#!/usr/bin/env bash

# concatenate_h5mu processing-workflows-quantile-filtering
# 
# This wrapper script is auto-generated by viash 0.9.7 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
# 
# The component may contain files which fall under a different license. The
# authors of this component should specify the license in the header of such
# files, or include a separate license file detailing the licenses of all included
# files.
# 
# Component authors:
#  * Dries Schaumont (maintainer)

set -e

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

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

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

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

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

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

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

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

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

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

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

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

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

# define meta fields
VIASH_META_NAME="concatenate_h5mu"
VIASH_META_FUNCTIONALITY_NAME="concatenate_h5mu"
VIASH_META_EXECUTABLE="$VIASH_META_RESOURCES_DIR/$VIASH_META_NAME"
VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
VIASH_META_TEMP_DIR="$VIASH_TEMP"



# initialise variables
VIASH_MODE='run'
VIASH_ENGINE_ID='docker'

######## Helper functions for setting up Docker images for viash ########
# expects: ViashDockerBuild

# ViashDockerInstallationCheck: check whether Docker is installed correctly
#
# examples:
#   ViashDockerInstallationCheck
function ViashDockerInstallationCheck {
  ViashDebug "Checking whether Docker is installed"
  if [ ! command -v docker &> /dev/null ]; then
    ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
    exit 1
  fi

  ViashDebug "Checking whether the Docker daemon is running"
  local save=$-; set +e
  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
  local out=$?
  [[ $save =~ e ]] && set -e
  if [ $out -ne 0 ]; then
    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
    ViashCritical "- Try running 'dockerd' in the command line"
    ViashCritical "- See https://docs.docker.com/config/daemon/"
    exit 1
  fi
}

# ViashDockerRemoteTagCheck: check whether a Docker image is available 
# on a remote. Assumes `docker login` has been performed, if relevant.
#
# $1                  : image identifier with format `[registry/]image[:tag]`
# exit code $?        : whether or not the image was found
# examples:
#   ViashDockerRemoteTagCheck python:latest
#   echo $?                                     # returns '0'
#   ViashDockerRemoteTagCheck sdaizudceahifu
#   echo $?                                     # returns '1'
function ViashDockerRemoteTagCheck {
  docker manifest inspect $1 > /dev/null 2> /dev/null
}

# ViashDockerLocalTagCheck: check whether a Docker image is available locally
#
# $1                  : image identifier with format `[registry/]image[:tag]`
# exit code $?        : whether or not the image was found
# examples:
#   docker pull python:latest
#   ViashDockerLocalTagCheck python:latest
#   echo $?                                     # returns '0'
#   ViashDockerLocalTagCheck sdaizudceahifu
#   echo $?                                     # returns '1'
function ViashDockerLocalTagCheck {
  [ -n "$(docker images -q $1)" ]
}

# ViashDockerPull: pull a Docker image
#
# $1                  : image identifier with format `[registry/]image[:tag]`
# exit code $?        : whether or not the image was found
# examples:
#   ViashDockerPull python:latest
#   echo $?                                     # returns '0'
#   ViashDockerPull sdaizudceahifu
#   echo $?                                     # returns '1'
function ViashDockerPull {
  ViashNotice "Checking if Docker image is available at '$1'"
  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
    docker pull $1 && return 0 || return 1
  else
    local save=$-; set +e
    docker pull $1 2> /dev/null > /dev/null
    local out=$?
    [[ $save =~ e ]] && set -e
    if [ $out -ne 0 ]; then
      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
    fi
    return $out
  fi
}

# ViashDockerPush: push a Docker image
#
# $1                  : image identifier with format `[registry/]image[:tag]`
# exit code $?        : whether or not the image was found
# examples:
#   ViashDockerPush python:latest
#   echo $?                                     # returns '0'
#   ViashDockerPush sdaizudceahifu
#   echo $?                                     # returns '1'
function ViashDockerPush {
  ViashNotice "Pushing image to '$1'"
  local save=$-; set +e
  local out
  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
    docker push $1
    out=$?
  else
    docker push $1 2> /dev/null > /dev/null
    out=$?
  fi
  [[ $save =~ e ]] && set -e
  if [ $out -eq 0 ]; then
    ViashNotice "Container '$1' push succeeded."
  else
    ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions."
  fi
  return $out
}

# ViashDockerPullElseBuild: pull a Docker image, else build it
#
# $1                  : image identifier with format `[registry/]image[:tag]`
# ViashDockerBuild    : a Bash function which builds a docker image, takes image identifier as argument.
# examples:
#   ViashDockerPullElseBuild mynewcomponent
function ViashDockerPullElseBuild {
  local save=$-; set +e
  ViashDockerPull $1
  local out=$?
  [[ $save =~ e ]] && set -e
  if [ $out -ne 0 ]; then
    ViashDockerBuild $@
  fi
}

# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
#
# $1          : image identifier with format `[registry/]image[:tag]`
# $2          : docker setup strategy, see DockerSetupStrategy.scala
# examples:
#   ViashDockerSetup mynewcomponent alwaysbuild
function ViashDockerSetup {
  local image_id="$1"
  local setup_strategy="$2"
  if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
    ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
  elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then
    ViashDockerPull $image_id
  elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then
    ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
  elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then
    ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
  elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then
    ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
  elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then
    local save=$-; set +e
    ViashDockerLocalTagCheck $image_id
    local outCheck=$?
    [[ $save =~ e ]] && set -e
    if [ $outCheck -eq 0 ]; then
      ViashInfo "Image $image_id already exists"
    elif [ "$setup_strategy" == "ifneedbebuild" ]; then
      ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
    elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then
      ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
    elif [ "$setup_strategy" == "ifneedbepull" ]; then
      ViashDockerPull $image_id
    elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then
      ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
    elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then
      ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
    else
      ViashError "Unrecognised Docker strategy: $setup_strategy"
      exit 1
    fi
  elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then
    ViashDockerPush "$image_id"
  elif [ "$setup_strategy" == "pushifnotpresent" -o "$setup_strategy" == "gentlepush" -o "$setup_strategy" == "maybepush" ]; then
    local save=$-; set +e
    ViashDockerRemoteTagCheck $image_id
    local outCheck=$?
    [[ $save =~ e ]] && set -e
    if [ $outCheck -eq 0 ]; then
      ViashNotice "Container '$image_id' exists, doing nothing."
    else
      ViashNotice "Container '$image_id' does not yet exist."
      ViashDockerPush "$image_id"
    fi
  elif [ "$setup_strategy" == "donothing" -o "$setup_strategy" == "meh" ]; then
    ViashNotice "Skipping setup."
  else
    ViashError "Unrecognised Docker strategy: $setup_strategy"
    exit 1
  fi
}

