#!/usr/bin/env bash

# busco_run seqtk_sample
# 
# This wrapper script is auto-generated by viash 0.9.0-RC6 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.

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 {
  SOURCE="$1"
  while [ -h "$SOURCE" ]; do
    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 {
  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="busco_run"
VIASH_META_FUNCTIONALITY_NAME="busco_run"
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"


# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
  echo "busco_run seqtk_sample"
  echo ""
  echo "Assessment of genome assembly and annotation completeness with single copy"
  echo "orthologs"
  echo ""
  echo "Inputs:"
  echo "    -i, --input"
  echo "        type: file, required parameter, file must exist"
  echo "        example: file.fasta"
  echo "        Input sequence file in FASTA format. Can be an assembled genome or"
  echo "        transcriptome (DNA), or protein sequences from an annotated gene set."
  echo "        Also possible to use a path to a directory containing multiple input"
  echo "        files."
  echo ""
  echo "    -m, --mode"
  echo "        type: string, required parameter"
  echo "        example: proteins"
  echo "        choices: [ genome, geno, transcriptome, tran, proteins, prot ]"
  echo "        Specify which BUSCO analysis mode to run. There are three valid modes:"
  echo "          - geno or genome, for genome assemblies (DNA)"
  echo "          - tran or transcriptome, for transcriptome assemblies (DNA)"
  echo "          - prot or proteins, for annotated gene sets (protein)"
  echo ""
  echo "    -l, --lineage_dataset"
  echo "        type: string"
  echo "        example: stramenopiles_odb10"
  echo "        Specify a BUSCO lineage dataset that is most closely related to the"
  echo "        assembly or gene set being assessed."
  echo "        The full list of available datasets can be viewed"
  echo "        [here](https://busco-data.ezlab.org/v5/data/lineages/) or by running the"
  echo "        busco/busco_list_datasets component."
  echo "        When unsure, the \"--auto_lineage\" flag can be set to automatically find"
  echo "        the optimal lineage path."
  echo "        BUSCO will automatically download the requested dataset if it is not"
  echo "        already present in the download folder."
  echo "        You can optionally provide a path to a local dataset instead of a name,"
  echo "        e.g. path/to/dataset."
  echo "        Datasets can be downloaded using the busco/busco_download_dataset"
  echo "        component."
  echo ""
  echo "Outputs:"
  echo "    --short_summary_json"
  echo "        type: file, output, file must exist"
  echo "        example: short_summary.json"
  echo "        Output file for short summary in JSON format."
  echo ""
  echo "    --short_summary_txt"
  echo "        type: file, output, file must exist"
  echo "        example: short_summary.txt"
  echo "        Output file for short summary in TXT format."
  echo ""
  echo "    --full_table"
  echo "        type: file, output, file must exist"
  echo "        example: full_table.tsv"
  echo "        Full table output in TSV format."
  echo ""
  echo "    --missing_busco_list"
  echo "        type: file, output, file must exist"
  echo "        example: missing_busco_list.tsv"
  echo "        Missing list output in TSV format."
  echo ""
  echo "    --output_dir"
  echo "        type: file, output, file must exist"
  echo "        example: output_dir"
  echo "        The full output directory, if so desired."
  echo ""
  echo "Resource and Run Settings:"
  echo "    --force"
  echo "        type: boolean_true"
  echo "        Force rewriting of existing files. Must be used when output files with"
  echo "        the provided name already exist."
  echo ""
  echo "    -q, --quiet"
  echo "        type: boolean_true"
  echo "        Disable the info logs, displays only errors."
  echo ""
  echo "    -r, --restart"
  echo "        type: boolean_true"
  echo "        Continue a run that had already partially completed. Restarting skips"
  echo "        calls to tools that have completed but performs all pre- and"
  echo "        post-processing steps."
  echo ""
  echo "    --tar"
  echo "        type: boolean_true"
  echo "        Compress some subdirectories with many files to save space."
  echo ""
  echo "Lineage Dataset Settings:"
  echo "    --auto_lineage"
  echo "        type: boolean_true"
  echo "        Run auto-lineage pipelilne to automatically determine BUSCO lineage"
  echo "        dataset that is most closely related to the assembly or gene set being"
  echo "        assessed."
  echo ""
  echo "    --auto_lineage_euk"
  echo "        type: boolean_true"
  echo "        Run auto-placement just on eukaryota tree to find optimal lineage path."
  echo ""
  echo "    --auto_lineage_prok"
  echo "        type: boolean_true"
  echo "        Run auto_lineage just on prokaryota trees to find optimum lineage path."
  echo ""
  echo "    --datasets_version"
  echo "        type: string"
  echo "        example: odb10"
  echo "        Specify the version of BUSCO datasets"
  echo ""
  echo "Augustus Settings:"
  echo "    --augustus"
  echo "        type: boolean_true"
  echo "        Use augustus gene predictor for eukaryote runs."
  echo ""
  echo "    --augustus_parameters"
  echo "        type: string"
  echo "        example: --PARAM1=VALUE1,--PARAM2=VALUE2"
  echo "        Additional parameters to be passed to Augustus (see Augustus"
  echo "        documentation:"
  echo "       "
  echo "https://github.com/Gaius-Augustus/Augustus/blob/master/docs/RUNNING-AUGUSTUS.md)."
  echo "        Parameters should be contained within a single string, without"
  echo "        whitespace and seperated by commas."
  echo ""
  echo "    --augustus_species"
  echo "        type: string"
  echo "        Specify the augustus species"
  echo ""
  echo "    --long"
  echo "        type: boolean_true"
  echo "        Optimize Augustus self-training mode. This adds considerably to the run"
  echo "        time, but can improve results for some non-model organisms."
  echo ""
  echo "BBTools Settings:"
  echo "    --contig_break"
  echo "        type: integer"
  echo "        Number of contiguous Ns to signify a break between contigs in BBTools"
  echo "        analysis."
  echo ""
  echo "    --limit"
  echo "        type: integer"
  echo "        Number of candidate regions (contig or transcript) from the BLAST output"
  echo "        to consider per BUSCO."
  echo "        This option is only effective in pipelines using BLAST, i.e. the genome"
  echo "        pipeline (see --augustus) or the prokaryota transcriptome pipeline."
  echo ""
  echo "    --scaffold_composition"
  echo "        type: boolean_true"
  echo "        Writes ACGTN content per scaffold to a file scaffold_composition.txt."
  echo ""
  echo "BLAST Settings:"
  echo "    --e_value"
  echo "        type: double"
  echo "        E-value cutoff for BLAST searches."
  echo ""
  echo "Protein Gene Prediction settings:"
  echo "    --miniprot"
  echo "        type: boolean_true"
  echo "        Use Miniprot gene predictor."
  echo ""
  echo "MetaEuk Settings:"
  echo "    --metaeuk_parameters"
  echo "        type: string"
  echo "        example: --max-overlap=15,--min-exon-aa=15"
  echo "        Pass additional arguments to Metaeuk for the first run (see Metaeuk"
  echo "        documentation https://github.com/soedinglab/metaeuk)."
  echo "        All parameters should be contained within a single string with no white"
  echo "        space, with each parameter separated by a comma."
  echo ""
  echo "    --metaeuk_rerun_parameters"
  echo "        type: string"
  echo "        example: --max-overlap=15,--min-exon-aa=15"
  echo "        Pass additional arguments to Metaeuk for the second run (see Metaeuk"
  echo "        documentation https://github.com/soedinglab/metaeuk)."
  echo "        All parameters should be contained within a single string with no white"
  echo "        space, with each parameter separated by a comma."
}

