#!/usr/bin/env bash

# bcftools_stats add_sgdemux
# 
# This wrapper script is auto-generated by viash 0.9.0 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:
#  * Theodoro Gasperin Terra Camargo (author)

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="bcftools_stats"
VIASH_META_FUNCTIONALITY_NAME="bcftools_stats"
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 "bcftools_stats add_sgdemux"
  echo ""
  echo "Parses VCF or BCF and produces a txt stats file which can be plotted using"
  echo "plot-vcfstats."
  echo "When two files are given, the program generates separate stats for intersection"
  echo "and the complements. By default only sites are compared, -s/-S must given to"
  echo "include"
  echo "also sample columns."
  echo ""
  echo "Inputs:"
  echo "    -i, --input"
  echo "        type: file, required parameter, multiple values allowed, file must exist"
  echo "        Input VCF/BCF file. Maximum of two files."
  echo ""
  echo "Outputs:"
  echo "    -o, --output"
  echo "        type: file, required parameter, output, file must exist"
  echo "        Output txt statistics file."
  echo ""
  echo "Options:"
  echo "    --af_bins, --allele_frequency_bins"
  echo "        type: string"
  echo "        example: 0.1,0.5,1"
  echo "        Allele frequency bins, a list of bin values (0.1,0.5,1)."
  echo ""
  echo "    --af_bins_file, --allele_frequency_bins_file"
  echo "        type: file, file must exist"
  echo "        Same as allele_frequency_bins, but in a file."
  echo "        Format of file is one value per line."
  echo "        e.g."
  echo "          0.1"
  echo "          0.5"
  echo "          1"
  echo ""
  echo "    --af_tag, --allele_frequency_tag"
  echo "        type: string"
  echo "        Allele frequency tag to use, by default estimated from AN,AC or GT."
  echo ""
  echo "    --first_only, --first_allele_only"
  echo "        type: boolean_true"
  echo "        Include only 1st allele at multiallelic sites."
  echo ""
  echo "    --c, --collapse"
  echo "        type: string"
  echo "        choices: [ snps, indels, both, all, some, none ]"
  echo "        Treat as identical records with <snps|indels|both|all|some|none>."
  echo "        See https://samtools.github.io/bcftools/bcftools.html#common_options for"
  echo "        details."
  echo ""
  echo "    --d, --depth"
  echo "        type: string"
  echo "        example: 0,500,1"
  echo "        Depth distribution: min,max,bin size."
  echo ""
  echo "    --e, --exclude"
  echo "        type: string"
  echo "        example: QUAL < 30 && DP < 10"
  echo "        Exclude sites for which the expression is true."
  echo "        See https://samtools.github.io/bcftools/bcftools.html#expressions for"
  echo "        details."
  echo ""
  echo "    --E, --exons"
  echo "        type: file, file must exist"
  echo "        tab-delimited file with exons for indel frameshifts statistics."
  echo "        The columns of the file are CHR, FROM, TO, with 1-based, inclusive,"
  echo "        positions."
  echo "        The file is BGZF-compressed and indexed with tabix (e.g. tabix -s1 -b2"
  echo "        -e3 file.gz)."
  echo ""
  echo "    --f, --apply_filters"
  echo "        type: string"
  echo "        Require at least one of the listed FILTER strings (e.g. \"PASS,.\")."
  echo ""
  echo "    --F, --fasta_reference"
  echo "        type: file, file must exist"
  echo "        Faidx indexed reference sequence file to determine INDEL context."
  echo ""
  echo "    --i, --include"
  echo "        type: string"
  echo "        example: QUAL >= 30 && DP >= 10"
  echo "        Select sites for which the expression is true."
  echo "        See https://samtools.github.io/bcftools/bcftools.html#expressions for"
  echo "        details."
  echo ""
  echo "    --I, --split_by_ID"
  echo "        type: boolean_true"
  echo "        Collect stats for sites with ID separately (known vs novel)."
  echo ""
  echo "    --r, --regions"
  echo "        type: string"
  echo "        example: 20:1000000-2000000"
  echo "        Restrict to comma-separated list of regions."
  echo "        Following formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​]."
  echo ""
  echo "    --R, --regions_file"
  echo "        type: file, file must exist"
  echo "        Restrict to regions listed in a file."
  echo "        Regions can be specified either on a VCF, BED, or tab-delimited file"
  echo "        (the default)."
  echo "        For more information check manual."
  echo ""
  echo "    --regions_overlap"
  echo "        type: string"
  echo "        choices: [ pos, record, variant, 0, 1, 2 ]"
  echo "        This option controls how overlapping records are determined:"
  echo "        set to 'pos' or '0' if the VCF record has to have POS inside a region"
  echo "        (this corresponds to the default behavior of -t/-T);"
  echo "        set to 'record' or '1' if also overlapping records with POS outside a"
  echo "        region should be included (this is the default behavior of -r/-R,"
  echo "        and includes indels with POS at the end of a region, which are"
  echo "        technically outside the region);"
  echo "        or set to 'variant' or '2' to include only true overlapping variation"
  echo "        (compare the full VCF representation \"TA>T-\" vs the true sequence"
  echo "        variation \"A>-\")."
  echo ""
  echo "    --s, --samples"
  echo "        type: string"
  echo "        List of samples for sample stats, \"-\" to include all samples."
  echo ""
  echo "    --S, --samples_file"
  echo "        type: file, file must exist"
  echo "        File of samples to include."
  echo "        e.g."
  echo "          sample1    1"
  echo "          sample2    2"
  echo "          sample3    2"
  echo ""
  echo "    --t, --targets"
  echo "        type: string"
  echo "        example: 20:1000000-2000000"
  echo "        Similar as -r, --regions, but the next position is accessed by streaming"
  echo "        the whole VCF/BCF"
  echo "        rather than using the tbi/csi index. Both -r and -t options can be"
  echo "        applied simultaneously: -r uses the"
  echo "        index to jump to a region and -t discards positions which are not in the"
  echo "        targets. Unlike -r, targets"
  echo "        can be prefixed with \"^\" to request logical complement. For example,"
  echo "        \"^X,Y,MT\" indicates that"
  echo "        sequences X, Y and MT should be skipped. Yet another difference between"
  echo "        the -t/-T and -r/-R is"
  echo "        that -r/-R checks for proper overlaps and considers both POS and the end"
  echo "        position of an indel,"
  echo "        while -t/-T considers the POS coordinate only (by default; see also"
  echo "        --regions-overlap and --targets-overlap)."
  echo "        Note that -t cannot be used in combination with -T."
  echo "        Following formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​]."
  echo ""
  echo "    --T, --targets_file"
  echo "        type: file, file must exist"
  echo "        Similar to --regions_file option but streams rather than index-jumps."
  echo ""
  echo "    --targets_overlaps"
  echo "        type: string"
  echo "        choices: [ pos, record, variant, 0, 1, 2 ]"
  echo "        Include if POS in the region (0), record overlaps (1), variant overlaps"
  echo "        (2)."
  echo ""
  echo "    --u, --user_tstv"
  echo "        type: string"
  echo "        Collect Ts/Tv stats for any tag using the given binning [0:1:100]."
  echo "        Format is <TAG[:min:max:n]>."
  echo "        A subfield can be selected as e.g. 'PV4[0]', here the first value of the"
  echo "        PV4 tag."
  echo ""
  echo "    --v, --verbose"
  echo "        type: boolean_true"
  echo "        Produce verbose per-site and per-sample output."
}

