#!/usr/bin/env bash

# bbmap_bbsplit v0.4.1
# 
# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
# 
# The component may contain files which fall under a different license. The
# authors of this component should specify the license in the header of such
# files, or include a separate license file detailing the licenses of all included
# files.

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="bbmap_bbsplit"
VIASH_META_FUNCTIONALITY_NAME="bbmap_bbsplit"
VIASH_META_EXECUTABLE="$VIASH_META_RESOURCES_DIR/$VIASH_META_NAME"
VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
VIASH_META_TEMP_DIR="$VIASH_TEMP"



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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

  if [[ "$engine_id" == "docker" ]]; then
    cat << 'VIASHDOCKER'
FROM ubuntu:22.04
ENTRYPOINT []
RUN apt-get update && \
apt-get install -y build-essential openjdk-17-jdk wget tar && \
wget --no-check-certificate https://sourceforge.net/projects/bbmap/files/BBMap_39.01.tar.gz && \
tar xzf BBMap_39.01.tar.gz && \
cp -r bbmap/* /usr/local/bin

RUN bbsplit.sh --version 2>&1 | awk '/BBMap version/{print "BBMAP:", $NF}' > /var/software_versions.txt

LABEL org.opencontainers.image.description="Companion container for running component bbmap bbmap_bbsplit"
LABEL org.opencontainers.image.created="2025-10-03T12:12:04Z"
LABEL org.opencontainers.image.source="https://github.com/BioInfoTools/BBMap/blob/master/sh/bbsplit.sh"
LABEL org.opencontainers.image.revision="69186bfc6beed075e81e10f17d24c4c999e87484"
LABEL org.opencontainers.image.version="v0.4.1"

VIASHDOCKER
  fi
}

# ViashDockerBuildArgs: return the arguments to pass to docker build
# $1    : engine identifier
# return : arguments to pass to docker build
function ViashDockerBuildArgs {
  local engine_id="$1"

  if [[ "$engine_id" == "docker" ]]; then
    echo ""
  fi
}

# ViashAbsolutePath: generate absolute path from relative path
# borrowed from https://stackoverflow.com/a/21951256
# $1     : relative filename
# return : absolute path
# examples:
#   ViashAbsolutePath some_file.txt   # returns /path/to/some_file.txt
#   ViashAbsolutePath /foo/bar/..     # returns /foo
function ViashAbsolutePath {
  local thePath
  local parr
  local outp
  local len
  if [[ ! "$1" =~ ^/ ]]; then
    thePath="$PWD/$1"
  else
    thePath="$1"
  fi
  echo "$thePath" | (
    IFS=/
    read -a parr
    declare -a outp
    for i in "${parr[@]}"; do
      case "$i" in
      ''|.) continue ;;
      ..)
        len=${#outp[@]}
        if ((len==0)); then
          continue
        else
          unset outp[$((len-1))]
        fi
        ;;
      *)
        len=${#outp[@]}
        outp[$len]="$i"
      ;;
      esac
    done
    echo /"${outp[*]}"
  )
}
# ViashDockerAutodetectMount: auto configuring docker mounts from parameters
# $1                             : The parameter value
# returns                        : New parameter
# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
# examples:
#   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
#   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
function ViashDockerAutodetectMount {
  local abs_path=$(ViashAbsolutePath "$1")
  local mount_source
  local base_name
  if [ -d "$abs_path" ]; then
    mount_source="$abs_path"
    base_name=""
  else
    mount_source=`dirname "$abs_path"`
    base_name=`basename "$abs_path"`
  fi
  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
  if [ -z "$base_name" ]; then
    echo "$mount_target"
  else
    echo "$mount_target/$base_name"
  fi
}
function ViashDockerAutodetectMountArg {
  local abs_path=$(ViashAbsolutePath "$1")
  local mount_source
  local base_name
  if [ -d "$abs_path" ]; then
    mount_source="$abs_path"
    base_name=""
  else
    mount_source=`dirname "$abs_path"`
    base_name=`basename "$abs_path"`
  fi
  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
  echo "--volume=\"$mount_source:$mount_target\""
}
function ViashDockerStripAutomount {
  local abs_path=$(ViashAbsolutePath "$1")
  echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
}
# initialise variables
VIASH_DIRECTORY_MOUNTS=()

# configure default docker automount prefix if it is unset
if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
  VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
fi

