#!/usr/bin/env bash

# from_cellranger_multi_to_h5mu v4.0.1
# 
# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
# 
# The component may contain files which fall under a different license. The
# authors of this component should specify the license in the header of such
# files, or include a separate license file detailing the licenses of all included
# files.
# 
# Component authors:
#  * Dries Schaumont (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="from_cellranger_multi_to_h5mu"
VIASH_META_FUNCTIONALITY_NAME="from_cellranger_multi_to_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~=0.12.7" "awkward" "mudata~=0.3.2" "scanpy~=1.11.4" "scirpy" && \
  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 convert from_cellranger_multi_to_h5mu"
LABEL org.opencontainers.image.created="2026-02-04T09:06:13Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
LABEL org.opencontainers.image.version="v4.0.1"

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 "from_cellranger_multi_to_h5mu v4.0.1"
  echo ""
  echo "Converts the output from cellranger multi to a single .h5mu file."
  echo "By default, will map the following library type names to modality names:"
  echo "  - Gene Expression: rna"
  echo "  - Peaks: atac"
  echo "  - Antibody Capture: prot"
  echo "  - VDJ: vdj"
  echo "  - VDJ-T: vdj_t"
  echo "  - VDJ-B: vdj_b"
  echo "  - CRISPR Guide Capture: crispr"
  echo "  - Multiplexing Capture: hashing"
  echo "Other library types have their whitepace removed and dashes replaced by"
  echo "underscores to generate the modality name."
  echo ""
  echo "Currently does not allow parsing the output from cell barcode demultiplexing."
  echo ""
  echo "Arguments:"
  echo "    -i, --input"
  echo "        type: file, required parameter, file must exist"
  echo "        example: input_dir_containing_modalities"
  echo "        Input folder. Must contain the output from a cellranger multi run."
  echo ""
  echo "    -o, --output"
  echo "        type: file, multiple values allowed, output, file must exist"
  echo "        example: *.h5mu"
  echo "        Locations for the output files. Must contain a wildcard (*) character,"
  echo "        which will be replaced with the sample name."
  echo ""
  echo "    --sample_csv"
  echo "        type: file, output, file must exist"
  echo "        example: samples.csv"
  echo "        CSV file describing the sample name per output file"
  echo ""
  echo "    --uns_metrics"
  echo "        type: string"
  echo "        default: metrics_cellranger"
  echo "        Name of the .uns slot under which to QC metrics (if any)."
  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 objects."
  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 "$1")"
            shift 1
            ;;
        --version)
            echo "from_cellranger_multi_to_h5mu v4.0.1"
            exit
            ;;
        --input)
            [ -n "$VIASH_PAR_INPUT" ] && ViashError Bad arguments for option \'--input\': \'$VIASH_PAR_INPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INPUT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --input. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --input=*)
            [ -n "$VIASH_PAR_INPUT" ] && ViashError Bad arguments for option \'--input=*\': \'$VIASH_PAR_INPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INPUT=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -i)
            [ -n "$VIASH_PAR_INPUT" ] && ViashError Bad arguments for option \'-i\': \'$VIASH_PAR_INPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INPUT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -i. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --output)
            [ -n "$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="$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"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -o. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --sample_csv)
            [ -n "$VIASH_PAR_SAMPLE_CSV" ] && ViashError Bad arguments for option \'--sample_csv\': \'$VIASH_PAR_SAMPLE_CSV\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SAMPLE_CSV="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --sample_csv. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --sample_csv=*)
            [ -n "$VIASH_PAR_SAMPLE_CSV" ] && ViashError Bad arguments for option \'--sample_csv=*\': \'$VIASH_PAR_SAMPLE_CSV\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SAMPLE_CSV=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --uns_metrics)
            [ -n "$VIASH_PAR_UNS_METRICS" ] && ViashError Bad arguments for option \'--uns_metrics\': \'$VIASH_PAR_UNS_METRICS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_UNS_METRICS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --uns_metrics. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --uns_metrics=*)
            [ -n "$VIASH_PAR_UNS_METRICS" ] && ViashError Bad arguments for option \'--uns_metrics=*\': \'$VIASH_PAR_UNS_METRICS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_UNS_METRICS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --output_compression)
            [ -n "$VIASH_PAR_OUTPUT_COMPRESSION" ] && ViashError Bad arguments for option \'--output_compression\': \'$VIASH_PAR_OUTPUT_COMPRESSION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_COMPRESSION="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --output_compression. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --output_compression=*)
            [ -n "$VIASH_PAR_OUTPUT_COMPRESSION" ] && ViashError Bad arguments for option \'--output_compression=*\': \'$VIASH_PAR_OUTPUT_COMPRESSION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_COMPRESSION=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        ---engine)
            VIASH_ENGINE_ID="$2"
            shift 2
            ;;
        ---engine=*)
            VIASH_ENGINE_ID="$(ViashRemoveFlags "$1")"
            shift 1
            ;;
        ---setup)
            VIASH_MODE='setup'
            VIASH_SETUP_STRATEGY="$2"
            shift 2
            ;;
        ---setup=*)
            VIASH_MODE='setup'
            VIASH_SETUP_STRATEGY="$(ViashRemoveFlags "$1")"
            shift 1
            ;;
        ---dockerfile)
            VIASH_MODE='dockerfile'
            shift 1
            ;;
        ---docker_run_args)
            VIASH_DOCKER_RUN_ARGS+=("$2")
            shift 2
            ;;
        ---docker_run_args=*)
            VIASH_DOCKER_RUN_ARGS+=("$(ViashRemoveFlags "$1")")
            shift 1
            ;;
        ---docker_image_id)
            VIASH_MODE='docker_image_id'
            shift 1
            ;;
        ---debug)
            VIASH_MODE='debug'
            shift 1
            ;;
        ---cpus)
            [ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_CPUS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to ---cpus. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        ---cpus=*)
            [ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus=*\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_CPUS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        ---memory)
            [ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_MEMORY="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to ---memory. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        ---memory=*)
            [ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory=*\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_MEMORY=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        *)  # positional arg or unknown option
            # since the positional args will be eval'd, can we always quote, instead of using ViashQuote
            VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'"
            [[ $1 == -* ]] && ViashWarning $1 looks like a parameter but is not a defined parameter and will instead be treated as a positional argument. Use "--help" to get more information on the parameters.
            shift # past argument
            ;;
    esac
done

