#!/usr/bin/env bash

# gene_program_mask v0.5.0
# 
# 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:
#  * Dorien Roosen (maintainer)
#  * Jakub Majercik (maintainer)
#  * Weiwei Schultz (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="gene_program_mask"
VIASH_META_FUNCTIONALITY_NAME="gene_program_mask"
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 nvidia/cuda:12.6.3-cudnn-devel-ubuntu24.04
ENTRYPOINT []
ENV PIP_BREAK_SYSTEM_PACKAGES=1
RUN apt-get update && \
  DEBIAN_FRONTEND=noninteractive apt-get install -y python3-pip python-is-python3 && \
  rm -rf /var/lib/apt/lists/*

RUN pip install --upgrade --no-cache-dir --ignore-installed pip
RUN pip install torch --index-url https://download.pytorch.org/whl/cu124 \
&& pip install pyg_lib torch-scatter torch-sparse -f https://data.pyg.org/whl/torch-2.6.0+cu124.html

RUN pip install --upgrade pip && \
  pip install --upgrade --no-cache-dir "numpy<2" "nichecompass" "decoupler~=2.1.6"

RUN cat > /NOTICE <<'EOF'
This image contains software provided by NVIDIA Corporation
and is governed by the NVIDIA Deep Learning Container License:
https://developer.download.nvidia.com/licenses/NVIDIA_Deep_Learning_Container_License.pdf

The source code for this project is licensed under MIT:
https://github.com/openpipelines-bio/openpipeline_spatial
EOF

LABEL org.opencontainers.image.authors="Dorien Roosen, Jakub Majercik, Weiwei Schultz"
LABEL org.opencontainers.image.description="Companion container for running component nichecompass gene_program_mask"
LABEL org.opencontainers.image.created="2026-06-02T07:59:41Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="56d3738b53a35d479550fa2fc88fabfe93c7a6bd"
LABEL org.opencontainers.image.version="v0.5.0"