# 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 debian:stable-slim
ENTRYPOINT []
RUN apt-get update && \
  DEBIAN_FRONTEND=noninteractive apt-get install -y bcftools procps && \
  rm -rf /var/lib/apt/lists/*

RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools //p')\"" > /var/software_versions.txt

LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_stats"
LABEL org.opencontainers.image.created="2024-11-14T12:50:47Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
LABEL org.opencontainers.image.revision="402ad6a813c0d0b141bbf8f9a3aab9c270a74812"
LABEL org.opencontainers.image.version="add_sgdemux"

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)

# 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 "$1")"
            shift 1
            ;;
        --version)
            echo "bcftools_stats add_sgdemux"
            exit
            ;;
        --input)
            if [ -z "$VIASH_PAR_INPUT" ]; then
              VIASH_PAR_INPUT="$2"
            else
              VIASH_PAR_INPUT="$VIASH_PAR_INPUT;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --input. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --input=*)
            if [ -z "$VIASH_PAR_INPUT" ]; then
              VIASH_PAR_INPUT=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_INPUT="$VIASH_PAR_INPUT;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        -i)
            if [ -z "$VIASH_PAR_INPUT" ]; then
              VIASH_PAR_INPUT="$2"
            else
              VIASH_PAR_INPUT="$VIASH_PAR_INPUT;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -i. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --output)
            [ -n "$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"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -o. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --allele_frequency_bins)
            [ -n "$VIASH_PAR_ALLELE_FREQUENCY_BINS" ] && ViashError Bad arguments for option \'--allele_frequency_bins\': \'$VIASH_PAR_ALLELE_FREQUENCY_BINS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALLELE_FREQUENCY_BINS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --allele_frequency_bins. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --allele_frequency_bins=*)
            [ -n "$VIASH_PAR_ALLELE_FREQUENCY_BINS" ] && ViashError Bad arguments for option \'--allele_frequency_bins=*\': \'$VIASH_PAR_ALLELE_FREQUENCY_BINS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALLELE_FREQUENCY_BINS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --af_bins)
            [ -n "$VIASH_PAR_ALLELE_FREQUENCY_BINS" ] && ViashError Bad arguments for option \'--af_bins\': \'$VIASH_PAR_ALLELE_FREQUENCY_BINS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALLELE_FREQUENCY_BINS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --af_bins. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --allele_frequency_bins_file)
            [ -n "$VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE" ] && ViashError Bad arguments for option \'--allele_frequency_bins_file\': \'$VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --allele_frequency_bins_file. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --allele_frequency_bins_file=*)
            [ -n "$VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE" ] && ViashError Bad arguments for option \'--allele_frequency_bins_file=*\': \'$VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --af_bins_file)
            [ -n "$VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE" ] && ViashError Bad arguments for option \'--af_bins_file\': \'$VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --af_bins_file. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --allele_frequency_tag)
            [ -n "$VIASH_PAR_ALLELE_FREQUENCY_TAG" ] && ViashError Bad arguments for option \'--allele_frequency_tag\': \'$VIASH_PAR_ALLELE_FREQUENCY_TAG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALLELE_FREQUENCY_TAG="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --allele_frequency_tag. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --allele_frequency_tag=*)
            [ -n "$VIASH_PAR_ALLELE_FREQUENCY_TAG" ] && ViashError Bad arguments for option \'--allele_frequency_tag=*\': \'$VIASH_PAR_ALLELE_FREQUENCY_TAG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALLELE_FREQUENCY_TAG=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --af_tag)
            [ -n "$VIASH_PAR_ALLELE_FREQUENCY_TAG" ] && ViashError Bad arguments for option \'--af_tag\': \'$VIASH_PAR_ALLELE_FREQUENCY_TAG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALLELE_FREQUENCY_TAG="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --af_tag. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --first_allele_only)
            [ -n "$VIASH_PAR_FIRST_ALLELE_ONLY" ] && ViashError Bad arguments for option \'--first_allele_only\': \'$VIASH_PAR_FIRST_ALLELE_ONLY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FIRST_ALLELE_ONLY=true
            shift 1
            ;;
        --first_only)
            [ -n "$VIASH_PAR_FIRST_ALLELE_ONLY" ] && ViashError Bad arguments for option \'--first_only\': \'$VIASH_PAR_FIRST_ALLELE_ONLY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FIRST_ALLELE_ONLY=true
            shift 1
            ;;
        --collapse)
            [ -n "$VIASH_PAR_COLLAPSE" ] && ViashError Bad arguments for option \'--collapse\': \'$VIASH_PAR_COLLAPSE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_COLLAPSE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --collapse. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --collapse=*)
            [ -n "$VIASH_PAR_COLLAPSE" ] && ViashError Bad arguments for option \'--collapse=*\': \'$VIASH_PAR_COLLAPSE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_COLLAPSE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --c)
            [ -n "$VIASH_PAR_COLLAPSE" ] && ViashError Bad arguments for option \'--c\': \'$VIASH_PAR_COLLAPSE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_COLLAPSE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --c. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --depth)
            [ -n "$VIASH_PAR_DEPTH" ] && ViashError Bad arguments for option \'--depth\': \'$VIASH_PAR_DEPTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_DEPTH="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --depth. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --depth=*)
            [ -n "$VIASH_PAR_DEPTH" ] && ViashError Bad arguments for option \'--depth=*\': \'$VIASH_PAR_DEPTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_DEPTH=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --d)
