#!/usr/bin/env bash

# highly_variable_features_scanpy v4.1.0
# 
# This wrapper script is auto-generated by viash 0.9.7 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 De Maeyer (contributor)
#  * Robrecht Cannoodt (maintainer, contributor)

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="highly_variable_features_scanpy"
VIASH_META_FUNCTIONALITY_NAME="highly_variable_features_scanpy"
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 python:3.12
ENTRYPOINT []
RUN pip install --upgrade pip && \
  pip install --upgrade --no-cache-dir "anndata~=0.12.16" "awkward" "scipy~=1.17.1" "mudata~=0.3.8" "scanpy~=1.11.4" "scikit-misc" && \
  python -c 'exec("try:\n  import zarr; from importlib.metadata import version\nexcept ModuleNotFoundError:\n  exit(0)\nelse:  assert int(version(\"zarr\").partition(\".\")[0]) > 2")'

LABEL org.opencontainers.image.authors="Dries De Maeyer, Robrecht Cannoodt"
LABEL org.opencontainers.image.description="Companion container for running component feature_annotation highly_variable_features_scanpy"
LABEL org.opencontainers.image.created="2026-05-27T07:39:06Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
LABEL org.opencontainers.image.revision="a6499fddaa8553874585c747370f919f4d7b729c"
LABEL org.opencontainers.image.version="v4.1.0"