# 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"
  save=$-; set +e
  docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
  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 $1 && return 0 || return 1
  else
    save=$-; set +e
    docker pull $1 2> /dev/null > /dev/null
    out=$?
    [[ $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 '$1'"
  save=$-; set +e
  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
#
# $1                  : image identifier with format `[registry/]image[:tag]`
# ViashDockerBuild    : a Bash function which builds a docker image, takes image identifier as argument.
# examples:
#   ViashDockerPullElseBuild mynewcomponent
function ViashDockerPullElseBuild {
  save=$-; set +e
  ViashDockerPull $1
  out=$?
  [[ $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 quay.io/biocontainers/busco:5.6.1--pyhdfd78af_0
ENTRYPOINT []
RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_versions.txt

LABEL org.opencontainers.image.description="Companion container for running component busco busco_run"
LABEL org.opencontainers.image.created="2024-06-27T09:29:45Z"
LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
LABEL org.opencontainers.image.revision="796c3bcdbb5f5fa578686cd33c28817d83f04427"
LABEL org.opencontainers.image.version="seqtk_sample"

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
  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
# $VIASH_DIRECTORY_MOUNTS : Added another parameter to be passed to docker
# examples:
#   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
#   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
function ViashDockerAutodetectMount {
  abs_path=$(ViashAbsolutePath "$1")
  if [ -d "$abs_path" ]; then
    mount_source="$abs_path"
    base_name=""
  else
    mount_source=`dirname "$abs_path"`
    base_name=`basename "$abs_path"`
  fi
  mount_target="/viash_automount$mount_source"
  if [ -z "$base_name" ]; then
    echo "$mount_target"
  else
    echo "$mount_target/$base_name"
  fi
}
function ViashDockerAutodetectMountArg {
  abs_path=$(ViashAbsolutePath "$1")
  if [ -d "$abs_path" ]; then
    mount_source="$abs_path"
    base_name=""
  else
    mount_source=`dirname "$abs_path"`
    base_name=`basename "$abs_path"`
  fi
  mount_target="/viash_automount$mount_source"
  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
  echo "--volume=\"$mount_source:$mount_target\""
}
function ViashDockerStripAutomount {
  abs_path=$(ViashAbsolutePath "$1")
  echo "${abs_path#/viash_automount}"
}
# initialise variables
VIASH_DIRECTORY_MOUNTS=()

# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)