            [ -n "$VIASH_PAR_DEPTH" ] && ViashError Bad arguments for option \'--d\': \'$VIASH_PAR_DEPTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_DEPTH="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --d. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --exclude)
            [ -n "$VIASH_PAR_EXCLUDE" ] && ViashError Bad arguments for option \'--exclude\': \'$VIASH_PAR_EXCLUDE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_EXCLUDE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --exclude. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --exclude=*)
            [ -n "$VIASH_PAR_EXCLUDE" ] && ViashError Bad arguments for option \'--exclude=*\': \'$VIASH_PAR_EXCLUDE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_EXCLUDE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --e)
            [ -n "$VIASH_PAR_EXCLUDE" ] && ViashError Bad arguments for option \'--e\': \'$VIASH_PAR_EXCLUDE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_EXCLUDE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --e. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --exons)
            [ -n "$VIASH_PAR_EXONS" ] && ViashError Bad arguments for option \'--exons\': \'$VIASH_PAR_EXONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_EXONS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --exons. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --exons=*)
            [ -n "$VIASH_PAR_EXONS" ] && ViashError Bad arguments for option \'--exons=*\': \'$VIASH_PAR_EXONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_EXONS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --E)
            [ -n "$VIASH_PAR_EXONS" ] && ViashError Bad arguments for option \'--E\': \'$VIASH_PAR_EXONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_EXONS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --E. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --apply_filters)
            [ -n "$VIASH_PAR_APPLY_FILTERS" ] && ViashError Bad arguments for option \'--apply_filters\': \'$VIASH_PAR_APPLY_FILTERS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_APPLY_FILTERS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --apply_filters. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --apply_filters=*)
            [ -n "$VIASH_PAR_APPLY_FILTERS" ] && ViashError Bad arguments for option \'--apply_filters=*\': \'$VIASH_PAR_APPLY_FILTERS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_APPLY_FILTERS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --f)
            [ -n "$VIASH_PAR_APPLY_FILTERS" ] && ViashError Bad arguments for option \'--f\': \'$VIASH_PAR_APPLY_FILTERS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_APPLY_FILTERS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --f. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --fasta_reference)
            [ -n "$VIASH_PAR_FASTA_REFERENCE" ] && ViashError Bad arguments for option \'--fasta_reference\': \'$VIASH_PAR_FASTA_REFERENCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FASTA_REFERENCE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --fasta_reference. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --fasta_reference=*)
            [ -n "$VIASH_PAR_FASTA_REFERENCE" ] && ViashError Bad arguments for option \'--fasta_reference=*\': \'$VIASH_PAR_FASTA_REFERENCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FASTA_REFERENCE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --F)
            [ -n "$VIASH_PAR_FASTA_REFERENCE" ] && ViashError Bad arguments for option \'--F\': \'$VIASH_PAR_FASTA_REFERENCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FASTA_REFERENCE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --F. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --include)
            [ -n "$VIASH_PAR_INCLUDE" ] && ViashError Bad arguments for option \'--include\': \'$VIASH_PAR_INCLUDE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INCLUDE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --include. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --include=*)
            [ -n "$VIASH_PAR_INCLUDE" ] && ViashError Bad arguments for option \'--include=*\': \'$VIASH_PAR_INCLUDE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INCLUDE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --i)
            [ -n "$VIASH_PAR_INCLUDE" ] && ViashError Bad arguments for option \'--i\': \'$VIASH_PAR_INCLUDE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INCLUDE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --i. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --split_by_ID)
            [ -n "$VIASH_PAR_SPLIT_BY_ID" ] && ViashError Bad arguments for option \'--split_by_ID\': \'$VIASH_PAR_SPLIT_BY_ID\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SPLIT_BY_ID=true
            shift 1
            ;;
        --I)
            [ -n "$VIASH_PAR_SPLIT_BY_ID" ] && ViashError Bad arguments for option \'--I\': \'$VIASH_PAR_SPLIT_BY_ID\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SPLIT_BY_ID=true
            shift 1
            ;;
        --regions)
            [ -n "$VIASH_PAR_REGIONS" ] && ViashError Bad arguments for option \'--regions\': \'$VIASH_PAR_REGIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_REGIONS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --regions. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --regions=*)
            [ -n "$VIASH_PAR_REGIONS" ] && ViashError Bad arguments for option \'--regions=*\': \'$VIASH_PAR_REGIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_REGIONS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --r)
            [ -n "$VIASH_PAR_REGIONS" ] && ViashError Bad arguments for option \'--r\': \'$VIASH_PAR_REGIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_REGIONS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --r. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --regions_file)
            [ -n "$VIASH_PAR_REGIONS_FILE" ] && ViashError Bad arguments for option \'--regions_file\': \'$VIASH_PAR_REGIONS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_REGIONS_FILE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --regions_file. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --regions_file=*)
            [ -n "$VIASH_PAR_REGIONS_FILE" ] && ViashError Bad arguments for option \'--regions_file=*\': \'$VIASH_PAR_REGIONS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_REGIONS_FILE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --R)
            [ -n "$VIASH_PAR_REGIONS_FILE" ] && ViashError Bad arguments for option \'--R\': \'$VIASH_PAR_REGIONS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_REGIONS_FILE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --R. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --regions_overlap)