# ViashDockerCheckCommands: Check whether a docker container has the required commands
#
# $1                  : image identifier with format `[registry/]image[:tag]`
# $@                  : commands to verify being present
# examples:
#   ViashDockerCheckCommands bash:4.0 bash ps foo
function ViashDockerCheckCommands {
  local image_id="$1"
  shift 1
  local commands="$@"
  local save=$-; set +e
  local missing # mark 'missing' as local in advance, otherwise the exit code of the command will be missing and always be '0'
  missing=$(docker run --rm --entrypoint=sh "$image_id" -c "for command in $commands; do command -v \$command >/dev/null 2>&1; if [ \$? -ne 0 ]; then echo \$command; exit 1; fi; done")
  local outCheck=$?
  [[ $save =~ e ]] && set -e
  if [ $outCheck -ne 0 ]; then
  	ViashError "Docker container '$image_id' does not contain command '$missing'."
  	exit 1
  fi
}

# ViashDockerBuild: build a docker image
# $1                               : image identifier with format `[registry/]image[:tag]`
# $...                             : additional arguments to pass to docker build
# $VIASH_META_TEMP_DIR             : temporary directory to store dockerfile & optional resources in
# $VIASH_META_NAME                 : name of the component
# $VIASH_META_RESOURCES_DIR        : directory containing the resources
# $VIASH_VERBOSITY                 : verbosity level
# exit code $?                     : whether or not the image was built successfully
function ViashDockerBuild {
  local image_id="$1"
  shift 1

  # create temporary directory to store dockerfile & optional resources in
  local tmpdir=$(mktemp -d "$VIASH_META_TEMP_DIR/dockerbuild-$VIASH_META_NAME-XXXXXX")
  local dockerfile="$tmpdir/Dockerfile"
  function clean_up {
    rm -rf "$tmpdir"
  }
  trap clean_up EXIT

  # store dockerfile and resources
  ViashDockerfile "$VIASH_ENGINE_ID" > "$dockerfile"

  # generate the build command
  local docker_build_cmd="docker build -t '$image_id' $@ '$VIASH_META_RESOURCES_DIR' -f '$dockerfile'"

  # build the container
  ViashNotice "Building container '$image_id' with Dockerfile"
  ViashInfo "$docker_build_cmd"
  local save=$-; set +e
  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
    eval $docker_build_cmd
  else
    eval $docker_build_cmd &> "$tmpdir/docker_build.log"
  fi

  # check exit code
  local out=$?
  [[ $save =~ e ]] && set -e
  if [ $out -ne 0 ]; then
    ViashError "Error occurred while building container '$image_id'"
    if [ $VIASH_VERBOSITY -lt $VIASH_LOGCODE_INFO ]; then
      ViashError "Transcript: --------------------------------"
      cat "$tmpdir/docker_build.log"
      ViashError "End of transcript --------------------------"
    fi
    exit 1
  fi
}

######## End of helper functions for setting up Docker images for viash ########

# ViashDockerFile: print the dockerfile to stdout
# $1    : engine identifier
# return : dockerfile required to run this component
# examples:
#   ViashDockerFile
function ViashDockerfile {
  local engine_id="$1"

  if [[ "$engine_id" == "docker" ]]; then
    cat << 'VIASHDOCKER'
FROM python:3.13-slim
ENTRYPOINT []
RUN apt-get update && \
  DEBIAN_FRONTEND=noninteractive apt-get install -y procps && \
  rm -rf /var/lib/apt/lists/*

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

LABEL org.opencontainers.image.authors="Dries Schaumont"
LABEL org.opencontainers.image.description="Companion container for running component dataflow concatenate_h5mu"
LABEL org.opencontainers.image.created="2026-06-09T16:27:35Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
LABEL org.opencontainers.image.revision="38f5f83d11f837ab6c211a98f36979405dd99e58"
LABEL org.opencontainers.image.version="processing-workflows-quantile-filtering"