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 "highly_variable_features_scanpy v4.1.0"
  echo ""
  echo "Annotate highly variable features [Satija15] [Zheng17] [Stuart19]."
  echo ""
  echo "Expects logarithmized data, except when flavor='seurat_v3' in which count data"
  echo "is expected."
  echo ""
  echo "Depending on flavor, this reproduces the R-implementations of Seurat [Satija15],"
  echo "Cell Ranger [Zheng17], and Seurat v3 [Stuart19]."
  echo ""
  echo "For the dispersion-based methods ([Satija15] and [Zheng17]), the normalized"
  echo "dispersion is obtained by scaling with the mean and standard deviation of the"
  echo "dispersions for features falling into a given bin for mean expression of"
  echo "features. This means that for each bin of mean expression, highly variable"
  echo "features are selected."
  echo ""
  echo "For [Stuart19], a normalized variance for each feature is computed. First, the"
  echo "data are standardized (i.e., z-score normalization per feature) with a"
  echo "regularized standard deviation. Next, the normalized variance is computed as the"
  echo "variance of each feature after the transformation. Features are ranked by the"
  echo "normalized variance."
  echo ""
  echo "Arguments:"
  echo "    --input"
  echo "        type: file, required parameter, file must exist"
  echo "        example: input.h5mu"
  echo "        Input h5mu file"
  echo ""
  echo "    --modality"
  echo "        type: string"
  echo "        default: rna"
  echo "        Which modality from the input MuData file to process."
  echo ""
  echo "    --layer"
  echo "        type: string"
  echo "        use adata.layers[layer] for expression values instead of adata.X."
  echo ""
  echo "    --var_input"
  echo "        type: string"
  echo "        If specified, use boolean array in adata.var[var_input] to calculate hvg"
  echo "        on subset of vars."
  echo ""
  echo "    --features_to_exclude"
  echo "        type: string, multiple values allowed"
  echo "        example: MT-CO1;MT-CO2;MT-ND1"
  echo "        User-defined list of feature names to exclude before HVG calculation."
  echo "        These features will be excluded from HVG selection but will remain in"
  echo "        the output data."
  echo ""
  echo "    --output"
  echo "        type: file, output, file must exist"
  echo "        example: output.h5mu"
  echo "        Output h5mu file."
  echo ""
  echo "    --var_name_filter"
  echo "        type: string"
  echo "        default: filter_with_hvg"
  echo "        In which .var slot to store a boolean array corresponding to which"
  echo "        observations should be filtered out."
  echo ""
  echo "    --varm_name"
  echo "        type: string"
  echo "        default: hvg"
  echo "        In which .varm slot to store additional metadata."
  echo ""
  echo "    --flavor"
  echo "        type: string"
  echo "        default: seurat"
  echo "        choices: [ seurat, cell_ranger, seurat_v3 ]"
  echo "        Choose the flavor for identifying highly variable features. For the"
  echo "        dispersion based methods"
  echo "        in their default workflows, Seurat passes the cutoffs whereas Cell"
  echo "        Ranger passes n_top_features."
  echo ""
  echo "    --n_top_features"
  echo "        type: integer"
  echo "        Number of highly-variable features to keep. Mandatory if"
  echo "        flavor='seurat_v3'."
  echo ""
  echo "    --min_mean"
  echo "        type: double"
  echo "        default: 0.0125"
  echo "        If n_top_features is defined, this and all other cutoffs for the means"
  echo "        and the normalized dispersions are ignored. Ignored if"
  echo "        flavor='seurat_v3'."
  echo ""
  echo "    --max_mean"
  echo "        type: double"
  echo "        default: 3.0"
  echo "        If n_top_features is defined, this and all other cutoffs for the means"
  echo "        and the normalized dispersions are ignored. Ignored if"
  echo "        flavor='seurat_v3'."
  echo ""
  echo "    --min_disp"
  echo "        type: double"
  echo "        default: 0.5"
  echo "        If n_top_features is defined, this and all other cutoffs for the means"
  echo "        and the normalized dispersions are ignored. Ignored if"
  echo "        flavor='seurat_v3'."
  echo ""
  echo "    --max_disp"
  echo "        type: double"
  echo "        If n_top_features is defined, this and all other cutoffs for the means"
  echo "        and the normalized dispersions are ignored. Ignored if"
  echo "        flavor='seurat_v3'. Default is +inf."
  echo ""
  echo "    --span"
  echo "        type: double"
  echo "        default: 0.3"
  echo "        The fraction of the data (cells) used when estimating the variance in"
  echo "        the loess model fit if flavor='seurat_v3'."
  echo ""
  echo "    --n_bins"
  echo "        type: integer"
  echo "        default: 20"
  echo "        Number of bins for binning the mean feature expression. Normalization is"
  echo "        done with respect to each bin. If just a single feature falls into a"
  echo "        bin, the normalized dispersion is artificially set to 1."
  echo ""
  echo "    --obs_batch_key"
  echo "        type: string"
  echo "        If specified, highly-variable features are selected within each batch"
  echo "        separately and merged. This simple"
  echo "        process avoids the selection of batch-specific features and acts as a"
  echo "        lightweight batch correction method."
  echo "        For all flavors, features are first sorted by how many batches they are"
  echo "        a HVG. For dispersion-based flavors"
  echo "        ties are broken by normalized dispersion. If flavor = 'seurat_v3', ties"
  echo "        are broken by the median (across"
  echo "        batches) rank based on within-batch normalized variance."
  echo ""
  echo "    --output_compression"
  echo "        type: string"
  echo "        example: gzip"
  echo "        choices: [ gzip, lzf ]"
  echo "        Compression format to use for the output AnnData and/or Mudata H5 files."
  echo "        By default no compression is applied."
  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 "$1")"
            shift 1
            ;;
        --version)
            echo "highly_variable_features_scanpy v4.1.0"
            exit
            ;;
        --input)
            [ -n "$VIASH_PAR_INPUT" ] && ViashError Bad arguments for option \'--input\': \'$VIASH_PAR_INPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INPUT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --input. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --input=*)
            [ -n "$VIASH_PAR_INPUT" ] && ViashError Bad arguments for option \'--input=*\': \'$VIASH_PAR_INPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INPUT=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --modality)
            [ -n "$VIASH_PAR_MODALITY" ] && ViashError Bad arguments for option \'--modality\': \'$VIASH_PAR_MODALITY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MODALITY="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --modality. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --modality=*)
            [ -n "$VIASH_PAR_MODALITY" ] && ViashError Bad arguments for option \'--modality=*\': \'$VIASH_PAR_MODALITY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MODALITY=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --layer)
            [ -n "$VIASH_PAR_LAYER" ] && ViashError Bad arguments for option \'--layer\': \'$VIASH_PAR_LAYER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LAYER="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --layer. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --layer=*)
            [ -n "$VIASH_PAR_LAYER" ] && ViashError Bad arguments for option \'--layer=*\': \'$VIASH_PAR_LAYER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LAYER=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --var_input)
            [ -n "$VIASH_PAR_VAR_INPUT" ] && ViashError Bad arguments for option \'--var_input\': \'$VIASH_PAR_VAR_INPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_VAR_INPUT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --var_input. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --var_input=*)
            [ -n "$VIASH_PAR_VAR_INPUT" ] && ViashError Bad arguments for option \'--var_input=*\': \'$VIASH_PAR_VAR_INPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_VAR_INPUT=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --features_to_exclude)
            if [ -z "$VIASH_PAR_FEATURES_TO_EXCLUDE" ]; then
              VIASH_PAR_FEATURES_TO_EXCLUDE="$2"
            else
              VIASH_PAR_FEATURES_TO_EXCLUDE="$VIASH_PAR_FEATURES_TO_EXCLUDE;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --features_to_exclude. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --features_to_exclude=*)
            if [ -z "$VIASH_PAR_FEATURES_TO_EXCLUDE" ]; then
              VIASH_PAR_FEATURES_TO_EXCLUDE=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_FEATURES_TO_EXCLUDE="$VIASH_PAR_FEATURES_TO_EXCLUDE;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --output)
            [ -n "$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 "$1")
            shift 1
            ;;
        --var_name_filter)
            [ -n "$VIASH_PAR_VAR_NAME_FILTER" ] && ViashError Bad arguments for option \'--var_name_filter\': \'$VIASH_PAR_VAR_NAME_FILTER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_VAR_NAME_FILTER="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --var_name_filter. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --var_name_filter=*)
            [ -n "$VIASH_PAR_VAR_NAME_FILTER" ] && ViashError Bad arguments for option \'--var_name_filter=*\': \'$VIASH_PAR_VAR_NAME_FILTER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_VAR_NAME_FILTER=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --varm_name)
            [ -n "$VIASH_PAR_VARM_NAME" ] && ViashError Bad arguments for option \'--varm_name\': \'$VIASH_PAR_VARM_NAME\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_VARM_NAME="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --varm_name. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --varm_name=*)
            [ -n "$VIASH_PAR_VARM_NAME" ] && ViashError Bad arguments for option \'--varm_name=*\': \'$VIASH_PAR_VARM_NAME\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_VARM_NAME=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --flavor)
            [ -n "$VIASH_PAR_FLAVOR" ] && ViashError Bad arguments for option \'--flavor\': \'$VIASH_PAR_FLAVOR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FLAVOR="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --flavor. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --flavor=*)
            [ -n "$VIASH_PAR_FLAVOR" ] && ViashError Bad arguments for option \'--flavor=*\': \'$VIASH_PAR_FLAVOR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FLAVOR=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --n_top_features)
            [ -n "$VIASH_PAR_N_TOP_FEATURES" ] && ViashError Bad arguments for option \'--n_top_features\': \'$VIASH_PAR_N_TOP_FEATURES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_N_TOP_FEATURES="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --n_top_features. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --n_top_features=*)
            [ -n "$VIASH_PAR_N_TOP_FEATURES" ] && ViashError Bad arguments for option \'--n_top_features=*\': \'$VIASH_PAR_N_TOP_FEATURES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_N_TOP_FEATURES=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --min_mean)
            [ -n "$VIASH_PAR_MIN_MEAN" ] && ViashError Bad arguments for option \'--min_mean\': \'$VIASH_PAR_MIN_MEAN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MIN_MEAN="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --min_mean. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --min_mean=*)
            [ -n "$VIASH_PAR_MIN_MEAN" ] && ViashError Bad arguments for option \'--min_mean=*\': \'$VIASH_PAR_MIN_MEAN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MIN_MEAN=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --max_mean)
            [ -n "$VIASH_PAR_MAX_MEAN" ] && ViashError Bad arguments for option \'--max_mean\': \'$VIASH_PAR_MAX_MEAN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_MEAN="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --max_mean. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --max_mean=*)
            [ -n "$VIASH_PAR_MAX_MEAN" ] && ViashError Bad arguments for option \'--max_mean=*\': \'$VIASH_PAR_MAX_MEAN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_MEAN=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --min_disp)
            [ -n "$VIASH_PAR_MIN_DISP" ] && ViashError Bad arguments for option \'--min_disp\': \'$VIASH_PAR_MIN_DISP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MIN_DISP="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --min_disp. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --min_disp=*)
            [ -n "$VIASH_PAR_MIN_DISP" ] && ViashError Bad arguments for option \'--min_disp=*\': \'$VIASH_PAR_MIN_DISP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MIN_DISP=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --max_disp)
            [ -n "$VIASH_PAR_MAX_DISP" ] && ViashError Bad arguments for option \'--max_disp\': \'$VIASH_PAR_MAX_DISP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_DISP="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --max_disp. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --max_disp=*)
            [ -n "$VIASH_PAR_MAX_DISP" ] && ViashError Bad arguments for option \'--max_disp=*\': \'$VIASH_PAR_MAX_DISP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_DISP=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --span)
            [ -n "$VIASH_PAR_SPAN" ] && ViashError Bad arguments for option \'--span\': \'$VIASH_PAR_SPAN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SPAN="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --span. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --span=*)
            [ -n "$VIASH_PAR_SPAN" ] && ViashError Bad arguments for option \'--span=*\': \'$VIASH_PAR_SPAN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SPAN=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --n_bins)
            [ -n "$VIASH_PAR_N_BINS" ] && ViashError Bad arguments for option \'--n_bins\': \'$VIASH_PAR_N_BINS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_N_BINS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --n_bins. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --n_bins=*)
            [ -n "$VIASH_PAR_N_BINS" ] && ViashError Bad arguments for option \'--n_bins=*\': \'$VIASH_PAR_N_BINS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_N_BINS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --obs_batch_key)
            [ -n "$VIASH_PAR_OBS_BATCH_KEY" ] && ViashError Bad arguments for option \'--obs_batch_key\': \'$VIASH_PAR_OBS_BATCH_KEY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OBS_BATCH_KEY="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --obs_batch_key. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --obs_batch_key=*)
            [ -n "$VIASH_PAR_OBS_BATCH_KEY" ] && ViashError Bad arguments for option \'--obs_batch_key=*\': \'$VIASH_PAR_OBS_BATCH_KEY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OBS_BATCH_KEY=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --output_compression)
            [ -n "$VIASH_PAR_OUTPUT_COMPRESSION" ] && ViashError Bad arguments for option \'--output_compression\': \'$VIASH_PAR_OUTPUT_COMPRESSION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_COMPRESSION="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --output_compression. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --output_compression=*)
            [ -n "$VIASH_PAR_OUTPUT_COMPRESSION" ] && ViashError Bad arguments for option \'--output_compression=*\': \'$VIASH_PAR_OUTPUT_COMPRESSION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_COMPRESSION=$(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/openpipeline/feature_annotation/highly_variable_features_scanpy:v4.1.0'
  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_INPUT+x} ]; then
  ViashError '--input' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_NAME+x} ]; then
  ViashError 'name' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then
  ViashError 'functionality_name' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_RESOURCES_DIR+x} ]; then
  ViashError 'resources_dir' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_EXECUTABLE+x} ]; then
  ViashError 'executable' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_CONFIG+x} ]; then
  ViashError 'config' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_TEMP_DIR+x} ]; then
  ViashError 'temp_dir' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi