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


# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
  echo "bbmap_bbsplit v0.4.1"
  echo ""
  echo "Split sequencing reads by mapping them to multiple references simultaneously."
  echo ""
  echo "Input:"
  echo "    --id"
  echo "        type: string"
  echo "        Sample ID"
  echo ""
  echo "    --paired"
  echo "        type: boolean_true"
  echo "        Paired fastq files or not?"
  echo ""
  echo "    --input"
  echo "        type: file, multiple values allowed, file must exist"
  echo "        example: reads.fastq"
  echo "        Input fastq files, either one or two (paired), separated by \";\"."
  echo ""
  echo "    --ref"
  echo "        type: file, multiple values allowed, file must exist"
  echo "        Reference FASTA files, separated by \";\". The primary reference should be"
  echo "        specified first."
  echo ""
  echo "    --only_build_index"
  echo "        type: boolean_true"
  echo "        If set, only builds the index. Otherwise, mapping is performed."
  echo ""
  echo "    --build"
  echo "        type: file, file must exist"
  echo "        Index to be used for mapping."
  echo ""
  echo "    --qin"
  echo "        type: string"
  echo "        Set to 33 or 64 to specify input quality value ASCII offset."
  echo "        Automatically detected if"
  echo "        not specified."
  echo ""
  echo "    --interleaved"
  echo "        type: boolean_true"
  echo "        True forces paired/interleaved input; false forces single-ended mapping."
  echo "        If not specified, interleaved status will be autodetected from read"
  echo "        names."
  echo ""
  echo "    --maxindel"
  echo "        type: integer"
  echo "        example: 20"
  echo "        Don't look for indels longer than this. Lower is faster. Set to >=100k"
  echo "        for RNA-seq."
  echo ""
  echo "    --minratio"
  echo "        type: double"
  echo "        example: 0.56"
  echo "        Fraction of max alignment score required to keep a site. Higher is"
  echo "        faster."
  echo ""
  echo "    --minhits"
  echo "        type: integer"
  echo "        example: 1"
  echo "        Minimum number of seed hits required for candidate sites. Higher is"
  echo "        faster."
  echo ""
  echo "    --ambiguous"
  echo "        type: string"
  echo "        example: best"
  echo "        choices: [ best, toss, random, all ]"
  echo "        Set behavior on ambiguously-mapped reads (with multiple top-scoring"
  echo "        mapping locations)."
  echo "          * best    Use the first best site (Default)"
  echo "          * toss    Consider unmapped"
  echo "          * random  Select one top-scoring site randomly"
  echo "          * all     Retain all top-scoring sites.  Does not work yet with SAM"
  echo "        output"
  echo ""
  echo "    --ambiguous2"
  echo "        type: string"
  echo "        example: best"
  echo "        choices: [ best, toss, all, split ]"
  echo "        Set behavior only for reads that map ambiguously to multiple different"
  echo "        references."
  echo "        Normal 'ambiguous=' controls behavior on all ambiguous reads;"
  echo "        Ambiguous2 excludes reads that map ambiguously within a single"
  echo "        reference."
  echo "          * best    Use the first best site (Default)"
  echo "          * toss    Consider unmapped"
  echo "          * all     Write a copy to the output for each reference to which it"
  echo "        maps"
  echo "          * split   Write a copy to the AMBIGUOUS_ output for each reference to"
  echo "        which it maps"
  echo ""
  echo "    --qtrim"
  echo "        type: string"
  echo "        choices: [ l, r, lr ]"
  echo "        Quality-trim ends to Q5 before mapping. Options are 'l' (left), 'r'"
  echo "        (right), and 'lr' (both)."
  echo ""
  echo "    --untrim"
  echo "        type: boolean_true"
  echo "        Undo trimming after mapping. Untrimmed bases will be soft-clipped in"
  echo "        cigar strings."
  echo ""
  echo "Output:"
  echo "    --index"
  echo "        type: file, output, file must exist"
  echo "        example: BBSplit_index"
  echo "        Location to write the index."
  echo ""
  echo "    --fastq_1"
  echo "        type: file, output, file must exist"
  echo "        example: read_out1.fastq"
  echo "        Output file for read 1."
  echo ""
  echo "    --fastq_2"
  echo "        type: file, output, file must exist"
  echo "        example: read_out2.fastq"
  echo "        Output file for read 2."
  echo ""
  echo "    --bs, --sam2bam"
  echo "        type: file, output, file must exist"
  echo "        example: script.sh"
  echo "        Write a shell script to 'file' that will turn the sam output into a"
  echo "        sorted, indexed bam file."
  echo ""
  echo "    --scafstats"
  echo "        type: file, output, file must exist"
  echo "        example: scaffold_stats.txt"
  echo "        Write statistics on how many reads mapped to which scaffold to this"
  echo "        file."
  echo ""
  echo "    --refstats"
  echo "        type: file, output, file must exist"
  echo "        example: reference_stats.txt"
  echo "        Write statistics on how many reads were assigned to which reference to"
  echo "        this file."
  echo "        Unmapped reads whose mate mapped to a reference are considered assigned"
  echo "        and will be counted."
  echo ""
  echo "    --nzo"
  echo "        type: boolean_true"
  echo "        Only print lines with nonzero coverage."
  echo ""
  echo "    --bbmap_args"
  echo "        type: string"
  echo "        Additional arguments from BBMap to pass to BBSplit."
  echo ""
  echo "Viash built in Computational Requirements:"
  echo "    ---cpus=INT"
  echo "        Number of CPUs to use"
  echo "    ---memory=STRING"
  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
  echo ""
  echo "Viash built in Docker:"
  echo "    ---setup=STRATEGY"
  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
  echo "        Default: ifneedbepullelsecachedbuild"
  echo "    ---dockerfile"
  echo "        Print the dockerfile to stdout."
  echo "    ---docker_run_args=ARG"
  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
  echo "    ---docker_image_id"
  echo "        Print the docker image id to stdout."
  echo "    ---debug"
  echo "        Enter the docker container for debugging purposes."
  echo ""
  echo "Viash built in Engines:"
  echo "    ---engine=ENGINE_ID"
  echo "        Specify the engine to use. Options are: docker, native."
  echo "        Default: docker"
}