# parse positional parameters
eval set -- $VIASH_POSITIONAL_ARGS


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

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

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_cellranger_multi_to_h5mu:v4.0.1'
  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_UNS_METRICS+x} ]; then
  VIASH_PAR_UNS_METRICS="metrics_cellranger"
fi

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

# check whether parameters values are of the right type
if [[ -n "$VIASH_PAR_OUTPUT" ]]; then
  if ! [[ "$VIASH_PAR_OUTPUT" =~ \* ]]; then
    ViashError '--output' has to be a path containing a wildcard, e.g. 'output_*.txt'. 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 "$VIASH_PAR_OUTPUT_COMPRESSION" ]; then
  VIASH_PAR_OUTPUT_COMPRESSION_CHOICES=("gzip;lzf")
  IFS=';'
  set -f
  if ! [[ ";${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 "$VIASH_PAR_OUTPUT")"
fi
if [ ! -z "$VIASH_PAR_SAMPLE_CSV" ] && [ ! -d "$(dirname "$VIASH_PAR_SAMPLE_CSV")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_SAMPLE_CSV")"
fi

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

if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  # detect volumes from file arguments
  VIASH_CHOWN_VARS=()
if [ ! -z "$VIASH_PAR_INPUT" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INPUT")" )
  VIASH_PAR_INPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_INPUT")
fi
if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
  VIASH_TEST_OUTPUT=()
  IFS=';'
  for var in $VIASH_PAR_OUTPUT; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_OUTPUT+=( "$var" )
    VIASH_CHOWN_VARS+=( "$var" )
  done
  VIASH_PAR_OUTPUT=$(IFS=';' ; echo "${VIASH_TEST_OUTPUT[*]}")
fi
if [ ! -z "$VIASH_PAR_SAMPLE_CSV" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_SAMPLE_CSV")" )
  VIASH_PAR_SAMPLE_CSV=$(ViashDockerAutodetectMount "$VIASH_PAR_SAMPLE_CSV")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_SAMPLE_CSV" )
fi
if [ ! -z "$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-from_cellranger_multi_to_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 pathlib import Path
import sys
import scanpy
import pandas as pd
import mudata
import numpy as np
from scirpy.io import read_10x_vdj
from collections import defaultdict
from functools import partial
import json
import csv
import tempfile