# filling in defaults
if [ -z ${VIASH_PAR_MODALITY+x} ]; then
  VIASH_PAR_MODALITY="rna"
fi
if [ -z ${VIASH_PAR_VAR_NAME_FILTER+x} ]; then
  VIASH_PAR_VAR_NAME_FILTER="filter_with_hvg"
fi
if [ -z ${VIASH_PAR_VARM_NAME+x} ]; then
  VIASH_PAR_VARM_NAME="hvg"
fi
if [ -z ${VIASH_PAR_FLAVOR+x} ]; then
  VIASH_PAR_FLAVOR="seurat"
fi
if [ -z ${VIASH_PAR_MIN_MEAN+x} ]; then
  VIASH_PAR_MIN_MEAN="0.0125"
fi
if [ -z ${VIASH_PAR_MAX_MEAN+x} ]; then
  VIASH_PAR_MAX_MEAN="3.0"
fi
if [ -z ${VIASH_PAR_MIN_DISP+x} ]; then
  VIASH_PAR_MIN_DISP="0.5"
fi
if [ -z ${VIASH_PAR_SPAN+x} ]; then
  VIASH_PAR_SPAN="0.3"
fi
if [ -z ${VIASH_PAR_N_BINS+x} ]; then
  VIASH_PAR_N_BINS="20"
fi

