#!/usr/bin/env bash

# samtools_fasta main
# 
# 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:
#  * Emma Rousseau (author, maintainer)

set -e

if [ -z "$VIASH_TEMP" ]; then
  VIASH_TEMP=${VIASH_TEMP:-$VIASH_TMPDIR}
  VIASH_TEMP=${VIASH_TEMP:-$VIASH_TEMPDIR}
  VIASH_TEMP=${VIASH_TEMP:-$VIASH_TMP}
  VIASH_TEMP=${VIASH_TEMP:-$TMPDIR}
  VIASH_TEMP=${VIASH_TEMP:-$TMP}
  VIASH_TEMP=${VIASH_TEMP:-$TEMPDIR}
  VIASH_TEMP=${VIASH_TEMP:-$TEMP}
  VIASH_TEMP=${VIASH_TEMP:-/tmp}
fi

# define helper functions
# ViashQuote: put quotes around non flag values
# $1     : unquoted string
# return : possibly quoted string
# examples:
#   ViashQuote --foo      # returns --foo
#   ViashQuote bar        # returns 'bar'
#   Viashquote --foo=bar  # returns --foo='bar'
function ViashQuote {
  if [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+=.+$ ]]; then
    echo "$1" | sed "s#=\(.*\)#='\1'#"
  elif [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+$ ]]; then
    echo "$1"
  else
    echo "'$1'"
  fi
}
# ViashRemoveFlags: Remove leading flag
# $1     : string with a possible leading flag
# return : string without possible leading flag
# examples:
#   ViashRemoveFlags --foo=bar  # returns bar
function ViashRemoveFlags {
  echo "$1" | sed 's/^--*[a-zA-Z0-9_\-]*=//'
}
# ViashSourceDir: return the path of a bash file, following symlinks
# usage   : ViashSourceDir ${BASH_SOURCE[0]}
# $1      : Should always be set to ${BASH_SOURCE[0]}
# returns : The absolute path of the bash file
function ViashSourceDir {
  local source="$1"
  while [ -h "$source" ]; do
    local dir="$( cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd )"
    source="$(readlink "$source")"
    [[ $source != /* ]] && source="$dir/$source"
  done
  cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd
}
# ViashFindTargetDir: return the path of the '.build.yaml' file, following symlinks
# usage   : ViashFindTargetDir 'ScriptPath'
# $1      : The location from where to start the upward search
# returns : The absolute path of the '.build.yaml' file
function ViashFindTargetDir {
  local source="$1"
  while [[ "$source" != "" && ! -e "$source/.build.yaml" ]]; do
    source=${source%/*}
  done
  echo $source
}
# see https://en.wikipedia.org/wiki/Syslog#Severity_level
VIASH_LOGCODE_EMERGENCY=0
VIASH_LOGCODE_ALERT=1
VIASH_LOGCODE_CRITICAL=2
VIASH_LOGCODE_ERROR=3
VIASH_LOGCODE_WARNING=4
VIASH_LOGCODE_NOTICE=5
VIASH_LOGCODE_INFO=6
VIASH_LOGCODE_DEBUG=7
VIASH_VERBOSITY=$VIASH_LOGCODE_NOTICE

# ViashLog: Log events depending on the verbosity level
# usage: ViashLog 1 alert Oh no something went wrong!
# $1: required verbosity level
# $2: display tag
# $3+: messages to display
# stdout: Your input, prepended by '[$2] '.
function ViashLog {
  local required_level="$1"
  local display_tag="$2"
  shift 2
  if [ $VIASH_VERBOSITY -ge $required_level ]; then
    >&2 echo "[$display_tag]" "$@"
  fi
}

# ViashEmergency: log events when the system is unstable
# usage: ViashEmergency Oh no something went wrong.
# stdout: Your input, prepended by '[emergency] '.
function ViashEmergency {
  ViashLog $VIASH_LOGCODE_EMERGENCY emergency "$@"
}

# ViashAlert: log events when actions must be taken immediately (e.g. corrupted system database)
# usage: ViashAlert Oh no something went wrong.
# stdout: Your input, prepended by '[alert] '.
function ViashAlert {
  ViashLog $VIASH_LOGCODE_ALERT alert "$@"
}

# ViashCritical: log events when a critical condition occurs
# usage: ViashCritical Oh no something went wrong.
# stdout: Your input, prepended by '[critical] '.
function ViashCritical {
  ViashLog $VIASH_LOGCODE_CRITICAL critical "$@"
}

# ViashError: log events when an error condition occurs
# usage: ViashError Oh no something went wrong.
# stdout: Your input, prepended by '[error] '.
function ViashError {
  ViashLog $VIASH_LOGCODE_ERROR error "$@"
}

# ViashWarning: log potentially abnormal events
# usage: ViashWarning Something may have gone wrong.
# stdout: Your input, prepended by '[warning] '.
function ViashWarning {
  ViashLog $VIASH_LOGCODE_WARNING warning "$@"
}

# ViashNotice: log significant but normal events
# usage: ViashNotice This just happened.
# stdout: Your input, prepended by '[notice] '.
function ViashNotice {
  ViashLog $VIASH_LOGCODE_NOTICE notice "$@"
}

# ViashInfo: log normal events
# usage: ViashInfo This just happened.
# stdout: Your input, prepended by '[info] '.
function ViashInfo {
  ViashLog $VIASH_LOGCODE_INFO info "$@"
}

# ViashDebug: log all events, for debugging purposes
# usage: ViashDebug This just happened.
# stdout: Your input, prepended by '[debug] '.
function ViashDebug {
  ViashLog $VIASH_LOGCODE_DEBUG debug "$@"
}

# find source folder of this component
VIASH_META_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}`

# find the root of the built components & dependencies
VIASH_TARGET_DIR=`ViashFindTargetDir $VIASH_META_RESOURCES_DIR`

# define meta fields
VIASH_META_NAME="samtools_fasta"
VIASH_META_FUNCTIONALITY_NAME="samtools_fasta"
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/samtools:1.19.2--h50ea8bc_1
ENTRYPOINT []
RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt