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 "gene_program_mask v0.5.0"
  echo ""
  echo "Generation of a prior knowledge gene program mask for NicheCompass."
  echo ""
  echo "Inputs:"
  echo "    --input_gene_orthologs_mapping_file"
  echo "        type: file, file must exist"
  echo "        Path to a CSV file mapping human genes to mouse orthologs."
  echo "        Required for the OmniPath and NicheNet masks if \`--species mouse\`."
  echo ""
  echo "    --input_metabolite_enzymes"
  echo "        type: file, file must exist"
  echo "        Path to the MeBocost metabolite-enzymes TSV file."
  echo "        Required for generating the MeBocost gene program mask."
  echo ""
  echo "    --input_metabolite_sensors"
  echo "        type: file, file must exist"
  echo "        Path to the MeBocost metabolite-sensors TSV file."
  echo "        Required for generating the MeBocost gene program mask."
  echo ""
  echo "    --input_omnipath_lr_network"
  echo "        type: file, file must exist"
  echo "        Path to the OmniPath ligand-receptor network CSV file."
  echo "        If provided, the network will be loaded from this file instead of"
  echo "        querying the OmniPath API."
  echo "        Cannot be used together with \`--output_omnipath_lr_network\`."
  echo ""
  echo "    --input_nichenet_ligand_target_matrix"
  echo "        type: file, file must exist"
  echo "        example: nichenet_ligand_target_matrix.csv"
  echo "        Path to the NicheNet ligand-target gene regulatory potential matrix"
  echo "        file."
  echo "        If provided, the matrix will be loaded from this file instead of"
  echo "        querying the NicheNet API."
  echo ""
  echo "    --input_nichenet_lrt_network"
  echo "        type: file, file must exist"
  echo "        Path to the NicheNet ligand-receptor network CSV file."
  echo "        If provided, the network will be loaded from this file instead of"
  echo "        querying the NicheNet API."
  echo ""
  echo "    --input_collectri_tf_network"
  echo "        type: file, file must exist"
  echo "        Path to the CollecTRI TF-target gene regulatory network CSV file."
  echo "        If provided, the network will be loaded from this file instead of"
  echo "        querying the CollecTRI API."
  echo ""
  echo "Parameters:"
  echo "    --species"
  echo "        type: string"
  echo "        default: human"
  echo "        choices: [ human, mouse ]"
  echo "        Species of the organism (human or mouse)."
  echo ""
  echo "    --create_omnipath_gene_program_mask"
  echo "        type: boolean"
  echo "        default: true"
  echo "        Whether to create the OmniPath gene program mask."
  echo ""
  echo "    --create_nichenet_gene_program_mask"
  echo "        type: boolean"
  echo "        default: true"
  echo "        Whether to create the NicheNet gene program mask."
  echo ""
  echo "    --create_mebocost_gene_program_mask"
  echo "        type: boolean"
  echo "        default: true"
  echo "        Whether to create the MeBocost gene program mask."
  echo ""
  echo "    --create_collectri_tf_gene_program_mask"
  echo "        type: boolean"
  echo "        default: true"
  echo "        Whether to create the CollecTRI TF gene program mask."
  echo ""
  echo "    --overlap_thresh_target_genes"
  echo "        type: double"
  echo "        default: 1.0"
  echo "        min: 0.0"
  echo "        max: 1.0"
  echo "        The minimum ratio of target genes that need to overlap between a GP"
  echo "        without source genes and another GP for the GP to be dropped."
  echo "        Gene programs with different source genes are never combined or dropped."
  echo ""
  echo "Omnipath Parameters:"
  echo "    --omnipath_min_curation_effort"
  echo "        type: integer"
  echo "        default: 2"
  echo "        Minimum number of times an interaction has to be described in a paper"
  echo "        and mentioned in a database to be included in the OmniPath gene"
  echo "        programs."
  echo ""
  echo "NicheNet Parameters:"
  echo "    --nichenet_version"
  echo "        type: string"
  echo "        default: v2"
  echo "        choices: [ v1, v2 ]"
  echo "        Version of the NicheNet ligand receptor network and ligand target gene"
  echo "        regulatory potential matrix."
  echo "        \`v2\` is an improved version of \`v1\`, and has separate files for mouse"
  echo "        and human."
  echo ""
  echo "    --nichenet_keep_target_genes_ratio"
  echo "        type: double"
  echo "        default: 1.0"
  echo "        Ratio of target genes that are kept compared to total target genes."
  echo "        This ratio is applied over the entire matrix (not on gene program"
  echo "        level), and determines the \`all_gps_score_keep_threshold\`, which will be"
  echo "        used to filter target genes according to their regulatory potential"
  echo "        scores."
  echo ""
  echo "    --nichenet_max_n_target_genes_per_gp"
  echo "        type: integer"
  echo "        default: 250"
  echo "        Maximum number of target genes per gene program. If a gene program has"
  echo "        more target genes than \`max_n_target_genes_per_gp\`, only the"
  echo "        \`max_n_target_genes_per_gp\` gene programs with the highest regulatory"
  echo "        potential scores will be kept."
  echo "        Default value is chosen based on MultiNicheNet specification (s."
  echo "        Browaeys, R. et al. MultiNicheNet: a flexible framework for differential"
  echo "        cell-cell communication analysis from multi-sample multi-condition"
  echo "        single-cell transcriptomics data. bioRxiv (2023)"
  echo "        doi:10.1101/2023.06.13.544751)."
  echo ""
  echo "Outputs:"
  echo "    --output"
  echo "        type: file, required parameter, output, file must exist"
  echo "        example: gp_mask.json"
  echo "        Path to the output gene program mask JSON file."
  echo ""
  echo "    --output_omnipath_lr_network"
  echo "        type: file, output, file must exist"
  echo "        example: omnipath_lr_network.csv"
  echo "        Path to the output OmniPath ligand-receptor network CSV file."
  echo "        If \`--input_omnipath_lr_network\` is not provided, the network will be"
  echo "        saved to this file after querying the OmniPath API."
  echo ""
  echo "    --output_nichenet_lrt_network"
  echo "        type: file, output, file must exist"
  echo "        example: nichenet_lrt_network.csv"
  echo "        Path to the output NicheNet ligand-receptor network CSV file."
  echo "        If \`--input_nichenet_lrt_network\` is not provided, the network will be"
  echo "        saved to this file after querying the NicheNet API."
  echo ""
  echo "    --output_nichenet_ligand_target_matrix"
  echo "        type: file, output, file must exist"
  echo "        example: nichenet_ligand_target_matrix.csv"
  echo "        Path to the output NicheNet ligand-target gene regulatory potential"
  echo "        matrix file."
  echo "        If \`--input_nichenet_ligand_target_matrix\` is not provided, the matrix"
  echo "        will be saved to this file after querying the NicheNet API."
  echo ""
  echo "    --output_collectri_tf_network"
  echo "        type: file, output, file must exist"
  echo "        example: collectri_tf_network.csv"
  echo "        Path to the output CollecTRI TF-target gene regulatory potential network"
  echo "        CSV file."
  echo "        If \`--input_collectri_tf_network\` is not provided, the network will be"
  echo "        saved to this file after querying the CollecTRI API."
  echo ""
  echo "    --output_omnipath_gp_gene_count_distributions"
  echo "        type: file, output, file must exist"
  echo "        example: omnipath_gp_gene_count_distributions.svg"
  echo "        Path to save the OmniPath gene program gene count distributions plot."
  echo ""
  echo "    --output_nichenet_gp_gene_count_distributions"
  echo "        type: file, output, file must exist"
  echo "        example: nichenet_gp_gene_count_distributions.svg"
  echo "        Path to save the NicheNet gene program gene count distributions plot."
  echo ""
  echo "    --output_mebocost_gp_gene_count_distributions"
  echo "        type: file, output, file must exist"
  echo "        example: mebocost_gp_gene_count_distributions.svg"
  echo "        Path to save the MeBocost gene program gene count distributions plot."
  echo ""
  echo "    --output_collectri_tf_gp_gene_count_distributions"
  echo "        type: file, output, file must exist"
  echo "        example: collectri_tf_gp_gene_count_distributions.svg"
  echo "        Path to save the CollecTRI TF gene program gene count distributions"
  echo "        plot."
  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 "$1")"
            shift 1
            ;;
        --version)
            echo "gene_program_mask v0.5.0"
            exit
            ;;
        --input_gene_orthologs_mapping_file)
            [ -n "$VIASH_PAR_INPUT_GENE_ORTHOLOGS_MAPPING_FILE" ] && ViashError Bad arguments for option \'--input_gene_orthologs_mapping_file\': \'$VIASH_PAR_INPUT_GENE_ORTHOLOGS_MAPPING_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INPUT_GENE_ORTHOLOGS_MAPPING_FILE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --input_gene_orthologs_mapping_file. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --input_gene_orthologs_mapping_file=*)
            [ -n "$VIASH_PAR_INPUT_GENE_ORTHOLOGS_MAPPING_FILE" ] && ViashError Bad arguments for option \'--input_gene_orthologs_mapping_file=*\': \'$VIASH_PAR_INPUT_GENE_ORTHOLOGS_MAPPING_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INPUT_GENE_ORTHOLOGS_MAPPING_FILE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --input_metabolite_enzymes)
            [ -n "$VIASH_PAR_INPUT_METABOLITE_ENZYMES" ] && ViashError Bad arguments for option \'--input_metabolite_enzymes\': \'$VIASH_PAR_INPUT_METABOLITE_ENZYMES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INPUT_METABOLITE_ENZYMES="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --input_metabolite_enzymes. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --input_metabolite_enzymes=*)
            [ -n "$VIASH_PAR_INPUT_METABOLITE_ENZYMES" ] && ViashError Bad arguments for option \'--input_metabolite_enzymes=*\': \'$VIASH_PAR_INPUT_METABOLITE_ENZYMES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INPUT_METABOLITE_ENZYMES=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --input_metabolite_sensors)
            [ -n "$VIASH_PAR_INPUT_METABOLITE_SENSORS" ] && ViashError Bad arguments for option \'--input_metabolite_sensors\': \'$VIASH_PAR_INPUT_METABOLITE_SENSORS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INPUT_METABOLITE_SENSORS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --input_metabolite_sensors. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --input_metabolite_sensors=*)
            [ -n "$VIASH_PAR_INPUT_METABOLITE_SENSORS" ] && ViashError Bad arguments for option \'--input_metabolite_sensors=*\': \'$VIASH_PAR_INPUT_METABOLITE_SENSORS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INPUT_METABOLITE_SENSORS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --input_omnipath_lr_network)
            [ -n "$VIASH_PAR_INPUT_OMNIPATH_LR_NETWORK" ] && ViashError Bad arguments for option \'--input_omnipath_lr_network\': \'$VIASH_PAR_INPUT_OMNIPATH_LR_NETWORK\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INPUT_OMNIPATH_LR_NETWORK="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --input_omnipath_lr_network. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --input_omnipath_lr_network=*)
            [ -n "$VIASH_PAR_INPUT_OMNIPATH_LR_NETWORK" ] && ViashError Bad arguments for option \'--input_omnipath_lr_network=*\': \'$VIASH_PAR_INPUT_OMNIPATH_LR_NETWORK\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INPUT_OMNIPATH_LR_NETWORK=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --input_nichenet_ligand_target_matrix)
            [ -n "$VIASH_PAR_INPUT_NICHENET_LIGAND_TARGET_MATRIX" ] && ViashError Bad arguments for option \'--input_nichenet_ligand_target_matrix\': \'$VIASH_PAR_INPUT_NICHENET_LIGAND_TARGET_MATRIX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INPUT_NICHENET_LIGAND_TARGET_MATRIX="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --input_nichenet_ligand_target_matrix. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --input_nichenet_ligand_target_matrix=*)
            [ -n "$VIASH_PAR_INPUT_NICHENET_LIGAND_TARGET_MATRIX" ] && ViashError Bad arguments for option \'--input_nichenet_ligand_target_matrix=*\': \'$VIASH_PAR_INPUT_NICHENET_LIGAND_TARGET_MATRIX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INPUT_NICHENET_LIGAND_TARGET_MATRIX=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --input_nichenet_lrt_network)
            [ -n "$VIASH_PAR_INPUT_NICHENET_LRT_NETWORK" ] && ViashError Bad arguments for option \'--input_nichenet_lrt_network\': \'$VIASH_PAR_INPUT_NICHENET_LRT_NETWORK\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INPUT_NICHENET_LRT_NETWORK="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --input_nichenet_lrt_network. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --input_nichenet_lrt_network=*)
            [ -n "$VIASH_PAR_INPUT_NICHENET_LRT_NETWORK" ] && ViashError Bad arguments for option \'--input_nichenet_lrt_network=*\': \'$VIASH_PAR_INPUT_NICHENET_LRT_NETWORK\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INPUT_NICHENET_LRT_NETWORK=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --input_collectri_tf_network)
            [ -n "$VIASH_PAR_INPUT_COLLECTRI_TF_NETWORK" ] && ViashError Bad arguments for option \'--input_collectri_tf_network\': \'$VIASH_PAR_INPUT_COLLECTRI_TF_NETWORK\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INPUT_COLLECTRI_TF_NETWORK="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --input_collectri_tf_network. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --input_collectri_tf_network=*)
            [ -n "$VIASH_PAR_INPUT_COLLECTRI_TF_NETWORK" ] && ViashError Bad arguments for option \'--input_collectri_tf_network=*\': \'$VIASH_PAR_INPUT_COLLECTRI_TF_NETWORK\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INPUT_COLLECTRI_TF_NETWORK=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --species)
            [ -n "$VIASH_PAR_SPECIES" ] && ViashError Bad arguments for option \'--species\': \'$VIASH_PAR_SPECIES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SPECIES="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --species. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --species=*)
            [ -n "$VIASH_PAR_SPECIES" ] && ViashError Bad arguments for option \'--species=*\': \'$VIASH_PAR_SPECIES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SPECIES=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --create_omnipath_gene_program_mask)
            [ -n "$VIASH_PAR_CREATE_OMNIPATH_GENE_PROGRAM_MASK" ] && ViashError Bad arguments for option \'--create_omnipath_gene_program_mask\': \'$VIASH_PAR_CREATE_OMNIPATH_GENE_PROGRAM_MASK\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CREATE_OMNIPATH_GENE_PROGRAM_MASK="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --create_omnipath_gene_program_mask. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --create_omnipath_gene_program_mask=*)
            [ -n "$VIASH_PAR_CREATE_OMNIPATH_GENE_PROGRAM_MASK" ] && ViashError Bad arguments for option \'--create_omnipath_gene_program_mask=*\': \'$VIASH_PAR_CREATE_OMNIPATH_GENE_PROGRAM_MASK\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CREATE_OMNIPATH_GENE_PROGRAM_MASK=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --create_nichenet_gene_program_mask)
            [ -n "$VIASH_PAR_CREATE_NICHENET_GENE_PROGRAM_MASK" ] && ViashError Bad arguments for option \'--create_nichenet_gene_program_mask\': \'$VIASH_PAR_CREATE_NICHENET_GENE_PROGRAM_MASK\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CREATE_NICHENET_GENE_PROGRAM_MASK="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --create_nichenet_gene_program_mask. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --create_nichenet_gene_program_mask=*)
            [ -n "$VIASH_PAR_CREATE_NICHENET_GENE_PROGRAM_MASK" ] && ViashError Bad arguments for option \'--create_nichenet_gene_program_mask=*\': \'$VIASH_PAR_CREATE_NICHENET_GENE_PROGRAM_MASK\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CREATE_NICHENET_GENE_PROGRAM_MASK=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --create_mebocost_gene_program_mask)
            [ -n "$VIASH_PAR_CREATE_MEBOCOST_GENE_PROGRAM_MASK" ] && ViashError Bad arguments for option \'--create_mebocost_gene_program_mask\': \'$VIASH_PAR_CREATE_MEBOCOST_GENE_PROGRAM_MASK\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CREATE_MEBOCOST_GENE_PROGRAM_MASK="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --create_mebocost_gene_program_mask. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --create_mebocost_gene_program_mask=*)
            [ -n "$VIASH_PAR_CREATE_MEBOCOST_GENE_PROGRAM_MASK" ] && ViashError Bad arguments for option \'--create_mebocost_gene_program_mask=*\': \'$VIASH_PAR_CREATE_MEBOCOST_GENE_PROGRAM_MASK\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CREATE_MEBOCOST_GENE_PROGRAM_MASK=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --create_collectri_tf_gene_program_mask)
            [ -n "$VIASH_PAR_CREATE_COLLECTRI_TF_GENE_PROGRAM_MASK" ] && ViashError Bad arguments for option \'--create_collectri_tf_gene_program_mask\': \'$VIASH_PAR_CREATE_COLLECTRI_TF_GENE_PROGRAM_MASK\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CREATE_COLLECTRI_TF_GENE_PROGRAM_MASK="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --create_collectri_tf_gene_program_mask. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --create_collectri_tf_gene_program_mask=*)
            [ -n "$VIASH_PAR_CREATE_COLLECTRI_TF_GENE_PROGRAM_MASK" ] && ViashError Bad arguments for option \'--create_collectri_tf_gene_program_mask=*\': \'$VIASH_PAR_CREATE_COLLECTRI_TF_GENE_PROGRAM_MASK\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CREATE_COLLECTRI_TF_GENE_PROGRAM_MASK=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --overlap_thresh_target_genes)
            [ -n "$VIASH_PAR_OVERLAP_THRESH_TARGET_GENES" ] && ViashError Bad arguments for option \'--overlap_thresh_target_genes\': \'$VIASH_PAR_OVERLAP_THRESH_TARGET_GENES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OVERLAP_THRESH_TARGET_GENES="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --overlap_thresh_target_genes. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --overlap_thresh_target_genes=*)
            [ -n "$VIASH_PAR_OVERLAP_THRESH_TARGET_GENES" ] && ViashError Bad arguments for option \'--overlap_thresh_target_genes=*\': \'$VIASH_PAR_OVERLAP_THRESH_TARGET_GENES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OVERLAP_THRESH_TARGET_GENES=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --omnipath_min_curation_effort)
            [ -n "$VIASH_PAR_OMNIPATH_MIN_CURATION_EFFORT" ] && ViashError Bad arguments for option \'--omnipath_min_curation_effort\': \'$VIASH_PAR_OMNIPATH_MIN_CURATION_EFFORT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OMNIPATH_MIN_CURATION_EFFORT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --omnipath_min_curation_effort. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --omnipath_min_curation_effort=*)
            [ -n "$VIASH_PAR_OMNIPATH_MIN_CURATION_EFFORT" ] && ViashError Bad arguments for option \'--omnipath_min_curation_effort=*\': \'$VIASH_PAR_OMNIPATH_MIN_CURATION_EFFORT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OMNIPATH_MIN_CURATION_EFFORT=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --nichenet_version)
            [ -n "$VIASH_PAR_NICHENET_VERSION" ] && ViashError Bad arguments for option \'--nichenet_version\': \'$VIASH_PAR_NICHENET_VERSION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_NICHENET_VERSION="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --nichenet_version. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --nichenet_version=*)
            [ -n "$VIASH_PAR_NICHENET_VERSION" ] && ViashError Bad arguments for option \'--nichenet_version=*\': \'$VIASH_PAR_NICHENET_VERSION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_NICHENET_VERSION=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --nichenet_keep_target_genes_ratio)
            [ -n "$VIASH_PAR_NICHENET_KEEP_TARGET_GENES_RATIO" ] && ViashError Bad arguments for option \'--nichenet_keep_target_genes_ratio\': \'$VIASH_PAR_NICHENET_KEEP_TARGET_GENES_RATIO\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_NICHENET_KEEP_TARGET_GENES_RATIO="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --nichenet_keep_target_genes_ratio. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --nichenet_keep_target_genes_ratio=*)
            [ -n "$VIASH_PAR_NICHENET_KEEP_TARGET_GENES_RATIO" ] && ViashError Bad arguments for option \'--nichenet_keep_target_genes_ratio=*\': \'$VIASH_PAR_NICHENET_KEEP_TARGET_GENES_RATIO\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_NICHENET_KEEP_TARGET_GENES_RATIO=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --nichenet_max_n_target_genes_per_gp)
            [ -n "$VIASH_PAR_NICHENET_MAX_N_TARGET_GENES_PER_GP" ] && ViashError Bad arguments for option \'--nichenet_max_n_target_genes_per_gp\': \'$VIASH_PAR_NICHENET_MAX_N_TARGET_GENES_PER_GP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_NICHENET_MAX_N_TARGET_GENES_PER_GP="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --nichenet_max_n_target_genes_per_gp. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --nichenet_max_n_target_genes_per_gp=*)
            [ -n "$VIASH_PAR_NICHENET_MAX_N_TARGET_GENES_PER_GP" ] && ViashError Bad arguments for option \'--nichenet_max_n_target_genes_per_gp=*\': \'$VIASH_PAR_NICHENET_MAX_N_TARGET_GENES_PER_GP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_NICHENET_MAX_N_TARGET_GENES_PER_GP=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --output)
            [ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --output. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --output=*)
            [ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output=*\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --output_omnipath_lr_network)
            [ -n "$VIASH_PAR_OUTPUT_OMNIPATH_LR_NETWORK" ] && ViashError Bad arguments for option \'--output_omnipath_lr_network\': \'$VIASH_PAR_OUTPUT_OMNIPATH_LR_NETWORK\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_OMNIPATH_LR_NETWORK="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --output_omnipath_lr_network. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --output_omnipath_lr_network=*)
            [ -n "$VIASH_PAR_OUTPUT_OMNIPATH_LR_NETWORK" ] && ViashError Bad arguments for option \'--output_omnipath_lr_network=*\': \'$VIASH_PAR_OUTPUT_OMNIPATH_LR_NETWORK\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_OMNIPATH_LR_NETWORK=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --output_nichenet_lrt_network)
            [ -n "$VIASH_PAR_OUTPUT_NICHENET_LRT_NETWORK" ] && ViashError Bad arguments for option \'--output_nichenet_lrt_network\': \'$VIASH_PAR_OUTPUT_NICHENET_LRT_NETWORK\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_NICHENET_LRT_NETWORK="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --output_nichenet_lrt_network. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --output_nichenet_lrt_network=*)
            [ -n "$VIASH_PAR_OUTPUT_NICHENET_LRT_NETWORK" ] && ViashError Bad arguments for option \'--output_nichenet_lrt_network=*\': \'$VIASH_PAR_OUTPUT_NICHENET_LRT_NETWORK\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_NICHENET_LRT_NETWORK=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --output_nichenet_ligand_target_matrix)
            [ -n "$VIASH_PAR_OUTPUT_NICHENET_LIGAND_TARGET_MATRIX" ] && ViashError Bad arguments for option \'--output_nichenet_ligand_target_matrix\': \'$VIASH_PAR_OUTPUT_NICHENET_LIGAND_TARGET_MATRIX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_NICHENET_LIGAND_TARGET_MATRIX="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --output_nichenet_ligand_target_matrix. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --output_nichenet_ligand_target_matrix=*)
            [ -n "$VIASH_PAR_OUTPUT_NICHENET_LIGAND_TARGET_MATRIX" ] && ViashError Bad arguments for option \'--output_nichenet_ligand_target_matrix=*\': \'$VIASH_PAR_OUTPUT_NICHENET_LIGAND_TARGET_MATRIX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_NICHENET_LIGAND_TARGET_MATRIX=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --output_collectri_tf_network)
            [ -n "$VIASH_PAR_OUTPUT_COLLECTRI_TF_NETWORK" ] && ViashError Bad arguments for option \'--output_collectri_tf_network\': \'$VIASH_PAR_OUTPUT_COLLECTRI_TF_NETWORK\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_COLLECTRI_TF_NETWORK="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --output_collectri_tf_network. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --output_collectri_tf_network=*)
            [ -n "$VIASH_PAR_OUTPUT_COLLECTRI_TF_NETWORK" ] && ViashError Bad arguments for option \'--output_collectri_tf_network=*\': \'$VIASH_PAR_OUTPUT_COLLECTRI_TF_NETWORK\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_COLLECTRI_TF_NETWORK=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --output_omnipath_gp_gene_count_distributions)
            [ -n "$VIASH_PAR_OUTPUT_OMNIPATH_GP_GENE_COUNT_DISTRIBUTIONS" ] && ViashError Bad arguments for option \'--output_omnipath_gp_gene_count_distributions\': \'$VIASH_PAR_OUTPUT_OMNIPATH_GP_GENE_COUNT_DISTRIBUTIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_OMNIPATH_GP_GENE_COUNT_DISTRIBUTIONS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --output_omnipath_gp_gene_count_distributions. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --output_omnipath_gp_gene_count_distributions=*)
            [ -n "$VIASH_PAR_OUTPUT_OMNIPATH_GP_GENE_COUNT_DISTRIBUTIONS" ] && ViashError Bad arguments for option \'--output_omnipath_gp_gene_count_distributions=*\': \'$VIASH_PAR_OUTPUT_OMNIPATH_GP_GENE_COUNT_DISTRIBUTIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_OMNIPATH_GP_GENE_COUNT_DISTRIBUTIONS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --output_nichenet_gp_gene_count_distributions)
            [ -n "$VIASH_PAR_OUTPUT_NICHENET_GP_GENE_COUNT_DISTRIBUTIONS" ] && ViashError Bad arguments for option \'--output_nichenet_gp_gene_count_distributions\': \'$VIASH_PAR_OUTPUT_NICHENET_GP_GENE_COUNT_DISTRIBUTIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_NICHENET_GP_GENE_COUNT_DISTRIBUTIONS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --output_nichenet_gp_gene_count_distributions. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --output_nichenet_gp_gene_count_distributions=*)
            [ -n "$VIASH_PAR_OUTPUT_NICHENET_GP_GENE_COUNT_DISTRIBUTIONS" ] && ViashError Bad arguments for option \'--output_nichenet_gp_gene_count_distributions=*\': \'$VIASH_PAR_OUTPUT_NICHENET_GP_GENE_COUNT_DISTRIBUTIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_NICHENET_GP_GENE_COUNT_DISTRIBUTIONS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --output_mebocost_gp_gene_count_distributions)
            [ -n "$VIASH_PAR_OUTPUT_MEBOCOST_GP_GENE_COUNT_DISTRIBUTIONS" ] && ViashError Bad arguments for option \'--output_mebocost_gp_gene_count_distributions\': \'$VIASH_PAR_OUTPUT_MEBOCOST_GP_GENE_COUNT_DISTRIBUTIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_MEBOCOST_GP_GENE_COUNT_DISTRIBUTIONS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --output_mebocost_gp_gene_count_distributions. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --output_mebocost_gp_gene_count_distributions=*)
            [ -n "$VIASH_PAR_OUTPUT_MEBOCOST_GP_GENE_COUNT_DISTRIBUTIONS" ] && ViashError Bad arguments for option \'--output_mebocost_gp_gene_count_distributions=*\': \'$VIASH_PAR_OUTPUT_MEBOCOST_GP_GENE_COUNT_DISTRIBUTIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_MEBOCOST_GP_GENE_COUNT_DISTRIBUTIONS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --output_collectri_tf_gp_gene_count_distributions)
            [ -n "$VIASH_PAR_OUTPUT_COLLECTRI_TF_GP_GENE_COUNT_DISTRIBUTIONS" ] && ViashError Bad arguments for option \'--output_collectri_tf_gp_gene_count_distributions\': \'$VIASH_PAR_OUTPUT_COLLECTRI_TF_GP_GENE_COUNT_DISTRIBUTIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_COLLECTRI_TF_GP_GENE_COUNT_DISTRIBUTIONS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --output_collectri_tf_gp_gene_count_distributions. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --output_collectri_tf_gp_gene_count_distributions=*)
            [ -n "$VIASH_PAR_OUTPUT_COLLECTRI_TF_GP_GENE_COUNT_DISTRIBUTIONS" ] && ViashError Bad arguments for option \'--output_collectri_tf_gp_gene_count_distributions=*\': \'$VIASH_PAR_OUTPUT_COLLECTRI_TF_GP_GENE_COUNT_DISTRIBUTIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_COLLECTRI_TF_GP_GENE_COUNT_DISTRIBUTIONS=$(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_spatial/nichecompass/gene_program_mask:v0.5.0'
  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_OUTPUT+x} ]; then
  ViashError '--output' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_NAME+x} ]; then
  ViashError 'name' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then
  ViashError 'functionality_name' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_RESOURCES_DIR+x} ]; then
  ViashError 'resources_dir' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_EXECUTABLE+x} ]; then
  ViashError 'executable' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_CONFIG+x} ]; then
  ViashError 'config' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_TEMP_DIR+x} ]; then
  ViashError 'temp_dir' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi

