#!/usr/bin/env bash

# bwa_mem 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.
# 
# Component authors:
#  * Robrecht Cannoodt (author, maintainer)
#  * Toni Verbeiren (reviewer)

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="bwa_mem"
VIASH_META_FUNCTIONALITY_NAME="bwa_mem"
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 quay.io/biocontainers/bwa:0.7.19--h577a1d6_1
ENTRYPOINT []
RUN bwa 2>&1 | grep "Version:" | sed 's/Version: /bwa: /' > /var/software_versions.txt

LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Toni Verbeiren"
LABEL org.opencontainers.image.description="Companion container for running component bwa bwa_mem"
LABEL org.opencontainers.image.created="2025-10-03T12:11:58Z"
LABEL org.opencontainers.image.source="https://github.com/lh3/bwa"
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 "bwa_mem v0.4.1"
  echo ""
  echo "BWA-MEM algorithm for aligning sequence reads to a reference genome."
  echo ""
  echo "Input:"
  echo "    --index"
  echo "        type: file, required parameter, file must exist"
  echo "        example: reference.fasta"
  echo "        BWA index base name (prefix of .amb, .ann, .bwt, .pac, .sa files)."
  echo ""
  echo "    --reads1"
  echo "        type: file, required parameter, file must exist"
  echo "        example: reads_R1.fastq"
  echo "        Input FASTQ file with first reads in pair (R1) or single-end reads."
  echo ""
  echo "    --reads2"
  echo "        type: file, file must exist"
  echo "        example: reads_R2.fastq"
  echo "        Input FASTQ file with second reads in pair (R2). Optional for"
  echo "        single-end."
  echo ""
  echo "Output:"
  echo "    -o, --output"
  echo "        type: file, output, file must exist"
  echo "        example: output.sam"
  echo "        Output SAM file. If not specified, output goes to stdout."
  echo ""
  echo "Algorithm Options:"
  echo "    -k, --min_seed_length"
  echo "        type: integer"
  echo "        example: 19"
  echo "        Minimum seed length. Default is 19."
  echo ""
  echo "    -w, --band_width"
  echo "        type: integer"
  echo "        example: 100"
  echo "        Band width for banded alignment. Default is 100."
  echo ""
  echo "    -d, --dropoff"
  echo "        type: integer"
  echo "        example: 100"
  echo "        Off-diagonal X-dropoff. Default is 100."
  echo ""
  echo "    -r, --reseed_ratio"
  echo "        type: double"
  echo "        example: 1.5"
  echo "        Look for internal seeds inside a seed longer than {-k} * FLOAT. Default"
  echo "        is 1.5."
  echo ""
  echo "    -y, --seed_occurrence"
  echo "        type: integer"
  echo "        example: 20"
  echo "        Seed occurrence for the 3rd round seeding. Default is 20."
  echo ""
  echo "    -c, --skip_seeds"
  echo "        type: integer"
  echo "        example: 500"
  echo "        Skip seeds with more than INT occurrences. Default is 500."
  echo ""
  echo "    -D, --chain_drop"
  echo "        type: double"
  echo "        example: 0.5"
  echo "        Drop chains shorter than FLOAT fraction of the longest overlapping"
  echo "        chain. Default is 0.50."
  echo ""
  echo "    -W, --seeded_bases"
  echo "        type: integer"
  echo "        example: 0"
  echo "        Discard a chain if seeded bases shorter than INT. Default is 0."
  echo ""
  echo "    -m, --mate_rescue"
  echo "        type: integer"
  echo "        example: 50"
  echo "        Perform at most INT rounds of mate rescues for each read. Default is 50."
  echo ""
  echo "    -S, --skip_mate_rescue"
  echo "        type: boolean_true"
  echo "        Skip mate rescue."
  echo ""
  echo "    -P, --skip_pairing"
  echo "        type: boolean_true"
  echo "        Skip pairing; mate rescue performed unless -S also in use."
  echo ""
  echo "Scoring Options:"
  echo "    -A, --match_score"
  echo "        type: integer"
  echo "        example: 1"
  echo "        Score for a sequence match. Default is 1."
  echo ""
  echo "    -B, --mismatch_penalty"
  echo "        type: integer"
  echo "        example: 4"
  echo "        Penalty for a mismatch. Default is 4."
  echo ""
  echo "    -O, --gap_open_penalty"
  echo "        type: string"
  echo "        example: 6,6"
  echo "        Gap open penalties for deletions and insertions. Default is 6,6."
  echo ""
  echo "    -E, --gap_extend_penalty"
  echo "        type: string"
  echo "        example: 1,1"
  echo "        Gap extension penalty. Default is 1,1."
  echo ""
  echo "    -L, --clipping_penalty"
  echo "        type: string"
  echo "        example: 5,5"
  echo "        Penalty for 5'- and 3'-end clipping. Default is 5,5."
  echo ""
  echo "    -U, --unpaired_penalty"
  echo "        type: integer"
  echo "        example: 17"
  echo "        Penalty for an unpaired read pair. Default is 17."
  echo ""
  echo "    -x, --read_type"
  echo "        type: string"
  echo "        choices: [ pacbio, ont2d, intractg ]"
  echo "        Read type preset (pacbio, ont2d, intractg)."
  echo ""
  echo "Input/Output Options:"
  echo "    -p, --smart_pairing"
  echo "        type: boolean_true"
  echo "        Smart pairing (ignoring in2.fq)."
  echo ""
  echo "    -R, --read_group"
  echo "        type: string"
  echo "        example: @RG ID:sample1 SM:sample1"
  echo "        Read group header line such as '@RG\\tID:foo\\tSM:bar'."
  echo ""
  echo "    -H, --header"
  echo "        type: string"
  echo "        Insert STR to header if it starts with @; or insert lines in FILE."
  echo ""
  echo "    -j, --ignore_alt"
  echo "        type: boolean_true"
  echo "        Treat ALT contigs as part of the primary assembly."
  echo ""
  echo "    -5, --primary_5prime"
  echo "        type: boolean_true"
  echo "        For split alignment, take the alignment with the smallest query (not"
  echo "        genomic) coordinate as primary."
  echo ""
  echo "    -q, --keep_mapq"
  echo "        type: boolean_true"
  echo "        Don't modify mapQ of supplementary alignments."
  echo ""
  echo "    -K, --batch_size"
  echo "        type: integer"
  echo "        Process INT input bases in each batch regardless of nThreads."
  echo ""
  echo "    -v, --verbosity"
  echo "        type: integer"
  echo "        choices: [ 1, 2, 3, 4 ]"
  echo "        Verbosity level (1=error, 2=warning, 3=message, 4+=debugging). Default"
  echo "        is 3."
  echo ""
  echo "    -T, --min_score"
  echo "        type: integer"
  echo "        example: 30"
  echo "        Minimum score to output. Default is 30."
  echo ""
  echo "    --max_hits_xa"
  echo "        type: string"
  echo "        example: 5,200"
  echo "        If there are <INT hits with score >80.00% of the max score, output all"
  echo "        in XA. Default is 5,200."
  echo ""
  echo "    -z, --score_fraction"
  echo "        type: double"
  echo "        example: 0.8"
  echo "        The fraction of the max score to use with -h. Default is 0.800000."
  echo ""
  echo "    -a, --output_all"
  echo "        type: boolean_true"
  echo "        Output all alignments for SE or unpaired PE."
  echo ""
  echo "    -C, --append_comment"
  echo "        type: boolean_true"
  echo "        Append FASTA/FASTQ comment to SAM output."
  echo ""
  echo "    -V, --output_ref_header"
  echo "        type: boolean_true"
  echo "        Output the reference FASTA header in the XR tag."
  echo ""
  echo "    -Y, --soft_clipping"
  echo "        type: boolean_true"
  echo "        Use soft clipping for supplementary alignments."
  echo ""
  echo "    -M, --mark_secondary"
  echo "        type: boolean_true"
  echo "        Mark shorter split hits as secondary."
  echo ""
  echo "    -u, --output_xb"
  echo "        type: boolean_true"
  echo "        Output XB instead of XA; XB is XA with the alignment score and mapping"
  echo "        quality added."
  echo ""
  echo "    -I, --insert_size"
  echo "        type: string"
  echo "        example: 500,50,800,100"
  echo "        Specify the mean, standard deviation, max and min of the insert size"
  echo "        distribution."
  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 "$1")"
            shift 1
            ;;
        --version)
            echo "bwa_mem v0.4.1"
            exit
            ;;
        --index)
            [ -n "$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 "$1")
            shift 1
            ;;
        --reads1)
            [ -n "$VIASH_PAR_READS1" ] && ViashError Bad arguments for option \'--reads1\': \'$VIASH_PAR_READS1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_READS1="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --reads1. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --reads1=*)
            [ -n "$VIASH_PAR_READS1" ] && ViashError Bad arguments for option \'--reads1=*\': \'$VIASH_PAR_READS1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_READS1=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --reads2)
            [ -n "$VIASH_PAR_READS2" ] && ViashError Bad arguments for option \'--reads2\': \'$VIASH_PAR_READS2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_READS2="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --reads2. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --reads2=*)