LABEL org.opencontainers.image.authors="Emma Rousseau"
LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_fasta"
LABEL org.opencontainers.image.created="2025-10-03T08:11:17Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="9991e9a4f5ddd5085a4e2becf962950b1daf594b"
LABEL org.opencontainers.image.version="main"

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 "samtools_fasta main"
  echo ""
  echo "Converts a SAM, BAM or CRAM to FASTA format."
  echo ""
  echo "Inputs:"
  echo "    --input"
  echo "        type: file, required parameter, file must exist"
  echo "        input SAM/BAM/CRAM file"
  echo ""
  echo "Outputs:"
  echo "    --output"
  echo "        type: file, required parameter, output, file must exist"
  echo "        output FASTA file"
  echo ""
  echo "Options:"
  echo "    -n, --no_suffix"
  echo "        type: boolean_true"
  echo "        By default, either '/1' or '/2' is added to the end of read names where"
  echo "        the corresponding"
  echo "        READ1 or READ2 FLAG bit is set. Using -n causes read names to be left as"
  echo "        they are."
  echo ""
  echo "    -N, --suffix"
  echo "        type: boolean_true"
  echo "        Always add either '/1' or '/2' to the end of read names even when put"
  echo "        into different files."
  echo ""
  echo "    -O, --use_oq"
  echo "        type: boolean_true"
  echo "        Use quality values from OQ tags in preference to standard quality string"
  echo "        if available."
  echo ""
  echo "    -s, --singleton"
  echo "        type: file, file must exist"
  echo "        write singleton reads to FILE."
  echo ""
  echo "    -t, --copy_tags"
  echo "        type: boolean_true"
  echo "        Copy RG, BC and QT tags to the FASTA header line, if they exist."
  echo ""
  echo "    -T, --copy_tags_list"
  echo "        type: string"
  echo "        Specify a comma-separated list of tags to copy to the FASTA header line,"
  echo "        if they exist."
  echo "        TAGLIST can be blank or \`*\` to indicate all tags should be copied to the"
  echo "        output. If using \`*\`,"
  echo "        be careful to quote it to avoid unwanted shell expansion."
  echo ""
  echo "    -1, --read1"
  echo "        type: file, output, file must exist"
  echo "        Write reads with the READ1 FLAG set (and READ2 not set) to FILE instead"
  echo "        of outputting them."
  echo "        If the -s option is used, only paired reads will be written to this"
  echo "        file."
  echo ""
  echo "    -2, --read2"
  echo "        type: file, output, file must exist"
  echo "        Write reads with the READ2 FLAG set (and READ1 not set) to FILE instead"
  echo "        of outputting them."
  echo "        If the -s option is used, only paired reads will be written to this"
  echo "        file."
  echo ""
  echo "    -o, --output_reads"
  echo "        type: file, output, file must exist"
  echo "        Write reads with either READ1 FLAG or READ2 flag set to FILE instead of"
  echo "        outputting them to stdout."
  echo "        This is equivalent to -1 FILE -2 FILE."
  echo ""
  echo "    0, --output_reads_both"
  echo "        type: file, output, file must exist"
  echo "        Write reads where the READ1 and READ2 FLAG bits set are either both set"
  echo "        or both unset to FILE"
  echo "        instead of outputting them."
  echo ""
  echo "    -f, --filter_flags"
  echo "        type: integer"
  echo "        example: 0"
  echo "        Only output alignments with all bits set in INT present in the FLAG"
  echo "        field. INT can be specified"
  echo "        in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/) or in octal by"
  echo "        beginning with '0'"
  echo "        (i.e. /^0[0-7]+/). Default: \`0\`."
  echo ""
  echo "    -F, --excl_flags"
  echo "        type: string"
  echo "        example: 0x900"
  echo "        Do not output alignments with any bits set in INT present in the FLAG"
  echo "        field. INT can be specified"
  echo "        in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/) or in octal by"
  echo "        beginning with '0'"
  echo "        (i.e. /^0[0-7]+/). This defaults to 0x900 representing filtering of"
  echo "        secondary and"
  echo "        supplementary alignments. Default: \`0x900\`."
  echo ""
  echo "    --rf, --incl_flags"
  echo "        type: string"
  echo "        example: 0"
  echo "        Only output alignments with any bits set in INT present in the FLAG"
  echo "        field. INT can be specified"
  echo "        in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/), in octal by"
  echo "        beginning with '0'"
  echo "        (i.e. /^0[0-7]+/), as a decimal number not beginning with '0' or as a"
  echo "        comma-separated list of"
  echo "        flag names. Default: \`0\`."
  echo ""
  echo "    -G, --excl_flags_all"
  echo "        type: integer"
  echo "        example: 0"
  echo "        Only EXCLUDE reads with all of the bits set in INT present in the FLAG"
  echo "        field. INT can be specified"
  echo "        in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/) or in octal by"
  echo "        beginning with '0' (i.e. /^0[0-7]+/)."
  echo "        Default: \`0\`."
  echo ""
  echo "    -d, --aux_tag"
  echo "        type: string"
  echo "        Only output alignments containing an auxiliary tag matching both TAG and"
  echo "        VAL. If VAL is omitted"
  echo "        then any value is accepted. The tag types supported are i, f, Z, A and"
  echo "        H. \"B\" arrays are not"
  echo "        supported. This is comparable to the method used in samtools view --tag."
  echo "        The option may be specified"
  echo "        multiple times and is equivalent to using the --aux_tag_file option."
  echo ""
  echo "    -D, --aux_tag_file"
  echo "        type: string"
  echo "        Only output alignments containing an auxiliary tag matching TAG and"
  echo "        having a value listed in FILE."
  echo "        The format of the file is one line per value. This is equivalent to"
  echo "        specifying --aux_tag multiple times."
  echo ""
  echo "    -i, --casava"
  echo "        type: boolean_true"
  echo "        add Illumina Casava 1.8 format entry to header (eg 1:N:0:ATCACG)"
  echo ""
  echo "    -c, --compression"
  echo "        type: integer"
  echo "        example: 0"
  echo "        set compression level when writing gz or bgzf fasta files."
  echo ""
  echo "    --i1, --index1"
  echo "        type: file, file must exist"
  echo "        write first index reads to FILE."
  echo ""
  echo "    --i2, --index2"
  echo "        type: file, file must exist"
  echo "        write second index reads to FILE."
  echo ""
  echo "    --barcode_tag"
  echo "        type: string"
  echo "        example: BC"
  echo "        Auxiliary tag to find index reads in. Default: \`BC\`."
  echo ""
  echo "    --quality_tag"
  echo "        type: string"