# filling in defaults
if [ -z ${VIASH_PAR_SPECIES+x} ]; then
  VIASH_PAR_SPECIES="human"
fi
if [ -z ${VIASH_PAR_CREATE_OMNIPATH_GENE_PROGRAM_MASK+x} ]; then
  VIASH_PAR_CREATE_OMNIPATH_GENE_PROGRAM_MASK="true"
fi
if [ -z ${VIASH_PAR_CREATE_NICHENET_GENE_PROGRAM_MASK+x} ]; then
  VIASH_PAR_CREATE_NICHENET_GENE_PROGRAM_MASK="true"
fi
if [ -z ${VIASH_PAR_CREATE_MEBOCOST_GENE_PROGRAM_MASK+x} ]; then
  VIASH_PAR_CREATE_MEBOCOST_GENE_PROGRAM_MASK="true"
fi
if [ -z ${VIASH_PAR_CREATE_COLLECTRI_TF_GENE_PROGRAM_MASK+x} ]; then
  VIASH_PAR_CREATE_COLLECTRI_TF_GENE_PROGRAM_MASK="true"
fi
if [ -z ${VIASH_PAR_OVERLAP_THRESH_TARGET_GENES+x} ]; then
  VIASH_PAR_OVERLAP_THRESH_TARGET_GENES="1.0"
fi
if [ -z ${VIASH_PAR_OMNIPATH_MIN_CURATION_EFFORT+x} ]; then
  VIASH_PAR_OMNIPATH_MIN_CURATION_EFFORT="2"
fi
if [ -z ${VIASH_PAR_NICHENET_VERSION+x} ]; then
  VIASH_PAR_NICHENET_VERSION="v2"
fi
if [ -z ${VIASH_PAR_NICHENET_KEEP_TARGET_GENES_RATIO+x} ]; then
  VIASH_PAR_NICHENET_KEEP_TARGET_GENES_RATIO="1.0"
fi
if [ -z ${VIASH_PAR_NICHENET_MAX_N_TARGET_GENES_PER_GP+x} ]; then
  VIASH_PAR_NICHENET_MAX_N_TARGET_GENES_PER_GP="250"
fi

