
  fi

  # check if docker image exists
  ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild
  ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bases2fastq' '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_ANALYSIS_DIRECTORY+x} ]; then
  ViashError '--analysis_directory' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_PAR_OUTPUT_DIRECTORY+x} ]; then
  ViashError '--output_directory' 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_DEMUX_ONLY+x} ]; then
  VIASH_PAR_DEMUX_ONLY="false"
fi
if [ -z ${VIASH_PAR_DETECT_ADAPTERS+x} ]; then
  VIASH_PAR_DETECT_ADAPTERS="false"
fi
if [ -z ${VIASH_PAR_ERROR_ON_MISSING+x} ]; then
  VIASH_PAR_ERROR_ON_MISSING="false"
fi
if [ -z ${VIASH_PAR_FORCE_INDEX_ORIENTATION+x} ]; then
  VIASH_PAR_FORCE_INDEX_ORIENTATION="false"
fi
if [ -z ${VIASH_PAR_GROUP_FASTQ+x} ]; then
  VIASH_PAR_GROUP_FASTQ="false"
fi
if [ -z ${VIASH_PAR_LEGACY_FASTQ+x} ]; then
  VIASH_PAR_LEGACY_FASTQ="false"
fi
if [ -z ${VIASH_PAR_NO_ERROR_ON_INVALID+x} ]; then
  VIASH_PAR_NO_ERROR_ON_INVALID="false"
fi
if [ -z ${VIASH_PAR_NO_PROJECTS+x} ]; then
  VIASH_PAR_NO_PROJECTS="false"
fi
if [ -z ${VIASH_PAR_QC_ONLY+x} ]; then
  VIASH_PAR_QC_ONLY="false"
fi
if [ -z ${VIASH_PAR_SPLIT_LANES+x} ]; then
  VIASH_PAR_SPLIT_LANES="false"
fi
if [ -z ${VIASH_PAR_SKIP_QC_REPORT+x} ]; then
  VIASH_PAR_SKIP_QC_REPORT="false"
fi
if [ -z ${VIASH_PAR_SKIP_MULTI_QC+x} ]; then
  VIASH_PAR_SKIP_MULTI_QC="false"
fi
if [ -z ${VIASH_PAR_PER_TARGET_FASTQ+x} ]; then
  VIASH_PAR_PER_TARGET_FASTQ="false"
fi

# check whether required files exist
if [ ! -z "$VIASH_PAR_ANALYSIS_DIRECTORY" ] && [ ! -e "$VIASH_PAR_ANALYSIS_DIRECTORY" ]; then
  ViashError "Input file '$VIASH_PAR_ANALYSIS_DIRECTORY' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_RUN_MANIFEST" ] && [ ! -e "$VIASH_PAR_RUN_MANIFEST" ]; then
  ViashError "Input file '$VIASH_PAR_RUN_MANIFEST' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_PANEL" ] && [ ! -e "$VIASH_PAR_PANEL" ]; then
  ViashError "Input file '$VIASH_PAR_PANEL' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_TCA_MANIFEST" ] && [ ! -e "$VIASH_PAR_TCA_MANIFEST" ]; then
  ViashError "Input file '$VIASH_PAR_TCA_MANIFEST' does not exist."
  exit 1
fi