  echo "        example: QT"
  echo "        Auxiliary tag to find index quality in. Default: \`QT\`."
  echo ""
  echo "    --index_format"
  echo "        type: string"
  echo "        string to describe how to parse the barcode and quality tags. For"
  echo "        example:"
  echo "        * \`i14i8\`: the first 14 characters are index 1, the next 8 characters"
  echo "        are index 2."
  echo "        * \`n8i14\`: ignore the first 8 characters, and use the next 14 characters"
  echo "        for index 1."
  echo "        If the tag contains a separator, then the numeric part can be replaced"
  echo "        with\`*\` to mean"
  echo "        'read until the separator or end of tag', for example: \`n*i*\`."
  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 "$1")"
            shift 1
            ;;
        --version)
            echo "samtools_fasta main"
            exit
            ;;
        --input)
            [ -n "$VIASH_PAR_INPUT" ] && ViashError Bad arguments for option \'--input\': \'$VIASH_PAR_INPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INPUT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --input. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --input=*)
            [ -n "$VIASH_PAR_INPUT" ] && ViashError Bad arguments for option \'--input=*\': \'$VIASH_PAR_INPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INPUT=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --output)
            [ -n "$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 "$1")
            shift 1
            ;;
        --no_suffix)
            [ -n "$VIASH_PAR_NO_SUFFIX" ] && ViashError Bad arguments for option \'--no_suffix\': \'$VIASH_PAR_NO_SUFFIX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_NO_SUFFIX=true
            shift 1
            ;;
        -n)
            [ -n "$VIASH_PAR_NO_SUFFIX" ] && ViashError Bad arguments for option \'-n\': \'$VIASH_PAR_NO_SUFFIX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_NO_SUFFIX=true
            shift 1
            ;;
        --suffix)
            [ -n "$VIASH_PAR_SUFFIX" ] && ViashError Bad arguments for option \'--suffix\': \'$VIASH_PAR_SUFFIX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SUFFIX=true
            shift 1
            ;;
        -N)
            [ -n "$VIASH_PAR_SUFFIX" ] && ViashError Bad arguments for option \'-N\': \'$VIASH_PAR_SUFFIX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SUFFIX=true
            shift 1
            ;;
        --use_oq)
            [ -n "$VIASH_PAR_USE_OQ" ] && ViashError Bad arguments for option \'--use_oq\': \'$VIASH_PAR_USE_OQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_USE_OQ=true
            shift 1
            ;;
        -O)
            [ -n "$VIASH_PAR_USE_OQ" ] && ViashError Bad arguments for option \'-O\': \'$VIASH_PAR_USE_OQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_USE_OQ=true
            shift 1
            ;;
        --singleton)
            [ -n "$VIASH_PAR_SINGLETON" ] && ViashError Bad arguments for option \'--singleton\': \'$VIASH_PAR_SINGLETON\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SINGLETON="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --singleton. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --singleton=*)
            [ -n "$VIASH_PAR_SINGLETON" ] && ViashError Bad arguments for option \'--singleton=*\': \'$VIASH_PAR_SINGLETON\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SINGLETON=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -s)
            [ -n "$VIASH_PAR_SINGLETON" ] && ViashError Bad arguments for option \'-s\': \'$VIASH_PAR_SINGLETON\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SINGLETON="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -s. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --copy_tags)
            [ -n "$VIASH_PAR_COPY_TAGS" ] && ViashError Bad arguments for option \'--copy_tags\': \'$VIASH_PAR_COPY_TAGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_COPY_TAGS=true
            shift 1
            ;;
        -t)
            [ -n "$VIASH_PAR_COPY_TAGS" ] && ViashError Bad arguments for option \'-t\': \'$VIASH_PAR_COPY_TAGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_COPY_TAGS=true
            shift 1
            ;;
        --copy_tags_list)
            [ -n "$VIASH_PAR_COPY_TAGS_LIST" ] && ViashError Bad arguments for option \'--copy_tags_list\': \'$VIASH_PAR_COPY_TAGS_LIST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_COPY_TAGS_LIST="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --copy_tags_list. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --copy_tags_list=*)
            [ -n "$VIASH_PAR_COPY_TAGS_LIST" ] && ViashError Bad arguments for option \'--copy_tags_list=*\': \'$VIASH_PAR_COPY_TAGS_LIST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_COPY_TAGS_LIST=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -T)
            [ -n "$VIASH_PAR_COPY_TAGS_LIST" ] && ViashError Bad arguments for option \'-T\': \'$VIASH_PAR_COPY_TAGS_LIST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_COPY_TAGS_LIST="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -T. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --read1)
            [ -n "$VIASH_PAR_READ1" ] && ViashError Bad arguments for option \'--read1\': \'$VIASH_PAR_READ1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_READ1="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --read1. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --read1=*)
            [ -n "$VIASH_PAR_READ1" ] && ViashError Bad arguments for option \'--read1=*\': \'$VIASH_PAR_READ1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_READ1=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -1)
            [ -n "$VIASH_PAR_READ1" ] && ViashError Bad arguments for option \'-1\': \'$VIASH_PAR_READ1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_READ1="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -1. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --read2)
            [ -n "$VIASH_PAR_READ2" ] && ViashError Bad arguments for option \'--read2\': \'$VIASH_PAR_READ2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_READ2="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --read2. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --read2=*)
            [ -n "$VIASH_PAR_READ2" ] && ViashError Bad arguments for option \'--read2=*\': \'$VIASH_PAR_READ2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_READ2=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -2)
            [ -n "$VIASH_PAR_READ2" ] && ViashError Bad arguments for option \'-2\': \'$VIASH_PAR_READ2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_READ2="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -2. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --output_reads)