# check whether required files exist
if [ ! -z "$VIASH_PAR_INPUT_GENE_ORTHOLOGS_MAPPING_FILE" ] && [ ! -e "$VIASH_PAR_INPUT_GENE_ORTHOLOGS_MAPPING_FILE" ]; then
  ViashError "Input file '$VIASH_PAR_INPUT_GENE_ORTHOLOGS_MAPPING_FILE' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_INPUT_METABOLITE_ENZYMES" ] && [ ! -e "$VIASH_PAR_INPUT_METABOLITE_ENZYMES" ]; then
  ViashError "Input file '$VIASH_PAR_INPUT_METABOLITE_ENZYMES' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_INPUT_METABOLITE_SENSORS" ] && [ ! -e "$VIASH_PAR_INPUT_METABOLITE_SENSORS" ]; then
  ViashError "Input file '$VIASH_PAR_INPUT_METABOLITE_SENSORS' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_INPUT_OMNIPATH_LR_NETWORK" ] && [ ! -e "$VIASH_PAR_INPUT_OMNIPATH_LR_NETWORK" ]; then
  ViashError "Input file '$VIASH_PAR_INPUT_OMNIPATH_LR_NETWORK' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_INPUT_NICHENET_LIGAND_TARGET_MATRIX" ] && [ ! -e "$VIASH_PAR_INPUT_NICHENET_LIGAND_TARGET_MATRIX" ]; then
  ViashError "Input file '$VIASH_PAR_INPUT_NICHENET_LIGAND_TARGET_MATRIX' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_INPUT_NICHENET_LRT_NETWORK" ] && [ ! -e "$VIASH_PAR_INPUT_NICHENET_LRT_NETWORK" ]; then
  ViashError "Input file '$VIASH_PAR_INPUT_NICHENET_LRT_NETWORK' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_INPUT_COLLECTRI_TF_NETWORK" ] && [ ! -e "$VIASH_PAR_INPUT_COLLECTRI_TF_NETWORK" ]; then
  ViashError "Input file '$VIASH_PAR_INPUT_COLLECTRI_TF_NETWORK' does not exist."
  exit 1
fi