# initialise array
VIASH_POSITIONAL_ARGS=''

while [[ $# -gt 0 ]]; do
    case "$1" in
        -h|--help)
            ViashHelp
            exit
            ;;
        ---v|---verbose)
            let "VIASH_VERBOSITY=VIASH_VERBOSITY+1"
            shift 1
            ;;
        ---verbosity)
            VIASH_VERBOSITY="$2"
            shift 2
            ;;
        ---verbosity=*)
            VIASH_VERBOSITY="$(ViashRemoveFlags "$1")"
            shift 1
            ;;
        --version)
            echo "bbmap_bbsplit v0.4.1"
            exit
            ;;
        --id)
            [ -n "$VIASH_PAR_ID" ] && ViashError Bad arguments for option \'--id\': \'$VIASH_PAR_ID\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ID="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --id. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --id=*)
            [ -n "$VIASH_PAR_ID" ] && ViashError Bad arguments for option \'--id=*\': \'$VIASH_PAR_ID\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ID=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --paired)
            [ -n "$VIASH_PAR_PAIRED" ] && ViashError Bad arguments for option \'--paired\': \'$VIASH_PAR_PAIRED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PAIRED=true
            shift 1
            ;;
        --input)
            if [ -z "$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 "$1")
            fi
            shift 1
            ;;
        --ref)
            if [ -z "$VIASH_PAR_REF" ]; then
              VIASH_PAR_REF="$2"
            else
              VIASH_PAR_REF="$VIASH_PAR_REF;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --ref. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --ref=*)
            if [ -z "$VIASH_PAR_REF" ]; then
              VIASH_PAR_REF=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_REF="$VIASH_PAR_REF;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --only_build_index)
            [ -n "$VIASH_PAR_ONLY_BUILD_INDEX" ] && ViashError Bad arguments for option \'--only_build_index\': \'$VIASH_PAR_ONLY_BUILD_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ONLY_BUILD_INDEX=true
            shift 1
            ;;
        --build)
            [ -n "$VIASH_PAR_BUILD" ] && ViashError Bad arguments for option \'--build\': \'$VIASH_PAR_BUILD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_BUILD="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --build. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --build=*)
            [ -n "$VIASH_PAR_BUILD" ] && ViashError Bad arguments for option \'--build=*\': \'$VIASH_PAR_BUILD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_BUILD=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --qin)
            [ -n "$VIASH_PAR_QIN" ] && ViashError Bad arguments for option \'--qin\': \'$VIASH_PAR_QIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_QIN="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --qin. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --qin=*)
            [ -n "$VIASH_PAR_QIN" ] && ViashError Bad arguments for option \'--qin=*\': \'$VIASH_PAR_QIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_QIN=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --interleaved)
            [ -n "$VIASH_PAR_INTERLEAVED" ] && ViashError Bad arguments for option \'--interleaved\': \'$VIASH_PAR_INTERLEAVED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INTERLEAVED=true
            shift 1
            ;;
        --maxindel)
            [ -n "$VIASH_PAR_MAXINDEL" ] && ViashError Bad arguments for option \'--maxindel\': \'$VIASH_PAR_MAXINDEL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAXINDEL="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --maxindel. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --maxindel=*)
            [ -n "$VIASH_PAR_MAXINDEL" ] && ViashError Bad arguments for option \'--maxindel=*\': \'$VIASH_PAR_MAXINDEL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAXINDEL=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --minratio)
            [ -n "$VIASH_PAR_MINRATIO" ] && ViashError Bad arguments for option \'--minratio\': \'$VIASH_PAR_MINRATIO\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MINRATIO="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --minratio. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --minratio=*)
            [ -n "$VIASH_PAR_MINRATIO" ] && ViashError Bad arguments for option \'--minratio=*\': \'$VIASH_PAR_MINRATIO\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MINRATIO=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --minhits)
            [ -n "$VIASH_PAR_MINHITS" ] && ViashError Bad arguments for option \'--minhits\': \'$VIASH_PAR_MINHITS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MINHITS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --minhits. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --minhits=*)
            [ -n "$VIASH_PAR_MINHITS" ] && ViashError Bad arguments for option \'--minhits=*\': \'$VIASH_PAR_MINHITS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MINHITS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --ambiguous)
            [ -n "$VIASH_PAR_AMBIGUOUS" ] && ViashError Bad arguments for option \'--ambiguous\': \'$VIASH_PAR_AMBIGUOUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_AMBIGUOUS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --ambiguous. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --ambiguous=*)
            [ -n "$VIASH_PAR_AMBIGUOUS" ] && ViashError Bad arguments for option \'--ambiguous=*\': \'$VIASH_PAR_AMBIGUOUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_AMBIGUOUS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --ambiguous2)
            [ -n "$VIASH_PAR_AMBIGUOUS2" ] && ViashError Bad arguments for option \'--ambiguous2\': \'$VIASH_PAR_AMBIGUOUS2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_AMBIGUOUS2="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --ambiguous2. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --ambiguous2=*)
            [ -n "$VIASH_PAR_AMBIGUOUS2" ] && ViashError Bad arguments for option \'--ambiguous2=*\': \'$VIASH_PAR_AMBIGUOUS2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_AMBIGUOUS2=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --qtrim)
            [ -n "$VIASH_PAR_QTRIM" ] && ViashError Bad arguments for option \'--qtrim\': \'$VIASH_PAR_QTRIM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_QTRIM="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --qtrim. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --qtrim=*)
            [ -n "$VIASH_PAR_QTRIM" ] && ViashError Bad arguments for option \'--qtrim=*\': \'$VIASH_PAR_QTRIM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_QTRIM=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --untrim)