            [ -n "$VIASH_PAR_REGIONS_OVERLAP" ] && ViashError Bad arguments for option \'--regions_overlap\': \'$VIASH_PAR_REGIONS_OVERLAP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_REGIONS_OVERLAP="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --regions_overlap. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --regions_overlap=*)
            [ -n "$VIASH_PAR_REGIONS_OVERLAP" ] && ViashError Bad arguments for option \'--regions_overlap=*\': \'$VIASH_PAR_REGIONS_OVERLAP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_REGIONS_OVERLAP=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --samples)
            [ -n "$VIASH_PAR_SAMPLES" ] && ViashError Bad arguments for option \'--samples\': \'$VIASH_PAR_SAMPLES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SAMPLES="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --samples. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --samples=*)
            [ -n "$VIASH_PAR_SAMPLES" ] && ViashError Bad arguments for option \'--samples=*\': \'$VIASH_PAR_SAMPLES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SAMPLES=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --s)
            [ -n "$VIASH_PAR_SAMPLES" ] && ViashError Bad arguments for option \'--s\': \'$VIASH_PAR_SAMPLES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SAMPLES="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --s. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --samples_file)
            [ -n "$VIASH_PAR_SAMPLES_FILE" ] && ViashError Bad arguments for option \'--samples_file\': \'$VIASH_PAR_SAMPLES_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SAMPLES_FILE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --samples_file. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --samples_file=*)
            [ -n "$VIASH_PAR_SAMPLES_FILE" ] && ViashError Bad arguments for option \'--samples_file=*\': \'$VIASH_PAR_SAMPLES_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SAMPLES_FILE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --S)
            [ -n "$VIASH_PAR_SAMPLES_FILE" ] && ViashError Bad arguments for option \'--S\': \'$VIASH_PAR_SAMPLES_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SAMPLES_FILE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --S. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --targets)
            [ -n "$VIASH_PAR_TARGETS" ] && ViashError Bad arguments for option \'--targets\': \'$VIASH_PAR_TARGETS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_TARGETS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --targets. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --targets=*)
            [ -n "$VIASH_PAR_TARGETS" ] && ViashError Bad arguments for option \'--targets=*\': \'$VIASH_PAR_TARGETS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_TARGETS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --t)
            [ -n "$VIASH_PAR_TARGETS" ] && ViashError Bad arguments for option \'--t\': \'$VIASH_PAR_TARGETS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_TARGETS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --t. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --targets_file)
            [ -n "$VIASH_PAR_TARGETS_FILE" ] && ViashError Bad arguments for option \'--targets_file\': \'$VIASH_PAR_TARGETS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_TARGETS_FILE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --targets_file. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --targets_file=*)
            [ -n "$VIASH_PAR_TARGETS_FILE" ] && ViashError Bad arguments for option \'--targets_file=*\': \'$VIASH_PAR_TARGETS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_TARGETS_FILE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --T)
            [ -n "$VIASH_PAR_TARGETS_FILE" ] && ViashError Bad arguments for option \'--T\': \'$VIASH_PAR_TARGETS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_TARGETS_FILE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --T. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --targets_overlaps)
            [ -n "$VIASH_PAR_TARGETS_OVERLAPS" ] && ViashError Bad arguments for option \'--targets_overlaps\': \'$VIASH_PAR_TARGETS_OVERLAPS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_TARGETS_OVERLAPS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --targets_overlaps. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --targets_overlaps=*)
            [ -n "$VIASH_PAR_TARGETS_OVERLAPS" ] && ViashError Bad arguments for option \'--targets_overlaps=*\': \'$VIASH_PAR_TARGETS_OVERLAPS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_TARGETS_OVERLAPS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --user_tstv)
            [ -n "$VIASH_PAR_USER_TSTV" ] && ViashError Bad arguments for option \'--user_tstv\': \'$VIASH_PAR_USER_TSTV\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_USER_TSTV="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --user_tstv. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --user_tstv=*)
            [ -n "$VIASH_PAR_USER_TSTV" ] && ViashError Bad arguments for option \'--user_tstv=*\': \'$VIASH_PAR_USER_TSTV\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_USER_TSTV=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --u)
            [ -n "$VIASH_PAR_USER_TSTV" ] && ViashError Bad arguments for option \'--u\': \'$VIASH_PAR_USER_TSTV\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_USER_TSTV="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --u. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --verbose)
            [ -n "$VIASH_PAR_VERBOSE" ] && ViashError Bad arguments for option \'--verbose\': \'$VIASH_PAR_VERBOSE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_VERBOSE=true
            shift 1
            ;;
        --v)
            [ -n "$VIASH_PAR_VERBOSE" ] && ViashError Bad arguments for option \'--v\': \'$VIASH_PAR_VERBOSE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_VERBOSE=true
            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/biobox/bcftools/bcftools_stats:add_sgdemux'
  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" '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_OUTPUT+x} ]; then
  ViashError '--output' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_NAME+x} ]; then
  ViashError 'name' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then
  ViashError 'functionality_name' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_RESOURCES_DIR+x} ]; then
  ViashError 'resources_dir' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_EXECUTABLE+x} ]; then
  ViashError 'executable' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_CONFIG+x} ]; then
  ViashError 'config' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_TEMP_DIR+x} ]; then
  ViashError 'temp_dir' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi

# filling in defaults
if [ -z ${VIASH_PAR_FIRST_ALLELE_ONLY+x} ]; then
  VIASH_PAR_FIRST_ALLELE_ONLY="false"
fi
if [ -z ${VIASH_PAR_SPLIT_BY_ID+x} ]; then
  VIASH_PAR_SPLIT_BY_ID="false"
fi
if [ -z ${VIASH_PAR_VERBOSE+x} ]; then
  VIASH_PAR_VERBOSE="false"
fi

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

# check whether parameters values are of the right type
if [[ -n "$VIASH_PAR_FIRST_ALLELE_ONLY" ]]; then
  if ! [[ "$VIASH_PAR_FIRST_ALLELE_ONLY" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--first_allele_only' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SPLIT_BY_ID" ]]; then
  if ! [[ "$VIASH_PAR_SPLIT_BY_ID" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--split_by_ID' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_VERBOSE" ]]; then
  if ! [[ "$VIASH_PAR_VERBOSE" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--verbose' 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 "$VIASH_PAR_COLLAPSE" ]; then
  VIASH_PAR_COLLAPSE_CHOICES=("snps;indels;both;all;some;none")
  IFS=';'
  set -f
  if ! [[ ";${VIASH_PAR_COLLAPSE_CHOICES[*]};" =~ ";$VIASH_PAR_COLLAPSE;" ]]; then
    ViashError '--collapse' specified value of \'$VIASH_PAR_COLLAPSE\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
    exit 1
  fi
  set +f
  unset IFS
fi