# check whether parameters values are of the right type
if [[ -n "$VIASH_PAR_CREATE_OMNIPATH_GENE_PROGRAM_MASK" ]]; then
  if ! [[ "$VIASH_PAR_CREATE_OMNIPATH_GENE_PROGRAM_MASK" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--create_omnipath_gene_program_mask' has to be a boolean. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_CREATE_NICHENET_GENE_PROGRAM_MASK" ]]; then
  if ! [[ "$VIASH_PAR_CREATE_NICHENET_GENE_PROGRAM_MASK" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--create_nichenet_gene_program_mask' has to be a boolean. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_CREATE_MEBOCOST_GENE_PROGRAM_MASK" ]]; then
  if ! [[ "$VIASH_PAR_CREATE_MEBOCOST_GENE_PROGRAM_MASK" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--create_mebocost_gene_program_mask' has to be a boolean. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_CREATE_COLLECTRI_TF_GENE_PROGRAM_MASK" ]]; then
  if ! [[ "$VIASH_PAR_CREATE_COLLECTRI_TF_GENE_PROGRAM_MASK" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--create_collectri_tf_gene_program_mask' has to be a boolean. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_OVERLAP_THRESH_TARGET_GENES" ]]; then
  if ! [[ "$VIASH_PAR_OVERLAP_THRESH_TARGET_GENES" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--overlap_thresh_target_genes' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
  if command -v bc &> /dev/null; then
    if ! [[ `echo $VIASH_PAR_OVERLAP_THRESH_TARGET_GENES '>=' 0.0 | bc` -eq 1 ]]; then
      ViashError '--overlap_thresh_target_genes' has be more than or equal to 0.0. Use "--help" to get more information on the parameters.
      exit 1
    fi
  elif command -v awk &> /dev/null; then
    if ! [[ `awk -v n1=$VIASH_PAR_OVERLAP_THRESH_TARGET_GENES -v n2=0.0 'BEGIN { print (n1 >= n2) ? "1" : "0" }'` -eq 1 ]]; then
      ViashError '--overlap_thresh_target_genes' has be more than or equal to 0.0. Use "--help" to get more information on the parameters.
      exit 1
    fi
  else
    ViashWarning '--overlap_thresh_target_genes' specifies a minimum value but the value was not verified as neither \'bc\' or \`awk\` are present on the system.
  fi
  if command -v bc &> /dev/null; then
    if ! [[ `echo $VIASH_PAR_OVERLAP_THRESH_TARGET_GENES '<=' 1.0 | bc` -eq 1 ]]; then
      ViashError '--overlap_thresh_target_genes' has to be less than or equal to 1.0. Use "--help" to get more information on the parameters.
      exit 1
    fi
  elif command -v awk &> /dev/null; then
    if ! [[ `awk -v n1=$VIASH_PAR_OVERLAP_THRESH_TARGET_GENES -v n2=1.0 'BEGIN { print (n1 <= n2) ? "1" : "0" }'` -eq 1 ]]; then
      ViashError '--overlap_thresh_target_genes' has be less than or equal to 1.0. Use "--help" to get more information on the parameters.
      exit 1
    fi
  else
    ViashWarning '--overlap_thresh_target_genes' specifies a maximum value but the value was not verified as neither \'bc\' or \'awk\' are present on the system.
  fi
fi
if [[ -n "$VIASH_PAR_OMNIPATH_MIN_CURATION_EFFORT" ]]; then
  if ! [[ "$VIASH_PAR_OMNIPATH_MIN_CURATION_EFFORT" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--omnipath_min_curation_effort' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_NICHENET_KEEP_TARGET_GENES_RATIO" ]]; then
  if ! [[ "$VIASH_PAR_NICHENET_KEEP_TARGET_GENES_RATIO" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--nichenet_keep_target_genes_ratio' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_NICHENET_MAX_N_TARGET_GENES_PER_GP" ]]; then
  if ! [[ "$VIASH_PAR_NICHENET_MAX_N_TARGET_GENES_PER_GP" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--nichenet_max_n_target_genes_per_gp' 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 "$VIASH_PAR_SPECIES" ]; then
  VIASH_PAR_SPECIES_CHOICES=("human;mouse")
  IFS=';'
  set -f
  if ! [[ ";${VIASH_PAR_SPECIES_CHOICES[*]};" =~ ";$VIASH_PAR_SPECIES;" ]]; then
    ViashError '--species' specified value of \'$VIASH_PAR_SPECIES\' 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 "$VIASH_PAR_NICHENET_VERSION" ]; then
  VIASH_PAR_NICHENET_VERSION_CHOICES=("v1;v2")
  IFS=';'
  set -f
  if ! [[ ";${VIASH_PAR_NICHENET_VERSION_CHOICES[*]};" =~ ";$VIASH_PAR_NICHENET_VERSION;" ]]; then
    ViashError '--nichenet_version' specified value of \'$VIASH_PAR_NICHENET_VERSION\' 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 "$VIASH_PAR_OUTPUT")"
fi
if [ ! -z "$VIASH_PAR_OUTPUT_OMNIPATH_LR_NETWORK" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT_OMNIPATH_LR_NETWORK")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_OUTPUT_OMNIPATH_LR_NETWORK")"
fi
if [ ! -z "$VIASH_PAR_OUTPUT_NICHENET_LRT_NETWORK" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT_NICHENET_LRT_NETWORK")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_OUTPUT_NICHENET_LRT_NETWORK")"
fi
if [ ! -z "$VIASH_PAR_OUTPUT_NICHENET_LIGAND_TARGET_MATRIX" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT_NICHENET_LIGAND_TARGET_MATRIX")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_OUTPUT_NICHENET_LIGAND_TARGET_MATRIX")"
fi
if [ ! -z "$VIASH_PAR_OUTPUT_COLLECTRI_TF_NETWORK" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT_COLLECTRI_TF_NETWORK")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_OUTPUT_COLLECTRI_TF_NETWORK")"
fi
if [ ! -z "$VIASH_PAR_OUTPUT_OMNIPATH_GP_GENE_COUNT_DISTRIBUTIONS" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT_OMNIPATH_GP_GENE_COUNT_DISTRIBUTIONS")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_OUTPUT_OMNIPATH_GP_GENE_COUNT_DISTRIBUTIONS")"
fi
if [ ! -z "$VIASH_PAR_OUTPUT_NICHENET_GP_GENE_COUNT_DISTRIBUTIONS" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT_NICHENET_GP_GENE_COUNT_DISTRIBUTIONS")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_OUTPUT_NICHENET_GP_GENE_COUNT_DISTRIBUTIONS")"
fi
if [ ! -z "$VIASH_PAR_OUTPUT_MEBOCOST_GP_GENE_COUNT_DISTRIBUTIONS" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT_MEBOCOST_GP_GENE_COUNT_DISTRIBUTIONS")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_OUTPUT_MEBOCOST_GP_GENE_COUNT_DISTRIBUTIONS")"
fi
if [ ! -z "$VIASH_PAR_OUTPUT_COLLECTRI_TF_GP_GENE_COUNT_DISTRIBUTIONS" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT_COLLECTRI_TF_GP_GENE_COUNT_DISTRIBUTIONS")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_OUTPUT_COLLECTRI_TF_GP_GENE_COUNT_DISTRIBUTIONS")"
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_GENE_ORTHOLOGS_MAPPING_FILE" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INPUT_GENE_ORTHOLOGS_MAPPING_FILE")" )
  VIASH_PAR_INPUT_GENE_ORTHOLOGS_MAPPING_FILE=$(ViashDockerAutodetectMount "$VIASH_PAR_INPUT_GENE_ORTHOLOGS_MAPPING_FILE")
fi
if [ ! -z "$VIASH_PAR_INPUT_METABOLITE_ENZYMES" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INPUT_METABOLITE_ENZYMES")" )
  VIASH_PAR_INPUT_METABOLITE_ENZYMES=$(ViashDockerAutodetectMount "$VIASH_PAR_INPUT_METABOLITE_ENZYMES")
fi
if [ ! -z "$VIASH_PAR_INPUT_METABOLITE_SENSORS" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INPUT_METABOLITE_SENSORS")" )
  VIASH_PAR_INPUT_METABOLITE_SENSORS=$(ViashDockerAutodetectMount "$VIASH_PAR_INPUT_METABOLITE_SENSORS")
fi
if [ ! -z "$VIASH_PAR_INPUT_OMNIPATH_LR_NETWORK" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INPUT_OMNIPATH_LR_NETWORK")" )
  VIASH_PAR_INPUT_OMNIPATH_LR_NETWORK=$(ViashDockerAutodetectMount "$VIASH_PAR_INPUT_OMNIPATH_LR_NETWORK")
fi
if [ ! -z "$VIASH_PAR_INPUT_NICHENET_LIGAND_TARGET_MATRIX" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INPUT_NICHENET_LIGAND_TARGET_MATRIX")" )
  VIASH_PAR_INPUT_NICHENET_LIGAND_TARGET_MATRIX=$(ViashDockerAutodetectMount "$VIASH_PAR_INPUT_NICHENET_LIGAND_TARGET_MATRIX")
fi
if [ ! -z "$VIASH_PAR_INPUT_NICHENET_LRT_NETWORK" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INPUT_NICHENET_LRT_NETWORK")" )
  VIASH_PAR_INPUT_NICHENET_LRT_NETWORK=$(ViashDockerAutodetectMount "$VIASH_PAR_INPUT_NICHENET_LRT_NETWORK")
fi
if [ ! -z "$VIASH_PAR_INPUT_COLLECTRI_TF_NETWORK" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INPUT_COLLECTRI_TF_NETWORK")" )
  VIASH_PAR_INPUT_COLLECTRI_TF_NETWORK=$(ViashDockerAutodetectMount "$VIASH_PAR_INPUT_COLLECTRI_TF_NETWORK")
fi
if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT")" )
  VIASH_PAR_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT" )
fi
if [ ! -z "$VIASH_PAR_OUTPUT_OMNIPATH_LR_NETWORK" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT_OMNIPATH_LR_NETWORK")" )
  VIASH_PAR_OUTPUT_OMNIPATH_LR_NETWORK=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT_OMNIPATH_LR_NETWORK")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT_OMNIPATH_LR_NETWORK" )
fi
if [ ! -z "$VIASH_PAR_OUTPUT_NICHENET_LRT_NETWORK" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT_NICHENET_LRT_NETWORK")" )
  VIASH_PAR_OUTPUT_NICHENET_LRT_NETWORK=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT_NICHENET_LRT_NETWORK")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT_NICHENET_LRT_NETWORK" )
fi
if [ ! -z "$VIASH_PAR_OUTPUT_NICHENET_LIGAND_TARGET_MATRIX" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT_NICHENET_LIGAND_TARGET_MATRIX")" )
  VIASH_PAR_OUTPUT_NICHENET_LIGAND_TARGET_MATRIX=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT_NICHENET_LIGAND_TARGET_MATRIX")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT_NICHENET_LIGAND_TARGET_MATRIX" )
fi
if [ ! -z "$VIASH_PAR_OUTPUT_COLLECTRI_TF_NETWORK" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT_COLLECTRI_TF_NETWORK")" )
  VIASH_PAR_OUTPUT_COLLECTRI_TF_NETWORK=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT_COLLECTRI_TF_NETWORK")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT_COLLECTRI_TF_NETWORK" )
fi
if [ ! -z "$VIASH_PAR_OUTPUT_OMNIPATH_GP_GENE_COUNT_DISTRIBUTIONS" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT_OMNIPATH_GP_GENE_COUNT_DISTRIBUTIONS")" )
  VIASH_PAR_OUTPUT_OMNIPATH_GP_GENE_COUNT_DISTRIBUTIONS=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT_OMNIPATH_GP_GENE_COUNT_DISTRIBUTIONS")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT_OMNIPATH_GP_GENE_COUNT_DISTRIBUTIONS" )
fi
if [ ! -z "$VIASH_PAR_OUTPUT_NICHENET_GP_GENE_COUNT_DISTRIBUTIONS" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT_NICHENET_GP_GENE_COUNT_DISTRIBUTIONS")" )
  VIASH_PAR_OUTPUT_NICHENET_GP_GENE_COUNT_DISTRIBUTIONS=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT_NICHENET_GP_GENE_COUNT_DISTRIBUTIONS")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT_NICHENET_GP_GENE_COUNT_DISTRIBUTIONS" )
fi
if [ ! -z "$VIASH_PAR_OUTPUT_MEBOCOST_GP_GENE_COUNT_DISTRIBUTIONS" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT_MEBOCOST_GP_GENE_COUNT_DISTRIBUTIONS")" )
  VIASH_PAR_OUTPUT_MEBOCOST_GP_GENE_COUNT_DISTRIBUTIONS=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT_MEBOCOST_GP_GENE_COUNT_DISTRIBUTIONS")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT_MEBOCOST_GP_GENE_COUNT_DISTRIBUTIONS" )
fi
if [ ! -z "$VIASH_PAR_OUTPUT_COLLECTRI_TF_GP_GENE_COUNT_DISTRIBUTIONS" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT_COLLECTRI_TF_GP_GENE_COUNT_DISTRIBUTIONS")" )
  VIASH_PAR_OUTPUT_COLLECTRI_TF_GP_GENE_COUNT_DISTRIBUTIONS=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT_COLLECTRI_TF_GP_GENE_COUNT_DISTRIBUTIONS")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT_COLLECTRI_TF_GP_GENE_COUNT_DISTRIBUTIONS" )
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-gene_program_mask-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 json
import os
import shutil
import sys
from pathlib import Path