            [ -n "$VIASH_PAR_OUTPUT_READS" ] && ViashError Bad arguments for option \'--output_reads\': \'$VIASH_PAR_OUTPUT_READS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_READS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --output_reads. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --output_reads=*)
            [ -n "$VIASH_PAR_OUTPUT_READS" ] && ViashError Bad arguments for option \'--output_reads=*\': \'$VIASH_PAR_OUTPUT_READS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_READS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -o)
            [ -n "$VIASH_PAR_OUTPUT_READS" ] && ViashError Bad arguments for option \'-o\': \'$VIASH_PAR_OUTPUT_READS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_READS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -o. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --output_reads_both)
            [ -n "$VIASH_PAR_OUTPUT_READS_BOTH" ] && ViashError Bad arguments for option \'--output_reads_both\': \'$VIASH_PAR_OUTPUT_READS_BOTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_READS_BOTH="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --output_reads_both. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --output_reads_both=*)
            [ -n "$VIASH_PAR_OUTPUT_READS_BOTH" ] && ViashError Bad arguments for option \'--output_reads_both=*\': \'$VIASH_PAR_OUTPUT_READS_BOTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_READS_BOTH=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        0)
            [ -n "$VIASH_PAR_OUTPUT_READS_BOTH" ] && ViashError Bad arguments for option \'0\': \'$VIASH_PAR_OUTPUT_READS_BOTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_READS_BOTH="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to 0. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --filter_flags)
            [ -n "$VIASH_PAR_FILTER_FLAGS" ] && ViashError Bad arguments for option \'--filter_flags\': \'$VIASH_PAR_FILTER_FLAGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FILTER_FLAGS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --filter_flags. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --filter_flags=*)
            [ -n "$VIASH_PAR_FILTER_FLAGS" ] && ViashError Bad arguments for option \'--filter_flags=*\': \'$VIASH_PAR_FILTER_FLAGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FILTER_FLAGS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -f)
            [ -n "$VIASH_PAR_FILTER_FLAGS" ] && ViashError Bad arguments for option \'-f\': \'$VIASH_PAR_FILTER_FLAGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FILTER_FLAGS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -f. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --excl_flags)
            [ -n "$VIASH_PAR_EXCL_FLAGS" ] && ViashError Bad arguments for option \'--excl_flags\': \'$VIASH_PAR_EXCL_FLAGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_EXCL_FLAGS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --excl_flags. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --excl_flags=*)
            [ -n "$VIASH_PAR_EXCL_FLAGS" ] && ViashError Bad arguments for option \'--excl_flags=*\': \'$VIASH_PAR_EXCL_FLAGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_EXCL_FLAGS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -F)
            [ -n "$VIASH_PAR_EXCL_FLAGS" ] && ViashError Bad arguments for option \'-F\': \'$VIASH_PAR_EXCL_FLAGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_EXCL_FLAGS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -F. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --incl_flags)
            [ -n "$VIASH_PAR_INCL_FLAGS" ] && ViashError Bad arguments for option \'--incl_flags\': \'$VIASH_PAR_INCL_FLAGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INCL_FLAGS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --incl_flags. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --incl_flags=*)
            [ -n "$VIASH_PAR_INCL_FLAGS" ] && ViashError Bad arguments for option \'--incl_flags=*\': \'$VIASH_PAR_INCL_FLAGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INCL_FLAGS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --rf)
            [ -n "$VIASH_PAR_INCL_FLAGS" ] && ViashError Bad arguments for option \'--rf\': \'$VIASH_PAR_INCL_FLAGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INCL_FLAGS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --rf. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --excl_flags_all)
            [ -n "$VIASH_PAR_EXCL_FLAGS_ALL" ] && ViashError Bad arguments for option \'--excl_flags_all\': \'$VIASH_PAR_EXCL_FLAGS_ALL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_EXCL_FLAGS_ALL="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --excl_flags_all. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --excl_flags_all=*)
            [ -n "$VIASH_PAR_EXCL_FLAGS_ALL" ] && ViashError Bad arguments for option \'--excl_flags_all=*\': \'$VIASH_PAR_EXCL_FLAGS_ALL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_EXCL_FLAGS_ALL=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -G)
            [ -n "$VIASH_PAR_EXCL_FLAGS_ALL" ] && ViashError Bad arguments for option \'-G\': \'$VIASH_PAR_EXCL_FLAGS_ALL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_EXCL_FLAGS_ALL="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -G. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --aux_tag)
            [ -n "$VIASH_PAR_AUX_TAG" ] && ViashError Bad arguments for option \'--aux_tag\': \'$VIASH_PAR_AUX_TAG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_AUX_TAG="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --aux_tag. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --aux_tag=*)
            [ -n "$VIASH_PAR_AUX_TAG" ] && ViashError Bad arguments for option \'--aux_tag=*\': \'$VIASH_PAR_AUX_TAG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_AUX_TAG=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -d)
            [ -n "$VIASH_PAR_AUX_TAG" ] && ViashError Bad arguments for option \'-d\': \'$VIASH_PAR_AUX_TAG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_AUX_TAG="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -d. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --aux_tag_file)
            [ -n "$VIASH_PAR_AUX_TAG_FILE" ] && ViashError Bad arguments for option \'--aux_tag_file\': \'$VIASH_PAR_AUX_TAG_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_AUX_TAG_FILE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --aux_tag_file. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --aux_tag_file=*)
            [ -n "$VIASH_PAR_AUX_TAG_FILE" ] && ViashError Bad arguments for option \'--aux_tag_file=*\': \'$VIASH_PAR_AUX_TAG_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_AUX_TAG_FILE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -D)
            [ -n "$VIASH_PAR_AUX_TAG_FILE" ] && ViashError Bad arguments for option \'-D\': \'$VIASH_PAR_AUX_TAG_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_AUX_TAG_FILE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -D. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --casava)