            [ -n "$VIASH_PAR_READS2" ] && ViashError Bad arguments for option \'--reads2=*\': \'$VIASH_PAR_READS2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_READS2=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --output)
            [ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --output. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --output=*)
            [ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output=*\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -o)
            [ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'-o\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -o. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --min_seed_length)
            [ -n "$VIASH_PAR_MIN_SEED_LENGTH" ] && ViashError Bad arguments for option \'--min_seed_length\': \'$VIASH_PAR_MIN_SEED_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MIN_SEED_LENGTH="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --min_seed_length. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --min_seed_length=*)
            [ -n "$VIASH_PAR_MIN_SEED_LENGTH" ] && ViashError Bad arguments for option \'--min_seed_length=*\': \'$VIASH_PAR_MIN_SEED_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MIN_SEED_LENGTH=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -k)
            [ -n "$VIASH_PAR_MIN_SEED_LENGTH" ] && ViashError Bad arguments for option \'-k\': \'$VIASH_PAR_MIN_SEED_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MIN_SEED_LENGTH="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -k. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --band_width)
            [ -n "$VIASH_PAR_BAND_WIDTH" ] && ViashError Bad arguments for option \'--band_width\': \'$VIASH_PAR_BAND_WIDTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_BAND_WIDTH="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --band_width. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --band_width=*)
            [ -n "$VIASH_PAR_BAND_WIDTH" ] && ViashError Bad arguments for option \'--band_width=*\': \'$VIASH_PAR_BAND_WIDTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_BAND_WIDTH=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -w)
            [ -n "$VIASH_PAR_BAND_WIDTH" ] && ViashError Bad arguments for option \'-w\': \'$VIASH_PAR_BAND_WIDTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_BAND_WIDTH="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -w. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --dropoff)
            [ -n "$VIASH_PAR_DROPOFF" ] && ViashError Bad arguments for option \'--dropoff\': \'$VIASH_PAR_DROPOFF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_DROPOFF="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --dropoff. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --dropoff=*)
            [ -n "$VIASH_PAR_DROPOFF" ] && ViashError Bad arguments for option \'--dropoff=*\': \'$VIASH_PAR_DROPOFF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_DROPOFF=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -d)
            [ -n "$VIASH_PAR_DROPOFF" ] && ViashError Bad arguments for option \'-d\': \'$VIASH_PAR_DROPOFF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_DROPOFF="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -d. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --reseed_ratio)
            [ -n "$VIASH_PAR_RESEED_RATIO" ] && ViashError Bad arguments for option \'--reseed_ratio\': \'$VIASH_PAR_RESEED_RATIO\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_RESEED_RATIO="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --reseed_ratio. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --reseed_ratio=*)
            [ -n "$VIASH_PAR_RESEED_RATIO" ] && ViashError Bad arguments for option \'--reseed_ratio=*\': \'$VIASH_PAR_RESEED_RATIO\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_RESEED_RATIO=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -r)
            [ -n "$VIASH_PAR_RESEED_RATIO" ] && ViashError Bad arguments for option \'-r\': \'$VIASH_PAR_RESEED_RATIO\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_RESEED_RATIO="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -r. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --seed_occurrence)
            [ -n "$VIASH_PAR_SEED_OCCURRENCE" ] && ViashError Bad arguments for option \'--seed_occurrence\': \'$VIASH_PAR_SEED_OCCURRENCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SEED_OCCURRENCE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --seed_occurrence. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --seed_occurrence=*)
            [ -n "$VIASH_PAR_SEED_OCCURRENCE" ] && ViashError Bad arguments for option \'--seed_occurrence=*\': \'$VIASH_PAR_SEED_OCCURRENCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SEED_OCCURRENCE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -y)
            [ -n "$VIASH_PAR_SEED_OCCURRENCE" ] && ViashError Bad arguments for option \'-y\': \'$VIASH_PAR_SEED_OCCURRENCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SEED_OCCURRENCE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -y. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --skip_seeds)
            [ -n "$VIASH_PAR_SKIP_SEEDS" ] && ViashError Bad arguments for option \'--skip_seeds\': \'$VIASH_PAR_SKIP_SEEDS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SKIP_SEEDS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --skip_seeds. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --skip_seeds=*)
            [ -n "$VIASH_PAR_SKIP_SEEDS" ] && ViashError Bad arguments for option \'--skip_seeds=*\': \'$VIASH_PAR_SKIP_SEEDS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SKIP_SEEDS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -c)
            [ -n "$VIASH_PAR_SKIP_SEEDS" ] && ViashError Bad arguments for option \'-c\': \'$VIASH_PAR_SKIP_SEEDS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SKIP_SEEDS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -c. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --chain_drop)
            [ -n "$VIASH_PAR_CHAIN_DROP" ] && ViashError Bad arguments for option \'--chain_drop\': \'$VIASH_PAR_CHAIN_DROP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CHAIN_DROP="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --chain_drop. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --chain_drop=*)
            [ -n "$VIASH_PAR_CHAIN_DROP" ] && ViashError Bad arguments for option \'--chain_drop=*\': \'$VIASH_PAR_CHAIN_DROP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CHAIN_DROP=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -D)
            [ -n "$VIASH_PAR_CHAIN_DROP" ] && ViashError Bad arguments for option \'-D\': \'$VIASH_PAR_CHAIN_DROP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CHAIN_DROP="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -D. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --seeded_bases)
            [ -n "$VIASH_PAR_SEEDED_BASES" ] && ViashError Bad arguments for option \'--seeded_bases\': \'$VIASH_PAR_SEEDED_BASES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SEEDED_BASES="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --seeded_bases. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --seeded_bases=*)
            [ -n "$VIASH_PAR_SEEDED_BASES" ] && ViashError Bad arguments for option \'--seeded_bases=*\': \'$VIASH_PAR_SEEDED_BASES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SEEDED_BASES=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -W)
            [ -n "$VIASH_PAR_SEEDED_BASES" ] && ViashError Bad arguments for option \'-W\': \'$VIASH_PAR_SEEDED_BASES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SEEDED_BASES="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -W. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --mate_rescue)
            [ -n "$VIASH_PAR_MATE_RESCUE" ] && ViashError Bad arguments for option \'--mate_rescue\': \'$VIASH_PAR_MATE_RESCUE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MATE_RESCUE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --mate_rescue. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --mate_rescue=*)
            [ -n "$VIASH_PAR_MATE_RESCUE" ] && ViashError Bad arguments for option \'--mate_rescue=*\': \'$VIASH_PAR_MATE_RESCUE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MATE_RESCUE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -m)
            [ -n "$VIASH_PAR_MATE_RESCUE" ] && ViashError Bad arguments for option \'-m\': \'$VIASH_PAR_MATE_RESCUE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MATE_RESCUE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -m. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --skip_mate_rescue)
            [ -n "$VIASH_PAR_SKIP_MATE_RESCUE" ] && ViashError Bad arguments for option \'--skip_mate_rescue\': \'$VIASH_PAR_SKIP_MATE_RESCUE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SKIP_MATE_RESCUE=true
            shift 1
            ;;
        -S)
            [ -n "$VIASH_PAR_SKIP_MATE_RESCUE" ] && ViashError Bad arguments for option \'-S\': \'$VIASH_PAR_SKIP_MATE_RESCUE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SKIP_MATE_RESCUE=true
            shift 1
            ;;
        --skip_pairing)
            [ -n "$VIASH_PAR_SKIP_PAIRING" ] && ViashError Bad arguments for option \'--skip_pairing\': \'$VIASH_PAR_SKIP_PAIRING\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SKIP_PAIRING=true