# check whether parameters values are of the right type
if [[ -n "$VIASH_PAR_DEMUX_ONLY" ]]; then
  if ! [[ "$VIASH_PAR_DEMUX_ONLY" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--demux_only' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_DETECT_ADAPTERS" ]]; then
  if ! [[ "$VIASH_PAR_DETECT_ADAPTERS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--detect_adapters' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_ERROR_ON_MISSING" ]]; then
  if ! [[ "$VIASH_PAR_ERROR_ON_MISSING" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--error_on_missing' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_FORCE_INDEX_ORIENTATION" ]]; then
  if ! [[ "$VIASH_PAR_FORCE_INDEX_ORIENTATION" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--force_index_orientation' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_GROUP_FASTQ" ]]; then
  if ! [[ "$VIASH_PAR_GROUP_FASTQ" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--group_fastq' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_I1_CYCLES" ]]; then
  if ! [[ "$VIASH_PAR_I1_CYCLES" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--i1_cycles' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
  if [[ $VIASH_PAR_I1_CYCLES -lt 1 ]]; then
    ViashError '--i1_cycles' has be more than or equal to 1. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_I2_CYCLES" ]]; then
  if ! [[ "$VIASH_PAR_I2_CYCLES" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--i2_cycles' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
  if [[ $VIASH_PAR_I2_CYCLES -lt 1 ]]; then
    ViashError '--i2_cycles' has be more than or equal to 1. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_LEGACY_FASTQ" ]]; then
  if ! [[ "$VIASH_PAR_LEGACY_FASTQ" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--legacy_fastq' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_NO_ERROR_ON_INVALID" ]]; then
  if ! [[ "$VIASH_PAR_NO_ERROR_ON_INVALID" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--no_error_on_invalid' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_NO_PROJECTS" ]]; then
  if ! [[ "$VIASH_PAR_NO_PROJECTS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--no_projects' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_NUM_UNASSIGNED" ]]; then
  if ! [[ "$VIASH_PAR_NUM_UNASSIGNED" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--num_unassigned' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
  if [[ $VIASH_PAR_NUM_UNASSIGNED -lt 0 ]]; then
    ViashError '--num_unassigned' has be more than or equal to 0. Use "--help" to get more information on the parameters.
    exit 1
  fi
  if [[ $VIASH_PAR_NUM_UNASSIGNED -gt 1000 ]]; then
    ViashError '--num_unassigned' has be less than or equal to 1000. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_QC_ONLY" ]]; then
  if ! [[ "$VIASH_PAR_QC_ONLY" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--qc_only' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_R1_CYCLES" ]]; then
  if ! [[ "$VIASH_PAR_R1_CYCLES" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--r1_cycles' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
  if [[ $VIASH_PAR_R1_CYCLES -lt 1 ]]; then
    ViashError '--r1_cycles' has be more than or equal to 1. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_R2_CYCLES" ]]; then
  if ! [[ "$VIASH_PAR_R2_CYCLES" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--r2_cycles' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
  if [[ $VIASH_PAR_R2_CYCLES -lt 1 ]]; then
    ViashError '--r2_cycles' has be more than or equal to 1. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SPLIT_LANES" ]]; then
  if ! [[ "$VIASH_PAR_SPLIT_LANES" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--split_lanes' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SKIP_QC_REPORT" ]]; then
  if ! [[ "$VIASH_PAR_SKIP_QC_REPORT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--skip_qc_report' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SKIP_MULTI_QC" ]]; then
  if ! [[ "$VIASH_PAR_SKIP_MULTI_QC" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--skip_multi_qc' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_PER_TARGET_FASTQ" ]]; then
  if ! [[ "$VIASH_PAR_PER_TARGET_FASTQ" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--per_target_fastq' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_CPUS" ]]; then
  if ! [[ "$VIASH_META_CPUS" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'cpus' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_B" ]]; then
  if ! [[ "$VIASH_META_MEMORY_B" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_b' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_KB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_KB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_kb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_MB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_MB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_mb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_GB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_GB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_gb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_TB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_TB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_tb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_PB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_PB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_pb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_KIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_KIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_kib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_MIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_MIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_mib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_GIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_GIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_gib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_TIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_TIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_tib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_PIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_PIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_pib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi

# check whether value is belongs to a set of choices
if [ ! -z "$VIASH_PAR_LOG_LEVEL" ]; then
  VIASH_PAR_LOG_LEVEL_CHOICES=("DEBUG;INFO;WARNING;ERROR")
  IFS=';'
  set -f
  if ! [[ ";${VIASH_PAR_LOG_LEVEL_CHOICES[*]};" =~ ";$VIASH_PAR_LOG_LEVEL;" ]]; then
    ViashError '--log_level' specified value of \'$VIASH_PAR_LOG_LEVEL\' 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 "$VIASH_PAR_OUTPUT_DIRECTORY" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT_DIRECTORY")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_OUTPUT_DIRECTORY")"
fi
if [ ! -z "$VIASH_PAR_REPORT" ] && [ ! -d "$(dirname "$VIASH_PAR_REPORT")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_REPORT")"
fi
if [ ! -z "$VIASH_PAR_LOGS" ] && [ ! -d "$(dirname "$VIASH_PAR_LOGS")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_LOGS")"
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_ANALYSIS_DIRECTORY" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_ANALYSIS_DIRECTORY")" )
  VIASH_PAR_ANALYSIS_DIRECTORY=$(ViashDockerAutodetectMount "$VIASH_PAR_ANALYSIS_DIRECTORY")
fi
if [ ! -z "$VIASH_PAR_RUN_MANIFEST" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_RUN_MANIFEST")" )
  VIASH_PAR_RUN_MANIFEST=$(ViashDockerAutodetectMount "$VIASH_PAR_RUN_MANIFEST")
fi
if [ ! -z "$VIASH_PAR_OUTPUT_DIRECTORY" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT_DIRECTORY")" )
  VIASH_PAR_OUTPUT_DIRECTORY=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT_DIRECTORY")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT_DIRECTORY" )
fi
if [ ! -z "$VIASH_PAR_REPORT" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_REPORT")" )
  VIASH_PAR_REPORT=$(ViashDockerAutodetectMount "$VIASH_PAR_REPORT")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_REPORT" )
fi
if [ ! -z "$VIASH_PAR_LOGS" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_LOGS")" )
  VIASH_PAR_LOGS=$(ViashDockerAutodetectMount "$VIASH_PAR_LOGS")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_LOGS" )
fi
if [ ! -z "$VIASH_PAR_PANEL" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_PANEL")" )
  VIASH_PAR_PANEL=$(ViashDockerAutodetectMount "$VIASH_PAR_PANEL")
fi
if [ ! -z "$VIASH_PAR_TCA_MANIFEST" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_TCA_MANIFEST")" )
  VIASH_PAR_TCA_MANIFEST=$(ViashDockerAutodetectMount "$VIASH_PAR_TCA_MANIFEST")
fi
if [ ! -z "$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-bases2fastq-XXXXXX").sh
function clean_up {
  rm "\$tempscript"
}
function interrupt {
  echo -e "\nCTRL-C Pressed..."
  exit 1
}
trap clean_up EXIT
trap interrupt INT SIGINT
cat > "\$tempscript" << 'VIASHMAIN'
#!/bin/bash