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

## VIASH END

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

logger = setup_logger()

POSSIBLE_LIBRARY_TYPES = (
    "vdj_t",
    "vdj_b",
    "vdj_t_gd",
    "count",
    "antigen_analysis",
    "multiplexing_analysis",
)

FEATURE_TYPES_NAMES = {
    "Gene Expression": "rna",
    "Peaks": "atac",
    "Antibody Capture": "prot",
    "VDJ": "vdj",
    "VDJ-T": "vdj_t",
    "VDJ-B": "vdj_b",
    "CRISPR Guide Capture": "gdo",
    "Multiplexing Capture": "hto",
    "Antigen Capture": "antigen",
    "Custom": "custom",
}


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 gather_input_data(dir: Path):
    # /
    # +-- multi
    # |    +-- count (raw output)
    # |    |    +-- feature_reference.csv
    # |    |    +-- raw_feature_bc_matrix.h5
    # |    +-- vdj_t
    # |    |    +-- all_contig_annotations.json
    # |    +-- vdj_b
    # |    |    +-- all_contig_annotations.json
    # |    +-- vdj_t_gd
    # |    |    +-- all_contig_annotations.json
    # |    +--  multiplexing_analysis
    # |         +-- cells_per_tag.json
    # +-- per_sample_outs (filtered outputs)
    #      +-- example_1
    #           +-- antigen_analysis
    #           |   +-- per_barcode.csv
    #           |   +-- antigen_specificity_scores.csv
    #           +-- count
    #           |   +-- antibody_analysis
    #           |   +-- crispr_analysis
    #           |       +-- perturbation_efficiencies_by_feature.csv
    #           |       +-- perturbation_efficiencies_by_target.csv
    #           +-- vdj_t (unused)
    #           +-- vdj_b (unused)
    #           +-- vdj_t_gd (unused)
    #           +-- metrics_summary.csv

    if not dir.is_dir():
        raise ValueError("Specified input is not a directory.")
    folder_contents = list(dir.iterdir())
    config = dir / "config.csv"
    if config not in folder_contents:
        logger.warning(
            "Config.csv not found in input directory, this folder might not be a valid cellranger multi output."
        )

    required_subfolders = [
        dir / subfolder_name for subfolder_name in ("per_sample_outs",)
    ]
    found_input = {key_: {} for key_ in POSSIBLE_LIBRARY_TYPES}
    for required_subfolder in required_subfolders:
        if required_subfolder not in folder_contents:
            raise ValueError(
                f"Input folder must contain the subfolder {required_subfolder} please make "
                "sure that the specified input folder is a valid cellranger multi output."
            )

    library_type_dir = multi_dir if (multi_dir := (dir / "multi")).is_dir() else dir
    for library_type in library_type_dir.iterdir():
        if library_type.name in POSSIBLE_LIBRARY_TYPES:
            if multi_dir.is_dir():
                if not library_type.is_dir():
                    logger.warning(
                        "%s is not a directory. Contents of the multi folder "
                        "must be directories to be recognized as valid input data",
                        library_type,
                    )
                    continue
            found_input[library_type.name] = library_type
            continue
        if multi_dir.is_dir():
            raise ValueError(
                f"Contents of the 'multi' folder must be found one of the following: {','.join(POSSIBLE_LIBRARY_TYPES)}."
            )
    if not found_input["count"]:
        found_input["count"] = dir

    feature_reference = found_input["count"] / "feature_reference.csv"
    if feature_reference:
        found_input["feature_reference"] = feature_reference

    per_sample_outs_dir = dir / "per_sample_outs"
    samples_dirs = [
        samplepath
        for samplepath in per_sample_outs_dir.iterdir()
        if samplepath.is_dir()
    ]
    for samples_dir in samples_dirs:
        for file_part in (
            "metrics_summary.csv",
            "count/crispr_analysis/perturbation_efficiencies_by_feature.csv",
            "crispr_analysis/perturbation_efficiencies_by_feature.csv",  # Cell Ranger v10
            "count/crispr_analysis/perturbation_efficiencies_by_target.csv",
            "crispr_analysis/perturbation_efficiencies_by_target.csv",  # Cell Ranger v10
            "antigen_analysis",
        ):
            found_file = samples_dir / file_part
            if found_file.exists():
                file_name = found_file.name.removesuffix(".csv")
                found_input.setdefault(file_name, {})[samples_dir.name] = found_file