            shift 1
            ;;
        -P)
            [ -n "$VIASH_PAR_SKIP_PAIRING" ] && ViashError Bad arguments for option \'-P\': \'$VIASH_PAR_SKIP_PAIRING\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SKIP_PAIRING=true
            shift 1
            ;;
        --match_score)
            [ -n "$VIASH_PAR_MATCH_SCORE" ] && ViashError Bad arguments for option \'--match_score\': \'$VIASH_PAR_MATCH_SCORE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MATCH_SCORE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --match_score. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --match_score=*)
            [ -n "$VIASH_PAR_MATCH_SCORE" ] && ViashError Bad arguments for option \'--match_score=*\': \'$VIASH_PAR_MATCH_SCORE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MATCH_SCORE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -A)
            [ -n "$VIASH_PAR_MATCH_SCORE" ] && ViashError Bad arguments for option \'-A\': \'$VIASH_PAR_MATCH_SCORE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MATCH_SCORE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -A. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --mismatch_penalty)
            [ -n "$VIASH_PAR_MISMATCH_PENALTY" ] && ViashError Bad arguments for option \'--mismatch_penalty\': \'$VIASH_PAR_MISMATCH_PENALTY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MISMATCH_PENALTY="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --mismatch_penalty. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --mismatch_penalty=*)
            [ -n "$VIASH_PAR_MISMATCH_PENALTY" ] && ViashError Bad arguments for option \'--mismatch_penalty=*\': \'$VIASH_PAR_MISMATCH_PENALTY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MISMATCH_PENALTY=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -B)
            [ -n "$VIASH_PAR_MISMATCH_PENALTY" ] && ViashError Bad arguments for option \'-B\': \'$VIASH_PAR_MISMATCH_PENALTY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MISMATCH_PENALTY="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -B. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --gap_open_penalty)
            [ -n "$VIASH_PAR_GAP_OPEN_PENALTY" ] && ViashError Bad arguments for option \'--gap_open_penalty\': \'$VIASH_PAR_GAP_OPEN_PENALTY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_GAP_OPEN_PENALTY="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --gap_open_penalty. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --gap_open_penalty=*)
            [ -n "$VIASH_PAR_GAP_OPEN_PENALTY" ] && ViashError Bad arguments for option \'--gap_open_penalty=*\': \'$VIASH_PAR_GAP_OPEN_PENALTY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_GAP_OPEN_PENALTY=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -O)
            [ -n "$VIASH_PAR_GAP_OPEN_PENALTY" ] && ViashError Bad arguments for option \'-O\': \'$VIASH_PAR_GAP_OPEN_PENALTY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_GAP_OPEN_PENALTY="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -O. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --gap_extend_penalty)
            [ -n "$VIASH_PAR_GAP_EXTEND_PENALTY" ] && ViashError Bad arguments for option \'--gap_extend_penalty\': \'$VIASH_PAR_GAP_EXTEND_PENALTY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_GAP_EXTEND_PENALTY="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --gap_extend_penalty. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --gap_extend_penalty=*)
            [ -n "$VIASH_PAR_GAP_EXTEND_PENALTY" ] && ViashError Bad arguments for option \'--gap_extend_penalty=*\': \'$VIASH_PAR_GAP_EXTEND_PENALTY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_GAP_EXTEND_PENALTY=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -E)
            [ -n "$VIASH_PAR_GAP_EXTEND_PENALTY" ] && ViashError Bad arguments for option \'-E\': \'$VIASH_PAR_GAP_EXTEND_PENALTY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_GAP_EXTEND_PENALTY="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -E. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --clipping_penalty)
            [ -n "$VIASH_PAR_CLIPPING_PENALTY" ] && ViashError Bad arguments for option \'--clipping_penalty\': \'$VIASH_PAR_CLIPPING_PENALTY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CLIPPING_PENALTY="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --clipping_penalty. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --clipping_penalty=*)
            [ -n "$VIASH_PAR_CLIPPING_PENALTY" ] && ViashError Bad arguments for option \'--clipping_penalty=*\': \'$VIASH_PAR_CLIPPING_PENALTY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CLIPPING_PENALTY=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -L)
            [ -n "$VIASH_PAR_CLIPPING_PENALTY" ] && ViashError Bad arguments for option \'-L\': \'$VIASH_PAR_CLIPPING_PENALTY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CLIPPING_PENALTY="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -L. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --unpaired_penalty)
            [ -n "$VIASH_PAR_UNPAIRED_PENALTY" ] && ViashError Bad arguments for option \'--unpaired_penalty\': \'$VIASH_PAR_UNPAIRED_PENALTY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_UNPAIRED_PENALTY="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --unpaired_penalty. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --unpaired_penalty=*)
            [ -n "$VIASH_PAR_UNPAIRED_PENALTY" ] && ViashError Bad arguments for option \'--unpaired_penalty=*\': \'$VIASH_PAR_UNPAIRED_PENALTY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_UNPAIRED_PENALTY=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -U)
            [ -n "$VIASH_PAR_UNPAIRED_PENALTY" ] && ViashError Bad arguments for option \'-U\': \'$VIASH_PAR_UNPAIRED_PENALTY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_UNPAIRED_PENALTY="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -U. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --read_type)
            [ -n "$VIASH_PAR_READ_TYPE" ] && ViashError Bad arguments for option \'--read_type\': \'$VIASH_PAR_READ_TYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_READ_TYPE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --read_type. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --read_type=*)
            [ -n "$VIASH_PAR_READ_TYPE" ] && ViashError Bad arguments for option \'--read_type=*\': \'$VIASH_PAR_READ_TYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_READ_TYPE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -x)
            [ -n "$VIASH_PAR_READ_TYPE" ] && ViashError Bad arguments for option \'-x\': \'$VIASH_PAR_READ_TYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_READ_TYPE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -x. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --smart_pairing)
            [ -n "$VIASH_PAR_SMART_PAIRING" ] && ViashError Bad arguments for option \'--smart_pairing\': \'$VIASH_PAR_SMART_PAIRING\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SMART_PAIRING=true
            shift 1
            ;;
        -p)
            [ -n "$VIASH_PAR_SMART_PAIRING" ] && ViashError Bad arguments for option \'-p\': \'$VIASH_PAR_SMART_PAIRING\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SMART_PAIRING=true
            shift 1
            ;;
        --read_group)
            [ -n "$VIASH_PAR_READ_GROUP" ] && ViashError Bad arguments for option \'--read_group\': \'$VIASH_PAR_READ_GROUP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_READ_GROUP="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --read_group. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --read_group=*)
            [ -n "$VIASH_PAR_READ_GROUP" ] && ViashError Bad arguments for option \'--read_group=*\': \'$VIASH_PAR_READ_GROUP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_READ_GROUP=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -R)
            [ -n "$VIASH_PAR_READ_GROUP" ] && ViashError Bad arguments for option \'-R\': \'$VIASH_PAR_READ_GROUP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_READ_GROUP="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -R. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --header)
            [ -n "$VIASH_PAR_HEADER" ] && ViashError Bad arguments for option \'--header\': \'$VIASH_PAR_HEADER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_HEADER="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --header. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --header=*)
            [ -n "$VIASH_PAR_HEADER" ] && ViashError Bad arguments for option \'--header=*\': \'$VIASH_PAR_HEADER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_HEADER=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -H)
            [ -n "$VIASH_PAR_HEADER" ] && ViashError Bad arguments for option \'-H\': \'$VIASH_PAR_HEADER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_HEADER="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -H. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --ignore_alt)
            [ -n "$VIASH_PAR_IGNORE_ALT" ] && ViashError Bad arguments for option \'--ignore_alt\': \'$VIASH_PAR_IGNORE_ALT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_IGNORE_ALT=true
            shift 1
            ;;
        -j)