import pandas as pd

from nichecompass.utils import (
    extract_gp_dict_from_mebocost_ms_interactions,
    extract_gp_dict_from_nichenet_lrt_interactions,
    extract_gp_dict_from_omnipath_lr_interactions,
    filter_and_combine_gp_dict_gps_v2,
    extract_gp_dict_from_collectri_tf_network,
)


## VIASH START
# The following code has been auto-generated by Viash.
par = {
  'input_gene_orthologs_mapping_file': $( if [ ! -z ${VIASH_PAR_INPUT_GENE_ORTHOLOGS_MAPPING_FILE+x} ]; then echo "r'${VIASH_PAR_INPUT_GENE_ORTHOLOGS_MAPPING_FILE//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'input_metabolite_enzymes': $( if [ ! -z ${VIASH_PAR_INPUT_METABOLITE_ENZYMES+x} ]; then echo "r'${VIASH_PAR_INPUT_METABOLITE_ENZYMES//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'input_metabolite_sensors': $( if [ ! -z ${VIASH_PAR_INPUT_METABOLITE_SENSORS+x} ]; then echo "r'${VIASH_PAR_INPUT_METABOLITE_SENSORS//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'input_omnipath_lr_network': $( if [ ! -z ${VIASH_PAR_INPUT_OMNIPATH_LR_NETWORK+x} ]; then echo "r'${VIASH_PAR_INPUT_OMNIPATH_LR_NETWORK//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'input_nichenet_ligand_target_matrix': $( if [ ! -z ${VIASH_PAR_INPUT_NICHENET_LIGAND_TARGET_MATRIX+x} ]; then echo "r'${VIASH_PAR_INPUT_NICHENET_LIGAND_TARGET_MATRIX//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'input_nichenet_lrt_network': $( if [ ! -z ${VIASH_PAR_INPUT_NICHENET_LRT_NETWORK+x} ]; then echo "r'${VIASH_PAR_INPUT_NICHENET_LRT_NETWORK//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'input_collectri_tf_network': $( if [ ! -z ${VIASH_PAR_INPUT_COLLECTRI_TF_NETWORK+x} ]; then echo "r'${VIASH_PAR_INPUT_COLLECTRI_TF_NETWORK//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'species': $( if [ ! -z ${VIASH_PAR_SPECIES+x} ]; then echo "r'${VIASH_PAR_SPECIES//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'create_omnipath_gene_program_mask': $( if [ ! -z ${VIASH_PAR_CREATE_OMNIPATH_GENE_PROGRAM_MASK+x} ]; then echo "r'${VIASH_PAR_CREATE_OMNIPATH_GENE_PROGRAM_MASK//\'/\'\"\'\"r\'}'.lower() == 'true'"; else echo None; fi ),
  'create_nichenet_gene_program_mask': $( if [ ! -z ${VIASH_PAR_CREATE_NICHENET_GENE_PROGRAM_MASK+x} ]; then echo "r'${VIASH_PAR_CREATE_NICHENET_GENE_PROGRAM_MASK//\'/\'\"\'\"r\'}'.lower() == 'true'"; else echo None; fi ),
  'create_mebocost_gene_program_mask': $( if [ ! -z ${VIASH_PAR_CREATE_MEBOCOST_GENE_PROGRAM_MASK+x} ]; then echo "r'${VIASH_PAR_CREATE_MEBOCOST_GENE_PROGRAM_MASK//\'/\'\"\'\"r\'}'.lower() == 'true'"; else echo None; fi ),
  'create_collectri_tf_gene_program_mask': $( if [ ! -z ${VIASH_PAR_CREATE_COLLECTRI_TF_GENE_PROGRAM_MASK+x} ]; then echo "r'${VIASH_PAR_CREATE_COLLECTRI_TF_GENE_PROGRAM_MASK//\'/\'\"\'\"r\'}'.lower() == 'true'"; else echo None; fi ),
  'overlap_thresh_target_genes': $( if [ ! -z ${VIASH_PAR_OVERLAP_THRESH_TARGET_GENES+x} ]; then echo "float(r'${VIASH_PAR_OVERLAP_THRESH_TARGET_GENES//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'omnipath_min_curation_effort': $( if [ ! -z ${VIASH_PAR_OMNIPATH_MIN_CURATION_EFFORT+x} ]; then echo "int(r'${VIASH_PAR_OMNIPATH_MIN_CURATION_EFFORT//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'nichenet_version': $( if [ ! -z ${VIASH_PAR_NICHENET_VERSION+x} ]; then echo "r'${VIASH_PAR_NICHENET_VERSION//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'nichenet_keep_target_genes_ratio': $( if [ ! -z ${VIASH_PAR_NICHENET_KEEP_TARGET_GENES_RATIO+x} ]; then echo "float(r'${VIASH_PAR_NICHENET_KEEP_TARGET_GENES_RATIO//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'nichenet_max_n_target_genes_per_gp': $( if [ ! -z ${VIASH_PAR_NICHENET_MAX_N_TARGET_GENES_PER_GP+x} ]; then echo "int(r'${VIASH_PAR_NICHENET_MAX_N_TARGET_GENES_PER_GP//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'output': $( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "r'${VIASH_PAR_OUTPUT//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'output_omnipath_lr_network': $( if [ ! -z ${VIASH_PAR_OUTPUT_OMNIPATH_LR_NETWORK+x} ]; then echo "r'${VIASH_PAR_OUTPUT_OMNIPATH_LR_NETWORK//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'output_nichenet_lrt_network': $( if [ ! -z ${VIASH_PAR_OUTPUT_NICHENET_LRT_NETWORK+x} ]; then echo "r'${VIASH_PAR_OUTPUT_NICHENET_LRT_NETWORK//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'output_nichenet_ligand_target_matrix': $( if [ ! -z ${VIASH_PAR_OUTPUT_NICHENET_LIGAND_TARGET_MATRIX+x} ]; then echo "r'${VIASH_PAR_OUTPUT_NICHENET_LIGAND_TARGET_MATRIX//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'output_collectri_tf_network': $( if [ ! -z ${VIASH_PAR_OUTPUT_COLLECTRI_TF_NETWORK+x} ]; then echo "r'${VIASH_PAR_OUTPUT_COLLECTRI_TF_NETWORK//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'output_omnipath_gp_gene_count_distributions': $( if [ ! -z ${VIASH_PAR_OUTPUT_OMNIPATH_GP_GENE_COUNT_DISTRIBUTIONS+x} ]; then echo "r'${VIASH_PAR_OUTPUT_OMNIPATH_GP_GENE_COUNT_DISTRIBUTIONS//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'output_nichenet_gp_gene_count_distributions': $( if [ ! -z ${VIASH_PAR_OUTPUT_NICHENET_GP_GENE_COUNT_DISTRIBUTIONS+x} ]; then echo "r'${VIASH_PAR_OUTPUT_NICHENET_GP_GENE_COUNT_DISTRIBUTIONS//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'output_mebocost_gp_gene_count_distributions': $( if [ ! -z ${VIASH_PAR_OUTPUT_MEBOCOST_GP_GENE_COUNT_DISTRIBUTIONS+x} ]; then echo "r'${VIASH_PAR_OUTPUT_MEBOCOST_GP_GENE_COUNT_DISTRIBUTIONS//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'output_collectri_tf_gp_gene_count_distributions': $( if [ ! -z ${VIASH_PAR_OUTPUT_COLLECTRI_TF_GP_GENE_COUNT_DISTRIBUTIONS+x} ]; then echo "r'${VIASH_PAR_OUTPUT_COLLECTRI_TF_GP_GENE_COUNT_DISTRIBUTIONS//\'/\'\"\'\"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

logger = setup_logger()


def _sanitize_omnipath_csv(file_path: str) -> None:
    """
    Sanitize the OmniPath CSV file format for compatibility with NicheCompass
    \`load_from_disk\`.

    Bug 1 - CSV index inconsistency:
    The library saves with \`to_csv(path, index=False)\` but loads with
    \`read_csv(path, index_col=0)\`. This causes the first data column to be
    incorrectly treated as the index when loading.