if [ ! -z "$VIASH_PAR_REGIONS_OVERLAP" ]; then
  VIASH_PAR_REGIONS_OVERLAP_CHOICES=("pos;record;variant;0;1;2")
  IFS=';'
  set -f
  if ! [[ ";${VIASH_PAR_REGIONS_OVERLAP_CHOICES[*]};" =~ ";$VIASH_PAR_REGIONS_OVERLAP;" ]]; then
    ViashError '--regions_overlap' specified value of \'$VIASH_PAR_REGIONS_OVERLAP\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
    exit 1
  fi
  set +f
  unset IFS
fi

if [ ! -z "$VIASH_PAR_TARGETS_OVERLAPS" ]; then
  VIASH_PAR_TARGETS_OVERLAPS_CHOICES=("pos;record;variant;0;1;2")
  IFS=';'
  set -f
  if ! [[ ";${VIASH_PAR_TARGETS_OVERLAPS_CHOICES[*]};" =~ ";$VIASH_PAR_TARGETS_OVERLAPS;" ]]; then
    ViashError '--targets_overlaps' specified value of \'$VIASH_PAR_TARGETS_OVERLAPS\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
    exit 1
  fi
  set +f
  unset IFS
fi

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

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

if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  # detect volumes from file arguments
  VIASH_CHOWN_VARS=()
if [ ! -z "$VIASH_PAR_INPUT" ]; then
  VIASH_TEST_INPUT=()
  IFS=';'
  for var in $VIASH_PAR_INPUT; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_INPUT+=( "$var" )
  done
  VIASH_PAR_INPUT=$(IFS=';' ; echo "${VIASH_TEST_INPUT[*]}")
fi
if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT")" )
  VIASH_PAR_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT" )
fi
if [ ! -z "$VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE")" )
  VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE=$(ViashDockerAutodetectMount "$VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE")
fi
if [ ! -z "$VIASH_PAR_EXONS" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_EXONS")" )
  VIASH_PAR_EXONS=$(ViashDockerAutodetectMount "$VIASH_PAR_EXONS")
fi
if [ ! -z "$VIASH_PAR_FASTA_REFERENCE" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_FASTA_REFERENCE")" )
  VIASH_PAR_FASTA_REFERENCE=$(ViashDockerAutodetectMount "$VIASH_PAR_FASTA_REFERENCE")
fi
if [ ! -z "$VIASH_PAR_REGIONS_FILE" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_REGIONS_FILE")" )
  VIASH_PAR_REGIONS_FILE=$(ViashDockerAutodetectMount "$VIASH_PAR_REGIONS_FILE")
fi
if [ ! -z "$VIASH_PAR_SAMPLES_FILE" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_SAMPLES_FILE")" )
  VIASH_PAR_SAMPLES_FILE=$(ViashDockerAutodetectMount "$VIASH_PAR_SAMPLES_FILE")
fi
if [ ! -z "$VIASH_PAR_TARGETS_FILE" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_TARGETS_FILE")" )
  VIASH_PAR_TARGETS_FILE=$(ViashDockerAutodetectMount "$VIASH_PAR_TARGETS_FILE")
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-bcftools_stats-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 ${VIASH_PAR_OUTPUT+x} ]; then echo "${VIASH_PAR_OUTPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_output='&'#" ; else echo "# par_output="; fi )
$( if [ ! -z ${VIASH_PAR_ALLELE_FREQUENCY_BINS+x} ]; then echo "${VIASH_PAR_ALLELE_FREQUENCY_BINS}" | sed "s#'#'\"'\"'#g;s#.*#par_allele_frequency_bins='&'#" ; else echo "# par_allele_frequency_bins="; fi )
$( if [ ! -z ${VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE+x} ]; then echo "${VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE}" | sed "s#'#'\"'\"'#g;s#.*#par_allele_frequency_bins_file='&'#" ; else echo "# par_allele_frequency_bins_file="; fi )