            [ -n "$VIASH_PAR_IGNORE_ALT" ] && ViashError Bad arguments for option \'-j\': \'$VIASH_PAR_IGNORE_ALT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_IGNORE_ALT=true
            shift 1
            ;;
        --primary_5prime)
            [ -n "$VIASH_PAR_PRIMARY_5PRIME" ] && ViashError Bad arguments for option \'--primary_5prime\': \'$VIASH_PAR_PRIMARY_5PRIME\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PRIMARY_5PRIME=true
            shift 1
            ;;
        -5)
            [ -n "$VIASH_PAR_PRIMARY_5PRIME" ] && ViashError Bad arguments for option \'-5\': \'$VIASH_PAR_PRIMARY_5PRIME\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PRIMARY_5PRIME=true
            shift 1
            ;;
        --keep_mapq)
            [ -n "$VIASH_PAR_KEEP_MAPQ" ] && ViashError Bad arguments for option \'--keep_mapq\': \'$VIASH_PAR_KEEP_MAPQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_KEEP_MAPQ=true
            shift 1
            ;;
        -q)
            [ -n "$VIASH_PAR_KEEP_MAPQ" ] && ViashError Bad arguments for option \'-q\': \'$VIASH_PAR_KEEP_MAPQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_KEEP_MAPQ=true
            shift 1
            ;;
        --batch_size)
            [ -n "$VIASH_PAR_BATCH_SIZE" ] && ViashError Bad arguments for option \'--batch_size\': \'$VIASH_PAR_BATCH_SIZE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_BATCH_SIZE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --batch_size. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --batch_size=*)
            [ -n "$VIASH_PAR_BATCH_SIZE" ] && ViashError Bad arguments for option \'--batch_size=*\': \'$VIASH_PAR_BATCH_SIZE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_BATCH_SIZE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -K)
            [ -n "$VIASH_PAR_BATCH_SIZE" ] && ViashError Bad arguments for option \'-K\': \'$VIASH_PAR_BATCH_SIZE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_BATCH_SIZE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -K. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --verbosity)
            [ -n "$VIASH_PAR_VERBOSITY" ] && ViashError Bad arguments for option \'--verbosity\': \'$VIASH_PAR_VERBOSITY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_VERBOSITY="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --verbosity. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --verbosity=*)
            [ -n "$VIASH_PAR_VERBOSITY" ] && ViashError Bad arguments for option \'--verbosity=*\': \'$VIASH_PAR_VERBOSITY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_VERBOSITY=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -v)
            [ -n "$VIASH_PAR_VERBOSITY" ] && ViashError Bad arguments for option \'-v\': \'$VIASH_PAR_VERBOSITY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_VERBOSITY="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -v. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --min_score)
            [ -n "$VIASH_PAR_MIN_SCORE" ] && ViashError Bad arguments for option \'--min_score\': \'$VIASH_PAR_MIN_SCORE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MIN_SCORE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --min_score. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --min_score=*)
            [ -n "$VIASH_PAR_MIN_SCORE" ] && ViashError Bad arguments for option \'--min_score=*\': \'$VIASH_PAR_MIN_SCORE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MIN_SCORE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -T)
            [ -n "$VIASH_PAR_MIN_SCORE" ] && ViashError Bad arguments for option \'-T\': \'$VIASH_PAR_MIN_SCORE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MIN_SCORE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -T. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --max_hits_xa)
            [ -n "$VIASH_PAR_MAX_HITS_XA" ] && ViashError Bad arguments for option \'--max_hits_xa\': \'$VIASH_PAR_MAX_HITS_XA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_HITS_XA="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --max_hits_xa. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --max_hits_xa=*)
            [ -n "$VIASH_PAR_MAX_HITS_XA" ] && ViashError Bad arguments for option \'--max_hits_xa=*\': \'$VIASH_PAR_MAX_HITS_XA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_HITS_XA=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --score_fraction)
            [ -n "$VIASH_PAR_SCORE_FRACTION" ] && ViashError Bad arguments for option \'--score_fraction\': \'$VIASH_PAR_SCORE_FRACTION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SCORE_FRACTION="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --score_fraction. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --score_fraction=*)
            [ -n "$VIASH_PAR_SCORE_FRACTION" ] && ViashError Bad arguments for option \'--score_fraction=*\': \'$VIASH_PAR_SCORE_FRACTION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SCORE_FRACTION=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -z)
            [ -n "$VIASH_PAR_SCORE_FRACTION" ] && ViashError Bad arguments for option \'-z\': \'$VIASH_PAR_SCORE_FRACTION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SCORE_FRACTION="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -z. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --output_all)
            [ -n "$VIASH_PAR_OUTPUT_ALL" ] && ViashError Bad arguments for option \'--output_all\': \'$VIASH_PAR_OUTPUT_ALL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_ALL=true
            shift 1
            ;;
        -a)
            [ -n "$VIASH_PAR_OUTPUT_ALL" ] && ViashError Bad arguments for option \'-a\': \'$VIASH_PAR_OUTPUT_ALL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_ALL=true
            shift 1
            ;;
        --append_comment)
            [ -n "$VIASH_PAR_APPEND_COMMENT" ] && ViashError Bad arguments for option \'--append_comment\': \'$VIASH_PAR_APPEND_COMMENT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_APPEND_COMMENT=true
            shift 1
            ;;
        -C)
            [ -n "$VIASH_PAR_APPEND_COMMENT" ] && ViashError Bad arguments for option \'-C\': \'$VIASH_PAR_APPEND_COMMENT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_APPEND_COMMENT=true
            shift 1
            ;;
        --output_ref_header)
            [ -n "$VIASH_PAR_OUTPUT_REF_HEADER" ] && ViashError Bad arguments for option \'--output_ref_header\': \'$VIASH_PAR_OUTPUT_REF_HEADER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_REF_HEADER=true
            shift 1
            ;;
        -V)
            [ -n "$VIASH_PAR_OUTPUT_REF_HEADER" ] && ViashError Bad arguments for option \'-V\': \'$VIASH_PAR_OUTPUT_REF_HEADER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_REF_HEADER=true
            shift 1
            ;;
        --soft_clipping)
            [ -n "$VIASH_PAR_SOFT_CLIPPING" ] && ViashError Bad arguments for option \'--soft_clipping\': \'$VIASH_PAR_SOFT_CLIPPING\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SOFT_CLIPPING=true
            shift 1
            ;;
        -Y)
            [ -n "$VIASH_PAR_SOFT_CLIPPING" ] && ViashError Bad arguments for option \'-Y\': \'$VIASH_PAR_SOFT_CLIPPING\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SOFT_CLIPPING=true
            shift 1
            ;;
        --mark_secondary)
            [ -n "$VIASH_PAR_MARK_SECONDARY" ] && ViashError Bad arguments for option \'--mark_secondary\': \'$VIASH_PAR_MARK_SECONDARY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MARK_SECONDARY=true
            shift 1
            ;;
        -M)
            [ -n "$VIASH_PAR_MARK_SECONDARY" ] && ViashError Bad arguments for option \'-M\': \'$VIASH_PAR_MARK_SECONDARY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MARK_SECONDARY=true
            shift 1
            ;;
        --output_xb)
            [ -n "$VIASH_PAR_OUTPUT_XB" ] && ViashError Bad arguments for option \'--output_xb\': \'$VIASH_PAR_OUTPUT_XB\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_XB=true
            shift 1
            ;;
        -u)
            [ -n "$VIASH_PAR_OUTPUT_XB" ] && ViashError Bad arguments for option \'-u\': \'$VIASH_PAR_OUTPUT_XB\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_XB=true
            shift 1
            ;;
        --insert_size)
            [ -n "$VIASH_PAR_INSERT_SIZE" ] && ViashError Bad arguments for option \'--insert_size\': \'$VIASH_PAR_INSERT_SIZE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INSERT_SIZE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --insert_size. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --insert_size=*)
            [ -n "$VIASH_PAR_INSERT_SIZE" ] && ViashError Bad arguments for option \'--insert_size=*\': \'$VIASH_PAR_INSERT_SIZE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INSERT_SIZE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -I)
            [ -n "$VIASH_PAR_INSERT_SIZE" ] && ViashError Bad arguments for option \'-I\': \'$VIASH_PAR_INSERT_SIZE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INSERT_SIZE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -I. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        ---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/bwa/bwa_mem: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" 'bwa' 'ps' 'bash'
    exit 0
  fi