            [ -n "$VIASH_PAR_UNTRIM" ] && ViashError Bad arguments for option \'--untrim\': \'$VIASH_PAR_UNTRIM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_UNTRIM=true
            shift 1
            ;;
        --index)
            [ -n "$VIASH_PAR_INDEX" ] && ViashError Bad arguments for option \'--index\': \'$VIASH_PAR_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INDEX="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --index. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --index=*)
            [ -n "$VIASH_PAR_INDEX" ] && ViashError Bad arguments for option \'--index=*\': \'$VIASH_PAR_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INDEX=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --fastq_1)
            [ -n "$VIASH_PAR_FASTQ_1" ] && ViashError Bad arguments for option \'--fastq_1\': \'$VIASH_PAR_FASTQ_1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FASTQ_1="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --fastq_1. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --fastq_1=*)
            [ -n "$VIASH_PAR_FASTQ_1" ] && ViashError Bad arguments for option \'--fastq_1=*\': \'$VIASH_PAR_FASTQ_1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FASTQ_1=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --fastq_2)
            [ -n "$VIASH_PAR_FASTQ_2" ] && ViashError Bad arguments for option \'--fastq_2\': \'$VIASH_PAR_FASTQ_2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FASTQ_2="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --fastq_2. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --fastq_2=*)
            [ -n "$VIASH_PAR_FASTQ_2" ] && ViashError Bad arguments for option \'--fastq_2=*\': \'$VIASH_PAR_FASTQ_2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FASTQ_2=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --sam2bam)
            [ -n "$VIASH_PAR_SAM2BAM" ] && ViashError Bad arguments for option \'--sam2bam\': \'$VIASH_PAR_SAM2BAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SAM2BAM="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --sam2bam. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --sam2bam=*)
            [ -n "$VIASH_PAR_SAM2BAM" ] && ViashError Bad arguments for option \'--sam2bam=*\': \'$VIASH_PAR_SAM2BAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SAM2BAM=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --bs)
            [ -n "$VIASH_PAR_SAM2BAM" ] && ViashError Bad arguments for option \'--bs\': \'$VIASH_PAR_SAM2BAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SAM2BAM="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --bs. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --scafstats)
            [ -n "$VIASH_PAR_SCAFSTATS" ] && ViashError Bad arguments for option \'--scafstats\': \'$VIASH_PAR_SCAFSTATS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SCAFSTATS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --scafstats. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --scafstats=*)
            [ -n "$VIASH_PAR_SCAFSTATS" ] && ViashError Bad arguments for option \'--scafstats=*\': \'$VIASH_PAR_SCAFSTATS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SCAFSTATS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --refstats)
            [ -n "$VIASH_PAR_REFSTATS" ] && ViashError Bad arguments for option \'--refstats\': \'$VIASH_PAR_REFSTATS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_REFSTATS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --refstats. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --refstats=*)
            [ -n "$VIASH_PAR_REFSTATS" ] && ViashError Bad arguments for option \'--refstats=*\': \'$VIASH_PAR_REFSTATS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_REFSTATS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --nzo)
            [ -n "$VIASH_PAR_NZO" ] && ViashError Bad arguments for option \'--nzo\': \'$VIASH_PAR_NZO\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_NZO=true
            shift 1
            ;;
        --bbmap_args)
            [ -n "$VIASH_PAR_BBMAP_ARGS" ] && ViashError Bad arguments for option \'--bbmap_args\': \'$VIASH_PAR_BBMAP_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_BBMAP_ARGS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --bbmap_args. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --bbmap_args=*)
            [ -n "$VIASH_PAR_BBMAP_ARGS" ] && ViashError Bad arguments for option \'--bbmap_args=*\': \'$VIASH_PAR_BBMAP_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_BBMAP_ARGS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        ---engine)
            VIASH_ENGINE_ID="$2"
            shift 2
            ;;
        ---engine=*)
            VIASH_ENGINE_ID="$(ViashRemoveFlags "$1")"
            shift 1
            ;;
        ---setup)
            VIASH_MODE='setup'
            VIASH_SETUP_STRATEGY="$2"
            shift 2
            ;;
        ---setup=*)
            VIASH_MODE='setup'
            VIASH_SETUP_STRATEGY="$(ViashRemoveFlags "$1")"
            shift 1
            ;;
        ---dockerfile)
            VIASH_MODE='dockerfile'
            shift 1
            ;;
        ---docker_run_args)
            VIASH_DOCKER_RUN_ARGS+=("$2")
            shift 2
            ;;
        ---docker_run_args=*)
            VIASH_DOCKER_RUN_ARGS+=("$(ViashRemoveFlags "$1")")
            shift 1
            ;;
        ---docker_image_id)
            VIASH_MODE='docker_image_id'
            shift 1
            ;;
        ---debug)
            VIASH_MODE='debug'
            shift 1
            ;;
        ---cpus)
            [ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_CPUS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to ---cpus. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        ---cpus=*)
            [ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus=*\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_CPUS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        ---memory)
            [ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_MEMORY="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to ---memory. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        ---memory=*)
            [ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory=*\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_MEMORY=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        *)  # positional arg or unknown option
            # since the positional args will be eval'd, can we always quote, instead of using ViashQuote
            VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'"
            [[ $1 == -* ]] && ViashWarning $1 looks like a parameter but is not a defined parameter and will instead be treated as a positional argument. Use "--help" to get more information on the parameters.
            shift # past argument
            ;;
    esac
done

