#!/usr/bin/env bash

# arriba 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:
#  * Robrecht Cannoodt (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="arriba"
VIASH_META_FUNCTIONALITY_NAME="arriba"
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/arriba:2.5.0--h87b9561_1
ENTRYPOINT []
RUN arriba -h 2>&1 | head -5 | grep 'Version:' | sed 's/Version:\s\(.*\)/arriba: "\1"/' > /var/software_versions.txt

LABEL org.opencontainers.image.authors="Robrecht Cannoodt"
LABEL org.opencontainers.image.description="Companion container for running component arriba"
LABEL org.opencontainers.image.created="2025-10-03T08:11:13Z"
LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba"
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 "arriba main"
  echo ""
  echo "Arriba is a command-line tool for the detection of gene fusions from RNA-Seq"
  echo "data. It was developed for the use in a clinical research setting. Therefore,"
  echo "short runtimes and high sensitivity were important design criteria."
  echo ""
  echo "Arriba is based on the STAR RNA-Seq aligner and post-processes the alignments"
  echo "(output from STAR) to:"
  echo ""
  echo "1. detect split reads and discordant mates, which are indicative of structural"
  echo "rearrangements,"
  echo "2. find reads supporting gene fusions (i.e., reads spanning the breakpoints of"
  echo "gene fusions),"
  echo "3. perform various filtering steps to remove false positives, and"
  echo "4. output the final predictions in a standardized format."
  echo ""
  echo "In contrast to many other fusion detection tools, Arriba does not require to"
  echo "reduce the STAR parameter \`--alignIntronMax\` (maximum intron size). Reducing"
  echo "this parameter impairs detection of long introns and may affect expression"
  echo "quantification. Arriba reliably filters translocation-based false positives even"
  echo "when large maximum intron sizes are used."
  echo ""
  echo "**Important**: Arriba requires BAM files that were aligned with STAR using"
  echo "specific chimeric alignment parameters, particularly \`--chimOutType WithinBAM"
  echo "HardClip\`. See the [official workflow"
  echo "documentation](https://github.com/suhrig/arriba/blob/master/run_arriba.sh) for"
  echo "the complete set of recommended STAR parameters."
  echo ""
  echo "Inputs:"
  echo "    -x, --bam"
  echo "        type: file, required parameter, file must exist"
  echo "        example: Aligned.out.bam"
  echo "        File in SAM/BAM/CRAM format with main alignments as generated by STAR"
  echo "        (Aligned.out.sam). **Important**: The BAM file must be generated by STAR"
  echo "        with"
  echo "        chimeric alignment parameters, specifically \`--chimOutType WithinBAM"
  echo "        HardClip\`."
  echo "        Arriba extracts candidate reads from this file, including both normal"
  echo "        and"
  echo "        chimeric alignments."
  echo ""
  echo "    -a, --genome"
  echo "        type: file, required parameter, file must exist"
  echo "        example: assembly.fa"
  echo "        FastA file with genome sequence (assembly). The file may be"
  echo "        gzip-compressed. An"
  echo "        index with the file extension .fai must exist only if CRAM files are"
  echo "        processed."
  echo ""
  echo "    -g, --gene_annotation"
  echo "        type: file, required parameter, file must exist"
  echo "        example: annotation.gtf"
  echo "        GTF file with gene annotation. The file may be gzip-compressed."
  echo ""
  echo "    -k, --known_fusions"
  echo "        type: file, file must exist"
  echo "        example: known_fusions.tsv"
  echo "        File containing known/recurrent fusions. Some cancer entities are often"
  echo "        characterized by fusions between the same pair of genes. In order to"
  echo "        boost"
  echo "        sensitivity, a list of known fusions can be supplied using this"
  echo "        parameter. The list"
  echo "        must contain two columns with the names of the fused genes, separated by"
  echo "        tabs."
  echo ""
  echo "    -b, --blacklist"
  echo "        type: file, file must exist"
  echo "        example: blacklist.tsv"
  echo "        File containing blacklisted events (recurrent artifacts and transcripts"
  echo "        observed in healthy tissue)."
  echo ""
  echo "    -d, --structural_variants"
  echo "        type: file, file must exist"
  echo "        example: structural_variants_from_WGS.tsv"
  echo "        Tab-separated file with coordinates of structural variants found using"
  echo "        whole-genome sequencing data. These coordinates serve to increase"
  echo "        sensitivity"
  echo "        towards weakly expressed fusions and to eliminate fusions with low"
  echo "        evidence."
  echo ""
  echo "    -t, --tags"
  echo "        type: file, file must exist"
  echo "        example: tags.tsv"
  echo "        Tab-separated file containing fusions to annotate with tags in the"
  echo "        'tags' column."
  echo "        The first two columns specify the genes; the third column specifies the"
  echo "        tag. The"
  echo "        file may be gzip-compressed."