  # check if docker image exists
  ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild
  ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bwa' '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_INDEX+x} ]; then
  ViashError '--index' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_PAR_READS1+x} ]; then
  ViashError '--reads1' 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_SKIP_MATE_RESCUE+x} ]; then
  VIASH_PAR_SKIP_MATE_RESCUE="false"
fi
if [ -z ${VIASH_PAR_SKIP_PAIRING+x} ]; then
  VIASH_PAR_SKIP_PAIRING="false"
fi
if [ -z ${VIASH_PAR_SMART_PAIRING+x} ]; then
  VIASH_PAR_SMART_PAIRING="false"
fi
if [ -z ${VIASH_PAR_IGNORE_ALT+x} ]; then
  VIASH_PAR_IGNORE_ALT="false"
fi
if [ -z ${VIASH_PAR_PRIMARY_5PRIME+x} ]; then
  VIASH_PAR_PRIMARY_5PRIME="false"
fi
if [ -z ${VIASH_PAR_KEEP_MAPQ+x} ]; then
  VIASH_PAR_KEEP_MAPQ="false"
fi
if [ -z ${VIASH_PAR_OUTPUT_ALL+x} ]; then
  VIASH_PAR_OUTPUT_ALL="false"
fi
if [ -z ${VIASH_PAR_APPEND_COMMENT+x} ]; then
  VIASH_PAR_APPEND_COMMENT="false"
fi
if [ -z ${VIASH_PAR_OUTPUT_REF_HEADER+x} ]; then
  VIASH_PAR_OUTPUT_REF_HEADER="false"
fi
if [ -z ${VIASH_PAR_SOFT_CLIPPING+x} ]; then
  VIASH_PAR_SOFT_CLIPPING="false"
fi
if [ -z ${VIASH_PAR_MARK_SECONDARY+x} ]; then
  VIASH_PAR_MARK_SECONDARY="false"
fi
if [ -z ${VIASH_PAR_OUTPUT_XB+x} ]; then
  VIASH_PAR_OUTPUT_XB="false"
fi