# 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 "$1")"
            shift 1
            ;;
        --version)
            echo "busco_run seqtk_sample"
            exit
            ;;
        --input)
            [ -n "$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"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -i. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --mode)
            [ -n "$VIASH_PAR_MODE" ] && ViashError Bad arguments for option \'--mode\': \'$VIASH_PAR_MODE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MODE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --mode. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --mode=*)
            [ -n "$VIASH_PAR_MODE" ] && ViashError Bad arguments for option \'--mode=*\': \'$VIASH_PAR_MODE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MODE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -m)
            [ -n "$VIASH_PAR_MODE" ] && ViashError Bad arguments for option \'-m\': \'$VIASH_PAR_MODE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MODE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -m. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --lineage_dataset)
            [ -n "$VIASH_PAR_LINEAGE_DATASET" ] && ViashError Bad arguments for option \'--lineage_dataset\': \'$VIASH_PAR_LINEAGE_DATASET\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LINEAGE_DATASET="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --lineage_dataset. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --lineage_dataset=*)
            [ -n "$VIASH_PAR_LINEAGE_DATASET" ] && ViashError Bad arguments for option \'--lineage_dataset=*\': \'$VIASH_PAR_LINEAGE_DATASET\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LINEAGE_DATASET=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -l)
            [ -n "$VIASH_PAR_LINEAGE_DATASET" ] && ViashError Bad arguments for option \'-l\': \'$VIASH_PAR_LINEAGE_DATASET\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LINEAGE_DATASET="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -l. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --short_summary_json)
            [ -n "$VIASH_PAR_SHORT_SUMMARY_JSON" ] && ViashError Bad arguments for option \'--short_summary_json\': \'$VIASH_PAR_SHORT_SUMMARY_JSON\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SHORT_SUMMARY_JSON="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --short_summary_json. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --short_summary_json=*)
            [ -n "$VIASH_PAR_SHORT_SUMMARY_JSON" ] && ViashError Bad arguments for option \'--short_summary_json=*\': \'$VIASH_PAR_SHORT_SUMMARY_JSON\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SHORT_SUMMARY_JSON=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --short_summary_txt)
            [ -n "$VIASH_PAR_SHORT_SUMMARY_TXT" ] && ViashError Bad arguments for option \'--short_summary_txt\': \'$VIASH_PAR_SHORT_SUMMARY_TXT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SHORT_SUMMARY_TXT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --short_summary_txt. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --short_summary_txt=*)
            [ -n "$VIASH_PAR_SHORT_SUMMARY_TXT" ] && ViashError Bad arguments for option \'--short_summary_txt=*\': \'$VIASH_PAR_SHORT_SUMMARY_TXT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SHORT_SUMMARY_TXT=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --full_table)
            [ -n "$VIASH_PAR_FULL_TABLE" ] && ViashError Bad arguments for option \'--full_table\': \'$VIASH_PAR_FULL_TABLE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FULL_TABLE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --full_table. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --full_table=*)
            [ -n "$VIASH_PAR_FULL_TABLE" ] && ViashError Bad arguments for option \'--full_table=*\': \'$VIASH_PAR_FULL_TABLE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FULL_TABLE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --missing_busco_list)
            [ -n "$VIASH_PAR_MISSING_BUSCO_LIST" ] && ViashError Bad arguments for option \'--missing_busco_list\': \'$VIASH_PAR_MISSING_BUSCO_LIST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MISSING_BUSCO_LIST="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --missing_busco_list. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --missing_busco_list=*)
            [ -n "$VIASH_PAR_MISSING_BUSCO_LIST" ] && ViashError Bad arguments for option \'--missing_busco_list=*\': \'$VIASH_PAR_MISSING_BUSCO_LIST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MISSING_BUSCO_LIST=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --output_dir)
            [ -n "$VIASH_PAR_OUTPUT_DIR" ] && ViashError Bad arguments for option \'--output_dir\': \'$VIASH_PAR_OUTPUT_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_DIR="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --output_dir. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --output_dir=*)
            [ -n "$VIASH_PAR_OUTPUT_DIR" ] && ViashError Bad arguments for option \'--output_dir=*\': \'$VIASH_PAR_OUTPUT_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_DIR=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --force)
            [ -n "$VIASH_PAR_FORCE" ] && ViashError Bad arguments for option \'--force\': \'$VIASH_PAR_FORCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FORCE=true
            shift 1
            ;;
        --quiet)
            [ -n "$VIASH_PAR_QUIET" ] && ViashError Bad arguments for option \'--quiet\': \'$VIASH_PAR_QUIET\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_QUIET=true
            shift 1
            ;;
        -q)
            [ -n "$VIASH_PAR_QUIET" ] && ViashError Bad arguments for option \'-q\': \'$VIASH_PAR_QUIET\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_QUIET=true
            shift 1
            ;;
        --restart)
            [ -n "$VIASH_PAR_RESTART" ] && ViashError Bad arguments for option \'--restart\': \'$VIASH_PAR_RESTART\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_RESTART=true
            shift 1
            ;;
        -r)
            [ -n "$VIASH_PAR_RESTART" ] && ViashError Bad arguments for option \'-r\': \'$VIASH_PAR_RESTART\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_RESTART=true
            shift 1
            ;;
        --tar)
            [ -n "$VIASH_PAR_TAR" ] && ViashError Bad arguments for option \'--tar\': \'$VIASH_PAR_TAR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_TAR=true
            shift 1
            ;;
        --auto_lineage)
            [ -n "$VIASH_PAR_AUTO_LINEAGE" ] && ViashError Bad arguments for option \'--auto_lineage\': \'$VIASH_PAR_AUTO_LINEAGE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_AUTO_LINEAGE=true
            shift 1
            ;;
        --auto_lineage_euk)
            [ -n "$VIASH_PAR_AUTO_LINEAGE_EUK" ] && ViashError Bad arguments for option \'--auto_lineage_euk\': \'$VIASH_PAR_AUTO_LINEAGE_EUK\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_AUTO_LINEAGE_EUK=true
            shift 1
            ;;
        --auto_lineage_prok)
            [ -n "$VIASH_PAR_AUTO_LINEAGE_PROK" ] && ViashError Bad arguments for option \'--auto_lineage_prok\': \'$VIASH_PAR_AUTO_LINEAGE_PROK\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_AUTO_LINEAGE_PROK=true
            shift 1
            ;;
        --datasets_version)