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

# check whether parameters values are of the right type
if [[ -n "$VIASH_PAR_N_TOP_FEATURES" ]]; then
  if ! [[ "$VIASH_PAR_N_TOP_FEATURES" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--n_top_features' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_MIN_MEAN" ]]; then
  if ! [[ "$VIASH_PAR_MIN_MEAN" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--min_mean' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_MAX_MEAN" ]]; then
  if ! [[ "$VIASH_PAR_MAX_MEAN" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--max_mean' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_MIN_DISP" ]]; then
  if ! [[ "$VIASH_PAR_MIN_DISP" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--min_disp' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_MAX_DISP" ]]; then
  if ! [[ "$VIASH_PAR_MAX_DISP" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--max_disp' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SPAN" ]]; then
  if ! [[ "$VIASH_PAR_SPAN" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--span' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_N_BINS" ]]; then
  if ! [[ "$VIASH_PAR_N_BINS" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--n_bins' has to be an integer. 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 "$VIASH_PAR_FLAVOR" ]; then
  VIASH_PAR_FLAVOR_CHOICES=("seurat;cell_ranger;seurat_v3")
  IFS=';'
  set -f
  if ! [[ ";${VIASH_PAR_FLAVOR_CHOICES[*]};" =~ ";$VIASH_PAR_FLAVOR;" ]]; then
    ViashError '--flavor' specified value of \'$VIASH_PAR_FLAVOR\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
    exit 1
  fi
  set +f
  unset IFS
fi