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 "concatenate_h5mu processing-workflows-quantile-filtering"
  echo ""
  echo "Concatenate observations from samples in several (uni- and/or multi-modal)"
  echo "MuData files into a single file."
  echo ""
  echo "Arguments:"
  echo "    -i, --input"
  echo "        type: file, required parameter, multiple values allowed, file must exist"
  echo "        example: sample_paths"
  echo "        Paths to the different samples to be concatenated."
  echo ""
  echo "    --modality"
  echo "        type: string, multiple values allowed"
  echo "        Only output concatenated objects for the provided modalities. Outputs"
  echo "        all modalities by default."
  echo ""
  echo "    --input_id"
  echo "        type: string, multiple values allowed"
  echo "        Names of the different samples that have to be concatenated.  Must be"
  echo "        specified when using '--mode move'."
  echo "        In this case, the ids will be used for the columns names of the"
  echo "        dataframes registring the conflicts."
  echo "        If specified, must be of same length as \`--input\`."
  echo ""
  echo "    -o, --output"
  echo "        type: file, output, file must exist"
  echo "        example: output.h5mu"
  echo "        Output location for the concatenated MuData object file."
  echo ""
  echo "    --other_axis_mode"
  echo "        type: string"
  echo "        default: move"
  echo "        choices: [ same, unique, first, only, concat, move ]"
  echo "        How to handle the merging of other axis (var, obs, ...)."
  echo "          - None: keep no data"
  echo "          - same: only keep elements of the matrices which are the same in each"
  echo "        of the samples"
  echo "          - unique: only keep elements for which there is only 1 possible value"
  echo "        (1 value that can occur in multiple samples)"
  echo "          - first: keep the annotation from the first sample"
  echo "          - only: keep elements that show up in only one of the objects (1"
  echo "        unique element in only 1 sample)"
  echo "          - move: identical to 'same', but moving the conflicting values to"
  echo "        .varm or .obsm"
  echo ""
  echo "    --uns_merge_mode"
  echo "        type: string"
  echo "        default: make_unique"
  echo "        choices: [ same, unique, first, only, make_unique ]"
  echo "        How to handle the merging of .uns across modalities"
  echo "          - None: keep no data"
  echo "          - same: only keep elements of the matrices which are the same in each"
  echo "        of the samples"
  echo "          - unique: only keep elements for which there is only 1 possible value"
  echo "        (1 value that can occur in multiple samples)"
  echo "          - first: keep the annotation from the first sample"
  echo "          - only: keep elements that show up in only one of the objects (1"
  echo "        unique element in only 1 sample)"
  echo "          - make_unique: identical to 'unique', but keys which are not unique"
  echo "        are made unique by prefixing them with the sample id."
  echo ""
  echo "    --obsp_keys"
  echo "        type: string, multiple values allowed"
  echo "        List of \`.obsp\` keys for which block-diagonal concatenation should be"
  echo "        performed."
  echo "        If not provided, no \`.obsp\` keys will be concatenated."
  echo "        Provided keys must be present in all samples for block concatenation to"
  echo "        be performed."
  echo ""
  echo "    --output_compression"
  echo "        type: string"
  echo "        example: gzip"
  echo "        choices: [ gzip, lzf ]"
  echo "        Compression format to use for the output AnnData and/or Mudata H5 files."
  echo "        By default no compression is applied."
  echo ""
  echo "Viash built in Computational Requirements:"
  echo "    ---cpus=INT"
  echo "        Number of CPUs to use"
  echo "    ---memory=STRING"
  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
  echo ""
  echo "Viash built in Docker:"
  echo "    ---setup=STRATEGY"
  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
  echo "        Default: ifneedbepullelsecachedbuild"
  echo "    ---dockerfile"
  echo "        Print the dockerfile to stdout."
  echo "    ---docker_run_args=ARG"
  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
  echo "    ---docker_image_id"
  echo "        Print the docker image id to stdout."
  echo "    ---debug"
  echo "        Enter the docker container for debugging purposes."
  echo ""
  echo "Viash built in Engines:"
  echo "    ---engine=ENGINE_ID"
  echo "        Specify the engine to use. Options are: docker, native."
  echo "        Default: docker"
}

# initialise array
VIASH_POSITIONAL_ARGS=''

while [[ $# -gt 0 ]]; do
    case "$1" in
        -h|--help)
            ViashHelp
            exit
            ;;
        ---v|---verbose)
            let "VIASH_VERBOSITY=VIASH_VERBOSITY+1"
            shift 1
            ;;
        ---verbosity)
            VIASH_VERBOSITY="$2"
            shift 2
            ;;
        ---verbosity=*)
            VIASH_VERBOSITY="$(ViashRemoveFlags "$1")"
            shift 1
            ;;
        --version)
            echo "concatenate_h5mu processing-workflows-quantile-filtering"
            exit
            ;;
        --input)
            if [ -z "$VIASH_PAR_INPUT" ]; then
              VIASH_PAR_INPUT="$2"
            else
              VIASH_PAR_INPUT="$VIASH_PAR_INPUT;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --input. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --input=*)
            if [ -z "$VIASH_PAR_INPUT" ]; then
              VIASH_PAR_INPUT=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_INPUT="$VIASH_PAR_INPUT;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        -i)
            if [ -z "$VIASH_PAR_INPUT" ]; then
              VIASH_PAR_INPUT="$2"
            else
              VIASH_PAR_INPUT="$VIASH_PAR_INPUT;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -i. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --modality)
            if [ -z "$VIASH_PAR_MODALITY" ]; then
              VIASH_PAR_MODALITY="$2"
            else
              VIASH_PAR_MODALITY="$VIASH_PAR_MODALITY;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --modality. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --modality=*)
            if [ -z "$VIASH_PAR_MODALITY" ]; then
              VIASH_PAR_MODALITY=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_MODALITY="$VIASH_PAR_MODALITY;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --input_id)
            if [ -z "$VIASH_PAR_INPUT_ID" ]; then
              VIASH_PAR_INPUT_ID="$2"
            else
              VIASH_PAR_INPUT_ID="$VIASH_PAR_INPUT_ID;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --input_id. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --input_id=*)
            if [ -z "$VIASH_PAR_INPUT_ID" ]; then
              VIASH_PAR_INPUT_ID=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_INPUT_ID="$VIASH_PAR_INPUT_ID;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --output)
            [ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --output. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --output=*)
            [ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output=*\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -o)
            [ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'-o\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -o. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --other_axis_mode)
            [ -n "$VIASH_PAR_OTHER_AXIS_MODE" ] && ViashError Bad arguments for option \'--other_axis_mode\': \'$VIASH_PAR_OTHER_AXIS_MODE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OTHER_AXIS_MODE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --other_axis_mode. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --other_axis_mode=*)
            [ -n "$VIASH_PAR_OTHER_AXIS_MODE" ] && ViashError Bad arguments for option \'--other_axis_mode=*\': \'$VIASH_PAR_OTHER_AXIS_MODE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OTHER_AXIS_MODE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --uns_merge_mode)
            [ -n "$VIASH_PAR_UNS_MERGE_MODE" ] && ViashError Bad arguments for option \'--uns_merge_mode\': \'$VIASH_PAR_UNS_MERGE_MODE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_UNS_MERGE_MODE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --uns_merge_mode. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --uns_merge_mode=*)
            [ -n "$VIASH_PAR_UNS_MERGE_MODE" ] && ViashError Bad arguments for option \'--uns_merge_mode=*\': \'$VIASH_PAR_UNS_MERGE_MODE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_UNS_MERGE_MODE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --obsp_keys)
            if [ -z "$VIASH_PAR_OBSP_KEYS" ]; then
              VIASH_PAR_OBSP_KEYS="$2"
            else
              VIASH_PAR_OBSP_KEYS="$VIASH_PAR_OBSP_KEYS;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --obsp_keys. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --obsp_keys=*)
            if [ -z "$VIASH_PAR_OBSP_KEYS" ]; then
              VIASH_PAR_OBSP_KEYS=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_OBSP_KEYS="$VIASH_PAR_OBSP_KEYS;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --output_compression)
            [ -n "$VIASH_PAR_OUTPUT_COMPRESSION" ] && ViashError Bad arguments for option \'--output_compression\': \'$VIASH_PAR_OUTPUT_COMPRESSION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_COMPRESSION="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --output_compression. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --output_compression=*)
            [ -n "$VIASH_PAR_OUTPUT_COMPRESSION" ] && ViashError Bad arguments for option \'--output_compression=*\': \'$VIASH_PAR_OUTPUT_COMPRESSION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_COMPRESSION=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        ---engine)
            VIASH_ENGINE_ID="$2"
            shift 2
            ;;
        ---engine=*)
            VIASH_ENGINE_ID="$(ViashRemoveFlags "$1")"
            shift 1
            ;;
        ---setup)
            VIASH_MODE='setup'
            VIASH_SETUP_STRATEGY="$2"
            shift 2
            ;;
        ---setup=*)
            VIASH_MODE='setup'
            VIASH_SETUP_STRATEGY="$(ViashRemoveFlags "$1")"
            shift 1
            ;;
        ---dockerfile)
            VIASH_MODE='dockerfile'
            shift 1
            ;;
        ---docker_run_args)
            VIASH_DOCKER_RUN_ARGS+=("$2")
            shift 2
            ;;
        ---docker_run_args=*)
            VIASH_DOCKER_RUN_ARGS+=("$(ViashRemoveFlags "$1")")
            shift 1
            ;;
        ---docker_image_id)
            VIASH_MODE='docker_image_id'
            shift 1
            ;;
        ---debug)
            VIASH_MODE='debug'
            shift 1
            ;;
        ---cpus)
            [ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_CPUS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to ---cpus. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        ---cpus=*)
            [ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus=*\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_CPUS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        ---memory)
            [ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_MEMORY="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to ---memory. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        ---memory=*)
            [ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory=*\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_MEMORY=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        *)  # positional arg or unknown option
            # since the positional args will be eval'd, can we always quote, instead of using ViashQuote
            VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'"
            [[ $1 == -* ]] && ViashWarning $1 looks like a parameter but is not a defined parameter and will instead be treated as a positional argument. Use "--help" to get more information on the parameters.
            shift # past argument
            ;;
    esac
done