            [ -n "$VIASH_PAR_DATASETS_VERSION" ] && ViashError Bad arguments for option \'--datasets_version\': \'$VIASH_PAR_DATASETS_VERSION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_DATASETS_VERSION="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --datasets_version. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --datasets_version=*)
            [ -n "$VIASH_PAR_DATASETS_VERSION" ] && ViashError Bad arguments for option \'--datasets_version=*\': \'$VIASH_PAR_DATASETS_VERSION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_DATASETS_VERSION=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --augustus)
            [ -n "$VIASH_PAR_AUGUSTUS" ] && ViashError Bad arguments for option \'--augustus\': \'$VIASH_PAR_AUGUSTUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_AUGUSTUS=true
            shift 1
            ;;
        --augustus_parameters)
            [ -n "$VIASH_PAR_AUGUSTUS_PARAMETERS" ] && ViashError Bad arguments for option \'--augustus_parameters\': \'$VIASH_PAR_AUGUSTUS_PARAMETERS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_AUGUSTUS_PARAMETERS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --augustus_parameters. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --augustus_parameters=*)
            [ -n "$VIASH_PAR_AUGUSTUS_PARAMETERS" ] && ViashError Bad arguments for option \'--augustus_parameters=*\': \'$VIASH_PAR_AUGUSTUS_PARAMETERS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_AUGUSTUS_PARAMETERS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --augustus_species)
            [ -n "$VIASH_PAR_AUGUSTUS_SPECIES" ] && ViashError Bad arguments for option \'--augustus_species\': \'$VIASH_PAR_AUGUSTUS_SPECIES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_AUGUSTUS_SPECIES="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --augustus_species. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --augustus_species=*)
            [ -n "$VIASH_PAR_AUGUSTUS_SPECIES" ] && ViashError Bad arguments for option \'--augustus_species=*\': \'$VIASH_PAR_AUGUSTUS_SPECIES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_AUGUSTUS_SPECIES=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --long)
            [ -n "$VIASH_PAR_LONG" ] && ViashError Bad arguments for option \'--long\': \'$VIASH_PAR_LONG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LONG=true
            shift 1
            ;;
        --contig_break)
            [ -n "$VIASH_PAR_CONTIG_BREAK" ] && ViashError Bad arguments for option \'--contig_break\': \'$VIASH_PAR_CONTIG_BREAK\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CONTIG_BREAK="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --contig_break. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --contig_break=*)
            [ -n "$VIASH_PAR_CONTIG_BREAK" ] && ViashError Bad arguments for option \'--contig_break=*\': \'$VIASH_PAR_CONTIG_BREAK\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CONTIG_BREAK=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --limit)
            [ -n "$VIASH_PAR_LIMIT" ] && ViashError Bad arguments for option \'--limit\': \'$VIASH_PAR_LIMIT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LIMIT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --limit. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --limit=*)
            [ -n "$VIASH_PAR_LIMIT" ] && ViashError Bad arguments for option \'--limit=*\': \'$VIASH_PAR_LIMIT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LIMIT=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --scaffold_composition)
            [ -n "$VIASH_PAR_SCAFFOLD_COMPOSITION" ] && ViashError Bad arguments for option \'--scaffold_composition\': \'$VIASH_PAR_SCAFFOLD_COMPOSITION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SCAFFOLD_COMPOSITION=true
            shift 1
            ;;
        --e_value)
            [ -n "$VIASH_PAR_E_VALUE" ] && ViashError Bad arguments for option \'--e_value\': \'$VIASH_PAR_E_VALUE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_E_VALUE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --e_value. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --e_value=*)
            [ -n "$VIASH_PAR_E_VALUE" ] && ViashError Bad arguments for option \'--e_value=*\': \'$VIASH_PAR_E_VALUE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_E_VALUE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --miniprot)
            [ -n "$VIASH_PAR_MINIPROT" ] && ViashError Bad arguments for option \'--miniprot\': \'$VIASH_PAR_MINIPROT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MINIPROT=true
            shift 1
            ;;
        --metaeuk_parameters)
            [ -n "$VIASH_PAR_METAEUK_PARAMETERS" ] && ViashError Bad arguments for option \'--metaeuk_parameters\': \'$VIASH_PAR_METAEUK_PARAMETERS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_METAEUK_PARAMETERS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --metaeuk_parameters. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --metaeuk_parameters=*)
            [ -n "$VIASH_PAR_METAEUK_PARAMETERS" ] && ViashError Bad arguments for option \'--metaeuk_parameters=*\': \'$VIASH_PAR_METAEUK_PARAMETERS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_METAEUK_PARAMETERS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --metaeuk_rerun_parameters)
            [ -n "$VIASH_PAR_METAEUK_RERUN_PARAMETERS" ] && ViashError Bad arguments for option \'--metaeuk_rerun_parameters\': \'$VIASH_PAR_METAEUK_RERUN_PARAMETERS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_METAEUK_RERUN_PARAMETERS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --metaeuk_rerun_parameters. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --metaeuk_rerun_parameters=*)
            [ -n "$VIASH_PAR_METAEUK_RERUN_PARAMETERS" ] && ViashError Bad arguments for option \'--metaeuk_rerun_parameters=*\': \'$VIASH_PAR_METAEUK_RERUN_PARAMETERS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_METAEUK_RERUN_PARAMETERS=$(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 "$1")"
            shift 1
            ;;
        ---dockerfile)
            VIASH_MODE='dockerfile'
            shift 1
            ;;
        ---debug)
            VIASH_MODE='debug'
            shift 1
            ;;
        ---cpus)
            [ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_CPUS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to ---cpus. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        ---cpus=*)
            [ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus=*\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_CPUS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        ---memory)
            [ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_MEMORY="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to ---memory. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        ---memory=*)
            [ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory=*\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_MEMORY=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        *)  # positional arg or unknown option
            # since the positional args will be eval'd, can we always quote, instead of using ViashQuote
            VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'"
            [[ $1 == -* ]] && ViashWarning $1 looks like a parameter but is not a defined parameter and will instead be treated as a positional argument. Use "--help" to get more information on the parameters.
            shift # past argument
            ;;
    esac
done