    Bug 2 - Missing NaN handling:
    OmniPath contains proteins (TrEMBL/unreviewed entries like A0A2R8YE73) that
    don't have gene symbol mappings. These appear as NaN in genesymbol columns.
    The \`resolve_protein_complexes\` function doesn't handle NaN, causing
    \`TypeError\`. When fetching from the API, groupby operations implicitly
    filter some NaN rows, but \`load_from_disk\` doesn't have this filtering.

    This function sanitizes the loaded CSV by:
     1. Dropping rows with NaN in genesymbol columns
         (unusable for gene programs)
    2. Rewriting with an index column (to fix the load inconsistency)

    See:
    https://github.com/Lotfollahi-lab/nichecompass/blob/main/src/nichecompass/utils/gene_programs.py

    Args:
        file_path: Path to the OmniPath CSV file to fix.
    """
    if not file_path or not os.path.exists(file_path):
        return

    df = pd.read_csv(file_path)

    # Find all genesymbol columns dynamically and drop rows where any are NaN.
    # These proteins don't have gene mappings and cannot be used in gene programs.
    genesymbol_cols = df.columns.str.lower().str.contains("genesymbol")
    if genesymbol_cols.any():
        df = df.dropna(subset=df.columns[genesymbol_cols])

    # Rewrite with an index column so downstream \`read_csv(..., index_col=0)\` is stable.
    os.makedirs(meta["temp_dir"], exist_ok=True)

    lr_network_file_path = os.path.join(
        meta["temp_dir"],
        "input_omnipath_lr_network_sanitized.csv",
    )
    df.to_csv(lr_network_file_path, index=True)
    return lr_network_file_path


def create_omnipath_gene_program_mask(
    output_lr_network: str | None,
    output_count_distr: str | None,
    input_lr_network: str | None,
    input_orthologs: str | None,
) -> dict:
    # Generate omnipath gene program mask
    # Determine output distribution
    plot_gp_gene_count_distributions = bool(output_count_distr)

    # Determine load_from_disk and save_to_disk from I/O params.
    load_from_disk = bool(input_lr_network)
    save_to_disk = bool(output_lr_network) and (not load_from_disk)

    # Warn if both input and output are provided
    if input_lr_network and output_lr_network:
        logger.warning(
            "Both Omnipath input and output paths are provided. "
            "Using input file; output will not be saved."
        )

    # Use input file path if provided, otherwise use output file path.
    if load_from_disk:
        lr_network_file_path = _sanitize_omnipath_csv(input_lr_network)
    else:
        lr_network_file_path = output_lr_network

    omnipath_gp_dict = extract_gp_dict_from_omnipath_lr_interactions(
        species=par["species"],
        min_curation_effort=par["omnipath_min_curation_effort"],
        load_from_disk=load_from_disk,
        save_to_disk=save_to_disk,
        lr_network_file_path=lr_network_file_path,
        gene_orthologs_mapping_file_path=input_orthologs,
        plot_gp_gene_count_distributions=plot_gp_gene_count_distributions,
        gp_gene_count_distributions_save_path=output_count_distr,
    )

    return omnipath_gp_dict


def create_nichenet_gene_program_mask(
    output_lrt_network: str | None,
    output_lt_matrix: str | None,
    output_count_distr: str | None,
    input_lrt_network: str | None,
    input_lt_matrix: str | None,
    input_orthologs: str | None,
) -> dict:
    plot_gp_gene_count_distributions = bool(output_count_distr)

    # Validate NicheNet I/O.
    load_from_disk = bool(input_lrt_network) and bool(input_lt_matrix)

    save_to_disk = (
        bool(output_lrt_network) or bool(output_lt_matrix) and not load_from_disk
    )

    # Warn if both input and output are provided.
    if load_from_disk and (bool(output_lrt_network) or bool(output_lt_matrix)):
        logger.warning(
            "Both NicheNet input and output paths are provided. "
            "Using input files; outputs will not be saved."
        )

    # Use input file path if provided, otherwise use output file path.
    if load_from_disk:
        lr_network_file_path = input_lrt_network
        ligand_target_matrix_file_path = input_lt_matrix
    else:
        lr_network_file_path = output_lrt_network
        ligand_target_matrix_file_path = output_lt_matrix

    nichenet_gp_dict = extract_gp_dict_from_nichenet_lrt_interactions(
        species=par["species"],
        version=par["nichenet_version"],
        keep_target_genes_ratio=par["nichenet_keep_target_genes_ratio"],
        max_n_target_genes_per_gp=par["nichenet_max_n_target_genes_per_gp"],
        load_from_disk=load_from_disk,
        save_to_disk=save_to_disk,
        lr_network_file_path=lr_network_file_path,
        ligand_target_matrix_file_path=ligand_target_matrix_file_path,
        gene_orthologs_mapping_file_path=input_orthologs,
        plot_gp_gene_count_distributions=plot_gp_gene_count_distributions,
        gp_gene_count_distributions_save_path=output_count_distr,
    )
    return nichenet_gp_dict


def create_mebocost_gene_program_mask(
    output_count_distr: str | None,
    input_metabolite_enzymes: str,
    input_metabolite_sensors: str,
) -> dict:
    os.makedirs(meta["temp_dir"], exist_ok=True)

    metabolite_enzymes_path = os.path.join(
        meta["temp_dir"],
        f"{par['species']}_metabolite_enzymes.tsv",
    )
    metabolite_sensors_path = os.path.join(
        meta["temp_dir"],
        f"{par['species']}_metabolite_sensors.tsv",
    )

    shutil.copy2(
        input_metabolite_enzymes,
        metabolite_enzymes_path,
    )
    shutil.copy2(
        input_metabolite_sensors,
        metabolite_sensors_path,
    )
    plot_gp_gene_count_distributions = bool(output_count_distr)

    mebocost_gp_dict = extract_gp_dict_from_mebocost_ms_interactions(
        dir_path=meta["temp_dir"],
        species=par["species"],
        plot_gp_gene_count_distributions=plot_gp_gene_count_distributions,
        gp_gene_count_distributions_save_path=output_count_distr,
    )
    return mebocost_gp_dict


def create_collectri_tf_gene_program_mask(
    output_count_distr: str | None,
    output_tf_network: str | None,
    input_tf_network: str | None,
) -> dict:
    plot_gp_gene_count_distributions = bool(output_count_distr)

    # Determine load_from_disk and save_to_disk from I/O params.
    load_from_disk = bool(input_tf_network)
    save_to_disk = bool(output_tf_network) and not load_from_disk

    # Warn if both input and output are provided
    if input_tf_network and output_tf_network:
        logger.warning(
            "Both CollecTRI input and output paths are provided. "
            "Using input file; output will not be saved."
        )

    # Use input file path if provided, otherwise use output file path
    tf_network_file_path = input_tf_network if load_from_disk else output_tf_network

    collectri_gp_dict = extract_gp_dict_from_collectri_tf_network(
        species=par["species"],
        load_from_disk=load_from_disk,
        save_to_disk=save_to_disk,
        tf_network_file_path=tf_network_file_path,
        plot_gp_gene_count_distributions=plot_gp_gene_count_distributions,
        gp_gene_count_distributions_save_path=output_count_distr,
    )
    return collectri_gp_dict


def main():
    # Validate that inputs are provided correctly
    if not any(
        [
            par["create_omnipath_gene_program_mask"],
            par["create_nichenet_gene_program_mask"],
            par["create_mebocost_gene_program_mask"],
            par["create_collectri_tf_gene_program_mask"],
        ]
    ):
        raise ValueError("At least one gene program mask must be set to True")
    if (
        par["create_omnipath_gene_program_mask"]
        and par["species"] == "mouse"
        and not par["input_gene_orthologs_mapping_file"]
    ):
        raise ValueError(
            "Mouse species requires --input_gene_orthologs_mapping_file "
            "to generate the Omnipath mask."
        )
    if (
        par["create_nichenet_gene_program_mask"]
        and par["species"] == "mouse"
        and not par["input_gene_orthologs_mapping_file"]
    ):
        raise ValueError(
            "Mouse species requires --input_gene_orthologs_mapping_file "
            "to generate the NicheNet mask."
        )
    if par["create_mebocost_gene_program_mask"] and (
        (not par["input_metabolite_enzymes"]) or (not par["input_metabolite_sensors"])
    ):
        raise ValueError(
            "MeBocost mask requires --input_metabolite_enzymes "
            "and --input_metabolite_sensors."
        )

    # Assemble gene program dictionaries
    gp_dicts = []

    masks = {
        "create_omnipath_gene_program_mask": (
            "Omnipath",
            create_omnipath_gene_program_mask,
        ),
        "create_nichenet_gene_program_mask": (
            "NicheNet",
            create_nichenet_gene_program_mask,
        ),
        "create_mebocost_gene_program_mask": (
            "MeBocost",
            create_mebocost_gene_program_mask,
        ),
        "create_collectri_tf_gene_program_mask": (
            "CollecTRI TF",
            create_collectri_tf_gene_program_mask,
        ),
    }

    mask_args = {
        "create_omnipath_gene_program_mask": (
            par["output_omnipath_lr_network"],
            par["output_omnipath_gp_gene_count_distributions"],
            par["input_omnipath_lr_network"],
            par["input_gene_orthologs_mapping_file"],
        ),
        "create_nichenet_gene_program_mask": (
            par["output_nichenet_lrt_network"],
            par["output_nichenet_ligand_target_matrix"],
            par["output_nichenet_gp_gene_count_distributions"],
            par["input_nichenet_lrt_network"],
            par["input_nichenet_ligand_target_matrix"],
            par["input_gene_orthologs_mapping_file"],
        ),
        "create_mebocost_gene_program_mask": (
            par["output_mebocost_gp_gene_count_distributions"],
            par["input_metabolite_enzymes"],
            par["input_metabolite_sensors"],
        ),
        "create_collectri_tf_gene_program_mask": (
            par["output_collectri_tf_gp_gene_count_distributions"],
            par["output_collectri_tf_network"],
            par["input_collectri_tf_network"],
        ),
    }

    for mask, (mask_name, mask_function) in masks.items():
        if par[mask]:
            logger.info(f"Generating {mask_name} gene program mask...")
            gp_dict = mask_function(*mask_args[mask])
            gp_dicts.append(gp_dict)