# parse positional parameters
eval set -- $VIASH_POSITIONAL_ARGS


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

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

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/dataflow/concatenate_h5mu:processing-workflows-quantile-filtering'
  fi

  # print dockerfile
  if [ "$VIASH_MODE" == "dockerfile" ]; then
    ViashDockerfile "$VIASH_ENGINE_ID"
    exit 0

  elif [ "$VIASH_MODE" == "docker_image_id" ]; then
    echo "$VIASH_DOCKER_IMAGE_ID"
    exit 0
  
  # enter docker container
  elif [[ "$VIASH_MODE" == "debug" ]]; then
    VIASH_CMD="docker run --entrypoint=bash ${VIASH_DOCKER_RUN_ARGS[@]} -v '$(pwd)':/pwd --workdir /pwd -t $VIASH_DOCKER_IMAGE_ID"
    ViashNotice "+ $VIASH_CMD"
    eval $VIASH_CMD
    exit 

  # build docker image
  elif [ "$VIASH_MODE" == "setup" ]; then
    ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY"
    ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bash'
    exit 0
  fi

  # check if docker image exists
  ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild
  ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bash'
fi

# setting computational defaults

# helper function for parsing memory strings
function ViashMemoryAsBytes {
  local memory=`echo "$1" | tr '[:upper:]' '[:lower:]' | tr -d '[:space:]'`
  local memory_regex='^([0-9]+)([kmgtp]i?b?|b)$'
  if [[ $memory =~ $memory_regex ]]; then
    local number=${memory/[^0-9]*/}
    local symbol=${memory/*[0-9]/}
    
    case $symbol in
      b)      memory_b=$number ;;
      kb|k)   memory_b=$(( $number * 1000 )) ;;
      mb|m)   memory_b=$(( $number * 1000 * 1000 )) ;;
      gb|g)   memory_b=$(( $number * 1000 * 1000 * 1000 )) ;;
      tb|t)   memory_b=$(( $number * 1000 * 1000 * 1000 * 1000 )) ;;
      pb|p)   memory_b=$(( $number * 1000 * 1000 * 1000 * 1000 * 1000 )) ;;
      kib|ki)   memory_b=$(( $number * 1024 )) ;;
      mib|mi)   memory_b=$(( $number * 1024 * 1024 )) ;;
      gib|gi)   memory_b=$(( $number * 1024 * 1024 * 1024 )) ;;
      tib|ti)   memory_b=$(( $number * 1024 * 1024 * 1024 * 1024 )) ;;
      pib|pi)   memory_b=$(( $number * 1024 * 1024 * 1024 * 1024 * 1024 )) ;;
    esac
    echo "$memory_b"
  fi
}
# compute memory in different units
if [ ! -z ${VIASH_META_MEMORY+x} ]; then
  VIASH_META_MEMORY_B=`ViashMemoryAsBytes $VIASH_META_MEMORY`
  # do not define other variables if memory_b is an empty string
  if [ ! -z "$VIASH_META_MEMORY_B" ]; then
    VIASH_META_MEMORY_KB=$(( ($VIASH_META_MEMORY_B+999) / 1000 ))
    VIASH_META_MEMORY_MB=$(( ($VIASH_META_MEMORY_KB+999) / 1000 ))
    VIASH_META_MEMORY_GB=$(( ($VIASH_META_MEMORY_MB+999) / 1000 ))
    VIASH_META_MEMORY_TB=$(( ($VIASH_META_MEMORY_GB+999) / 1000 ))
    VIASH_META_MEMORY_PB=$(( ($VIASH_META_MEMORY_TB+999) / 1000 ))
    VIASH_META_MEMORY_KIB=$(( ($VIASH_META_MEMORY_B+1023) / 1024 ))
    VIASH_META_MEMORY_MIB=$(( ($VIASH_META_MEMORY_KIB+1023) / 1024 ))
    VIASH_META_MEMORY_GIB=$(( ($VIASH_META_MEMORY_MIB+1023) / 1024 ))
    VIASH_META_MEMORY_TIB=$(( ($VIASH_META_MEMORY_GIB+1023) / 1024 ))
    VIASH_META_MEMORY_PIB=$(( ($VIASH_META_MEMORY_TIB+1023) / 1024 ))
  else
    # unset memory if string is empty
    unset $VIASH_META_MEMORY_B
  fi
fi
# unset nproc if string is empty
if [ -z "$VIASH_META_CPUS" ]; then
  unset $VIASH_META_CPUS
fi