## VIASH START
# The following code has been auto-generated by Viash.
$( if [ ! -z ${VIASH_PAR_ANALYSIS_DIRECTORY+x} ]; then echo "${VIASH_PAR_ANALYSIS_DIRECTORY}" | sed "s#'#'\"'\"'#g;s#.*#par_analysis_directory='&'#" ; else echo "# par_analysis_directory="; fi )
$( if [ ! -z ${VIASH_PAR_RUN_MANIFEST+x} ]; then echo "${VIASH_PAR_RUN_MANIFEST}" | sed "s#'#'\"'\"'#g;s#.*#par_run_manifest='&'#" ; else echo "# par_run_manifest="; fi )
$( if [ ! -z ${VIASH_PAR_OUTPUT_DIRECTORY+x} ]; then echo "${VIASH_PAR_OUTPUT_DIRECTORY}" | sed "s#'#'\"'\"'#g;s#.*#par_output_directory='&'#" ; else echo "# par_output_directory="; fi )
$( if [ ! -z ${VIASH_PAR_REPORT+x} ]; then echo "${VIASH_PAR_REPORT}" | sed "s#'#'\"'\"'#g;s#.*#par_report='&'#" ; else echo "# par_report="; fi )
$( if [ ! -z ${VIASH_PAR_LOGS+x} ]; then echo "${VIASH_PAR_LOGS}" | sed "s#'#'\"'\"'#g;s#.*#par_logs='&'#" ; else echo "# par_logs="; fi )
$( if [ ! -z ${VIASH_PAR_CHEMISTRY_VERSION+x} ]; then echo "${VIASH_PAR_CHEMISTRY_VERSION}" | sed "s#'#'\"'\"'#g;s#.*#par_chemistry_version='&'#" ; else echo "# par_chemistry_version="; fi )
$( if [ ! -z ${VIASH_PAR_DEMUX_ONLY+x} ]; then echo "${VIASH_PAR_DEMUX_ONLY}" | sed "s#'#'\"'\"'#g;s#.*#par_demux_only='&'#" ; else echo "# par_demux_only="; fi )
$( if [ ! -z ${VIASH_PAR_DETECT_ADAPTERS+x} ]; then echo "${VIASH_PAR_DETECT_ADAPTERS}" | sed "s#'#'\"'\"'#g;s#.*#par_detect_adapters='&'#" ; else echo "# par_detect_adapters="; fi )
$( if [ ! -z ${VIASH_PAR_ERROR_ON_MISSING+x} ]; then echo "${VIASH_PAR_ERROR_ON_MISSING}" | sed "s#'#'\"'\"'#g;s#.*#par_error_on_missing='&'#" ; else echo "# par_error_on_missing="; fi )
$( if [ ! -z ${VIASH_PAR_EXCLUDE_TILE+x} ]; then echo "${VIASH_PAR_EXCLUDE_TILE}" | sed "s#'#'\"'\"'#g;s#.*#par_exclude_tile='&'#" ; else echo "# par_exclude_tile="; fi )
$( if [ ! -z ${VIASH_PAR_FILTER_MASK+x} ]; then echo "${VIASH_PAR_FILTER_MASK}" | sed "s#'#'\"'\"'#g;s#.*#par_filter_mask='&'#" ; else echo "# par_filter_mask="; fi )
$( if [ ! -z ${VIASH_PAR_FLOWCELL_ID+x} ]; then echo "${VIASH_PAR_FLOWCELL_ID}" | sed "s#'#'\"'\"'#g;s#.*#par_flowcell_id='&'#" ; else echo "# par_flowcell_id="; fi )
$( if [ ! -z ${VIASH_PAR_FORCE_INDEX_ORIENTATION+x} ]; then echo "${VIASH_PAR_FORCE_INDEX_ORIENTATION}" | sed "s#'#'\"'\"'#g;s#.*#par_force_index_orientation='&'#" ; else echo "# par_force_index_orientation="; fi )
$( if [ ! -z ${VIASH_PAR_GROUP_FASTQ+x} ]; then echo "${VIASH_PAR_GROUP_FASTQ}" | sed "s#'#'\"'\"'#g;s#.*#par_group_fastq='&'#" ; else echo "# par_group_fastq="; fi )
$( if [ ! -z ${VIASH_PAR_I1_CYCLES+x} ]; then echo "${VIASH_PAR_I1_CYCLES}" | sed "s#'#'\"'\"'#g;s#.*#par_i1_cycles='&'#" ; else echo "# par_i1_cycles="; fi )
$( if [ ! -z ${VIASH_PAR_I2_CYCLES+x} ]; then echo "${VIASH_PAR_I2_CYCLES}" | sed "s#'#'\"'\"'#g;s#.*#par_i2_cycles='&'#" ; else echo "# par_i2_cycles="; fi )
$( if [ ! -z ${VIASH_PAR_INCLUDE_TILE+x} ]; then echo "${VIASH_PAR_INCLUDE_TILE}" | sed "s#'#'\"'\"'#g;s#.*#par_include_tile='&'#" ; else echo "# par_include_tile="; fi )
$( if [ ! -z ${VIASH_PAR_KIT_CONFIGURATION+x} ]; then echo "${VIASH_PAR_KIT_CONFIGURATION}" | sed "s#'#'\"'\"'#g;s#.*#par_kit_configuration='&'#" ; else echo "# par_kit_configuration="; fi )