$( if [ ! -z ${VIASH_PAR_ALLELE_FREQUENCY_TAG+x} ]; then echo "${VIASH_PAR_ALLELE_FREQUENCY_TAG}" | sed "s#'#'\"'\"'#g;s#.*#par_allele_frequency_tag='&'#" ; else echo "# par_allele_frequency_tag="; fi )
$( if [ ! -z ${VIASH_PAR_FIRST_ALLELE_ONLY+x} ]; then echo "${VIASH_PAR_FIRST_ALLELE_ONLY}" | sed "s#'#'\"'\"'#g;s#.*#par_first_allele_only='&'#" ; else echo "# par_first_allele_only="; fi )
$( if [ ! -z ${VIASH_PAR_COLLAPSE+x} ]; then echo "${VIASH_PAR_COLLAPSE}" | sed "s#'#'\"'\"'#g;s#.*#par_collapse='&'#" ; else echo "# par_collapse="; fi )
$( if [ ! -z ${VIASH_PAR_DEPTH+x} ]; then echo "${VIASH_PAR_DEPTH}" | sed "s#'#'\"'\"'#g;s#.*#par_depth='&'#" ; else echo "# par_depth="; fi )
$( if [ ! -z ${VIASH_PAR_EXCLUDE+x} ]; then echo "${VIASH_PAR_EXCLUDE}" | sed "s#'#'\"'\"'#g;s#.*#par_exclude='&'#" ; else echo "# par_exclude="; fi )
$( if [ ! -z ${VIASH_PAR_EXONS+x} ]; then echo "${VIASH_PAR_EXONS}" | sed "s#'#'\"'\"'#g;s#.*#par_exons='&'#" ; else echo "# par_exons="; fi )
$( if [ ! -z ${VIASH_PAR_APPLY_FILTERS+x} ]; then echo "${VIASH_PAR_APPLY_FILTERS}" | sed "s#'#'\"'\"'#g;s#.*#par_apply_filters='&'#" ; else echo "# par_apply_filters="; fi )
$( if [ ! -z ${VIASH_PAR_FASTA_REFERENCE+x} ]; then echo "${VIASH_PAR_FASTA_REFERENCE}" | sed "s#'#'\"'\"'#g;s#.*#par_fasta_reference='&'#" ; else echo "# par_fasta_reference="; fi )
$( if [ ! -z ${VIASH_PAR_INCLUDE+x} ]; then echo "${VIASH_PAR_INCLUDE}" | sed "s#'#'\"'\"'#g;s#.*#par_include='&'#" ; else echo "# par_include="; fi )
$( if [ ! -z ${VIASH_PAR_SPLIT_BY_ID+x} ]; then echo "${VIASH_PAR_SPLIT_BY_ID}" | sed "s#'#'\"'\"'#g;s#.*#par_split_by_ID='&'#" ; else echo "# par_split_by_ID="; fi )
$( if [ ! -z ${VIASH_PAR_REGIONS+x} ]; then echo "${VIASH_PAR_REGIONS}" | sed "s#'#'\"'\"'#g;s#.*#par_regions='&'#" ; else echo "# par_regions="; fi )
$( if [ ! -z ${VIASH_PAR_REGIONS_FILE+x} ]; then echo "${VIASH_PAR_REGIONS_FILE}" | sed "s#'#'\"'\"'#g;s#.*#par_regions_file='&'#" ; else echo "# par_regions_file="; fi )
$( if [ ! -z ${VIASH_PAR_REGIONS_OVERLAP+x} ]; then echo "${VIASH_PAR_REGIONS_OVERLAP}" | sed "s#'#'\"'\"'#g;s#.*#par_regions_overlap='&'#" ; else echo "# par_regions_overlap="; fi )
$( if [ ! -z ${VIASH_PAR_SAMPLES+x} ]; then echo "${VIASH_PAR_SAMPLES}" | sed "s#'#'\"'\"'#g;s#.*#par_samples='&'#" ; else echo "# par_samples="; fi )
$( if [ ! -z ${VIASH_PAR_SAMPLES_FILE+x} ]; then echo "${VIASH_PAR_SAMPLES_FILE}" | sed "s#'#'\"'\"'#g;s#.*#par_samples_file='&'#" ; else echo "# par_samples_file="; fi )
$( if [ ! -z ${VIASH_PAR_TARGETS+x} ]; then echo "${VIASH_PAR_TARGETS}" | sed "s#'#'\"'\"'#g;s#.*#par_targets='&'#" ; else echo "# par_targets="; fi )
$( if [ ! -z ${VIASH_PAR_TARGETS_FILE+x} ]; then echo "${VIASH_PAR_TARGETS_FILE}" | sed "s#'#'\"'\"'#g;s#.*#par_targets_file='&'#" ; else echo "# par_targets_file="; fi )
$( if [ ! -z ${VIASH_PAR_TARGETS_OVERLAPS+x} ]; then echo "${VIASH_PAR_TARGETS_OVERLAPS}" | sed "s#'#'\"'\"'#g;s#.*#par_targets_overlaps='&'#" ; else echo "# par_targets_overlaps="; fi )
$( if [ ! -z ${VIASH_PAR_USER_TSTV+x} ]; then echo "${VIASH_PAR_USER_TSTV}" | sed "s#'#'\"'\"'#g;s#.*#par_user_tstv='&'#" ; else echo "# par_user_tstv="; fi )
$( if [ ! -z ${VIASH_PAR_VERBOSE+x} ]; then echo "${VIASH_PAR_VERBOSE}" | sed "s#'#'\"'\"'#g;s#.*#par_verbose='&'#" ; else echo "# par_verbose="; 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