# check whether required parameters exist
if [ -z ${VIASH_PAR_INPUT+x} ]; then
  ViashError '--input' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_NAME+x} ]; then
  ViashError 'name' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then
  ViashError 'functionality_name' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_RESOURCES_DIR+x} ]; then
  ViashError 'resources_dir' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_EXECUTABLE+x} ]; then
  ViashError 'executable' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_CONFIG+x} ]; then
  ViashError 'config' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_TEMP_DIR+x} ]; then
  ViashError 'temp_dir' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi

# filling in defaults
if [ -z ${VIASH_PAR_OTHER_AXIS_MODE+x} ]; then
  VIASH_PAR_OTHER_AXIS_MODE="move"
fi
if [ -z ${VIASH_PAR_UNS_MERGE_MODE+x} ]; then
  VIASH_PAR_UNS_MERGE_MODE="make_unique"
fi

# check whether required files exist
if [ ! -z "$VIASH_PAR_INPUT" ]; then
  IFS=';'
  set -f
  for file in $VIASH_PAR_INPUT; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi

# check whether parameters values are of the right type
if [[ -n "$VIASH_META_CPUS" ]]; then
  if ! [[ "$VIASH_META_CPUS" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'cpus' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_B" ]]; then
  if ! [[ "$VIASH_META_MEMORY_B" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_b' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_KB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_KB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_kb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_MB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_MB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_mb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_GB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_GB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_gb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_TB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_TB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_tb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_PB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_PB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_pb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_KIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_KIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_kib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_MIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_MIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_mib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_GIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_GIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_gib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_TIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_TIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_tib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_PIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_PIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_pib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi

# check whether value is belongs to a set of choices
if [ ! -z "$VIASH_PAR_OTHER_AXIS_MODE" ]; then
  VIASH_PAR_OTHER_AXIS_MODE_CHOICES=("same;unique;first;only;concat;move")
  IFS=';'
  set -f
  if ! [[ ";${VIASH_PAR_OTHER_AXIS_MODE_CHOICES[*]};" =~ ";$VIASH_PAR_OTHER_AXIS_MODE;" ]]; then
    ViashError '--other_axis_mode' specified value of \'$VIASH_PAR_OTHER_AXIS_MODE\' 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 "$VIASH_PAR_UNS_MERGE_MODE" ]; then
  VIASH_PAR_UNS_MERGE_MODE_CHOICES=("same;unique;first;only;make_unique")
  IFS=';'
  set -f
  if ! [[ ";${VIASH_PAR_UNS_MERGE_MODE_CHOICES[*]};" =~ ";$VIASH_PAR_UNS_MERGE_MODE;" ]]; then
    ViashError '--uns_merge_mode' specified value of \'$VIASH_PAR_UNS_MERGE_MODE\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
    exit 1
  fi
  set +f
  unset IFS
fi

if [ ! -z "$VIASH_PAR_OUTPUT_COMPRESSION" ]; then
  VIASH_PAR_OUTPUT_COMPRESSION_CHOICES=("gzip;lzf")
  IFS=';'
  set -f
  if ! [[ ";${VIASH_PAR_OUTPUT_COMPRESSION_CHOICES[*]};" =~ ";$VIASH_PAR_OUTPUT_COMPRESSION;" ]]; then
    ViashError '--output_compression' specified value of \'$VIASH_PAR_OUTPUT_COMPRESSION\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
    exit 1
  fi
  set +f
  unset IFS
fi

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

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

if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  # detect volumes from file arguments
  VIASH_CHOWN_VARS=()
if [ ! -z "$VIASH_PAR_INPUT" ]; then
  VIASH_TEST_INPUT=()
  IFS=';'
  for var in $VIASH_PAR_INPUT; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_INPUT+=( "$var" )
  done
  VIASH_PAR_INPUT=$(IFS=';' ; echo "${VIASH_TEST_INPUT[*]}")
fi
if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT")" )
  VIASH_PAR_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT" )
fi
if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_RESOURCES_DIR")" )
  VIASH_META_RESOURCES_DIR=$(ViashDockerAutodetectMount "$VIASH_META_RESOURCES_DIR")
fi
if [ ! -z "$VIASH_META_EXECUTABLE" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_EXECUTABLE")" )
  VIASH_META_EXECUTABLE=$(ViashDockerAutodetectMount "$VIASH_META_EXECUTABLE")
fi
if [ ! -z "$VIASH_META_CONFIG" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_CONFIG")" )
  VIASH_META_CONFIG=$(ViashDockerAutodetectMount "$VIASH_META_CONFIG")
fi
if [ ! -z "$VIASH_META_TEMP_DIR" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_TEMP_DIR")" )
  VIASH_META_TEMP_DIR=$(ViashDockerAutodetectMount "$VIASH_META_TEMP_DIR")
fi
  
  # get unique mounts
  VIASH_UNIQUE_MOUNTS=($(for val in "${VIASH_DIRECTORY_MOUNTS[@]}"; do echo "$val"; done | sort -u))
fi