    return found_input


def proces_perturbation(
    key_name: str, mudatas: dict[str, mudata.MuData], efficiency_files: dict[str, Path]
):
    for sample_name, mudata_obj in mudatas.items():
        efficiency_file = efficiency_files[sample_name]
        assert "gdo" in mudata_obj.mod
        eff_df = pd.read_csv(
            efficiency_file,
            index_col="Perturbation",
            sep=",",
            decimal=".",
            quotechar='"',
        )
        mudata_obj.mod["gdo"].uns[key_name] = eff_df
    return mudatas


def process_feature_reference(
    mudatas: dict[str, mudata.MuData], efficiency_file: dict[str, Path]
):
    df_all = pd.read_csv(
        efficiency_file, index_col="id", sep=",", decimal=".", quotechar='"'
    )
    assert "feature_type" in df_all.columns, (
        "Columns 'feature_type' should be present in features_reference file."
    )
    for _, mudata_obj in mudatas.items():
        df = df_all.copy(deep=True)
        feature_types = df["feature_type"]
        missing_features = set(feature_types) - set(FEATURE_TYPES_NAMES)
        if missing_features:
            raise ValueError(
                "Not all feature types present in the features_reference file are supported by this component.\\n"
                f"Missing support for features: {','.join(missing_features)}."
            )
        for feature_type in feature_types:
            modality = FEATURE_TYPES_NAMES[feature_type]
            subset_df = df.loc[df["feature_type"] == feature_type]
            mudata_obj.mod[modality].uns["feature_reference"] = subset_df
    return mudatas


def process_counts(counts_folder: Path, multiplexing_info, metrics_files):
    counts_matrix_file = counts_folder / "raw_feature_bc_matrix.h5"
    logger.info("Reading %s.", counts_matrix_file)
    adata = scanpy.read_10x_h5(counts_matrix_file, gex_only=False)

    # set the gene ids as var_names
    logger.info("Renaming var columns")
    adata.var = adata.var.rename_axis("gene_symbol").reset_index().set_index("gene_ids")

    # generate output
    logger.info("Convert to mudata")

    def modality_name_factory(library_type):
        return ("".join(library_type.replace("-", "_").split())).lower()

    feature_types = defaultdict(modality_name_factory, FEATURE_TYPES_NAMES)
    mudata_all_samples = mudata.MuData(adata, feature_types_names=feature_types)
    if multiplexing_info:
        # Get the mapping between the barcode and the sample ID from one of the metrics files
        metrics_file = pd.read_csv(
            list(metrics_files.values())[0], decimal=".", quotechar='"', thousands=","
        )
        sample_ids = metrics_file[metrics_file["Metric Name"] == "Sample ID"]
        barcode_sample_mapping = (
            sample_ids.loc[:, ["Group Name", "Metric Value"]]
            .set_index("Group Name")
            .squeeze()
            .to_dict()
        )
        # When probe barcodes are combined with multiplexing barcodes; the probe barcode (BC)
        # is paired with other sample with other sample information using the syntax "{BC}+{antibody}"
        # (or even "{BC}+{antibody}+{crispr guide}"). The cells_per_tag
        # file only encodes the BCs; so we need to strip the other information.
        barcode_sample_mapping = {
            key_.partition("+")[0]: value_
            for key_, value_ in barcode_sample_mapping.items()
        }
        return split_samples(
            mudata_all_samples, multiplexing_info, barcode_sample_mapping
        )
    return {"run": mudata_all_samples}


def split_samples(mudata_obj, multiplexing_analysis_folder, barcode_sample_mapping):
    result = {}
    cells_per_tag_file = multiplexing_analysis_folder / "cells_per_tag.json"
    with cells_per_tag_file.open("r") as open_json:
        sample_cell_mapping = json.load(open_json)