# parse positional parameters
eval set -- $VIASH_POSITIONAL_ARGS


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

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

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bbmap/bbmap_bbsplit:v0.4.1'
  fi

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

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

  # build docker image
  elif [ "$VIASH_MODE" == "setup" ]; then
    ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY"
    ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" '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_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_PAIRED+x} ]; then
  VIASH_PAR_PAIRED="false"
fi
if [ -z ${VIASH_PAR_ONLY_BUILD_INDEX+x} ]; then
  VIASH_PAR_ONLY_BUILD_INDEX="false"
fi
if [ -z ${VIASH_PAR_INTERLEAVED+x} ]; then
  VIASH_PAR_INTERLEAVED="false"
fi
if [ -z ${VIASH_PAR_UNTRIM+x} ]; then
  VIASH_PAR_UNTRIM="false"
fi
if [ -z ${VIASH_PAR_NZO+x} ]; then
  VIASH_PAR_NZO="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_REF" ]; then
  IFS=';'
  set -f
  for file in $VIASH_PAR_REF; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_BUILD" ] && [ ! -e "$VIASH_PAR_BUILD" ]; then
  ViashError "Input file '$VIASH_PAR_BUILD' does not exist."
  exit 1
fi

# check whether parameters values are of the right type
if [[ -n "$VIASH_PAR_PAIRED" ]]; then
  if ! [[ "$VIASH_PAR_PAIRED" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--paired' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_ONLY_BUILD_INDEX" ]]; then
  if ! [[ "$VIASH_PAR_ONLY_BUILD_INDEX" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--only_build_index' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_INTERLEAVED" ]]; then
  if ! [[ "$VIASH_PAR_INTERLEAVED" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--interleaved' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_MAXINDEL" ]]; then
  if ! [[ "$VIASH_PAR_MAXINDEL" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--maxindel' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_MINRATIO" ]]; then
  if ! [[ "$VIASH_PAR_MINRATIO" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--minratio' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_MINHITS" ]]; then
  if ! [[ "$VIASH_PAR_MINHITS" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--minhits' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_UNTRIM" ]]; then
  if ! [[ "$VIASH_PAR_UNTRIM" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--untrim' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_NZO" ]]; then
  if ! [[ "$VIASH_PAR_NZO" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--nzo' 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 "$VIASH_PAR_AMBIGUOUS" ]; then
  VIASH_PAR_AMBIGUOUS_CHOICES=("best;toss;random;all")
  IFS=';'
  set -f
  if ! [[ ";${VIASH_PAR_AMBIGUOUS_CHOICES[*]};" =~ ";$VIASH_PAR_AMBIGUOUS;" ]]; then
    ViashError '--ambiguous' specified value of \'$VIASH_PAR_AMBIGUOUS\' 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 "$VIASH_PAR_AMBIGUOUS2" ]; then
  VIASH_PAR_AMBIGUOUS2_CHOICES=("best;toss;all;split")
  IFS=';'
  set -f
  if ! [[ ";${VIASH_PAR_AMBIGUOUS2_CHOICES[*]};" =~ ";$VIASH_PAR_AMBIGUOUS2;" ]]; then
    ViashError '--ambiguous2' specified value of \'$VIASH_PAR_AMBIGUOUS2\' 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 "$VIASH_PAR_QTRIM" ]; then
  VIASH_PAR_QTRIM_CHOICES=("l;r;lr")
  IFS=';'
  set -f
  if ! [[ ";${VIASH_PAR_QTRIM_CHOICES[*]};" =~ ";$VIASH_PAR_QTRIM;" ]]; then
    ViashError '--qtrim' specified value of \'$VIASH_PAR_QTRIM\' 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 "$VIASH_PAR_INDEX" ] && [ ! -d "$(dirname "$VIASH_PAR_INDEX")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_INDEX")"
fi
if [ ! -z "$VIASH_PAR_FASTQ_1" ] && [ ! -d "$(dirname "$VIASH_PAR_FASTQ_1")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_FASTQ_1")"
fi
if [ ! -z "$VIASH_PAR_FASTQ_2" ] && [ ! -d "$(dirname "$VIASH_PAR_FASTQ_2")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_FASTQ_2")"
fi
if [ ! -z "$VIASH_PAR_SAM2BAM" ] && [ ! -d "$(dirname "$VIASH_PAR_SAM2BAM")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_SAM2BAM")"
fi
if [ ! -z "$VIASH_PAR_SCAFSTATS" ] && [ ! -d "$(dirname "$VIASH_PAR_SCAFSTATS")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_SCAFSTATS")"
fi
if [ ! -z "$VIASH_PAR_REFSTATS" ] && [ ! -d "$(dirname "$VIASH_PAR_REFSTATS")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_REFSTATS")"
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_REF" ]; then
  VIASH_TEST_REF=()
  IFS=';'
  for var in $VIASH_PAR_REF; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_REF+=( "$var" )
  done
  VIASH_PAR_REF=$(IFS=';' ; echo "${VIASH_TEST_REF[*]}")
fi
if [ ! -z "$VIASH_PAR_BUILD" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_BUILD")" )
  VIASH_PAR_BUILD=$(ViashDockerAutodetectMount "$VIASH_PAR_BUILD")
fi
if [ ! -z "$VIASH_PAR_INDEX" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INDEX")" )