if [ ! -z "$VIASH_PAR_OUTPUT_COMPRESSION" ]; then
  VIASH_PAR_OUTPUT_COMPRESSION_CHOICES=("gzip;lzf")
  IFS=';'
  set -f
  if ! [[ ";${VIASH_PAR_OUTPUT_COMPRESSION_CHOICES[*]};" =~ ";$VIASH_PAR_OUTPUT_COMPRESSION;" ]]; then
    ViashError '--output_compression' specified value of \'$VIASH_PAR_OUTPUT_COMPRESSION\' 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_INPUT" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INPUT")" )
  VIASH_PAR_INPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_INPUT")
fi
if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT")" )
  VIASH_PAR_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT" )
fi
if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_RESOURCES_DIR")" )
  VIASH_META_RESOURCES_DIR=$(ViashDockerAutodetectMount "$VIASH_META_RESOURCES_DIR")
fi
if [ ! -z "$VIASH_META_EXECUTABLE" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_EXECUTABLE")" )
  VIASH_META_EXECUTABLE=$(ViashDockerAutodetectMount "$VIASH_META_EXECUTABLE")
fi
if [ ! -z "$VIASH_META_CONFIG" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_CONFIG")" )
  VIASH_META_CONFIG=$(ViashDockerAutodetectMount "$VIASH_META_CONFIG")
fi
if [ ! -z "$VIASH_META_TEMP_DIR" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_TEMP_DIR")" )
  VIASH_META_TEMP_DIR=$(ViashDockerAutodetectMount "$VIASH_META_TEMP_DIR")
fi
  
  # get unique mounts
  VIASH_UNIQUE_MOUNTS=($(for val in "${VIASH_DIRECTORY_MOUNTS[@]}"; do echo "$val"; done | sort -u))
fi

if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  # change file ownership
  function ViashPerformChown {
    if (( ${#VIASH_CHOWN_VARS[@]} )); then
      set +e
      VIASH_CMD="docker run --entrypoint=bash --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_DOCKER_IMAGE_ID -c 'chown $(id -u):$(id -g) --silent --recursive ${VIASH_CHOWN_VARS[@]}'"
      ViashDebug "+ $VIASH_CMD"
      eval $VIASH_CMD
      set -e
    fi
  }
  trap ViashPerformChown EXIT
fi

if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  # helper function for filling in extra docker args
  if [ ! -z "$VIASH_META_MEMORY_B" ]; then
    VIASH_DOCKER_RUN_ARGS+=("--memory=${VIASH_META_MEMORY_B}")
  fi
  if [ ! -z "$VIASH_META_CPUS" ]; then
    VIASH_DOCKER_RUN_ARGS+=("--cpus=${VIASH_META_CPUS}")
  fi
fi

if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  VIASH_CMD="docker run --entrypoint=bash ${VIASH_DOCKER_RUN_ARGS[@]} ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_DOCKER_IMAGE_ID"
fi


# set dependency paths


ViashDebug "Running command: $(echo $VIASH_CMD)"
cat << VIASHEOF | eval $VIASH_CMD
set -e
tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-highly_variable_features_scanpy-XXXXXX").py
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'
import scanpy as sc
import mudata as mu
import anndata as ad
import pandas as pd
import sys
import re