    for barcode, indices in sample_cell_mapping.items():
        if indices:
            sample_mudata = mudata_obj[indices]
            sample = barcode_sample_mapping[barcode]
            result[sample] = sample_mudata.copy()
    return result


def process_metrics_summary(
    mudatas: dict[str, mudata.MuData], metrics_files: dict[str, Path]
):
    def read_percentage(val):
        try:
            if str(val).endswith("%"):
                return float(val.strip("%")) / 100
            else:
                return val
        except (AttributeError, ValueError):
            return val

    for sample, mudata_obj in mudatas.items():
        metrics_file = metrics_files[sample]
        metrics_summary = pd.read_csv(
            metrics_file, decimal=".", quotechar='"', thousands=","
        ).applymap(read_percentage)

        mudata_obj.uns[par["uns_metrics"]] = metrics_summary
        for colname, coldata in metrics_summary.items():
            try:
                new_column = coldata.astype(str, copy=True).astype(
                    {colname: "category"}
                )
                metrics_summary[colname] = new_column
            except (ValueError, TypeError):
                logger.warning(f"Could not store column {colname} from metrics.")
                pass
    return mudatas


def process_antigen_analysis(
    mudatas: dict[str, mudata.MuData], antigen_analysis_folder_paths: dict[str, Path]
):
    for sample_id, mudata_obj in mudatas.items():
        antigen_analysis_folder_path = antigen_analysis_folder_paths[sample_id]
        assert "antigen" in mudata_obj.mod
        per_barcodes_file = antigen_analysis_folder_path / "per_barcode.csv"
        assert per_barcodes_file.is_file(), (
            "Expected a per_barcode.csv file to be present."
        )
        per_barcodes_df = pd.read_csv(
            per_barcodes_file, index_col="barcode", sep=",", decimal=".", quotechar='"'
        )
        is_gex_cell = per_barcodes_df["is_gex_cell"]
        assert len(set(is_gex_cell.unique().tolist()) - set([False, True])) == 0, (
            "Expected 'is_gex_cell' column to be boolean. Please report this as a bug."
        )
        barcodes_in_gex = per_barcodes_df[is_gex_cell]
        # All of the barcodes listed in the per_barcode.csv with is_gex_cell set to 'True'
        # must be in the 'rna' (an thus also 'antigen') modality
        assert barcodes_in_gex.index.difference(mudata_obj["rna"].obs_names).empty
        orig_obs_names = mudata_obj["antigen"].obs_names.copy()
        mudata_obj["antigen"].obs = cast_to_writeable_dtype(
            pd.concat(
                [mudata_obj["antigen"].obs, barcodes_in_gex],
                axis="columns",
                join="outer",
                verify_integrity=True,
                sort=False,
            )
        )
        assert orig_obs_names.equals(mudata_obj["antigen"].obs_names)
        del orig_obs_names

        # The antigen_specificity_scores.csv file is only present when cellranger
        # multi was run with a [antigen-specificity] section in config
        specificity_file = (
            antigen_analysis_folder_path / "antigen_specificity_scores.csv"
        )
        if specificity_file.is_file():
            antigen_scores_df = pd.read_csv(
                specificity_file,
                index_col=["barcode", "antigen"],
                sep=",",
                decimal=".",
                quotechar='"',
            )
            score = antigen_scores_df.unstack()
            assert score.index.difference(mudata_obj["rna"].obs_names).empty
            antigens = score.columns.unique(level="antigen")
            for antigen in antigens:
                score_antigen = score.loc[:, (slice(None), antigen)].droplevel(
                    "antigen", axis=1
                )
                score_antigen = score_antigen.reindex(mudata_obj["rna"].obs_names)
                mudata_obj["antigen"].obsm[f"antigen_specificity_scores_{antigen}"] = (
                    cast_to_writeable_dtype(score_antigen)
                )
    return mudatas