    # Filter and combine GPs
    assert len(gp_dicts) > 0, "No gene program dictionaries were created."

    combined_gp_dict = filter_and_combine_gp_dict_gps_v2(
        gp_dicts,
        overlap_thresh_target_genes=par["overlap_thresh_target_genes"],
        verbose=True,
    )

    logger.info("Gene program mask generation completed.")
    logger.info(
        "Number of gene programs after filtering and combining: %s.",
        len(combined_gp_dict),
    )

    output_path = Path(par["output"])
    output_path.parent.mkdir(parents=True, exist_ok=True)

    logger.info("Saving combined gene program mask to: %s", str(output_path))
    with output_path.open("w", encoding="utf-8") as f:
        json.dump(combined_gp_dict, f)


if __name__ == "__main__":
    main()
VIASHMAIN
python -B "\$tempscript" &
wait "\$!"

VIASHEOF


if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  # strip viash automount from file paths
  
  if [ ! -z "$VIASH_PAR_INPUT_GENE_ORTHOLOGS_MAPPING_FILE" ]; then
    VIASH_PAR_INPUT_GENE_ORTHOLOGS_MAPPING_FILE=$(ViashDockerStripAutomount "$VIASH_PAR_INPUT_GENE_ORTHOLOGS_MAPPING_FILE")
  fi
  if [ ! -z "$VIASH_PAR_INPUT_METABOLITE_ENZYMES" ]; then
    VIASH_PAR_INPUT_METABOLITE_ENZYMES=$(ViashDockerStripAutomount "$VIASH_PAR_INPUT_METABOLITE_ENZYMES")
  fi
  if [ ! -z "$VIASH_PAR_INPUT_METABOLITE_SENSORS" ]; then
    VIASH_PAR_INPUT_METABOLITE_SENSORS=$(ViashDockerStripAutomount "$VIASH_PAR_INPUT_METABOLITE_SENSORS")
  fi
  if [ ! -z "$VIASH_PAR_INPUT_OMNIPATH_LR_NETWORK" ]; then
    VIASH_PAR_INPUT_OMNIPATH_LR_NETWORK=$(ViashDockerStripAutomount "$VIASH_PAR_INPUT_OMNIPATH_LR_NETWORK")
  fi
  if [ ! -z "$VIASH_PAR_INPUT_NICHENET_LIGAND_TARGET_MATRIX" ]; then
    VIASH_PAR_INPUT_NICHENET_LIGAND_TARGET_MATRIX=$(ViashDockerStripAutomount "$VIASH_PAR_INPUT_NICHENET_LIGAND_TARGET_MATRIX")
  fi
  if [ ! -z "$VIASH_PAR_INPUT_NICHENET_LRT_NETWORK" ]; then
    VIASH_PAR_INPUT_NICHENET_LRT_NETWORK=$(ViashDockerStripAutomount "$VIASH_PAR_INPUT_NICHENET_LRT_NETWORK")
  fi
  if [ ! -z "$VIASH_PAR_INPUT_COLLECTRI_TF_NETWORK" ]; then
    VIASH_PAR_INPUT_COLLECTRI_TF_NETWORK=$(ViashDockerStripAutomount "$VIASH_PAR_INPUT_COLLECTRI_TF_NETWORK")
  fi
  if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
    VIASH_PAR_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT")
  fi
  if [ ! -z "$VIASH_PAR_OUTPUT_OMNIPATH_LR_NETWORK" ]; then
    VIASH_PAR_OUTPUT_OMNIPATH_LR_NETWORK=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT_OMNIPATH_LR_NETWORK")
  fi
  if [ ! -z "$VIASH_PAR_OUTPUT_NICHENET_LRT_NETWORK" ]; then
    VIASH_PAR_OUTPUT_NICHENET_LRT_NETWORK=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT_NICHENET_LRT_NETWORK")
  fi
  if [ ! -z "$VIASH_PAR_OUTPUT_NICHENET_LIGAND_TARGET_MATRIX" ]; then
    VIASH_PAR_OUTPUT_NICHENET_LIGAND_TARGET_MATRIX=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT_NICHENET_LIGAND_TARGET_MATRIX")
  fi
  if [ ! -z "$VIASH_PAR_OUTPUT_COLLECTRI_TF_NETWORK" ]; then
    VIASH_PAR_OUTPUT_COLLECTRI_TF_NETWORK=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT_COLLECTRI_TF_NETWORK")
  fi
  if [ ! -z "$VIASH_PAR_OUTPUT_OMNIPATH_GP_GENE_COUNT_DISTRIBUTIONS" ]; then
    VIASH_PAR_OUTPUT_OMNIPATH_GP_GENE_COUNT_DISTRIBUTIONS=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT_OMNIPATH_GP_GENE_COUNT_DISTRIBUTIONS")
  fi
  if [ ! -z "$VIASH_PAR_OUTPUT_NICHENET_GP_GENE_COUNT_DISTRIBUTIONS" ]; then
    VIASH_PAR_OUTPUT_NICHENET_GP_GENE_COUNT_DISTRIBUTIONS=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT_NICHENET_GP_GENE_COUNT_DISTRIBUTIONS")
  fi
  if [ ! -z "$VIASH_PAR_OUTPUT_MEBOCOST_GP_GENE_COUNT_DISTRIBUTIONS" ]; then
    VIASH_PAR_OUTPUT_MEBOCOST_GP_GENE_COUNT_DISTRIBUTIONS=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT_MEBOCOST_GP_GENE_COUNT_DISTRIBUTIONS")
  fi
  if [ ! -z "$VIASH_PAR_OUTPUT_COLLECTRI_TF_GP_GENE_COUNT_DISTRIBUTIONS" ]; then
    VIASH_PAR_OUTPUT_COLLECTRI_TF_GP_GENE_COUNT_DISTRIBUTIONS=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT_COLLECTRI_TF_GP_GENE_COUNT_DISTRIBUTIONS")
  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 '$VIASH_PAR_OUTPUT' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_OUTPUT_OMNIPATH_LR_NETWORK" ] && [ ! -e "$VIASH_PAR_OUTPUT_OMNIPATH_LR_NETWORK" ]; then
  ViashError "Output file '$VIASH_PAR_OUTPUT_OMNIPATH_LR_NETWORK' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_OUTPUT_NICHENET_LRT_NETWORK" ] && [ ! -e "$VIASH_PAR_OUTPUT_NICHENET_LRT_NETWORK" ]; then
  ViashError "Output file '$VIASH_PAR_OUTPUT_NICHENET_LRT_NETWORK' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_OUTPUT_NICHENET_LIGAND_TARGET_MATRIX" ] && [ ! -e "$VIASH_PAR_OUTPUT_NICHENET_LIGAND_TARGET_MATRIX" ]; then
  ViashError "Output file '$VIASH_PAR_OUTPUT_NICHENET_LIGAND_TARGET_MATRIX' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_OUTPUT_COLLECTRI_TF_NETWORK" ] && [ ! -e "$VIASH_PAR_OUTPUT_COLLECTRI_TF_NETWORK" ]; then
  ViashError "Output file '$VIASH_PAR_OUTPUT_COLLECTRI_TF_NETWORK' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_OUTPUT_OMNIPATH_GP_GENE_COUNT_DISTRIBUTIONS" ] && [ ! -e "$VIASH_PAR_OUTPUT_OMNIPATH_GP_GENE_COUNT_DISTRIBUTIONS" ]; then
  ViashError "Output file '$VIASH_PAR_OUTPUT_OMNIPATH_GP_GENE_COUNT_DISTRIBUTIONS' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_OUTPUT_NICHENET_GP_GENE_COUNT_DISTRIBUTIONS" ] && [ ! -e "$VIASH_PAR_OUTPUT_NICHENET_GP_GENE_COUNT_DISTRIBUTIONS" ]; then
  ViashError "Output file '$VIASH_PAR_OUTPUT_NICHENET_GP_GENE_COUNT_DISTRIBUTIONS' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_OUTPUT_MEBOCOST_GP_GENE_COUNT_DISTRIBUTIONS" ] && [ ! -e "$VIASH_PAR_OUTPUT_MEBOCOST_GP_GENE_COUNT_DISTRIBUTIONS" ]; then
  ViashError "Output file '$VIASH_PAR_OUTPUT_MEBOCOST_GP_GENE_COUNT_DISTRIBUTIONS' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_OUTPUT_COLLECTRI_TF_GP_GENE_COUNT_DISTRIBUTIONS" ] && [ ! -e "$VIASH_PAR_OUTPUT_COLLECTRI_TF_GP_GENE_COUNT_DISTRIBUTIONS" ]; then
  ViashError "Output file '$VIASH_PAR_OUTPUT_COLLECTRI_TF_GP_GENE_COUNT_DISTRIBUTIONS' does not exist."
  exit 1
fi


exit 0