## VIASH START
# The following code has been auto-generated by Viash.
par = {
  'input': $( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "r'${VIASH_PAR_INPUT//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'modality': $( if [ ! -z ${VIASH_PAR_MODALITY+x} ]; then echo "r'${VIASH_PAR_MODALITY//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'layer': $( if [ ! -z ${VIASH_PAR_LAYER+x} ]; then echo "r'${VIASH_PAR_LAYER//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'var_input': $( if [ ! -z ${VIASH_PAR_VAR_INPUT+x} ]; then echo "r'${VIASH_PAR_VAR_INPUT//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'features_to_exclude': $( if [ ! -z ${VIASH_PAR_FEATURES_TO_EXCLUDE+x} ]; then echo "r'${VIASH_PAR_FEATURES_TO_EXCLUDE//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'output': $( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "r'${VIASH_PAR_OUTPUT//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'var_name_filter': $( if [ ! -z ${VIASH_PAR_VAR_NAME_FILTER+x} ]; then echo "r'${VIASH_PAR_VAR_NAME_FILTER//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'varm_name': $( if [ ! -z ${VIASH_PAR_VARM_NAME+x} ]; then echo "r'${VIASH_PAR_VARM_NAME//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'flavor': $( if [ ! -z ${VIASH_PAR_FLAVOR+x} ]; then echo "r'${VIASH_PAR_FLAVOR//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'n_top_features': $( if [ ! -z ${VIASH_PAR_N_TOP_FEATURES+x} ]; then echo "int(r'${VIASH_PAR_N_TOP_FEATURES//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'min_mean': $( if [ ! -z ${VIASH_PAR_MIN_MEAN+x} ]; then echo "float(r'${VIASH_PAR_MIN_MEAN//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'max_mean': $( if [ ! -z ${VIASH_PAR_MAX_MEAN+x} ]; then echo "float(r'${VIASH_PAR_MAX_MEAN//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'min_disp': $( if [ ! -z ${VIASH_PAR_MIN_DISP+x} ]; then echo "float(r'${VIASH_PAR_MIN_DISP//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'max_disp': $( if [ ! -z ${VIASH_PAR_MAX_DISP+x} ]; then echo "float(r'${VIASH_PAR_MAX_DISP//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'span': $( if [ ! -z ${VIASH_PAR_SPAN+x} ]; then echo "float(r'${VIASH_PAR_SPAN//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'n_bins': $( if [ ! -z ${VIASH_PAR_N_BINS+x} ]; then echo "int(r'${VIASH_PAR_N_BINS//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'obs_batch_key': $( if [ ! -z ${VIASH_PAR_OBS_BATCH_KEY+x} ]; then echo "r'${VIASH_PAR_OBS_BATCH_KEY//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'output_compression': $( if [ ! -z ${VIASH_PAR_OUTPUT_COMPRESSION+x} ]; then echo "r'${VIASH_PAR_OUTPUT_COMPRESSION//\'/\'\"\'\"r\'}'"; else echo None; fi )
}
meta = {
  'name': $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "r'${VIASH_META_NAME//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'functionality_name': $( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "r'${VIASH_META_FUNCTIONALITY_NAME//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'resources_dir': $( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "r'${VIASH_META_RESOURCES_DIR//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'executable': $( if [ ! -z ${VIASH_META_EXECUTABLE+x} ]; then echo "r'${VIASH_META_EXECUTABLE//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'config': $( if [ ! -z ${VIASH_META_CONFIG+x} ]; then echo "r'${VIASH_META_CONFIG//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'temp_dir': $( if [ ! -z ${VIASH_META_TEMP_DIR+x} ]; then echo "r'${VIASH_META_TEMP_DIR//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'cpus': $( if [ ! -z ${VIASH_META_CPUS+x} ]; then echo "int(r'${VIASH_META_CPUS//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_b': $( if [ ! -z ${VIASH_META_MEMORY_B+x} ]; then echo "int(r'${VIASH_META_MEMORY_B//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_kb': $( if [ ! -z ${VIASH_META_MEMORY_KB+x} ]; then echo "int(r'${VIASH_META_MEMORY_KB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_mb': $( if [ ! -z ${VIASH_META_MEMORY_MB+x} ]; then echo "int(r'${VIASH_META_MEMORY_MB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_gb': $( if [ ! -z ${VIASH_META_MEMORY_GB+x} ]; then echo "int(r'${VIASH_META_MEMORY_GB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_tb': $( if [ ! -z ${VIASH_META_MEMORY_TB+x} ]; then echo "int(r'${VIASH_META_MEMORY_TB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_pb': $( if [ ! -z ${VIASH_META_MEMORY_PB+x} ]; then echo "int(r'${VIASH_META_MEMORY_PB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_kib': $( if [ ! -z ${VIASH_META_MEMORY_KIB+x} ]; then echo "int(r'${VIASH_META_MEMORY_KIB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_mib': $( if [ ! -z ${VIASH_META_MEMORY_MIB+x} ]; then echo "int(r'${VIASH_META_MEMORY_MIB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_gib': $( if [ ! -z ${VIASH_META_MEMORY_GIB+x} ]; then echo "int(r'${VIASH_META_MEMORY_GIB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_tib': $( if [ ! -z ${VIASH_META_MEMORY_TIB+x} ]; then echo "int(r'${VIASH_META_MEMORY_TIB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_pib': $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "int(r'${VIASH_META_MEMORY_PIB//\'/\'\"\'\"r\'}')"; else echo None; fi )
}
dep = {
  