$( if [ ! -z ${VIASH_PAR_LEGACY_FASTQ+x} ]; then echo "${VIASH_PAR_LEGACY_FASTQ}" | sed "s#'#'\"'\"'#g;s#.*#par_legacy_fastq='&'#" ; else echo "# par_legacy_fastq="; fi )
$( if [ ! -z ${VIASH_PAR_LOG_LEVEL+x} ]; then echo "${VIASH_PAR_LOG_LEVEL}" | sed "s#'#'\"'\"'#g;s#.*#par_log_level='&'#" ; else echo "# par_log_level="; fi )
$( if [ ! -z ${VIASH_PAR_NO_ERROR_ON_INVALID+x} ]; then echo "${VIASH_PAR_NO_ERROR_ON_INVALID}" | sed "s#'#'\"'\"'#g;s#.*#par_no_error_on_invalid='&'#" ; else echo "# par_no_error_on_invalid="; fi )
$( if [ ! -z ${VIASH_PAR_NO_PROJECTS+x} ]; then echo "${VIASH_PAR_NO_PROJECTS}" | sed "s#'#'\"'\"'#g;s#.*#par_no_projects='&'#" ; else echo "# par_no_projects="; fi )
$( if [ ! -z ${VIASH_PAR_NUM_UNASSIGNED+x} ]; then echo "${VIASH_PAR_NUM_UNASSIGNED}" | sed "s#'#'\"'\"'#g;s#.*#par_num_unassigned='&'#" ; else echo "# par_num_unassigned="; fi )
$( if [ ! -z ${VIASH_PAR_PREPARATION_WORKFLOW+x} ]; then echo "${VIASH_PAR_PREPARATION_WORKFLOW}" | sed "s#'#'\"'\"'#g;s#.*#par_preparation_workflow='&'#" ; else echo "# par_preparation_workflow="; fi )
$( if [ ! -z ${VIASH_PAR_QC_ONLY+x} ]; then echo "${VIASH_PAR_QC_ONLY}" | sed "s#'#'\"'\"'#g;s#.*#par_qc_only='&'#" ; else echo "# par_qc_only="; fi )
$( if [ ! -z ${VIASH_PAR_R1_CYCLES+x} ]; then echo "${VIASH_PAR_R1_CYCLES}" | sed "s#'#'\"'\"'#g;s#.*#par_r1_cycles='&'#" ; else echo "# par_r1_cycles="; fi )
$( if [ ! -z ${VIASH_PAR_R2_CYCLES+x} ]; then echo "${VIASH_PAR_R2_CYCLES}" | sed "s#'#'\"'\"'#g;s#.*#par_r2_cycles='&'#" ; else echo "# par_r2_cycles="; fi )
$( if [ ! -z ${VIASH_PAR_SPLIT_LANES+x} ]; then echo "${VIASH_PAR_SPLIT_LANES}" | sed "s#'#'\"'\"'#g;s#.*#par_split_lanes='&'#" ; else echo "# par_split_lanes="; fi )
$( if [ ! -z ${VIASH_PAR_SKIP_QC_REPORT+x} ]; then echo "${VIASH_PAR_SKIP_QC_REPORT}" | sed "s#'#'\"'\"'#g;s#.*#par_skip_qc_report='&'#" ; else echo "# par_skip_qc_report="; fi )
$( if [ ! -z ${VIASH_PAR_SKIP_MULTI_QC+x} ]; then echo "${VIASH_PAR_SKIP_MULTI_QC}" | sed "s#'#'\"'\"'#g;s#.*#par_skip_multi_qc='&'#" ; else echo "# par_skip_multi_qc="; fi )
$( if [ ! -z ${VIASH_PAR_SETTINGS+x} ]; then echo "${VIASH_PAR_SETTINGS}" | sed "s#'#'\"'\"'#g;s#.*#par_settings='&'#" ; else echo "# par_settings="; fi )
$( if [ ! -z ${VIASH_PAR_BATCH+x} ]; then echo "${VIASH_PAR_BATCH}" | sed "s#'#'\"'\"'#g;s#.*#par_batch='&'#" ; else echo "# par_batch="; fi )
$( if [ ! -z ${VIASH_PAR_CYTO_FASTQ_MASK+x} ]; then echo "${VIASH_PAR_CYTO_FASTQ_MASK}" | sed "s#'#'\"'\"'#g;s#.*#par_cyto_fastq_mask='&'#" ; else echo "# par_cyto_fastq_mask="; fi )
$( if [ ! -z ${VIASH_PAR_PANEL+x} ]; then echo "${VIASH_PAR_PANEL}" | sed "s#'#'\"'\"'#g;s#.*#par_panel='&'#" ; else echo "# par_panel="; fi )
$( if [ ! -z ${VIASH_PAR_PER_TARGET_FASTQ+x} ]; then echo "${VIASH_PAR_PER_TARGET_FASTQ}" | sed "s#'#'\"'\"'#g;s#.*#par_per_target_fastq='&'#" ; else echo "# par_per_target_fastq="; fi )
$( if [ ! -z ${VIASH_PAR_TCA_MANIFEST+x} ]; then echo "${VIASH_PAR_TCA_MANIFEST}" | sed "s#'#'\"'\"'#g;s#.*#par_tca_manifest='&'#" ; else echo "# par_tca_manifest="; 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