# parse positional parameters
eval set -- $VIASH_POSITIONAL_ARGS


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

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

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/busco/busco_run:seqtk_sample'
  fi

  # print dockerfile
  if [ "$VIASH_MODE" == "dockerfile" ]; then
    ViashDockerfile "$VIASH_ENGINE_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" 'ps' 'bash'
    exit 0
  fi

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

# setting computational defaults

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


# check whether required parameters exist
if [ -z ${VIASH_PAR_INPUT+x} ]; then
  ViashError '--input' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_PAR_MODE+x} ]; then
  ViashError '--mode' 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_FORCE+x} ]; then
  VIASH_PAR_FORCE="false"
fi
if [ -z ${VIASH_PAR_QUIET+x} ]; then
  VIASH_PAR_QUIET="false"
fi
if [ -z ${VIASH_PAR_RESTART+x} ]; then
  VIASH_PAR_RESTART="false"
fi
if [ -z ${VIASH_PAR_TAR+x} ]; then
  VIASH_PAR_TAR="false"
fi
if [ -z ${VIASH_PAR_AUTO_LINEAGE+x} ]; then
  VIASH_PAR_AUTO_LINEAGE="false"
fi
if [ -z ${VIASH_PAR_AUTO_LINEAGE_EUK+x} ]; then
  VIASH_PAR_AUTO_LINEAGE_EUK="false"
fi
if [ -z ${VIASH_PAR_AUTO_LINEAGE_PROK+x} ]; then
  VIASH_PAR_AUTO_LINEAGE_PROK="false"
fi
if [ -z ${VIASH_PAR_AUGUSTUS+x} ]; then
  VIASH_PAR_AUGUSTUS="false"
fi
if [ -z ${VIASH_PAR_LONG+x} ]; then
  VIASH_PAR_LONG="false"
fi
if [ -z ${VIASH_PAR_SCAFFOLD_COMPOSITION+x} ]; then
  VIASH_PAR_SCAFFOLD_COMPOSITION="false"
fi
if [ -z ${VIASH_PAR_MINIPROT+x} ]; then
  VIASH_PAR_MINIPROT="false"
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 "$VIASH_PAR_FORCE" ]]; then
  if ! [[ "$VIASH_PAR_FORCE" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--force' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_QUIET" ]]; then
  if ! [[ "$VIASH_PAR_QUIET" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--quiet' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_RESTART" ]]; then
  if ! [[ "$VIASH_PAR_RESTART" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--restart' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_TAR" ]]; then
  if ! [[ "$VIASH_PAR_TAR" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--tar' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_AUTO_LINEAGE" ]]; then
  if ! [[ "$VIASH_PAR_AUTO_LINEAGE" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--auto_lineage' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_AUTO_LINEAGE_EUK" ]]; then
  if ! [[ "$VIASH_PAR_AUTO_LINEAGE_EUK" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--auto_lineage_euk' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_AUTO_LINEAGE_PROK" ]]; then
  if ! [[ "$VIASH_PAR_AUTO_LINEAGE_PROK" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--auto_lineage_prok' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_AUGUSTUS" ]]; then
  if ! [[ "$VIASH_PAR_AUGUSTUS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--augustus' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_LONG" ]]; then
  if ! [[ "$VIASH_PAR_LONG" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--long' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_CONTIG_BREAK" ]]; then
  if ! [[ "$VIASH_PAR_CONTIG_BREAK" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--contig_break' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_LIMIT" ]]; then
  if ! [[ "$VIASH_PAR_LIMIT" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--limit' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SCAFFOLD_COMPOSITION" ]]; then
  if ! [[ "$VIASH_PAR_SCAFFOLD_COMPOSITION" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--scaffold_composition' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_E_VALUE" ]]; then
  if ! [[ "$VIASH_PAR_E_VALUE" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--e_value' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_MINIPROT" ]]; then
  if ! [[ "$VIASH_PAR_MINIPROT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--miniprot' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_CPUS" ]]; then
  if ! [[ "$VIASH_META_CPUS" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'cpus' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_B" ]]; then
  if ! [[ "$VIASH_META_MEMORY_B" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_b' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_KB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_KB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_kb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_MB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_MB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_mb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_GB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_GB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_gb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_TB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_TB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_tb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_PB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_PB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_pb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_KIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_KIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_kib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_MIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_MIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_mib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_GIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_GIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_gib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_TIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_TIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_tib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_PIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_PIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_pib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi

# check whether value is belongs to a set of choices
if [ ! -z "$VIASH_PAR_MODE" ]; then
  VIASH_PAR_MODE_CHOICES=("genome;geno;transcriptome;tran;proteins;prot")
  IFS=';'
  set -f
  if ! [[ ";${VIASH_PAR_MODE_CHOICES[*]};" =~ ";$VIASH_PAR_MODE;" ]]; then
    ViashError '--mode' specified value of \'$VIASH_PAR_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

# create parent directories of output files, if so desired
if [ ! -z "$VIASH_PAR_SHORT_SUMMARY_JSON" ] && [ ! -d "$(dirname "$VIASH_PAR_SHORT_SUMMARY_JSON")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_SHORT_SUMMARY_JSON")"
fi
if [ ! -z "$VIASH_PAR_SHORT_SUMMARY_TXT" ] && [ ! -d "$(dirname "$VIASH_PAR_SHORT_SUMMARY_TXT")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_SHORT_SUMMARY_TXT")"
fi
if [ ! -z "$VIASH_PAR_FULL_TABLE" ] && [ ! -d "$(dirname "$VIASH_PAR_FULL_TABLE")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_FULL_TABLE")"
fi
if [ ! -z "$VIASH_PAR_MISSING_BUSCO_LIST" ] && [ ! -d "$(dirname "$VIASH_PAR_MISSING_BUSCO_LIST")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_MISSING_BUSCO_LIST")"
fi
if [ ! -z "$VIASH_PAR_OUTPUT_DIR" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT_DIR")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_OUTPUT_DIR")"
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 "$VIASH_PAR_SHORT_SUMMARY_JSON" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_SHORT_SUMMARY_JSON")" )
  VIASH_PAR_SHORT_SUMMARY_JSON=$(ViashDockerAutodetectMount "$VIASH_PAR_SHORT_SUMMARY_JSON")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_SHORT_SUMMARY_JSON" )
fi
if [ ! -z "$VIASH_PAR_SHORT_SUMMARY_TXT" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_SHORT_SUMMARY_TXT")" )
  VIASH_PAR_SHORT_SUMMARY_TXT=$(ViashDockerAutodetectMount "$VIASH_PAR_SHORT_SUMMARY_TXT")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_SHORT_SUMMARY_TXT" )
fi
if [ ! -z "$VIASH_PAR_FULL_TABLE" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_FULL_TABLE")" )
  VIASH_PAR_FULL_TABLE=$(ViashDockerAutodetectMount "$VIASH_PAR_FULL_TABLE")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_FULL_TABLE" )
fi
if [ ! -z "$VIASH_PAR_MISSING_BUSCO_LIST" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_MISSING_BUSCO_LIST")" )
  VIASH_PAR_MISSING_BUSCO_LIST=$(ViashDockerAutodetectMount "$VIASH_PAR_MISSING_BUSCO_LIST")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_MISSING_BUSCO_LIST" )
fi
if [ ! -z "$VIASH_PAR_OUTPUT_DIR" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT_DIR")" )
  VIASH_PAR_OUTPUT_DIR=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT_DIR")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT_DIR" )
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-busco_run-XXXXXX").sh
function clean_up {
  rm "\$tempscript"
}
function interrupt {
  echo -e "\nCTRL-C Pressed..."
  exit 1
}
trap clean_up EXIT
trap interrupt INT SIGINT
cat > "\$tempscript" << 'VIASHMAIN'
#!/bin/bash