  VIASH_PAR_INDEX=$(ViashDockerAutodetectMount "$VIASH_PAR_INDEX")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_INDEX" )
fi
if [ ! -z "$VIASH_PAR_FASTQ_1" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_FASTQ_1")" )
  VIASH_PAR_FASTQ_1=$(ViashDockerAutodetectMount "$VIASH_PAR_FASTQ_1")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_FASTQ_1" )
fi
if [ ! -z "$VIASH_PAR_FASTQ_2" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_FASTQ_2")" )
  VIASH_PAR_FASTQ_2=$(ViashDockerAutodetectMount "$VIASH_PAR_FASTQ_2")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_FASTQ_2" )
fi
if [ ! -z "$VIASH_PAR_SAM2BAM" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_SAM2BAM")" )
  VIASH_PAR_SAM2BAM=$(ViashDockerAutodetectMount "$VIASH_PAR_SAM2BAM")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_SAM2BAM" )
fi
if [ ! -z "$VIASH_PAR_SCAFSTATS" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_SCAFSTATS")" )
  VIASH_PAR_SCAFSTATS=$(ViashDockerAutodetectMount "$VIASH_PAR_SCAFSTATS")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_SCAFSTATS" )
fi
if [ ! -z "$VIASH_PAR_REFSTATS" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_REFSTATS")" )
  VIASH_PAR_REFSTATS=$(ViashDockerAutodetectMount "$VIASH_PAR_REFSTATS")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_REFSTATS" )
fi
if [ ! -z "$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-bbmap_bbsplit-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 ${VIASH_PAR_ID+x} ]; then echo "${VIASH_PAR_ID}" | sed "s#'#'\"'\"'#g;s#.*#par_id='&'#" ; else echo "# par_id="; fi )
$( if [ ! -z ${VIASH_PAR_PAIRED+x} ]; then echo "${VIASH_PAR_PAIRED}" | sed "s#'#'\"'\"'#g;s#.*#par_paired='&'#" ; else echo "# par_paired="; fi )
$( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_input='&'#" ; else echo "# par_input="; fi )
$( if [ ! -z ${VIASH_PAR_REF+x} ]; then echo "${VIASH_PAR_REF}" | sed "s#'#'\"'\"'#g;s#.*#par_ref='&'#" ; else echo "# par_ref="; fi )
$( if [ ! -z ${VIASH_PAR_ONLY_BUILD_INDEX+x} ]; then echo "${VIASH_PAR_ONLY_BUILD_INDEX}" | sed "s#'#'\"'\"'#g;s#.*#par_only_build_index='&'#" ; else echo "# par_only_build_index="; fi )
$( if [ ! -z ${VIASH_PAR_BUILD+x} ]; then echo "${VIASH_PAR_BUILD}" | sed "s#'#'\"'\"'#g;s#.*#par_build='&'#" ; else echo "# par_build="; fi )
$( if [ ! -z ${VIASH_PAR_QIN+x} ]; then echo "${VIASH_PAR_QIN}" | sed "s#'#'\"'\"'#g;s#.*#par_qin='&'#" ; else echo "# par_qin="; fi )
$( if [ ! -z ${VIASH_PAR_INTERLEAVED+x} ]; then echo "${VIASH_PAR_INTERLEAVED}" | sed "s#'#'\"'\"'#g;s#.*#par_interleaved='&'#" ; else echo "# par_interleaved="; fi )
$( if [ ! -z ${VIASH_PAR_MAXINDEL+x} ]; then echo "${VIASH_PAR_MAXINDEL}" | sed "s#'#'\"'\"'#g;s#.*#par_maxindel='&'#" ; else echo "# par_maxindel="; fi )
$( if [ ! -z ${VIASH_PAR_MINRATIO+x} ]; then echo "${VIASH_PAR_MINRATIO}" | sed "s#'#'\"'\"'#g;s#.*#par_minratio='&'#" ; else echo "# par_minratio="; fi )
$( if [ ! -z ${VIASH_PAR_MINHITS+x} ]; then echo "${VIASH_PAR_MINHITS}" | sed "s#'#'\"'\"'#g;s#.*#par_minhits='&'#" ; else echo "# par_minhits="; fi )
$( if [ ! -z ${VIASH_PAR_AMBIGUOUS+x} ]; then echo "${VIASH_PAR_AMBIGUOUS}" | sed "s#'#'\"'\"'#g;s#.*#par_ambiguous='&'#" ; else echo "# par_ambiguous="; fi )
$( if [ ! -z ${VIASH_PAR_AMBIGUOUS2+x} ]; then echo "${VIASH_PAR_AMBIGUOUS2}" | sed "s#'#'\"'\"'#g;s#.*#par_ambiguous2='&'#" ; else echo "# par_ambiguous2="; fi )
$( if [ ! -z ${VIASH_PAR_QTRIM+x} ]; then echo "${VIASH_PAR_QTRIM}" | sed "s#'#'\"'\"'#g;s#.*#par_qtrim='&'#" ; else echo "# par_qtrim="; fi )
$( if [ ! -z ${VIASH_PAR_UNTRIM+x} ]; then echo "${VIASH_PAR_UNTRIM}" | sed "s#'#'\"'\"'#g;s#.*#par_untrim='&'#" ; else echo "# par_untrim="; fi )
$( if [ ! -z ${VIASH_PAR_INDEX+x} ]; then echo "${VIASH_PAR_INDEX}" | sed "s#'#'\"'\"'#g;s#.*#par_index='&'#" ; else echo "# par_index="; fi )
$( if [ ! -z ${VIASH_PAR_FASTQ_1+x} ]; then echo "${VIASH_PAR_FASTQ_1}" | sed "s#'#'\"'\"'#g;s#.*#par_fastq_1='&'#" ; else echo "# par_fastq_1="; fi )
$( if [ ! -z ${VIASH_PAR_FASTQ_2+x} ]; then echo "${VIASH_PAR_FASTQ_2}" | sed "s#'#'\"'\"'#g;s#.*#par_fastq_2='&'#" ; else echo "# par_fastq_2="; fi )
$( if [ ! -z ${VIASH_PAR_SAM2BAM+x} ]; then echo "${VIASH_PAR_SAM2BAM}" | sed "s#'#'\"'\"'#g;s#.*#par_sam2bam='&'#" ; else echo "# par_sam2bam="; fi )
$( if [ ! -z ${VIASH_PAR_SCAFSTATS+x} ]; then echo "${VIASH_PAR_SCAFSTATS}" | sed "s#'#'\"'\"'#g;s#.*#par_scafstats='&'#" ; else echo "# par_scafstats="; fi )
$( if [ ! -z ${VIASH_PAR_REFSTATS+x} ]; then echo "${VIASH_PAR_REFSTATS}" | sed "s#'#'\"'\"'#g;s#.*#par_refstats='&'#" ; else echo "# par_refstats="; fi )
$( if [ ! -z ${VIASH_PAR_NZO+x} ]; then echo "${VIASH_PAR_NZO}" | sed "s#'#'\"'\"'#g;s#.*#par_nzo='&'#" ; else echo "# par_nzo="; fi )
$( if [ ! -z ${VIASH_PAR_BBMAP_ARGS+x} ]; then echo "${VIASH_PAR_BBMAP_ARGS}" | sed "s#'#'\"'\"'#g;s#.*#par_bbmap_args='&'#" ; else echo "# par_bbmap_args="; 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