# Exit on error
set -eo pipefail

# Unset parameters
unset_if_false=(
  par_demux_only
  par_detect_adapters
  par_error_on_missing
  par_group_fastq
  par_legacy_fastq
  par_no_error_on_invalid
  par_no_projects
  par_qc_only
  par_split_lanes
  par_skip_qc_report
  par_skip_multi_qc
  par_force_index_orientation
  par_per_target_fastq
)

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

# Create arrays for inputs that contain multiple arguments
IFS=";" read -ra exclude_tile <<< "\$par_exclude_tile"
IFS=";" read -ra include_tile <<< "\$par_include_tile"
IFS=";" read -ra settings <<< "\$par_settings"
IFS=";" read -ra cyto_fastq_mask <<< "\$par_cyto_fastq_mask"

echo "> Creating temporary directory."
# create temporary directory and clean up on exit
TMPDIR=\$(mktemp -d "\$meta_temp_dir/\$meta_name-XXXXXX")
echo "> Created \$TMPDIR"
function clean_up {
  [[ -d "\$TMPDIR" ]] && rm -rf "\$TMPDIR"
}
trap clean_up EXIT

# NOTE: --preparation-workflow is bugged in bases2fastq
args=(
  \${par_demux_only:+--demux-only}
  \${par_detect_adapters:+--detect-adapters}
  \${par_error_on_missing:+--error-on-missing}
  \${par_group_fastq:+--group-fastq}
  \${par_legacy_fastq:+--legacy-fastq}
  \${par_no_error_on_invalid:+--no-error-on-invalid}
  \${par_no_projects:+--no-projects}
  \${par_split_lanes:+--split-lanes}
  \${par_force_index_orientation:+--force-index-orientation}
  \${par_skip_qc_report:+--skip-qc-report}
  \${par_skip_multi_qc:+--skip-multi-qc}
  \${par_per_target_fastq:+--per-target-fastq}
  \${par_chemistry_version:+--chemistry-version "\$par_chemistry_version"}
  \${par_filter_mask:+--filter-mask "\$par_filter_mask"}
  \${par_flowcell_id:+--flowcell-id "\$par_flowcell_id"}
  \${par_i1_cycles:+--i1-cycles "\$par_i1_cycles"}
  \${par_i2_cycles:+--i2-cycles "\$par_i2_cycles"}
  \${par_r1_cycles:+--r1-cycles "\$par_r1_cycles"}
  \${par_r2_cycles:+--r2-cycles "\$par_r2_cycles"}
  \${par_kit_configuration:+--kit-configuration "\$par_kit_configuration"}
  \${par_log_level:+--log-level "\$par_log_level"}
  \${par_num_unassigned:+--num-unassigned "\$par_num_unassigned"}
  \${par_preparation_workflow:+--preparation-workflow "\$par_preparation_workflow"}
  \${par_batch:+--batch "\$par_batch"}
  \${par_panel:+--panel "\$par_panel"}
  \${par_tca_manifest:+--tca-manifest "\$par_tca_manifest"}
  \${meta_cpus:+--num-threads "\$meta_cpus"}
  \${par_run_manifest:+--run-manifest "\$par_run_manifest"}
)

if [ -z "\$par_report" ]; then
  args+=( --skip-qc-report )
fi

for arg_value in "\${exclude_tile[@]}"; do
  args+=( "--exclude-tile" "\$arg_value" )
done

for arg_value in "\${include_tile[@]}"; do
  args+=( "--include-tile" "\$arg_value" )
done