# check whether required files exist
if [ ! -z "$VIASH_PAR_INDEX" ] && [ ! -e "$VIASH_PAR_INDEX" ]; then
  ViashError "Input file '$VIASH_PAR_INDEX' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_READS1" ] && [ ! -e "$VIASH_PAR_READS1" ]; then
  ViashError "Input file '$VIASH_PAR_READS1' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_READS2" ] && [ ! -e "$VIASH_PAR_READS2" ]; then
  ViashError "Input file '$VIASH_PAR_READS2' does not exist."
  exit 1
fi

# check whether parameters values are of the right type
if [[ -n "$VIASH_PAR_MIN_SEED_LENGTH" ]]; then
  if ! [[ "$VIASH_PAR_MIN_SEED_LENGTH" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--min_seed_length' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_BAND_WIDTH" ]]; then
  if ! [[ "$VIASH_PAR_BAND_WIDTH" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--band_width' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_DROPOFF" ]]; then
  if ! [[ "$VIASH_PAR_DROPOFF" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--dropoff' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_RESEED_RATIO" ]]; then
  if ! [[ "$VIASH_PAR_RESEED_RATIO" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--reseed_ratio' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SEED_OCCURRENCE" ]]; then
  if ! [[ "$VIASH_PAR_SEED_OCCURRENCE" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--seed_occurrence' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SKIP_SEEDS" ]]; then
  if ! [[ "$VIASH_PAR_SKIP_SEEDS" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--skip_seeds' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_CHAIN_DROP" ]]; then
  if ! [[ "$VIASH_PAR_CHAIN_DROP" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--chain_drop' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SEEDED_BASES" ]]; then
  if ! [[ "$VIASH_PAR_SEEDED_BASES" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--seeded_bases' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_MATE_RESCUE" ]]; then
  if ! [[ "$VIASH_PAR_MATE_RESCUE" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--mate_rescue' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SKIP_MATE_RESCUE" ]]; then
  if ! [[ "$VIASH_PAR_SKIP_MATE_RESCUE" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--skip_mate_rescue' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SKIP_PAIRING" ]]; then
  if ! [[ "$VIASH_PAR_SKIP_PAIRING" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--skip_pairing' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_MATCH_SCORE" ]]; then
  if ! [[ "$VIASH_PAR_MATCH_SCORE" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--match_score' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_MISMATCH_PENALTY" ]]; then
  if ! [[ "$VIASH_PAR_MISMATCH_PENALTY" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--mismatch_penalty' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_UNPAIRED_PENALTY" ]]; then
  if ! [[ "$VIASH_PAR_UNPAIRED_PENALTY" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--unpaired_penalty' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SMART_PAIRING" ]]; then
  if ! [[ "$VIASH_PAR_SMART_PAIRING" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--smart_pairing' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_IGNORE_ALT" ]]; then
  if ! [[ "$VIASH_PAR_IGNORE_ALT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--ignore_alt' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_PRIMARY_5PRIME" ]]; then
  if ! [[ "$VIASH_PAR_PRIMARY_5PRIME" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--primary_5prime' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_KEEP_MAPQ" ]]; then
  if ! [[ "$VIASH_PAR_KEEP_MAPQ" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--keep_mapq' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_BATCH_SIZE" ]]; then
  if ! [[ "$VIASH_PAR_BATCH_SIZE" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--batch_size' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_VERBOSITY" ]]; then
  if ! [[ "$VIASH_PAR_VERBOSITY" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--verbosity' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_MIN_SCORE" ]]; then
  if ! [[ "$VIASH_PAR_MIN_SCORE" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--min_score' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SCORE_FRACTION" ]]; then
  if ! [[ "$VIASH_PAR_SCORE_FRACTION" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--score_fraction' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_OUTPUT_ALL" ]]; then
  if ! [[ "$VIASH_PAR_OUTPUT_ALL" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--output_all' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_APPEND_COMMENT" ]]; then
  if ! [[ "$VIASH_PAR_APPEND_COMMENT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--append_comment' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_OUTPUT_REF_HEADER" ]]; then
  if ! [[ "$VIASH_PAR_OUTPUT_REF_HEADER" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--output_ref_header' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SOFT_CLIPPING" ]]; then
  if ! [[ "$VIASH_PAR_SOFT_CLIPPING" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--soft_clipping' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_MARK_SECONDARY" ]]; then
  if ! [[ "$VIASH_PAR_MARK_SECONDARY" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--mark_secondary' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_OUTPUT_XB" ]]; then
  if ! [[ "$VIASH_PAR_OUTPUT_XB" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--output_xb' 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 "$VIASH_PAR_READ_TYPE" ]; then
  VIASH_PAR_READ_TYPE_CHOICES=("pacbio;ont2d;intractg")
  IFS=';'
  set -f
  if ! [[ ";${VIASH_PAR_READ_TYPE_CHOICES[*]};" =~ ";$VIASH_PAR_READ_TYPE;" ]]; then
    ViashError '--read_type' specified value of \'$VIASH_PAR_READ_TYPE\' 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 "$VIASH_PAR_VERBOSITY" ]; then
  VIASH_PAR_VERBOSITY_CHOICES=("1;2;3;4")
  IFS=';'
  set -f
  if ! [[ ";${VIASH_PAR_VERBOSITY_CHOICES[*]};" =~ ";$VIASH_PAR_VERBOSITY;" ]]; then
    ViashError '--verbosity' specified value of \'$VIASH_PAR_VERBOSITY\' 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_INDEX" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INDEX")" )
  VIASH_PAR_INDEX=$(ViashDockerAutodetectMount "$VIASH_PAR_INDEX")
fi
if [ ! -z "$VIASH_PAR_READS1" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_READS1")" )
  VIASH_PAR_READS1=$(ViashDockerAutodetectMount "$VIASH_PAR_READS1")
fi
if [ ! -z "$VIASH_PAR_READS2" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_READS2")" )
  VIASH_PAR_READS2=$(ViashDockerAutodetectMount "$VIASH_PAR_READS2")
fi
if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT")" )
  VIASH_PAR_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT" )
fi
if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_RESOURCES_DIR")" )
  VIASH_META_RESOURCES_DIR=$(ViashDockerAutodetectMount "$VIASH_META_RESOURCES_DIR")
fi
if [ ! -z "$VIASH_META_EXECUTABLE" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_EXECUTABLE")" )
  VIASH_META_EXECUTABLE=$(ViashDockerAutodetectMount "$VIASH_META_EXECUTABLE")
fi
if [ ! -z "$VIASH_META_CONFIG" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_CONFIG")" )
  VIASH_META_CONFIG=$(ViashDockerAutodetectMount "$VIASH_META_CONFIG")
fi
if [ ! -z "$VIASH_META_TEMP_DIR" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_TEMP_DIR")" )
  VIASH_META_TEMP_DIR=$(ViashDockerAutodetectMount "$VIASH_META_TEMP_DIR")
fi
  