set -eo pipefail

function clean_up {
    rm -rf "\$tmpdir"
}
trap clean_up EXIT 

unset_if_false=( par_paired par_only_build_index par_interleaved par_untrim par_nzo)

for var in "\${unset_if_false[@]}"; do
    if [ -z "\${!var}" ]; then
        unset \$var
    fi
done

if [ ! -d "\$par_build" ]; then
    IFS=";" read -ra ref_files <<< "\$par_ref"
    primary_ref="\${ref_files[0]}"
    refs=()
    for file in "\${ref_files[@]:1}"
    do
        name=\$(basename "\$file" | sed 's/\\.[^.]*\$//')
        refs+=("ref_\$name=\$file")
    done
fi

if \$par_only_build_index; then
    if [ "\${#refs[@]}" -gt 1 ]; then
        bbsplit.sh \\
            --ref_primary="\$primary_ref" \\
            "\${refs[@]}" \\
            path=\$par_index
    else
        echo "ERROR: Please specify at least two reference fasta files."
    fi
else
    IFS=";" read -ra input <<< "\$par_input"
    tmpdir=\$(mktemp -d "\$meta_temp_dir/\$meta_name-XXXXXXXX")
    index_files=''
    if [ -d "\$par_build" ]; then
        index_files="path=\$par_build"
    elif [ \${#refs[@]} -gt 0 ]; then
        index_files="--ref_primary=\$primary_ref \${refs[*]}"
    else
        echo "ERROR: Please either specify a BBSplit index as input or at least two reference fasta files."
    fi