            [ -n "$VIASH_PAR_CASAVA" ] && ViashError Bad arguments for option \'--casava\': \'$VIASH_PAR_CASAVA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CASAVA=true
            shift 1
            ;;
        -i)
            [ -n "$VIASH_PAR_CASAVA" ] && ViashError Bad arguments for option \'-i\': \'$VIASH_PAR_CASAVA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CASAVA=true
            shift 1
            ;;
        --compression)
            [ -n "$VIASH_PAR_COMPRESSION" ] && ViashError Bad arguments for option \'--compression\': \'$VIASH_PAR_COMPRESSION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_COMPRESSION="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --compression. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --compression=*)
            [ -n "$VIASH_PAR_COMPRESSION" ] && ViashError Bad arguments for option \'--compression=*\': \'$VIASH_PAR_COMPRESSION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_COMPRESSION=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -c)
            [ -n "$VIASH_PAR_COMPRESSION" ] && ViashError Bad arguments for option \'-c\': \'$VIASH_PAR_COMPRESSION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_COMPRESSION="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -c. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --index1)
            [ -n "$VIASH_PAR_INDEX1" ] && ViashError Bad arguments for option \'--index1\': \'$VIASH_PAR_INDEX1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INDEX1="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --index1. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --index1=*)
            [ -n "$VIASH_PAR_INDEX1" ] && ViashError Bad arguments for option \'--index1=*\': \'$VIASH_PAR_INDEX1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INDEX1=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --i1)
            [ -n "$VIASH_PAR_INDEX1" ] && ViashError Bad arguments for option \'--i1\': \'$VIASH_PAR_INDEX1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INDEX1="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --i1. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --index2)
            [ -n "$VIASH_PAR_INDEX2" ] && ViashError Bad arguments for option \'--index2\': \'$VIASH_PAR_INDEX2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INDEX2="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --index2. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --index2=*)
            [ -n "$VIASH_PAR_INDEX2" ] && ViashError Bad arguments for option \'--index2=*\': \'$VIASH_PAR_INDEX2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INDEX2=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --i2)
            [ -n "$VIASH_PAR_INDEX2" ] && ViashError Bad arguments for option \'--i2\': \'$VIASH_PAR_INDEX2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INDEX2="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --i2. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --barcode_tag)
            [ -n "$VIASH_PAR_BARCODE_TAG" ] && ViashError Bad arguments for option \'--barcode_tag\': \'$VIASH_PAR_BARCODE_TAG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_BARCODE_TAG="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --barcode_tag. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --barcode_tag=*)
            [ -n "$VIASH_PAR_BARCODE_TAG" ] && ViashError Bad arguments for option \'--barcode_tag=*\': \'$VIASH_PAR_BARCODE_TAG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_BARCODE_TAG=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --quality_tag)
            [ -n "$VIASH_PAR_QUALITY_TAG" ] && ViashError Bad arguments for option \'--quality_tag\': \'$VIASH_PAR_QUALITY_TAG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_QUALITY_TAG="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --quality_tag. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --quality_tag=*)
            [ -n "$VIASH_PAR_QUALITY_TAG" ] && ViashError Bad arguments for option \'--quality_tag=*\': \'$VIASH_PAR_QUALITY_TAG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_QUALITY_TAG=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --index_format)
            [ -n "$VIASH_PAR_INDEX_FORMAT" ] && ViashError Bad arguments for option \'--index_format\': \'$VIASH_PAR_INDEX_FORMAT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INDEX_FORMAT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --index_format. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --index_format=*)
            [ -n "$VIASH_PAR_INDEX_FORMAT" ] && ViashError Bad arguments for option \'--index_format=*\': \'$VIASH_PAR_INDEX_FORMAT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INDEX_FORMAT=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        ---engine)
            VIASH_ENGINE_ID="$2"
            shift 2
            ;;
        ---engine=*)
            VIASH_ENGINE_ID="$(ViashRemoveFlags "$1")"
            shift 1
            ;;
        ---setup)
            VIASH_MODE='setup'
            VIASH_SETUP_STRATEGY="$2"
            shift 2
            ;;
        ---setup=*)
            VIASH_MODE='setup'
            VIASH_SETUP_STRATEGY="$(ViashRemoveFlags "$1")"
            shift 1
            ;;
        ---dockerfile)
            VIASH_MODE='dockerfile'
            shift 1
            ;;
        ---docker_run_args)
            VIASH_DOCKER_RUN_ARGS+=("$2")
            shift 2
            ;;
        ---docker_run_args=*)
            VIASH_DOCKER_RUN_ARGS+=("$(ViashRemoveFlags "$1")")
            shift 1
            ;;
        ---docker_image_id)
            VIASH_MODE='docker_image_id'
            shift 1
            ;;
        ---debug)
            VIASH_MODE='debug'
            shift 1
            ;;
        ---cpus)
            [ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_CPUS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to ---cpus. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        ---cpus=*)
            [ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus=*\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_CPUS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        ---memory)
            [ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_MEMORY="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to ---memory. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        ---memory=*)
            [ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory=*\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_MEMORY=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        *)  # positional arg or unknown option
            # since the positional args will be eval'd, can we always quote, instead of using ViashQuote
            VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'"
            [[ $1 == -* ]] && ViashWarning $1 looks like a parameter but is not a defined parameter and will instead be treated as a positional argument. Use "--help" to get more information on the parameters.
            shift # past argument
            ;;
    esac
done