# Exit on error
set -eo pipefail

# Unset parameters
unset_if_false=(
    par_first_allele_only
    par_split_by_ID
    par_verbose 
)

for par in \${unset_if_false[@]}; do
    test_val="\${!par}"
    [[ "\$test_val" == "false" ]] && unset \$par
done

# Create input array 
IFS=";" read -ra input <<< \$par_input

# Check the size of the input array
if [[ \${#input[@]} -gt 2 ]]; then
    echo "Error: --input only takes a max of two files!"
    exit 1
fi

# Execute bcftools stats with the provided arguments
bcftools stats \\
    \${par_first_allele_only:+--1st-allele-only} \\
    \${par_split_by_ID:+--split-by-ID} \\
    \${par_verbose:+--verbose} \\
    \${par_allele_frequency_bins:+--af-bins "\${par_allele_frequency_bins}"} \\
    \${par_allele_frequency_bins_file:+--af-bins "\${par_allele_frequency_bins_file}"} \\
    \${par_allele_frequency_tag:+--af-tag "\${par_allele_frequency_tag}"} \\
    \${par_collapse:+-c "\${par_collapse}"} \\
    \${par_depth:+-d "\${par_depth}"} \\
    \${par_exclude:+-e "\${par_exclude}"} \\
    \${par_exons:+-E "\${par_exons}"} \\
    \${par_apply_filters:+-f "\${par_apply_filters}"} \\
    \${par_fasta_reference:+-F "\${par_fasta_reference}"} \\
    \${par_include:+-i "\${par_include}"} \\
    \${par_regions:+-r "\${par_regions}"} \\
    \${par_regions_file:+-R "\${par_regions_file}"} \\
    \${par_regions_overlap:+--regions-overlap "\${par_regions_overlap}"} \\
    \${par_samples:+-s "\${par_samples}"} \\
    \${par_samples_file:+-S "\${par_samples_file}"} \\
    \${par_targets:+-t "\${par_targets}"} \\
    \${par_targets_file:+-T "\${par_targets_file}"} \\
    \${par_targets_overlaps:+--targets-overlap "\${par_targets_overlaps}"} \\
    \${par_user_tstv:+-u "\${par_user_tstv}"} \\
    "\${input[@]}" \\
    > \$par_output
VIASHMAIN
bash "\$tempscript" &
wait "\$!"

VIASHEOF


if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  # strip viash automount from file paths
  
  if [ ! -z "$VIASH_PAR_INPUT" ]; then
    unset VIASH_TEST_INPUT
    IFS=';'
    for var in $VIASH_PAR_INPUT; do
      unset IFS
      if [ -z "$VIASH_TEST_INPUT" ]; then
      VIASH_TEST_INPUT="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_INPUT="$VIASH_TEST_INPUT;""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_INPUT="$VIASH_TEST_INPUT"
  fi
  if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
    VIASH_PAR_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT")
  fi
  if [ ! -z "$VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE" ]; then
    VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE=$(ViashDockerStripAutomount "$VIASH_PAR_ALLELE_FREQUENCY_BINS_FILE")
  fi
  if [ ! -z "$VIASH_PAR_EXONS" ]; then
    VIASH_PAR_EXONS=$(ViashDockerStripAutomount "$VIASH_PAR_EXONS")
  fi
  if [ ! -z "$VIASH_PAR_FASTA_REFERENCE" ]; then
    VIASH_PAR_FASTA_REFERENCE=$(ViashDockerStripAutomount "$VIASH_PAR_FASTA_REFERENCE")
  fi
  if [ ! -z "$VIASH_PAR_REGIONS_FILE" ]; then
    VIASH_PAR_REGIONS_FILE=$(ViashDockerStripAutomount "$VIASH_PAR_REGIONS_FILE")
  fi
  if [ ! -z "$VIASH_PAR_SAMPLES_FILE" ]; then
    VIASH_PAR_SAMPLES_FILE=$(ViashDockerStripAutomount "$VIASH_PAR_SAMPLES_FILE")
  fi
  if [ ! -z "$VIASH_PAR_TARGETS_FILE" ]; then
    VIASH_PAR_TARGETS_FILE=$(ViashDockerStripAutomount "$VIASH_PAR_TARGETS_FILE")
  fi
  if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
    VIASH_META_RESOURCES_DIR=$(ViashDockerStripAutomount "$VIASH_META_RESOURCES_DIR")
  fi
  if [ ! -z "$VIASH_META_EXECUTABLE" ]; then
    VIASH_META_EXECUTABLE=$(ViashDockerStripAutomount "$VIASH_META_EXECUTABLE")
  fi
  if [ ! -z "$VIASH_META_CONFIG" ]; then
    VIASH_META_CONFIG=$(ViashDockerStripAutomount "$VIASH_META_CONFIG")
  fi
  if [ ! -z "$VIASH_META_TEMP_DIR" ]; then
    VIASH_META_TEMP_DIR=$(ViashDockerStripAutomount "$VIASH_META_TEMP_DIR")
  fi
fi


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


exit 0