    extra_args=""
    if [ -f "\$par_refstats" ]; then extra_args+=" --refstats \$par_refstats"; fi
    if [ -n "\$par_ambiguous" ]; then extra_args+=" --ambiguous \$par_ambiguous"; fi
    if [ -n "\$par_ambiguous2" ]; then extra_args+=" --ambiguous2 \$par_ambiguous2"; fi
    if [ -n "\$par_minratio" ]; then extra_args+=" --minratio \$par_minratio"; fi
    if [ -n "\$par_minhits" ]; then extra_args+=" --minhits \$par_minhits"; fi
    if [ -n "\$par_maxindel" ]; then extra_args+=" --maxindel \$par_maxindel"; fi
    if [ -n "\$par_qin" ]; then extra_args+=" --qin \$par_qin"; fi
    if [ -n "\$par_qtrim" ]; then extra_args+=" --qtrim \$par_qtrim"; fi
    if [ "\$par_interleaved" = true ]; then extra_args+=" --interleaved"; fi
    if [ "\$par_untrim" = true ]; then extra_args+=" --untrim"; fi
    if [ "\$par_nzo" = true ]; then extra_args+=" --nzo"; fi

    if [ -n "\$par_bbmap_args" ]; then extra_args+=" \$par_bbmap_args"; fi

    
    if \$par_paired; then
        bbsplit.sh \\
            \$index_files \\
            in=\${input[0]} \\
            in2=\${input[1]} \\
            basename=\${tmpdir}/%_#.fastq \\
            \$extra_args
        read1=\$(find \$tmpdir/ -iname primary_1*)
        read2=\$(find \$tmpdir/ -iname primary_2*)
        cp \$read1 \$par_fastq_1
        cp \$read2 \$par_fastq_2
    else
        bbsplit.sh \\
            \$index_files \\
            in=\${input[0]} \\
            basename=\${tmpdir}/%.fastq \\
            \$extra_args
        read1=\$(find \$tmpdir/ -iname primary*)
        cp \$read1 \$par_fastq_1
    fi
fi

exit 0
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_REF" ]; then
    unset VIASH_TEST_REF
    IFS=';'
    for var in $VIASH_PAR_REF; do
      unset IFS
      if [ -z "$VIASH_TEST_REF" ]; then
      VIASH_TEST_REF="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_REF="$VIASH_TEST_REF;""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_REF="$VIASH_TEST_REF"
  fi
  if [ ! -z "$VIASH_PAR_BUILD" ]; then
    VIASH_PAR_BUILD=$(ViashDockerStripAutomount "$VIASH_PAR_BUILD")
  fi
  if [ ! -z "$VIASH_PAR_INDEX" ]; then
    VIASH_PAR_INDEX=$(ViashDockerStripAutomount "$VIASH_PAR_INDEX")
  fi
  if [ ! -z "$VIASH_PAR_FASTQ_1" ]; then
    VIASH_PAR_FASTQ_1=$(ViashDockerStripAutomount "$VIASH_PAR_FASTQ_1")
  fi
  if [ ! -z "$VIASH_PAR_FASTQ_2" ]; then
    VIASH_PAR_FASTQ_2=$(ViashDockerStripAutomount "$VIASH_PAR_FASTQ_2")
  fi
  if [ ! -z "$VIASH_PAR_SAM2BAM" ]; then
    VIASH_PAR_SAM2BAM=$(ViashDockerStripAutomount "$VIASH_PAR_SAM2BAM")
  fi
  if [ ! -z "$VIASH_PAR_SCAFSTATS" ]; then
    VIASH_PAR_SCAFSTATS=$(ViashDockerStripAutomount "$VIASH_PAR_SCAFSTATS")
  fi
  if [ ! -z "$VIASH_PAR_REFSTATS" ]; then
    VIASH_PAR_REFSTATS=$(ViashDockerStripAutomount "$VIASH_PAR_REFSTATS")
  fi
  if [ ! -z "$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 "$VIASH_PAR_INDEX" ] && [ ! -e "$VIASH_PAR_INDEX" ]; then
  ViashError "Output file '$VIASH_PAR_INDEX' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_FASTQ_1" ] && [ ! -e "$VIASH_PAR_FASTQ_1" ]; then
  ViashError "Output file '$VIASH_PAR_FASTQ_1' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_FASTQ_2" ] && [ ! -e "$VIASH_PAR_FASTQ_2" ]; then
  ViashError "Output file '$VIASH_PAR_FASTQ_2' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_SAM2BAM" ] && [ ! -e "$VIASH_PAR_SAM2BAM" ]; then
  ViashError "Output file '$VIASH_PAR_SAM2BAM' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_SCAFSTATS" ] && [ ! -e "$VIASH_PAR_SCAFSTATS" ]; then
  ViashError "Output file '$VIASH_PAR_SCAFSTATS' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_REFSTATS" ] && [ ! -e "$VIASH_PAR_REFSTATS" ]; then
  ViashError "Output file '$VIASH_PAR_REFSTATS' does not exist."
  exit 1
fi


exit 0