# parse positional parameters
eval set -- $VIASH_POSITIONAL_ARGS


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

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

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

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

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

  # build docker image
  elif [ "$VIASH_MODE" == "setup" ]; then
    ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY"
    ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash'
    exit 0
  fi

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

# setting computational defaults

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


# check whether required parameters exist
if [ -z ${VIASH_PAR_INPUT+x} ]; then
  ViashError '--input' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_PAR_OUTPUT+x} ]; then
  ViashError '--output' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_NAME+x} ]; then
  ViashError 'name' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then
  ViashError 'functionality_name' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_RESOURCES_DIR+x} ]; then
  ViashError 'resources_dir' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_EXECUTABLE+x} ]; then
  ViashError 'executable' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_CONFIG+x} ]; then
  ViashError 'config' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_TEMP_DIR+x} ]; then
  ViashError 'temp_dir' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi

# filling in defaults
if [ -z ${VIASH_PAR_NO_SUFFIX+x} ]; then
  VIASH_PAR_NO_SUFFIX="false"
fi
if [ -z ${VIASH_PAR_SUFFIX+x} ]; then
  VIASH_PAR_SUFFIX="false"
fi
if [ -z ${VIASH_PAR_USE_OQ+x} ]; then
  VIASH_PAR_USE_OQ="false"
fi
if [ -z ${VIASH_PAR_COPY_TAGS+x} ]; then
  VIASH_PAR_COPY_TAGS="false"
fi
if [ -z ${VIASH_PAR_CASAVA+x} ]; then
  VIASH_PAR_CASAVA="false"
fi

# check whether required files exist
if [ ! -z "$VIASH_PAR_INPUT" ] && [ ! -e "$VIASH_PAR_INPUT" ]; then
  ViashError "Input file '$VIASH_PAR_INPUT' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_SINGLETON" ] && [ ! -e "$VIASH_PAR_SINGLETON" ]; then
  ViashError "Input file '$VIASH_PAR_SINGLETON' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_INDEX1" ] && [ ! -e "$VIASH_PAR_INDEX1" ]; then
  ViashError "Input file '$VIASH_PAR_INDEX1' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_INDEX2" ] && [ ! -e "$VIASH_PAR_INDEX2" ]; then
  ViashError "Input file '$VIASH_PAR_INDEX2' does not exist."
  exit 1
fi

# check whether parameters values are of the right type
if [[ -n "$VIASH_PAR_NO_SUFFIX" ]]; then
  if ! [[ "$VIASH_PAR_NO_SUFFIX" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--no_suffix' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SUFFIX" ]]; then
  if ! [[ "$VIASH_PAR_SUFFIX" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--suffix' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_USE_OQ" ]]; then
  if ! [[ "$VIASH_PAR_USE_OQ" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--use_oq' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_COPY_TAGS" ]]; then
  if ! [[ "$VIASH_PAR_COPY_TAGS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--copy_tags' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_FILTER_FLAGS" ]]; then
  if ! [[ "$VIASH_PAR_FILTER_FLAGS" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--filter_flags' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_EXCL_FLAGS_ALL" ]]; then
  if ! [[ "$VIASH_PAR_EXCL_FLAGS_ALL" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--excl_flags_all' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_CASAVA" ]]; then
  if ! [[ "$VIASH_PAR_CASAVA" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--casava' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_COMPRESSION" ]]; then
  if ! [[ "$VIASH_PAR_COMPRESSION" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--compression' has to be an integer. 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

# create parent directories of output files, if so desired
if [ ! -z "$VIASH_PAR_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_OUTPUT")"
fi
if [ ! -z "$VIASH_PAR_READ1" ] && [ ! -d "$(dirname "$VIASH_PAR_READ1")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_READ1")"
fi
if [ ! -z "$VIASH_PAR_READ2" ] && [ ! -d "$(dirname "$VIASH_PAR_READ2")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_READ2")"
fi
if [ ! -z "$VIASH_PAR_OUTPUT_READS" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT_READS")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_OUTPUT_READS")"
fi
if [ ! -z "$VIASH_PAR_OUTPUT_READS_BOTH" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT_READS_BOTH")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_OUTPUT_READS_BOTH")"
fi

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

if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  # detect volumes from file arguments
  VIASH_CHOWN_VARS=()
if [ ! -z "$VIASH_PAR_INPUT" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INPUT")" )
  VIASH_PAR_INPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_INPUT")
fi
if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT")" )
  VIASH_PAR_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT" )
fi
if [ ! -z "$VIASH_PAR_SINGLETON" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_SINGLETON")" )
  VIASH_PAR_SINGLETON=$(ViashDockerAutodetectMount "$VIASH_PAR_SINGLETON")
fi
if [ ! -z "$VIASH_PAR_READ1" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_READ1")" )
  VIASH_PAR_READ1=$(ViashDockerAutodetectMount "$VIASH_PAR_READ1")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_READ1" )
fi
if [ ! -z "$VIASH_PAR_READ2" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_READ2")" )
  VIASH_PAR_READ2=$(ViashDockerAutodetectMount "$VIASH_PAR_READ2")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_READ2" )
fi
if [ ! -z "$VIASH_PAR_OUTPUT_READS" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT_READS")" )
  VIASH_PAR_OUTPUT_READS=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT_READS")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT_READS" )
fi
if [ ! -z "$VIASH_PAR_OUTPUT_READS_BOTH" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT_READS_BOTH")" )
  VIASH_PAR_OUTPUT_READS_BOTH=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT_READS_BOTH")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT_READS_BOTH" )
fi
if [ ! -z "$VIASH_PAR_INDEX1" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INDEX1")" )
  VIASH_PAR_INDEX1=$(ViashDockerAutodetectMount "$VIASH_PAR_INDEX1")
fi
if [ ! -z "$VIASH_PAR_INDEX2" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INDEX2")" )
  VIASH_PAR_INDEX2=$(ViashDockerAutodetectMount "$VIASH_PAR_INDEX2")
fi
if [ ! -z "$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-samtools_fasta-XXXXXX").sh
function clean_up {
  rm "\$tempscript"
}
function interrupt {
  echo -e "\nCTRL-C Pressed..."
  exit 1
}
trap clean_up EXIT
trap interrupt INT SIGINT
cat > "\$tempscript" << 'VIASHMAIN'
#!/bin/bash