  echo ""
  echo "    -p, --protein_domains"
  echo "        type: file, file must exist"
  echo "        example: protein_domains.gff3"
  echo "        File in GFF3 format containing coordinates of the protein domains of"
  echo "        genes. The"
  echo "        protein domains retained in a fusion are listed in the column"
  echo "        'retained_protein_domains'. The file may be gzip-compressed."
  echo ""
  echo "Outputs:"
  echo "    -o, --fusions"
  echo "        type: file, required parameter, output, file must exist"
  echo "        example: fusions.tsv"
  echo "        Output file with fusions that have passed all filters."
  echo ""
  echo "    -O, --fusions_discarded"
  echo "        type: file, output, file must exist"
  echo "        example: fusions.discarded.tsv"
  echo "        Output file with fusions that were discarded due to filtering."
  echo ""
  echo "Arguments:"
  echo "    -D, --max_genomic_breakpoint_distance"
  echo "        type: long"
  echo "        When a file with genomic breakpoints obtained via"
  echo "        whole-genome sequencing is supplied via the --structural_variants"
  echo "        parameter, this parameter determines how far a"
  echo "        genomic breakpoint may be away from a"
  echo "        transcriptomic breakpoint to consider it as a"
  echo "        related event. For events inside genes, the"
  echo "        distance is added to the end of the gene; for"
  echo "        intergenic events, the distance threshold is"
  echo "        applied as is. Default: 100000."
  echo ""
  echo "    -s, --strandedness"
  echo "        type: string"
  echo "        choices: [ auto, yes, no, reverse ]"
  echo "        Whether a strand-specific protocol was used for library preparation,"
  echo "        and if so, the type of strandedness (auto/yes/no/reverse). When"
  echo "        unstranded data is processed, the strand can sometimes be inferred from"
  echo "        splice-patterns. But in unclear situations, stranded data helps"
  echo "        resolve ambiguities. Default: auto"
  echo ""
  echo "    -i, --interesting_contigs"
  echo "        type: string, multiple values allowed"
  echo "        example: 1;2;AC_*;NC_*"
  echo "        List of interesting contigs. Fusions between genes"
  echo "        on other contigs are ignored. Contigs can be specified with or without"
  echo "        the"
  echo "        prefix \"chr\". Asterisks (*) are treated as wild-cards."
  echo "        Default: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y"
  echo "        AC_* NC_*"
  echo ""
  echo "    -v, --viral_contigs"
  echo "        type: string, multiple values allowed"
  echo "        example: AC_*;NC_*"
  echo "        List of viral contigs. Asterisks (*) are treated as"
  echo "        wild-cards."
  echo "        Default: AC_* NC_*"
  echo ""
  echo "    -f, --disable_filters"
  echo "        type: string, multiple values allowed"
  echo "        choices: [ homologs, low_entropy, isoforms, top_expressed_viral_contigs,"
  echo "viral_contigs, uninteresting_contigs, non_coding_neighbors, mismatches,"
  echo "duplicates, no_genomic_support, genomic_support, intronic, end_to_end,"
  echo "relative_support, low_coverage_viral_contigs, merge_adjacent, mismappers,"
  echo "multimappers, same_gene, long_gap, internal_tandem_duplication,"
  echo "small_insert_size, read_through, inconsistently_clipped, intragenic_exonic,"
  echo "marginal_read_through, spliced, hairpin, blacklist, min_support, select_best,"
  echo "in_vitro, short_anchor, known_fusions, no_coverage, homopolymer, many_spliced ]"
  echo "        List of filters to disable. By default all filters are"
  echo "        enabled."
  echo ""
  echo "    -E, --max_e_value"
  echo "        type: double"
  echo "        Arriba estimates the number of fusions with a given number of supporting"
  echo "        reads which one would expect to see by random chance. If the expected"
  echo "        number"
  echo "        of fusions (e-value) is higher than this threshold, the fusion is"
  echo "        discarded by the 'relative_support' filter. Note: Increasing this"
  echo "        threshold can dramatically increase the number of false positives and"
  echo "        may"
  echo "        increase the runtime of resource-intensive steps. Fractional values are"
  echo "        possible. Default: 0.300000"
  echo ""
  echo "    -S, --min_supporting_reads"
  echo "        type: integer"
  echo "        example: 2"
  echo "        The 'min_support' filter discards all fusions with fewer than"
  echo "        this many supporting reads (split reads and discordant mates"
  echo "        combined). Default: 2"
  echo ""
  echo "    -m, --max_mismappers"
  echo "        type: double"
  echo "        example: 0.8"
  echo "        When more than this fraction of supporting reads turns out to be"
  echo "        mismappers, the 'mismappers' filter discards the fusion. Default:"
  echo "        0.800000"
  echo ""
  echo "    -L, --max_homolog_identity"
  echo "        type: double"
  echo "        example: 0.3"
  echo "        Genes with more than the given fraction of sequence identity are"
  echo "        considered homologs and removed by the 'homologs' filter."