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

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

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


# set dependency paths


ViashDebug "Running command: $(echo $VIASH_CMD)"
cat << VIASHEOF | eval $VIASH_CMD
set -e
tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-concatenate_h5mu-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'
from __future__ import annotations
import sys
import anndata
import mudata as mu
import pandas as pd
import numpy as np
from collections.abc import Iterable
from multiprocessing import Pool
from pathlib import Path
from h5py import File as H5File
from typing import Literal
import shutil

### VIASH START
# The following code has been auto-generated by Viash.
par = {
  'input': $( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "r'${VIASH_PAR_INPUT//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'modality': $( if [ ! -z ${VIASH_PAR_MODALITY+x} ]; then echo "r'${VIASH_PAR_MODALITY//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'input_id': $( if [ ! -z ${VIASH_PAR_INPUT_ID+x} ]; then echo "r'${VIASH_PAR_INPUT_ID//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'output': $( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "r'${VIASH_PAR_OUTPUT//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'other_axis_mode': $( if [ ! -z ${VIASH_PAR_OTHER_AXIS_MODE+x} ]; then echo "r'${VIASH_PAR_OTHER_AXIS_MODE//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'uns_merge_mode': $( if [ ! -z ${VIASH_PAR_UNS_MERGE_MODE+x} ]; then echo "r'${VIASH_PAR_UNS_MERGE_MODE//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'obsp_keys': $( if [ ! -z ${VIASH_PAR_OBSP_KEYS+x} ]; then echo "r'${VIASH_PAR_OBSP_KEYS//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'output_compression': $( if [ ! -z ${VIASH_PAR_OUTPUT_COMPRESSION+x} ]; then echo "r'${VIASH_PAR_OUTPUT_COMPRESSION//\'/\'\"\'\"r\'}'"; else echo None; fi )
}
meta = {
  'name': $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "r'${VIASH_META_NAME//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'functionality_name': $( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "r'${VIASH_META_FUNCTIONALITY_NAME//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'resources_dir': $( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "r'${VIASH_META_RESOURCES_DIR//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'executable': $( if [ ! -z ${VIASH_META_EXECUTABLE+x} ]; then echo "r'${VIASH_META_EXECUTABLE//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'config': $( if [ ! -z ${VIASH_META_CONFIG+x} ]; then echo "r'${VIASH_META_CONFIG//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'temp_dir': $( if [ ! -z ${VIASH_META_TEMP_DIR+x} ]; then echo "r'${VIASH_META_TEMP_DIR//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'cpus': $( if [ ! -z ${VIASH_META_CPUS+x} ]; then echo "int(r'${VIASH_META_CPUS//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_b': $( if [ ! -z ${VIASH_META_MEMORY_B+x} ]; then echo "int(r'${VIASH_META_MEMORY_B//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_kb': $( if [ ! -z ${VIASH_META_MEMORY_KB+x} ]; then echo "int(r'${VIASH_META_MEMORY_KB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_mb': $( if [ ! -z ${VIASH_META_MEMORY_MB+x} ]; then echo "int(r'${VIASH_META_MEMORY_MB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_gb': $( if [ ! -z ${VIASH_META_MEMORY_GB+x} ]; then echo "int(r'${VIASH_META_MEMORY_GB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_tb': $( if [ ! -z ${VIASH_META_MEMORY_TB+x} ]; then echo "int(r'${VIASH_META_MEMORY_TB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_pb': $( if [ ! -z ${VIASH_META_MEMORY_PB+x} ]; then echo "int(r'${VIASH_META_MEMORY_PB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_kib': $( if [ ! -z ${VIASH_META_MEMORY_KIB+x} ]; then echo "int(r'${VIASH_META_MEMORY_KIB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_mib': $( if [ ! -z ${VIASH_META_MEMORY_MIB+x} ]; then echo "int(r'${VIASH_META_MEMORY_MIB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_gib': $( if [ ! -z ${VIASH_META_MEMORY_GIB+x} ]; then echo "int(r'${VIASH_META_MEMORY_GIB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_tib': $( if [ ! -z ${VIASH_META_MEMORY_TIB+x} ]; then echo "int(r'${VIASH_META_MEMORY_TIB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_pib': $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "int(r'${VIASH_META_MEMORY_PIB//\'/\'\"\'\"r\'}')"; else echo None; fi )
}
dep = {
  
}

### VIASH END

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

logger = setup_logger()


def nunique(row):
    unique = pd.unique(row)
    unique_without_na = pd.core.dtypes.missing.remove_na_arraylike(unique)
    return len(unique_without_na) > 1


def any_row_contains_duplicate_values(n_processes: int, frame: pd.DataFrame) -> bool:
    """
    Check if any row contains duplicate values, that are not NA.
    """
    numpy_array = frame.to_numpy()
    with Pool(n_processes) as pool:
        is_duplicated = pool.map(nunique, iter(numpy_array))
    return any(is_duplicated)


def concatenate_matrices(
    n_processes: int, matrices: dict[str, pd.DataFrame], align_to: pd.Index
) -> tuple[
    dict[str, pd.DataFrame], pd.DataFrame | None, dict[str, pd.core.dtypes.dtypes.Dtype]
]:
    """
    Merge matrices by combining columns that have the same name.
    Columns that contain conflicting values (e.i. the columns have different values),
    are not merged, but instead moved to a new dataframe.
    """
    column_names = set(column_name for var in matrices.values() for column_name in var)
    logger.debug("Trying to concatenate columns: %s.", ",".join(column_names))
    if not column_names:
        return {}, pd.DataFrame(index=align_to)
    conflicts, concatenated_matrix = split_conflicts_and_concatenated_columns(
        n_processes, matrices, column_names, align_to
    )
    concatenated_matrix = cast_to_writeable_dtype(concatenated_matrix)
    conflicts = {
        conflict_name: cast_to_writeable_dtype(conflict_df)
        for conflict_name, conflict_df in conflicts.items()
    }
    return conflicts, concatenated_matrix


def get_first_non_na_value_vector(df):
    numpy_arr = df.to_numpy()
    n_rows, n_cols = numpy_arr.shape
    col_index = pd.isna(numpy_arr).argmin(axis=1)
    flat_index = n_cols * np.arange(n_rows) + col_index
    return pd.Series(numpy_arr.ravel()[flat_index], index=df.index, name=df.columns[0])