## VIASH START
# The following code has been auto-generated by Viash.
$( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_input='&'#" ; else echo "# par_input="; fi )
$( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "${VIASH_PAR_OUTPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_output='&'#" ; else echo "# par_output="; fi )
$( if [ ! -z ${VIASH_PAR_NO_SUFFIX+x} ]; then echo "${VIASH_PAR_NO_SUFFIX}" | sed "s#'#'\"'\"'#g;s#.*#par_no_suffix='&'#" ; else echo "# par_no_suffix="; fi )
$( if [ ! -z ${VIASH_PAR_SUFFIX+x} ]; then echo "${VIASH_PAR_SUFFIX}" | sed "s#'#'\"'\"'#g;s#.*#par_suffix='&'#" ; else echo "# par_suffix="; fi )
$( if [ ! -z ${VIASH_PAR_USE_OQ+x} ]; then echo "${VIASH_PAR_USE_OQ}" | sed "s#'#'\"'\"'#g;s#.*#par_use_oq='&'#" ; else echo "# par_use_oq="; fi )
$( if [ ! -z ${VIASH_PAR_SINGLETON+x} ]; then echo "${VIASH_PAR_SINGLETON}" | sed "s#'#'\"'\"'#g;s#.*#par_singleton='&'#" ; else echo "# par_singleton="; fi )
$( if [ ! -z ${VIASH_PAR_COPY_TAGS+x} ]; then echo "${VIASH_PAR_COPY_TAGS}" | sed "s#'#'\"'\"'#g;s#.*#par_copy_tags='&'#" ; else echo "# par_copy_tags="; fi )
$( if [ ! -z ${VIASH_PAR_COPY_TAGS_LIST+x} ]; then echo "${VIASH_PAR_COPY_TAGS_LIST}" | sed "s#'#'\"'\"'#g;s#.*#par_copy_tags_list='&'#" ; else echo "# par_copy_tags_list="; fi )
$( if [ ! -z ${VIASH_PAR_READ1+x} ]; then echo "${VIASH_PAR_READ1}" | sed "s#'#'\"'\"'#g;s#.*#par_read1='&'#" ; else echo "# par_read1="; fi )
$( if [ ! -z ${VIASH_PAR_READ2+x} ]; then echo "${VIASH_PAR_READ2}" | sed "s#'#'\"'\"'#g;s#.*#par_read2='&'#" ; else echo "# par_read2="; fi )
$( if [ ! -z ${VIASH_PAR_OUTPUT_READS+x} ]; then echo "${VIASH_PAR_OUTPUT_READS}" | sed "s#'#'\"'\"'#g;s#.*#par_output_reads='&'#" ; else echo "# par_output_reads="; fi )
$( if [ ! -z ${VIASH_PAR_OUTPUT_READS_BOTH+x} ]; then echo "${VIASH_PAR_OUTPUT_READS_BOTH}" | sed "s#'#'\"'\"'#g;s#.*#par_output_reads_both='&'#" ; else echo "# par_output_reads_both="; fi )
$( if [ ! -z ${VIASH_PAR_FILTER_FLAGS+x} ]; then echo "${VIASH_PAR_FILTER_FLAGS}" | sed "s#'#'\"'\"'#g;s#.*#par_filter_flags='&'#" ; else echo "# par_filter_flags="; fi )
$( if [ ! -z ${VIASH_PAR_EXCL_FLAGS+x} ]; then echo "${VIASH_PAR_EXCL_FLAGS}" | sed "s#'#'\"'\"'#g;s#.*#par_excl_flags='&'#" ; else echo "# par_excl_flags="; fi )
$( if [ ! -z ${VIASH_PAR_INCL_FLAGS+x} ]; then echo "${VIASH_PAR_INCL_FLAGS}" | sed "s#'#'\"'\"'#g;s#.*#par_incl_flags='&'#" ; else echo "# par_incl_flags="; fi )
$( if [ ! -z ${VIASH_PAR_EXCL_FLAGS_ALL+x} ]; then echo "${VIASH_PAR_EXCL_FLAGS_ALL}" | sed "s#'#'\"'\"'#g;s#.*#par_excl_flags_all='&'#" ; else echo "# par_excl_flags_all="; fi )
$( if [ ! -z ${VIASH_PAR_AUX_TAG+x} ]; then echo "${VIASH_PAR_AUX_TAG}" | sed "s#'#'\"'\"'#g;s#.*#par_aux_tag='&'#" ; else echo "# par_aux_tag="; fi )
$( if [ ! -z ${VIASH_PAR_AUX_TAG_FILE+x} ]; then echo "${VIASH_PAR_AUX_TAG_FILE}" | sed "s#'#'\"'\"'#g;s#.*#par_aux_tag_file='&'#" ; else echo "# par_aux_tag_file="; fi )
$( if [ ! -z ${VIASH_PAR_CASAVA+x} ]; then echo "${VIASH_PAR_CASAVA}" | sed "s#'#'\"'\"'#g;s#.*#par_casava='&'#" ; else echo "# par_casava="; fi )
$( if [ ! -z ${VIASH_PAR_COMPRESSION+x} ]; then echo "${VIASH_PAR_COMPRESSION}" | sed "s#'#'\"'\"'#g;s#.*#par_compression='&'#" ; else echo "# par_compression="; fi )
$( if [ ! -z ${VIASH_PAR_INDEX1+x} ]; then echo "${VIASH_PAR_INDEX1}" | sed "s#'#'\"'\"'#g;s#.*#par_index1='&'#" ; else echo "# par_index1="; fi )
$( if [ ! -z ${VIASH_PAR_INDEX2+x} ]; then echo "${VIASH_PAR_INDEX2}" | sed "s#'#'\"'\"'#g;s#.*#par_index2='&'#" ; else echo "# par_index2="; fi )
$( if [ ! -z ${VIASH_PAR_BARCODE_TAG+x} ]; then echo "${VIASH_PAR_BARCODE_TAG}" | sed "s#'#'\"'\"'#g;s#.*#par_barcode_tag='&'#" ; else echo "# par_barcode_tag="; fi )
$( if [ ! -z ${VIASH_PAR_QUALITY_TAG+x} ]; then echo "${VIASH_PAR_QUALITY_TAG}" | sed "s#'#'\"'\"'#g;s#.*#par_quality_tag='&'#" ; else echo "# par_quality_tag="; fi )
$( if [ ! -z ${VIASH_PAR_INDEX_FORMAT+x} ]; then echo "${VIASH_PAR_INDEX_FORMAT}" | sed "s#'#'\"'\"'#g;s#.*#par_index_format='&'#" ; else echo "# par_index_format="; 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 -e