## VIASH START
# The following code has been auto-generated by Viash.
$( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_input='&'#" ; else echo "# par_input="; fi )
$( if [ ! -z ${VIASH_PAR_MODE+x} ]; then echo "${VIASH_PAR_MODE}" | sed "s#'#'\"'\"'#g;s#.*#par_mode='&'#" ; else echo "# par_mode="; fi )
$( if [ ! -z ${VIASH_PAR_LINEAGE_DATASET+x} ]; then echo "${VIASH_PAR_LINEAGE_DATASET}" | sed "s#'#'\"'\"'#g;s#.*#par_lineage_dataset='&'#" ; else echo "# par_lineage_dataset="; fi )
$( if [ ! -z ${VIASH_PAR_SHORT_SUMMARY_JSON+x} ]; then echo "${VIASH_PAR_SHORT_SUMMARY_JSON}" | sed "s#'#'\"'\"'#g;s#.*#par_short_summary_json='&'#" ; else echo "# par_short_summary_json="; fi )
$( if [ ! -z ${VIASH_PAR_SHORT_SUMMARY_TXT+x} ]; then echo "${VIASH_PAR_SHORT_SUMMARY_TXT}" | sed "s#'#'\"'\"'#g;s#.*#par_short_summary_txt='&'#" ; else echo "# par_short_summary_txt="; fi )
$( if [ ! -z ${VIASH_PAR_FULL_TABLE+x} ]; then echo "${VIASH_PAR_FULL_TABLE}" | sed "s#'#'\"'\"'#g;s#.*#par_full_table='&'#" ; else echo "# par_full_table="; fi )
$( if [ ! -z ${VIASH_PAR_MISSING_BUSCO_LIST+x} ]; then echo "${VIASH_PAR_MISSING_BUSCO_LIST}" | sed "s#'#'\"'\"'#g;s#.*#par_missing_busco_list='&'#" ; else echo "# par_missing_busco_list="; fi )
$( if [ ! -z ${VIASH_PAR_OUTPUT_DIR+x} ]; then echo "${VIASH_PAR_OUTPUT_DIR}" | sed "s#'#'\"'\"'#g;s#.*#par_output_dir='&'#" ; else echo "# par_output_dir="; fi )
$( if [ ! -z ${VIASH_PAR_FORCE+x} ]; then echo "${VIASH_PAR_FORCE}" | sed "s#'#'\"'\"'#g;s#.*#par_force='&'#" ; else echo "# par_force="; fi )
$( if [ ! -z ${VIASH_PAR_QUIET+x} ]; then echo "${VIASH_PAR_QUIET}" | sed "s#'#'\"'\"'#g;s#.*#par_quiet='&'#" ; else echo "# par_quiet="; fi )
$( if [ ! -z ${VIASH_PAR_RESTART+x} ]; then echo "${VIASH_PAR_RESTART}" | sed "s#'#'\"'\"'#g;s#.*#par_restart='&'#" ; else echo "# par_restart="; fi )
$( if [ ! -z ${VIASH_PAR_TAR+x} ]; then echo "${VIASH_PAR_TAR}" | sed "s#'#'\"'\"'#g;s#.*#par_tar='&'#" ; else echo "# par_tar="; fi )
$( if [ ! -z ${VIASH_PAR_AUTO_LINEAGE+x} ]; then echo "${VIASH_PAR_AUTO_LINEAGE}" | sed "s#'#'\"'\"'#g;s#.*#par_auto_lineage='&'#" ; else echo "# par_auto_lineage="; fi )
$( if [ ! -z ${VIASH_PAR_AUTO_LINEAGE_EUK+x} ]; then echo "${VIASH_PAR_AUTO_LINEAGE_EUK}" | sed "s#'#'\"'\"'#g;s#.*#par_auto_lineage_euk='&'#" ; else echo "# par_auto_lineage_euk="; fi )
$( if [ ! -z ${VIASH_PAR_AUTO_LINEAGE_PROK+x} ]; then echo "${VIASH_PAR_AUTO_LINEAGE_PROK}" | sed "s#'#'\"'\"'#g;s#.*#par_auto_lineage_prok='&'#" ; else echo "# par_auto_lineage_prok="; fi )
$( if [ ! -z ${VIASH_PAR_DATASETS_VERSION+x} ]; then echo "${VIASH_PAR_DATASETS_VERSION}" | sed "s#'#'\"'\"'#g;s#.*#par_datasets_version='&'#" ; else echo "# par_datasets_version="; fi )
$( if [ ! -z ${VIASH_PAR_AUGUSTUS+x} ]; then echo "${VIASH_PAR_AUGUSTUS}" | sed "s#'#'\"'\"'#g;s#.*#par_augustus='&'#" ; else echo "# par_augustus="; fi )
$( if [ ! -z ${VIASH_PAR_AUGUSTUS_PARAMETERS+x} ]; then echo "${VIASH_PAR_AUGUSTUS_PARAMETERS}" | sed "s#'#'\"'\"'#g;s#.*#par_augustus_parameters='&'#" ; else echo "# par_augustus_parameters="; fi )
$( if [ ! -z ${VIASH_PAR_AUGUSTUS_SPECIES+x} ]; then echo "${VIASH_PAR_AUGUSTUS_SPECIES}" | sed "s#'#'\"'\"'#g;s#.*#par_augustus_species='&'#" ; else echo "# par_augustus_species="; fi )
$( if [ ! -z ${VIASH_PAR_LONG+x} ]; then echo "${VIASH_PAR_LONG}" | sed "s#'#'\"'\"'#g;s#.*#par_long='&'#" ; else echo "# par_long="; fi )
$( if [ ! -z ${VIASH_PAR_CONTIG_BREAK+x} ]; then echo "${VIASH_PAR_CONTIG_BREAK}" | sed "s#'#'\"'\"'#g;s#.*#par_contig_break='&'#" ; else echo "# par_contig_break="; fi )
$( if [ ! -z ${VIASH_PAR_LIMIT+x} ]; then echo "${VIASH_PAR_LIMIT}" | sed "s#'#'\"'\"'#g;s#.*#par_limit='&'#" ; else echo "# par_limit="; fi )