  # get unique mounts
  VIASH_UNIQUE_MOUNTS=($(for val in "${VIASH_DIRECTORY_MOUNTS[@]}"; do echo "$val"; done | sort -u))
fi

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

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

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


# set dependency paths


ViashDebug "Running command: $(echo $VIASH_CMD)"
cat << VIASHEOF | eval $VIASH_CMD
set -e
tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-bwa_mem-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 ${VIASH_PAR_INDEX+x} ]; then echo "${VIASH_PAR_INDEX}" | sed "s#'#'\"'\"'#g;s#.*#par_index='&'#" ; else echo "# par_index="; fi )
$( if [ ! -z ${VIASH_PAR_READS1+x} ]; then echo "${VIASH_PAR_READS1}" | sed "s#'#'\"'\"'#g;s#.*#par_reads1='&'#" ; else echo "# par_reads1="; fi )
$( if [ ! -z ${VIASH_PAR_READS2+x} ]; then echo "${VIASH_PAR_READS2}" | sed "s#'#'\"'\"'#g;s#.*#par_reads2='&'#" ; else echo "# par_reads2="; 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 ${VIASH_PAR_MIN_SEED_LENGTH+x} ]; then echo "${VIASH_PAR_MIN_SEED_LENGTH}" | sed "s#'#'\"'\"'#g;s#.*#par_min_seed_length='&'#" ; else echo "# par_min_seed_length="; fi )
$( if [ ! -z ${VIASH_PAR_BAND_WIDTH+x} ]; then echo "${VIASH_PAR_BAND_WIDTH}" | sed "s#'#'\"'\"'#g;s#.*#par_band_width='&'#" ; else echo "# par_band_width="; fi )
$( if [ ! -z ${VIASH_PAR_DROPOFF+x} ]; then echo "${VIASH_PAR_DROPOFF}" | sed "s#'#'\"'\"'#g;s#.*#par_dropoff='&'#" ; else echo "# par_dropoff="; fi )
$( if [ ! -z ${VIASH_PAR_RESEED_RATIO+x} ]; then echo "${VIASH_PAR_RESEED_RATIO}" | sed "s#'#'\"'\"'#g;s#.*#par_reseed_ratio='&'#" ; else echo "# par_reseed_ratio="; fi )
$( if [ ! -z ${VIASH_PAR_SEED_OCCURRENCE+x} ]; then echo "${VIASH_PAR_SEED_OCCURRENCE}" | sed "s#'#'\"'\"'#g;s#.*#par_seed_occurrence='&'#" ; else echo "# par_seed_occurrence="; fi )
$( if [ ! -z ${VIASH_PAR_SKIP_SEEDS+x} ]; then echo "${VIASH_PAR_SKIP_SEEDS}" | sed "s#'#'\"'\"'#g;s#.*#par_skip_seeds='&'#" ; else echo "# par_skip_seeds="; fi )
$( if [ ! -z ${VIASH_PAR_CHAIN_DROP+x} ]; then echo "${VIASH_PAR_CHAIN_DROP}" | sed "s#'#'\"'\"'#g;s#.*#par_chain_drop='&'#" ; else echo "# par_chain_drop="; fi )
$( if [ ! -z ${VIASH_PAR_SEEDED_BASES+x} ]; then echo "${VIASH_PAR_SEEDED_BASES}" | sed "s#'#'\"'\"'#g;s#.*#par_seeded_bases='&'#" ; else echo "# par_seeded_bases="; fi )
$( if [ ! -z ${VIASH_PAR_MATE_RESCUE+x} ]; then echo "${VIASH_PAR_MATE_RESCUE}" | sed "s#'#'\"'\"'#g;s#.*#par_mate_rescue='&'#" ; else echo "# par_mate_rescue="; fi )
$( if [ ! -z ${VIASH_PAR_SKIP_MATE_RESCUE+x} ]; then echo "${VIASH_PAR_SKIP_MATE_RESCUE}" | sed "s#'#'\"'\"'#g;s#.*#par_skip_mate_rescue='&'#" ; else echo "# par_skip_mate_rescue="; fi )
$( if [ ! -z ${VIASH_PAR_SKIP_PAIRING+x} ]; then echo "${VIASH_PAR_SKIP_PAIRING}" | sed "s#'#'\"'\"'#g;s#.*#par_skip_pairing='&'#" ; else echo "# par_skip_pairing="; fi )
$( if [ ! -z ${VIASH_PAR_MATCH_SCORE+x} ]; then echo "${VIASH_PAR_MATCH_SCORE}" | sed "s#'#'\"'\"'#g;s#.*#par_match_score='&'#" ; else echo "# par_match_score="; fi )
$( if [ ! -z ${VIASH_PAR_MISMATCH_PENALTY+x} ]; then echo "${VIASH_PAR_MISMATCH_PENALTY}" | sed "s#'#'\"'\"'#g;s#.*#par_mismatch_penalty='&'#" ; else echo "# par_mismatch_penalty="; fi )
$( if [ ! -z ${VIASH_PAR_GAP_OPEN_PENALTY+x} ]; then echo "${VIASH_PAR_GAP_OPEN_PENALTY}" | sed "s#'#'\"'\"'#g;s#.*#par_gap_open_penalty='&'#" ; else echo "# par_gap_open_penalty="; fi )
$( if [ ! -z ${VIASH_PAR_GAP_EXTEND_PENALTY+x} ]; then echo "${VIASH_PAR_GAP_EXTEND_PENALTY}" | sed "s#'#'\"'\"'#g;s#.*#par_gap_extend_penalty='&'#" ; else echo "# par_gap_extend_penalty="; fi )
$( if [ ! -z ${VIASH_PAR_CLIPPING_PENALTY+x} ]; then echo "${VIASH_PAR_CLIPPING_PENALTY}" | sed "s#'#'\"'\"'#g;s#.*#par_clipping_penalty='&'#" ; else echo "# par_clipping_penalty="; fi )
$( if [ ! -z ${VIASH_PAR_UNPAIRED_PENALTY+x} ]; then echo "${VIASH_PAR_UNPAIRED_PENALTY}" | sed "s#'#'\"'\"'#g;s#.*#par_unpaired_penalty='&'#" ; else echo "# par_unpaired_penalty="; fi )
$( if [ ! -z ${VIASH_PAR_READ_TYPE+x} ]; then echo "${VIASH_PAR_READ_TYPE}" | sed "s#'#'\"'\"'#g;s#.*#par_read_type='&'#" ; else echo "# par_read_type="; fi )
$( if [ ! -z ${VIASH_PAR_SMART_PAIRING+x} ]; then echo "${VIASH_PAR_SMART_PAIRING}" | sed "s#'#'\"'\"'#g;s#.*#par_smart_pairing='&'#" ; else echo "# par_smart_pairing="; fi )
$( if [ ! -z ${VIASH_PAR_READ_GROUP+x} ]; then echo "${VIASH_PAR_READ_GROUP}" | sed "s#'#'\"'\"'#g;s#.*#par_read_group='&'#" ; else echo "# par_read_group="; fi )
$( if [ ! -z ${VIASH_PAR_HEADER+x} ]; then echo "${VIASH_PAR_HEADER}" | sed "s#'#'\"'\"'#g;s#.*#par_header='&'#" ; else echo "# par_header="; fi )
$( if [ ! -z ${VIASH_PAR_IGNORE_ALT+x} ]; then echo "${VIASH_PAR_IGNORE_ALT}" | sed "s#'#'\"'\"'#g;s#.*#par_ignore_alt='&'#" ; else echo "# par_ignore_alt="; fi )
$( if [ ! -z ${VIASH_PAR_PRIMARY_5PRIME+x} ]; then echo "${VIASH_PAR_PRIMARY_5PRIME}" | sed "s#'#'\"'\"'#g;s#.*#par_primary_5prime='&'#" ; else echo "# par_primary_5prime="; fi )
$( if [ ! -z ${VIASH_PAR_KEEP_MAPQ+x} ]; then echo "${VIASH_PAR_KEEP_MAPQ}" | sed "s#'#'\"'\"'#g;s#.*#par_keep_mapq='&'#" ; else echo "# par_keep_mapq="; fi )
$( if [ ! -z ${VIASH_PAR_BATCH_SIZE+x} ]; then echo "${VIASH_PAR_BATCH_SIZE}" | sed "s#'#'\"'\"'#g;s#.*#par_batch_size='&'#" ; else echo "# par_batch_size="; fi )
$( if [ ! -z ${VIASH_PAR_VERBOSITY+x} ]; then echo "${VIASH_PAR_VERBOSITY}" | sed "s#'#'\"'\"'#g;s#.*#par_verbosity='&'#" ; else echo "# par_verbosity="; fi )
$( if [ ! -z ${VIASH_PAR_MIN_SCORE+x} ]; then echo "${VIASH_PAR_MIN_SCORE}" | sed "s#'#'\"'\"'#g;s#.*#par_min_score='&'#" ; else echo "# par_min_score="; fi )
$( if [ ! -z ${VIASH_PAR_MAX_HITS_XA+x} ]; then echo "${VIASH_PAR_MAX_HITS_XA}" | sed "s#'#'\"'\"'#g;s#.*#par_max_hits_xa='&'#" ; else echo "# par_max_hits_xa="; fi )
$( if [ ! -z ${VIASH_PAR_SCORE_FRACTION+x} ]; then echo "${VIASH_PAR_SCORE_FRACTION}" | sed "s#'#'\"'\"'#g;s#.*#par_score_fraction='&'#" ; else echo "# par_score_fraction="; fi )
$( if [ ! -z ${VIASH_PAR_OUTPUT_ALL+x} ]; then echo "${VIASH_PAR_OUTPUT_ALL}" | sed "s#'#'\"'\"'#g;s#.*#par_output_all='&'#" ; else echo "# par_output_all="; fi )
$( if [ ! -z ${VIASH_PAR_APPEND_COMMENT+x} ]; then echo "${VIASH_PAR_APPEND_COMMENT}" | sed "s#'#'\"'\"'#g;s#.*#par_append_comment='&'#" ; else echo "# par_append_comment="; fi )
$( if [ ! -z ${VIASH_PAR_OUTPUT_REF_HEADER+x} ]; then echo "${VIASH_PAR_OUTPUT_REF_HEADER}" | sed "s#'#'\"'\"'#g;s#.*#par_output_ref_header='&'#" ; else echo "# par_output_ref_header="; fi )
$( if [ ! -z ${VIASH_PAR_SOFT_CLIPPING+x} ]; then echo "${VIASH_PAR_SOFT_CLIPPING}" | sed "s#'#'\"'\"'#g;s#.*#par_soft_clipping='&'#" ; else echo "# par_soft_clipping="; fi )
$( if [ ! -z ${VIASH_PAR_MARK_SECONDARY+x} ]; then echo "${VIASH_PAR_MARK_SECONDARY}" | sed "s#'#'\"'\"'#g;s#.*#par_mark_secondary='&'#" ; else echo "# par_mark_secondary="; fi )
$( if [ ! -z ${VIASH_PAR_OUTPUT_XB+x} ]; then echo "${VIASH_PAR_OUTPUT_XB}" | sed "s#'#'\"'\"'#g;s#.*#par_output_xb='&'#" ; else echo "# par_output_xb="; fi )
$( if [ ! -z ${VIASH_PAR_INSERT_SIZE+x} ]; then echo "${VIASH_PAR_INSERT_SIZE}" | sed "s#'#'\"'\"'#g;s#.*#par_insert_size='&'#" ; else echo "# par_insert_size="; 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