for arg_value in "\${settings[@]}"; do
  args+=( "--settings" "\$arg_value" )
done

for arg_value in "\${cyto_fastq_mask[@]}"; do
  args+=( "--cyto-fastq-mask" "\$arg_value" )
done

args+=( "\$par_analysis_directory" "\$TMPDIR")
echo "> Running bases2fastq with arguments: \${args[@]}"
bases2fastq \${args[@]}
echo "> Done running sgdemux"

echo "> Moving FASTQ files into final output directory"
mkdir -p "\$par_output_directory/"
mv "\$TMPDIR"/Samples/* --target-directory="\$par_output_directory"

if [ ! -z "\$par_report" ]; then
  echo "> Moving HTML report to the output (\$par_report)"
  # Find HTML files in TMPDIR
  html_files=("\$TMPDIR"/*.html)
  if [ -f "\${html_files[0]}" ]; then
    # If there's only one HTML file, move it to the specified report path
    if [ \${#html_files[@]} -eq 1 ]; then
      mv "\${html_files[0]}" "\$par_report"
    else
      # Multiple HTML files - find the main QC report and move it to the specified path
      # bases2fastq generates both QC report and MultiQC report
      for html_file in "\${html_files[@]}"; do
        # The main QC report is usually not named multiqc_report.html
        if [[ ! "\$(basename "\$html_file")" =~ ^multiqc.*\\.html\$ ]]; then
          mv "\$html_file" "\$par_report"
          break
        fi
      done
    fi
  fi
else
  echo " > Leaving reports alone"
fi

# Logs is everything else
if [ ! -z "\$par_logs" ]; then
  mkdir -p "\$par_logs"
  echo "> Moving logs to their own location (\$par_logs)"
  mv "\$TMPDIR/"* "\$par_logs/"
else
  echo "> Not moving logs"
fi
VIASHMAIN
bash "\$tempscript" &
wait "\$!"

VIASHEOF


if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  # strip viash automount from file paths
  
  if [ ! -z "$VIASH_PAR_ANALYSIS_DIRECTORY" ]; then
    VIASH_PAR_ANALYSIS_DIRECTORY=$(ViashDockerStripAutomount "$VIASH_PAR_ANALYSIS_DIRECTORY")
  fi
  if [ ! -z "$VIASH_PAR_RUN_MANIFEST" ]; then
    VIASH_PAR_RUN_MANIFEST=$(ViashDockerStripAutomount "$VIASH_PAR_RUN_MANIFEST")
  fi
  if [ ! -z "$VIASH_PAR_OUTPUT_DIRECTORY" ]; then
    VIASH_PAR_OUTPUT_DIRECTORY=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT_DIRECTORY")
  fi
  if [ ! -z "$VIASH_PAR_REPORT" ]; then
    VIASH_PAR_REPORT=$(ViashDockerStripAutomount "$VIASH_PAR_REPORT")
  fi
  if [ ! -z "$VIASH_PAR_LOGS" ]; then
    VIASH_PAR_LOGS=$(ViashDockerStripAutomount "$VIASH_PAR_LOGS")
  fi
  if [ ! -z "$VIASH_PAR_PANEL" ]; then
    VIASH_PAR_PANEL=$(ViashDockerStripAutomount "$VIASH_PAR_PANEL")
  fi
  if [ ! -z "$VIASH_PAR_TCA_MANIFEST" ]; then
    VIASH_PAR_TCA_MANIFEST=$(ViashDockerStripAutomount "$VIASH_PAR_TCA_MANIFEST")
  fi
  if [ ! -z "$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 "$VIASH_PAR_OUTPUT_DIRECTORY" ] && [ ! -e "$VIASH_PAR_OUTPUT_DIRECTORY" ]; then
  ViashError "Output file '$VIASH_PAR_OUTPUT_DIRECTORY' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_REPORT" ] && [ ! -e "$VIASH_PAR_REPORT" ]; then
  ViashError "Output file '$VIASH_PAR_REPORT' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_LOGS" ] && [ ! -e "$VIASH_PAR_LOGS" ]; then
  ViashError "Output file '$VIASH_PAR_LOGS' does not exist."
  exit 1
fi


exit 0