unset_if_false=(
  par_no_suffix
  par_suffix
  par_use_oq
  par_copy_tags
  par_casava
)

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

if [[ "\$meta_name" == "samtools_fasta" ]]; then
  subcommand=fasta
elif [[ "\$meta_name" == "samtools_fastq" ]]; then
  subcommand=fastq
else
  echo "Unrecognized component name" && exit 1
fi
samtools "\$subcommand" \\
    \${par_no_suffix:+-n} \\
    \${par_suffix:+-N} \\
    \${par_use_oq:+-O} \\
    \${par_singleton:+-s "\$par_singleton"} \\
    \${par_copy_tags:+-t} \\
    \${par_copy_tags_list:+-T "\$par_copy_tags_list"} \\
    \${par_read1:+-1 "\$par_read1"} \\
    \${par_read2:+-2 "\$par_read2"} \\
    \${par_output_reads:+-o "\$par_output_reads"} \\
    \${par_output_reads_both:+-0 "\$par_output_reads_both"} \\
    \${par_filter_flags:+-f "\$par_filter_flags"} \\
    \${par_excl_flags:+-F "\$par_excl_flags"} \\
    \${par_incl_flags:+--rf "\$par_incl_flags"} \\
    \${par_excl_flags_all:+-G "\$par_excl_flags_all"} \\
    \${par_aux_tag:+-d "\$par_aux_tag"} \\
    \${par_aux_tag_file:+-D "\$par_aux_tag_file"} \\
    \${par_casava:+-i} \\
    \${par_compression:+-c "\$par_compression"} \\
    \${par_index1:+--i1 "\$par_index1"} \\
    \${par_index2:+--i2 "\$par_index2"} \\
    \${par_barcode_tag:+--barcode-tag "\$par_barcode_tag"} \\
    \${par_quality_tag:+--quality-tag "\$par_quality_tag"} \\
    \${par_index_format:+--index-format "\$par_index_format"} \\
    "\$par_input" \\
    > "\$par_output"
VIASHMAIN
bash "\$tempscript" &
wait "\$!"

VIASHEOF


if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  # strip viash automount from file paths
  
  if [ ! -z "$VIASH_PAR_INPUT" ]; then
    VIASH_PAR_INPUT=$(ViashDockerStripAutomount "$VIASH_PAR_INPUT")
  fi
  if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
    VIASH_PAR_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT")
  fi
  if [ ! -z "$VIASH_PAR_SINGLETON" ]; then
    VIASH_PAR_SINGLETON=$(ViashDockerStripAutomount "$VIASH_PAR_SINGLETON")
  fi
  if [ ! -z "$VIASH_PAR_READ1" ]; then
    VIASH_PAR_READ1=$(ViashDockerStripAutomount "$VIASH_PAR_READ1")
  fi
  if [ ! -z "$VIASH_PAR_READ2" ]; then
    VIASH_PAR_READ2=$(ViashDockerStripAutomount "$VIASH_PAR_READ2")
  fi
  if [ ! -z "$VIASH_PAR_OUTPUT_READS" ]; then
    VIASH_PAR_OUTPUT_READS=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT_READS")
  fi
  if [ ! -z "$VIASH_PAR_OUTPUT_READS_BOTH" ]; then
    VIASH_PAR_OUTPUT_READS_BOTH=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT_READS_BOTH")
  fi
  if [ ! -z "$VIASH_PAR_INDEX1" ]; then
    VIASH_PAR_INDEX1=$(ViashDockerStripAutomount "$VIASH_PAR_INDEX1")
  fi
  if [ ! -z "$VIASH_PAR_INDEX2" ]; then
    VIASH_PAR_INDEX2=$(ViashDockerStripAutomount "$VIASH_PAR_INDEX2")
  fi
  if [ ! -z "$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 '$VIASH_PAR_OUTPUT' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_READ1" ] && [ ! -e "$VIASH_PAR_READ1" ]; then
  ViashError "Output file '$VIASH_PAR_READ1' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_READ2" ] && [ ! -e "$VIASH_PAR_READ2" ]; then
  ViashError "Output file '$VIASH_PAR_READ2' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_OUTPUT_READS" ] && [ ! -e "$VIASH_PAR_OUTPUT_READS" ]; then
  ViashError "Output file '$VIASH_PAR_OUTPUT_READS' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_OUTPUT_READS_BOTH" ] && [ ! -e "$VIASH_PAR_OUTPUT_READS_BOTH" ]; then
  ViashError "Output file '$VIASH_PAR_OUTPUT_READS_BOTH' does not exist."
  exit 1
fi


exit 0