def process_vdj(mudatas: dict[str, mudata.MuData], vdj_folder_path: str):
    # https://scverse.org/scirpy/latest/generated/scirpy.io.read_10x_vdj.html#scirpy-io-read-10x-vdj
    # According to docs, using the json is preferred as this file includes intron info.
    all_config_json_file = vdj_folder_path / "all_contig_annotations.json"
    vdj_type = vdj_folder_path.name
    with all_config_json_file.open("r") as open_json:
        json_obj = json.load(open_json)
    for _, mudata_obj in mudatas.items():
        json_for_sample = [
            entry for entry in json_obj if entry["barcode"] in mudata_obj.obs_names
        ]
        with tempfile.NamedTemporaryFile(mode="w", suffix=".json") as tfile:
            json.dump(json_for_sample, tfile, indent=4)
            tfile.flush()
            vdj_anndata = read_10x_vdj(tfile.name)
        mudata_obj.mod[vdj_type] = vdj_anndata
    return mudatas


def get_modalities(input_data):
    dispatcher = {
        "multiplexing_analysis": split_samples,
        "vdj_t": process_vdj,
        "vdj_b": process_vdj,
        "vdj_t_gd": process_vdj,
        "metrics_summary": process_metrics_summary,
        "feature_reference": process_feature_reference,
        "perturbation_efficiencies_by_feature": partial(
            proces_perturbation, "perturbation_efficiencies_by_feature"
        ),
        "perturbation_efficiencies_by_target": partial(
            proces_perturbation, "perturbation_efficiencies_by_target"
        ),
        "antigen_analysis": process_antigen_analysis,
    }
    mudata_per_sample = process_counts(
        input_data["count"],
        input_data["multiplexing_analysis"],
        input_data["metrics_summary"],
    )
    for modality_name, modality_data_path in input_data.items():
        if (
            modality_name in ("count", "multiplexing_analysis")
            or not modality_data_path
        ):
            continue
        try:
            parser_function = dispatcher[modality_name]
        except KeyError as e:
            raise ValueError(
                "This component does not support the "
                f"parsing of the '{modality_name}' yet."
            ) from e
        mudata_per_sample = parser_function(mudata_per_sample, modality_data_path)
    return mudata_per_sample


def main():
    cellranger_multi_dir = Path(par["input"])
    # TODO: remove when issue https://github.com/viash-io/viash/issues/706 is resolved.
    if isinstance(par["output"], (list, set, tuple)):
        assert len(par["output"]) == 1, (
            "A single output file template should have been provided."
        )
        par["output"] = par["output"][0]
    assert par["output"].count("*") == 1, (
        f"Expected exactly one wildcard character (*) in output "
        f"files template ({par['output']}). Found {par['output'].count('*')}"
    )
    input_data = gather_input_data(cellranger_multi_dir)
    result = get_modalities(input_data)
    output_files = {
        par["output"].replace("*", sample_name) for sample_name in result.keys()
    }
    assert len(output_files) == len(result.keys()), (
        "Replacing the wildcard in the output files "
        "template did not produce unique file paths."
    )
    logger.info(
        "Writing output for samples: '%s' to '%s'",
        "".join(result.keys()),
        par["output"],
    )
    with Path(par["sample_csv"]).open("w", newline="") as open_csv:
        csvwriter = csv.DictWriter(open_csv, fieldnames=["sample_name", "file"])
        csvwriter.writeheader()
        for sample_name, mudata_obj in result.items():
            output_file = Path(par["output"].replace("*", sample_name))
            mudata_obj.write_h5mu(output_file, compression=par["output_compression"])
            csvwriter.writerow({"sample_name": sample_name, "file": output_file.name})


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

VIASHEOF


if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  # strip viash automount from file paths
  
  if [ ! -z "$VIASH_PAR_INPUT" ]; then
    VIASH_PAR_INPUT=$(ViashDockerStripAutomount "$VIASH_PAR_INPUT")
  fi
  if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
    VIASH_PAR_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT")
  fi
  if [ ! -z "$VIASH_PAR_SAMPLE_CSV" ]; then
    VIASH_PAR_SAMPLE_CSV=$(ViashDockerStripAutomount "$VIASH_PAR_SAMPLE_CSV")
  fi
  if [ ! -z "$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 "$VIASH_PAR_OUTPUT" ] && ! compgen -G "$VIASH_PAR_OUTPUT" > /dev/null; then
  ViashError "Output file '$VIASH_PAR_OUTPUT' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_SAMPLE_CSV" ] && [ ! -e "$VIASH_PAR_SAMPLE_CSV" ]; then
  ViashError "Output file '$VIASH_PAR_SAMPLE_CSV' does not exist."
  exit 1
fi


exit 0