}

## VIASH END

sys.path.append(meta["resources_dir"])
from setup_logger import setup_logger
from subset_vars import subset_vars
from compress_h5mu import write_h5ad_to_h5mu_with_compression

logger = setup_logger()
modality_name = par["modality"]
data = mu.read_h5ad(par["input"], mod=modality_name)
assert data.var_names.is_unique, "Expected var_names of input modality to be unique."

logger.info("Processing modality '%s'", modality_name)

if par["layer"] and par["layer"] not in data.layers:
    raise ValueError(
        f"Layer '{par['layer']}' not found in layers for modality '{modality_name}'. "
        f"Found layers are: {','.join(data.layers)}"
    )

# input layer argument does not work when batch_key is specified because
# it still uses .X to filter out genes with 0 counts, even if .X might not exist.
# So create a custom anndata as input that always uses .X
input_layer = data.X if not par["layer"] else data.layers[par["layer"]]
obs = pd.DataFrame(index=data.obs_names.copy())
var = pd.DataFrame(index=data.var_names.copy())
if par["obs_batch_key"]:
    obs = data.obs.loc[:, par["obs_batch_key"]].to_frame()
input_anndata = ad.AnnData(X=input_layer.copy(), obs=obs, var=var)
if "log1p" in data.uns:
    input_anndata.uns["log1p"] = data.uns["log1p"]

# Workaround for issue
# https://github.com/scverse/scanpy/issues/2239
# https://github.com/scverse/scanpy/issues/2181
if par["flavor"] != "seurat_v3":
    # This component requires log normalized data when flavor is not seurat_v3
    # We assume that the data is correctly normalized but scanpy will look at
    # .uns to check the transformations performed on the data.
    # To prevent scanpy from automatically tranforming the counts when they are
    # already transformed, we set the appropriate values to .uns.
    if "log1p" not in input_anndata.uns:
        logger.warning(
            "When flavor is not set to 'seurat_v3', "
            "the input data for this component must be log-transformed. "
            "However, the 'log1p' dictionairy in .uns has not been set. "
            "This is fine if you did not log transform your data with scanpy."
            "Otherwise, please check if you are providing log transformed "
            "data using --layer."
        )
        input_anndata.uns["log1p"] = {"base": None}
    elif "log1p" in input_anndata.uns and "base" not in input_anndata.uns["log1p"]:
        input_anndata.uns["log1p"]["base"] = None

# Enable calculating the HVG only on a subset of vars
# e.g for cell type annotation, only calculate HVG on variables that are common between query and reference
if par["var_input"]:
    input_anndata.var[par["var_input"]] = data.var[par["var_input"]]
    input_anndata = subset_vars(input_anndata, par["var_input"])

# Exclude user-specified features from HVG calculation
excluded_features_mask = None
if par.get("features_to_exclude"):
    features_to_exclude = set(par["features_to_exclude"])
    logger.info(
        "\\tExcluding %d specified features from HVG calculation",
        len(features_to_exclude),
    )
    excluded_features_mask = input_anndata.var_names.isin(features_to_exclude)
    n_excluded = excluded_features_mask.sum()
    n_not_found = len(features_to_exclude) - n_excluded
    if n_not_found > 0:
        not_found = features_to_exclude - set(
            input_anndata.var_names[excluded_features_mask]
        )
        logger.warning(
            "\\t%d features to exclude were not found in the data: %s",
            n_not_found,
            list(not_found)[:10],
        )
    logger.info("\\tExcluding %d features from HVG calculation", n_excluded)
    if n_excluded == input_anndata.n_vars:
        raise ValueError(
            f"All features ({n_excluded}) are in the exclusion list. "
            "Please check your --features_to_exclude list."
        )
    # Store original var_names for later reindexing
    original_var_names = input_anndata.var_names.copy()
    # Subset to non-excluded features for HVG calculation using subset_vars
    input_anndata = subset_vars(input_anndata, ~excluded_features_mask)
    logger.info("\\t%d features remaining for HVG calculation", input_anndata.n_vars)