def make_uns_keys_unique(mod_data, concatenated_data):
    """
    Check if the uns keys across samples are unique before adding them
    to the final concatenated object. If a conflict occurs between the samples,
    add the sample ID to make the key unique again.
    """
    all_uns_keys = {}
    for sample_id, mod in mod_data.items():
        for uns_key, _ in mod.uns.items():
            all_uns_keys.setdefault(uns_key, []).append(sample_id)
    for uns_key, samples_ids in all_uns_keys.items():
        assert samples_ids
        if len(samples_ids) == 1:
            sample_id = samples_ids[0]
            concatenated_data.uns[uns_key] = mod_data[sample_id].uns[uns_key]
        else:
            for sample_id in samples_ids:
                concatenated_data.uns[f"{sample_id}_{uns_key}"] = mod_data[
                    sample_id
                ].uns[uns_key]
    return concatenated_data


def split_conflicts_and_concatenated_columns(
    n_processes: int,
    matrices: dict[str, pd.DataFrame],
    column_names: Iterable[str],
    align_to: pd.Index,
) -> tuple[dict[str, pd.DataFrame], pd.DataFrame]:
    """
    Retrieve columns with the same name from a list of dataframes which are
    identical across all the frames (ignoring NA values).
    Columns which are not the same are regarded as 'conflicts',
    which are stored in seperate dataframes, one per columns
    with the same name that store conflicting values.
    """
    conflicts = {}
    concatenated_matrix = []
    for column_name in column_names:
        columns = {
            input_id: var[column_name]
            for input_id, var in matrices.items()
            if column_name in var
        }
        assert columns, "Some columns should have been found."
        concatenated_columns = pd.concat(
            columns.values(), axis=1, join="outer", sort=False
        )
        if any_row_contains_duplicate_values(n_processes, concatenated_columns):
            concatenated_columns.columns = (
                columns.keys()
            )  # Use the sample id as column name
            concatenated_columns = concatenated_columns.reindex(align_to, copy=False)
            conflicts[f"conflict_{column_name}"] = concatenated_columns
        else:
            unique_values = get_first_non_na_value_vector(concatenated_columns)
            concatenated_matrix.append(unique_values)
    if not concatenated_matrix:
        return conflicts, pd.DataFrame(index=align_to)
    concatenated_matrix = pd.concat(
        concatenated_matrix, join="outer", axis=1, sort=False
    )
    concatenated_matrix = concatenated_matrix.reindex(align_to, copy=False)
    return conflicts, concatenated_matrix


def cast_to_writeable_dtype(result: pd.DataFrame) -> pd.DataFrame:
    """
    Cast the dataframe to dtypes that can be written by mudata.
    """
    # dtype inferral workfs better with np.nan
    result = result.replace({pd.NA: np.nan})

    # MuData supports nullable booleans and ints
    # ie. \`IntegerArray\` and \`BooleanArray\`
    result = result.convert_dtypes(
        infer_objects=True,
        convert_integer=True,
        convert_string=False,
        convert_boolean=True,
        convert_floating=False,
    )

    # Convert leftover 'object' columns to string
    # However, na values are supported, so convert all values except NA's to string
    object_cols = result.select_dtypes(include="object").columns.values
    for obj_col in object_cols:
        result[obj_col] = (
            result[obj_col]
            .where(result[obj_col].isna(), result[obj_col].astype(str))
            .astype("category")
        )
    return result


def split_conflicts_modalities(
    n_processes: int, samples: dict[str, anndata.AnnData], output: anndata.AnnData
) -> anndata.AnnData:
    """
    Merge .var and .obs matrices of the anndata objects. Columns are merged
    when the values (excl NA) are the same in each of the matrices.
    Conflicting columns are moved to a separate dataframe (one dataframe for each column,
    containing all the corresponding column from each sample).
    """
    matrices_to_parse = ("var", "obs")
    for matrix_name in matrices_to_parse:
        matrices = {
            sample_id: getattr(sample, matrix_name)
            for sample_id, sample in samples.items()
        }
        output_index = getattr(output, matrix_name).index
        conflicts, concatenated_matrix = concatenate_matrices(
            n_processes, matrices, output_index
        )
        if concatenated_matrix.empty:
            concatenated_matrix.index = output_index

        # Even though we did not touch the varm and obsm matrices that were already present,
        # the joining of observations might have caused a dtype change in these matrices as well
        # so these also need to be casted to a writable dtype...
        for multidim_name, multidim_data in getattr(output, f"{matrix_name}m").items():
            new_data = (
                cast_to_writeable_dtype(multidim_data)
                if isinstance(multidim_data, pd.DataFrame)
                else multidim_data
            )
            getattr(output, f"{matrix_name}m")[multidim_name] = new_data

        # Write the conflicts to the output
        for conflict_name, conflict_data in conflicts.items():
            getattr(output, f"{matrix_name}m")[conflict_name] = conflict_data

        # Set other annotation matrices in the output
        setattr(output, matrix_name, concatenated_matrix)

    return output


def concatenate_modality(
    n_processes: int,
    mod: str | None,
    input_files: Iterable[str | Path],
    other_axis_mode: str,
    uns_merge_mode: str,
    input_ids: tuple[str],
) -> anndata.AnnData:
    concat_modes = {
        "move": "unique",
    }
    other_axis_mode_to_apply = concat_modes.get(other_axis_mode, other_axis_mode)

    uns_merge_modes = {"make_unique": None}
    uns_merge_mode_to_apply = uns_merge_modes.get(uns_merge_mode, uns_merge_mode)

    mod_data = {}
    mod_indices_combined = pd.Index([])
    for input_id, input_file in zip(input_ids, input_files):
        if mod is not None:
            try:
                data = mu.read_h5ad(input_file, mod=mod)