$( if [ ! -z ${VIASH_PAR_SCAFFOLD_COMPOSITION+x} ]; then echo "${VIASH_PAR_SCAFFOLD_COMPOSITION}" | sed "s#'#'\"'\"'#g;s#.*#par_scaffold_composition='&'#" ; else echo "# par_scaffold_composition="; fi )
$( if [ ! -z ${VIASH_PAR_E_VALUE+x} ]; then echo "${VIASH_PAR_E_VALUE}" | sed "s#'#'\"'\"'#g;s#.*#par_e_value='&'#" ; else echo "# par_e_value="; fi )
$( if [ ! -z ${VIASH_PAR_MINIPROT+x} ]; then echo "${VIASH_PAR_MINIPROT}" | sed "s#'#'\"'\"'#g;s#.*#par_miniprot='&'#" ; else echo "# par_miniprot="; fi )
$( if [ ! -z ${VIASH_PAR_METAEUK_PARAMETERS+x} ]; then echo "${VIASH_PAR_METAEUK_PARAMETERS}" | sed "s#'#'\"'\"'#g;s#.*#par_metaeuk_parameters='&'#" ; else echo "# par_metaeuk_parameters="; fi )
$( if [ ! -z ${VIASH_PAR_METAEUK_RERUN_PARAMETERS+x} ]; then echo "${VIASH_PAR_METAEUK_RERUN_PARAMETERS}" | sed "s#'#'\"'\"'#g;s#.*#par_metaeuk_rerun_parameters='&'#" ; else echo "# par_metaeuk_rerun_parameters="; fi )
$( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi )
$( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi )
$( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "${VIASH_META_RESOURCES_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_resources_dir='&'#" ; else echo "# meta_resources_dir="; fi )
$( if [ ! -z ${VIASH_META_EXECUTABLE+x} ]; then echo "${VIASH_META_EXECUTABLE}" | sed "s#'#'\"'\"'#g;s#.*#meta_executable='&'#" ; else echo "# meta_executable="; fi )
$( if [ ! -z ${VIASH_META_CONFIG+x} ]; then echo "${VIASH_META_CONFIG}" | sed "s#'#'\"'\"'#g;s#.*#meta_config='&'#" ; else echo "# meta_config="; fi )
$( if [ ! -z ${VIASH_META_TEMP_DIR+x} ]; then echo "${VIASH_META_TEMP_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_temp_dir='&'#" ; else echo "# meta_temp_dir="; fi )
$( if [ ! -z ${VIASH_META_CPUS+x} ]; then echo "${VIASH_META_CPUS}" | sed "s#'#'\"'\"'#g;s#.*#meta_cpus='&'#" ; else echo "# meta_cpus="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_B+x} ]; then echo "${VIASH_META_MEMORY_B}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_b='&'#" ; else echo "# meta_memory_b="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_KB+x} ]; then echo "${VIASH_META_MEMORY_KB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_kb='&'#" ; else echo "# meta_memory_kb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_MB+x} ]; then echo "${VIASH_META_MEMORY_MB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_mb='&'#" ; else echo "# meta_memory_mb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_GB+x} ]; then echo "${VIASH_META_MEMORY_GB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_gb='&'#" ; else echo "# meta_memory_gb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_TB+x} ]; then echo "${VIASH_META_MEMORY_TB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_tb='&'#" ; else echo "# meta_memory_tb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_PB+x} ]; then echo "${VIASH_META_MEMORY_PB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_pb='&'#" ; else echo "# meta_memory_pb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_KIB+x} ]; then echo "${VIASH_META_MEMORY_KIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_kib='&'#" ; else echo "# meta_memory_kib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_MIB+x} ]; then echo "${VIASH_META_MEMORY_MIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_mib='&'#" ; else echo "# meta_memory_mib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_GIB+x} ]; then echo "${VIASH_META_MEMORY_GIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_gib='&'#" ; else echo "# meta_memory_gib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_TIB+x} ]; then echo "${VIASH_META_MEMORY_TIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_tib='&'#" ; else echo "# meta_memory_tib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_pib='&'#" ; else echo "# meta_memory_pib="; fi )