logger.info("\\tUnfiltered data: %s", data)

logger.info("\\tComputing hvg")
# construct arguments
hvg_args = {
    "adata": input_anndata,
    "n_top_genes": par["n_top_features"],
    "min_mean": par["min_mean"],
    "max_mean": par["max_mean"],
    "min_disp": par["min_disp"],
    "span": par["span"],
    "n_bins": par["n_bins"],
    "flavor": par["flavor"],
    "subset": False,
    "inplace": False,
    "layer": None,  # Always uses .X because the input layer was already handled
}

optional_parameters = {
    "max_disp": "max_disp",
    "obs_batch_key": "batch_key",
    "n_top_genes": "n_top_features",
}
# only add parameter if it's passed
for par_name, dest_name in optional_parameters.items():
    if par.get(par_name):
        hvg_args[dest_name] = par[par_name]

# scanpy does not do this check, although it is stated in the documentation
if par["flavor"] == "seurat_v3" and not par["n_top_features"]:
    raise ValueError(
        "When flavor is set to 'seurat_v3', you are required to set 'n_top_features'."
    )

# call function
try:
    out = sc.pp.highly_variable_genes(**hvg_args)
    if par["var_input"] is not None:
        out.index = input_anndata.var.index
        out = out.reindex(index=data.var.index, method=None)
        out.highly_variable = out.highly_variable.fillna(False)
        assert (out.index == data.var.index).all(), (
            "Expected output index values to be equivalent to the input index"
        )
    elif par.get("features_to_exclude") is not None:
        # Reindex to include excluded features, marking them as non-HVG
        out.index = input_anndata.var.index
        out = out.reindex(index=original_var_names, method=None)
        out.highly_variable = out.highly_variable.fillna(False)
        # Further reindex to match data.var.index (for consistency with var_input path)
        out = out.reindex(index=data.var.index, method=None)
        out.highly_variable = out.highly_variable.fillna(False)
        assert (out.index == data.var.index).all(), (
            "Expected output index values to be equivalent to the input index"
        )
    elif par["obs_batch_key"] is not None:
        out = out.reindex(index=data.var.index, method=None)
        assert (out.index == data.var.index).all(), (
            "Expected output index values to be equivalent to the input index"
        )

except ValueError as err:
    if str(err) == "cannot specify integer \`bins\` when input data contains infinity":
        err.args = (
            "Cannot specify integer \`bins\` when input data contains infinity. "
            "Perhaps input data has not been log normalized?",
        )
    if re.search("Bin edges must be unique:", str(err)):
        raise RuntimeError(
            "Scanpy failed to calculate hvg. The error "
            "returned by scanpy (see above) could be the "
            "result from trying to use this component on unfiltered data."
        ) from err
    raise err

out.index = data.var.index
logger.info("\\tStoring output into .var")
if par.get("var_name_filter", None) is not None:
    data.var[par["var_name_filter"]] = out["highly_variable"]

if par.get("varm_name", None) is not None and "mean_bin" in out:
    # drop mean_bin as mudata/anndata doesn't support tuples
    data.varm[par["varm_name"]] = out.drop("mean_bin", axis=1)

logger.info("Writing h5mu to file")
write_h5ad_to_h5mu_with_compression(
    par["output"], par["input"], modality_name, data, par["output_compression"]
)
VIASHMAIN
python -B "\$tempscript" &
wait "\$!"

VIASHEOF


if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  # strip viash automount from file paths
  
  if [ ! -z "$VIASH_PAR_INPUT" ]; then
    VIASH_PAR_INPUT=$(ViashDockerStripAutomount "$VIASH_PAR_INPUT")
  fi
  if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
    VIASH_PAR_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT")
  fi
  if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
    VIASH_META_RESOURCES_DIR=$(ViashDockerStripAutomount "$VIASH_META_RESOURCES_DIR")
  fi
  if [ ! -z "$VIASH_META_EXECUTABLE" ]; then
    VIASH_META_EXECUTABLE=$(ViashDockerStripAutomount "$VIASH_META_EXECUTABLE")
  fi
  if [ ! -z "$VIASH_META_CONFIG" ]; then
    VIASH_META_CONFIG=$(ViashDockerStripAutomount "$VIASH_META_CONFIG")
  fi
  if [ ! -z "$VIASH_META_TEMP_DIR" ]; then
    VIASH_META_TEMP_DIR=$(ViashDockerStripAutomount "$VIASH_META_TEMP_DIR")
  fi
fi


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


exit 0