                # Remove obsp keys that are not in par["obsp_keys"]
                obsp_keys_to_keep = par.get("obsp_keys") or []
                obsp_keys_to_remove = set(data.obsp.keys()) - set(obsp_keys_to_keep)
                for key in obsp_keys_to_remove:
                    try:
                        del data.obsp[key]
                    except KeyError:
                        pass

                mod_data[input_id] = data
                mod_indices_combined = mod_indices_combined.append(data.obs.index)

            except KeyError as e:  # Modality does not exist for this sample, skip it
                if (
                    f"Unable to synchronously open object (object '{mod}' doesn't exist)"
                    not in str(e)
                ):
                    raise e
                pass
        else:  # When mod=None, process the 'global' h5mu state
            with H5File(input_file, "r") as input_h5:
                if "uns" in input_h5.keys():
                    uns_data = anndata.experimental.read_elem(input_h5["uns"])
                    if uns_data:
                        mod_data[input_id] = anndata.AnnData(uns=uns_data)

    if not mod_indices_combined.is_unique:
        raise ValueError("Observations are not unique across samples.")

    if not mod_data:
        return anndata.AnnData()

    concatenated_data = anndata.concat(
        mod_data.values(),
        join="outer",
        pairwise=True if par["obsp_keys"] else False,
        merge=other_axis_mode_to_apply,
        uns_merge=uns_merge_mode_to_apply,
    )

    if other_axis_mode == "move":
        concatenated_data = split_conflicts_modalities(
            n_processes, mod_data, concatenated_data
        )

    if uns_merge_mode == "make_unique":
        concatenated_data = make_uns_keys_unique(mod_data, concatenated_data)

    return concatenated_data


def concatenate_modalities(
    n_processes: int,
    modalities: list[str],
    input_files: Path | str,
    other_axis_mode: str,
    uns_merge_mode: str,
    output_file: Path | str,
    compression: Literal["gzip"] | Literal["lzf"],
    input_ids: tuple[str] | None = None,
) -> None:
    """
    Join the modalities together into a single multimodal sample.
    """
    logger.info("Concatenating samples.")
    output_file, input_files = (
        Path(output_file),
        [Path(input_file) for input_file in input_files],
    )
    output_file_uncompressed = output_file.with_name(
        output_file.stem + "_uncompressed.h5mu"
    )
    output_file_uncompressed.touch()
    # Create empty mudata file
    mdata = mu.MuData({modality: anndata.AnnData() for modality in modalities})
    mdata.write(output_file_uncompressed, compression=compression)

    # Use "None" for the global slots (not assigned to any modality)
    for mod_name in modalities + [
        None,
    ]:
        new_mod = concatenate_modality(
            n_processes,
            mod_name,
            input_files,
            other_axis_mode,
            uns_merge_mode,
            input_ids,
        )
        if mod_name is None:
            if new_mod.uns:
                with H5File(output_file_uncompressed, "r+") as open_h5mu_file:
                    anndata.experimental.write_elem(
                        open_h5mu_file, "uns", dict(new_mod.uns)
                    )
            continue
        logger.info(
            "Writing out modality '%s' to '%s' with compression '%s'.",
            mod_name,
            output_file_uncompressed,
            compression,
        )
        mu.write_h5ad(output_file_uncompressed, data=new_mod, mod=mod_name)

    if compression:
        compress_h5mu(output_file_uncompressed, output_file, compression=compression)
        output_file_uncompressed.unlink()
    else:
        shutil.move(output_file_uncompressed, output_file)

    logger.info("Concatenation successful.")


def main() -> None:
    # Get a list of all possible modalities
    mods = set()
    for path in par["input"]:
        try:
            with H5File(path, "r") as f_root:
                mods = mods | set(f_root["mod"].keys())
        except OSError:
            raise OSError(f"Failed to load {path}. Is it a valid h5 file?")

    input_ids = None
    if par["input_id"]:
        input_ids: tuple[str] = tuple(i.strip() for i in par["input_id"])
        if len(input_ids) != len(par["input"]):
            raise ValueError(
                "The number of sample names must match the number of sample files."
            )

        if len(set(input_ids)) != len(input_ids):
            raise ValueError("The sample names should be unique.")

    logger.info("\\nConcatenating data from paths:\\n\\t%s", "\\n\\t".join(par["input"]))

    if par["other_axis_mode"] == "move" and not input_ids:
        raise ValueError("--mode 'move' requires --input_ids.")

    n_processes = meta["cpus"] if meta["cpus"] else 1

    if par["modality"]:
        par["modality"] = set(par["modality"])
        if not par["modality"].issubset(mods):
            mods_joined, input_mods_joined = ", ".join(mods), ", ".join(par["modality"])
            raise ValueError(
                f"One of the modalities provided ({input_mods_joined}) is not available in the input data {mods_joined}"
            )
        mods = par["modality"]

    concatenate_modalities(
        n_processes,
        list(mods),
        par["input"],
        par["other_axis_mode"],
        par["uns_merge_mode"],
        par["output"],
        par["output_compression"],
        input_ids=input_ids,
    )


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" ]; then
    unset VIASH_TEST_INPUT
    IFS=';'
    for var in $VIASH_PAR_INPUT; do
      unset IFS
      if [ -z "$VIASH_TEST_INPUT" ]; then
      VIASH_TEST_INPUT="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_INPUT="$VIASH_TEST_INPUT;""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_INPUT="$VIASH_TEST_INPUT"
  fi
  if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
    VIASH_PAR_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT")
  fi
  if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
    VIASH_META_RESOURCES_DIR=$(ViashDockerStripAutomount "$VIASH_META_RESOURCES_DIR")
  fi
  if [ ! -z "$VIASH_META_EXECUTABLE" ]; then
    VIASH_META_EXECUTABLE=$(ViashDockerStripAutomount "$VIASH_META_EXECUTABLE")
  fi
  if [ ! -z "$VIASH_META_CONFIG" ]; then
    VIASH_META_CONFIG=$(ViashDockerStripAutomount "$VIASH_META_CONFIG")
  fi
  if [ ! -z "$VIASH_META_TEMP_DIR" ]; then
    VIASH_META_TEMP_DIR=$(ViashDockerStripAutomount "$VIASH_META_TEMP_DIR")
  fi
fi


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


exit 0