## VIASH END


[[ "\$par_tar" == "false" ]] && unset par_tar
[[ "\$par_force" == "false" ]] && unset par_force
[[ "\$par_quiet" == "false" ]] && unset par_quiet
[[ "\$par_restart" == "false" ]] && unset par_restart
[[ "\$par_auto_lineage" == "false" ]] && unset par_auto_lineage
[[ "\$par_auto_lineage_euk" == "false" ]] && unset par_auto_lineage_euk
[[ "\$par_auto_lineage_prok" == "false" ]] && unset par_auto_lineage_prok
[[ "\$par_augustus" == "false" ]] && unset par_augustus
[[ "\$par_long" == "false" ]] && unset par_long
[[ "\$par_scaffold_composition" == "false" ]] && unset par_scaffold_composition
[[ "\$par_miniprot" == "false" ]] && unset par_miniprot

tmp_dir=\$(mktemp -d -p "\$meta_temp_dir" busco_XXXXXXXXX)
prefix=\$(openssl rand -hex 8)

busco \\
    --in "\$par_input" \\
    --mode "\$par_mode" \\
    --out "\$prefix" \\
    --out_path "\$tmp_dir" \\
    --opt-out-run-stats \\
    \${meta_cpus:+--cpu "\${meta_cpus}"} \\
    \${par_lineage_dataset:+--lineage_dataset "\$par_lineage_dataset"} \\
    \${par_augustus:+--augustus} \\
    \${par_augustus_parameters:+--augustus_parameters "\$par_augustus_parameters"} \\
    \${par_augustus_species:+--augustus_species "\$par_augustus_species"} \\
    \${par_auto_lineage:+--auto-lineage} \\
    \${par_auto_lineage_euk:+--auto-lineage-euk} \\
    \${par_auto_lineage_prok:+--auto-lineage-prok} \\
    \${par_contig_break:+--contig_break \$par_contig_break} \\
    \${par_datasets_version:+--datasets_version "\$par_datasets_version"} \\
    \${par_e_value:+--evalue "\$par_e_value"} \\
    \${par_force:+--force} \\
    \${par_limit:+--limit "\$par_limit"} \\
    \${par_long:+--long} \\
    \${par_metaeuk_parameters:+--metaeuk_parameters "\$par_metaeuk_parameters"} \\
    \${par_metaeuk_rerun_parameters:+--metaeuk_rerun_parameters "\$par_metaeuk_rerun_parameters"} \\
    \${par_miniprot:+--miniprot} \\
    \${par_quiet:+--quiet} \\
    \${par_restart:+--restart} \\
    \${par_scaffold_composition:+--scaffold_composition} \\
    \${par_tar:+--tar} \\


out_dir=\$(find "\$tmp_dir/\$prefix" -maxdepth 1 -name 'run_*')

if [[ -n "\$par_short_summary_json" ]]; then
    cp "\$out_dir/short_summary.json" "\$par_short_summary_json"
fi
if [[ -n "\$par_short_summary_txt" ]]; then
    cp "\$out_dir/short_summary.txt" "\$par_short_summary_txt"
fi
if [[ -n "\$par_full_table" ]]; then
    cp "\$out_dir/full_table.tsv" "\$par_full_table"
fi
if [[ -n "\$par_missing_busco_list" ]]; then
    cp "\$out_dir/missing_busco_list.tsv" "\$par_missing_busco_list"
fi
if [[ -n "\$par_output_dir" ]]; then
    if [[ -d "\$par_output_dir" ]]; then
        rm -r "\$par_output_dir"
    fi
    cp -r -L "\$out_dir" "\$par_output_dir"
fi
VIASHMAIN
bash "\$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_SHORT_SUMMARY_JSON" ]; then
    VIASH_PAR_SHORT_SUMMARY_JSON=$(ViashDockerStripAutomount "$VIASH_PAR_SHORT_SUMMARY_JSON")
  fi
  if [ ! -z "$VIASH_PAR_SHORT_SUMMARY_TXT" ]; then
    VIASH_PAR_SHORT_SUMMARY_TXT=$(ViashDockerStripAutomount "$VIASH_PAR_SHORT_SUMMARY_TXT")
  fi
  if [ ! -z "$VIASH_PAR_FULL_TABLE" ]; then
    VIASH_PAR_FULL_TABLE=$(ViashDockerStripAutomount "$VIASH_PAR_FULL_TABLE")
  fi
  if [ ! -z "$VIASH_PAR_MISSING_BUSCO_LIST" ]; then
    VIASH_PAR_MISSING_BUSCO_LIST=$(ViashDockerStripAutomount "$VIASH_PAR_MISSING_BUSCO_LIST")
  fi
  if [ ! -z "$VIASH_PAR_OUTPUT_DIR" ]; then
    VIASH_PAR_OUTPUT_DIR=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT_DIR")
  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 "$VIASH_PAR_SHORT_SUMMARY_JSON" ] && [ ! -e "$VIASH_PAR_SHORT_SUMMARY_JSON" ]; then
  ViashError "Output file '$VIASH_PAR_SHORT_SUMMARY_JSON' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_SHORT_SUMMARY_TXT" ] && [ ! -e "$VIASH_PAR_SHORT_SUMMARY_TXT" ]; then
  ViashError "Output file '$VIASH_PAR_SHORT_SUMMARY_TXT' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_FULL_TABLE" ] && [ ! -e "$VIASH_PAR_FULL_TABLE" ]; then
  ViashError "Output file '$VIASH_PAR_FULL_TABLE' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_MISSING_BUSCO_LIST" ] && [ ! -e "$VIASH_PAR_MISSING_BUSCO_LIST" ]; then
  ViashError "Output file '$VIASH_PAR_MISSING_BUSCO_LIST' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_OUTPUT_DIR" ] && [ ! -e "$VIASH_PAR_OUTPUT_DIR" ]; then
  ViashError "Output file '$VIASH_PAR_OUTPUT_DIR' does not exist."
  exit 1
fi


exit 0