# unset flags
[[ "\$par_skip_mate_rescue" == "false" ]] && unset par_skip_mate_rescue
[[ "\$par_skip_pairing" == "false" ]] && unset par_skip_pairing
[[ "\$par_smart_pairing" == "false" ]] && unset par_smart_pairing
[[ "\$par_ignore_alt" == "false" ]] && unset par_ignore_alt
[[ "\$par_primary_5prime" == "false" ]] && unset par_primary_5prime
[[ "\$par_keep_mapq" == "false" ]] && unset par_keep_mapq
[[ "\$par_output_all" == "false" ]] && unset par_output_all
[[ "\$par_append_comment" == "false" ]] && unset par_append_comment
[[ "\$par_output_ref_header" == "false" ]] && unset par_output_ref_header
[[ "\$par_soft_clipping" == "false" ]] && unset par_soft_clipping
[[ "\$par_mark_secondary" == "false" ]] && unset par_mark_secondary
[[ "\$par_output_xb" == "false" ]] && unset par_output_xb

# Build the command
cmd_args=(
    # Algorithm options
    \${meta_cpus:+-t "\$meta_cpus"}
    \${par_min_seed_length:+-k "\$par_min_seed_length"}
    \${par_band_width:+-w "\$par_band_width"}
    \${par_dropoff:+-d "\$par_dropoff"}
    \${par_reseed_ratio:+-r "\$par_reseed_ratio"}
    \${par_seed_occurrence:+-y "\$par_seed_occurrence"}
    \${par_skip_seeds:+-c "\$par_skip_seeds"}
    \${par_chain_drop:+-D "\$par_chain_drop"}
    \${par_seeded_bases:+-W "\$par_seeded_bases"}
    \${par_mate_rescue:+-m "\$par_mate_rescue"}
    \${par_skip_mate_rescue:+-S}
    \${par_skip_pairing:+-P}
    
    # Scoring options
    \${par_match_score:+-A "\$par_match_score"}
    \${par_mismatch_penalty:+-B "\$par_mismatch_penalty"}
    \${par_gap_open_penalty:+-O "\$par_gap_open_penalty"}
    \${par_gap_extend_penalty:+-E "\$par_gap_extend_penalty"}
    \${par_clipping_penalty:+-L "\$par_clipping_penalty"}
    \${par_unpaired_penalty:+-U "\$par_unpaired_penalty"}
    \${par_read_type:+-x "\$par_read_type"}
    
    # Input/Output options
    \${par_smart_pairing:+-p}
    \${par_read_group:+-R "\$par_read_group"}
    \${par_header:+-H "\$par_header"}
    \${par_output:+-o "\$par_output"}
    \${par_ignore_alt:+-j}
    \${par_primary_5prime:+-5}
    \${par_keep_mapq:+-q}
    \${par_batch_size:+-K "\$par_batch_size"}
    \${par_verbosity:+-v "\$par_verbosity"}
    \${par_min_score:+-T "\$par_min_score"}
    \${par_max_hits_xa:+-h "\$par_max_hits_xa"}
    \${par_score_fraction:+-z "\$par_score_fraction"}
    \${par_output_all:+-a}
    \${par_append_comment:+-C}
    \${par_output_ref_header:+-V}
    \${par_soft_clipping:+-Y}
    \${par_mark_secondary:+-M}
    \${par_output_xb:+-u}
    \${par_insert_size:+-I "\$par_insert_size"}
    
    # Index and input files
    "\$par_index"
    "\$par_reads1"
    \${par_reads2:+"\$par_reads2"}
)

# Run bwa mem
bwa mem "\${cmd_args[@]}"
VIASHMAIN
bash "\$tempscript" &
wait "\$!"

VIASHEOF


if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  # strip viash automount from file paths
  
  if [ ! -z "$VIASH_PAR_INDEX" ]; then
    VIASH_PAR_INDEX=$(ViashDockerStripAutomount "$VIASH_PAR_INDEX")
  fi
  if [ ! -z "$VIASH_PAR_READS1" ]; then
    VIASH_PAR_READS1=$(ViashDockerStripAutomount "$VIASH_PAR_READS1")
  fi
  if [ ! -z "$VIASH_PAR_READS2" ]; then
    VIASH_PAR_READS2=$(ViashDockerStripAutomount "$VIASH_PAR_READS2")
  fi
  if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
    VIASH_PAR_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT")
  fi
  if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
    VIASH_META_RESOURCES_DIR=$(ViashDockerStripAutomount "$VIASH_META_RESOURCES_DIR")
  fi
  if [ ! -z "$VIASH_META_EXECUTABLE" ]; then
    VIASH_META_EXECUTABLE=$(ViashDockerStripAutomount "$VIASH_META_EXECUTABLE")
  fi
  if [ ! -z "$VIASH_META_CONFIG" ]; then
    VIASH_META_CONFIG=$(ViashDockerStripAutomount "$VIASH_META_CONFIG")
  fi
  if [ ! -z "$VIASH_META_TEMP_DIR" ]; then
    VIASH_META_TEMP_DIR=$(ViashDockerStripAutomount "$VIASH_META_TEMP_DIR")
  fi
fi


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


exit 0