  echo "        Default: 0.300000"
  echo ""
  echo "    -H, --homopolymer_length"
  echo "        type: integer"
  echo "        example: 6"
  echo "        The 'homopolymer' filter removes breakpoints adjacent to"
  echo "        homopolymers of the given length or more. Default: 6"
  echo ""
  echo "    -R, --read_through_distance"
  echo "        type: integer"
  echo "        example: 10000"
  echo "        The 'read_through' filter removes read-through fusions"
  echo "        where the breakpoints are less than the given distance away"
  echo "        from each other. Default: 10000"
  echo ""
  echo "    -A, --min_anchor_length"
  echo "        type: integer"
  echo "        example: 23"
  echo "        Alignment artifacts are often characterized by split reads coming"
  echo "        from only one gene and no discordant mates. Moreover, the split"
  echo "        reads only align to a short stretch in one of the genes. The"
  echo "        'short_anchor' filter removes these fusions. This parameter sets"
  echo "        the threshold in bp for what the filter considers short. Default: 23"
  echo ""
  echo "    -M, --many_spliced_events"
  echo "        type: integer"
  echo "        example: 4"
  echo "        The 'many_spliced' filter recovers fusions between genes that"
  echo "        have at least this many spliced breakpoints. Default: 4"
  echo ""
  echo "    -K, --max_kmer_content"
  echo "        type: double"
  echo "        example: 0.6"
  echo "        The 'low_entropy' filter removes reads with repetitive 3-mers. If"
  echo "        the 3-mers make up more than the given fraction of the sequence, then"
  echo "        the read is discarded. Default: 0.600000"
  echo ""
  echo "    -V, --max_mismatch_pvalue"
  echo "        type: double"
  echo "        example: 0.05"
  echo "        The 'mismatches' filter uses a binomial model to calculate a"
  echo "        p-value for observing a given number of mismatches in a read. If"
  echo "        the number of mismatches is too high, the read is discarded."
  echo "        Default: 0.010000"
  echo ""
  echo "    -F, --fragment_length"
  echo "        type: integer"
  echo "        example: 200"
  echo "        When paired-end data is given, the fragment length is estimated"
  echo "        automatically and this parameter has no effect. But when single-end"
  echo "        data is given, the mean fragment length should be specified to"
  echo "        effectively filter fusions that arise from hairpin structures."
  echo "        Default: 200"
  echo ""
  echo "    -U, --max_reads"
  echo "        type: integer"
  echo "        example: 300"
  echo "        Subsample fusions with more than the given number of supporting reads."
  echo "        This"
  echo "        improves performance without compromising sensitivity, as long as the"
  echo "        threshold is high. Counting of supporting reads beyond the threshold is"
  echo "        inaccurate, obviously. Default: 300"
  echo ""
  echo "    -Q, --quantile"
  echo "        type: double"
  echo "        example: 0.998"
  echo "        Highly expressed genes are prone to produce artifacts during library"
  echo "        preparation. Genes with an expression above the given quantile are"
  echo "        eligible"
  echo "        for filtering by the 'in_vitro' filter. Default: 0.998000"
  echo ""
  echo "    -e, --exonic_fraction"
  echo "        type: double"
  echo "        example: 0.33"
  echo "        The breakpoints of false-positive predictions of intragenic events"
  echo "        are often both in exons. True predictions are more likely to have at"
  echo "        least one breakpoint in an intron, because introns are larger. If the"
  echo "        fraction of exonic sequence between two breakpoints is smaller than"
  echo "        the given fraction, the 'intragenic_exonic' filter discards the"
  echo "        event. Default: 0.330000"
  echo ""
  echo "    -T, --top_n"
  echo "        type: integer"
  echo "        example: 5"
  echo "        Only report viral integration sites of the top N most highly expressed"
  echo "        viral"
  echo "        contigs. Default: 5"
  echo ""
  echo "    -C, --covered_fraction"
  echo "        type: double"
  echo "        example: 0.05"
  echo "        Ignore virally associated events if the virus is not fully"
  echo "        expressed, i.e., less than the given fraction of the viral contig is"
  echo "        transcribed. Default: 0.050000"
  echo ""
  echo "    -l, --max_itd_length"
  echo "        type: integer"
  echo "        example: 100"
  echo "        Maximum length of internal tandem duplications. Note: Increasing"
  echo "        this value beyond the default can impair performance and lead to many"
  echo "        false positives. Default: 100"
  echo ""
  echo "    -z, --min_itd_allele_fraction"
  echo "        type: double"
  echo "        example: 0.07"
  echo "        Required fraction of supporting reads to report an internal"
  echo "        tandem duplication. Default: 0.070000"
  echo ""
  echo "    -Z, --min_itd_supporting_reads"
  echo "        type: integer"
  echo "        example: 10"
  echo "        Required absolute number of supporting reads to report an"
  echo "        internal tandem duplication. Default: 10"
  echo ""
  echo "    -u, --skip_duplicate_marking"
  echo "        type: boolean_true"
  echo "        Instead of performing duplicate marking itself, Arriba relies on"
  echo "        duplicate marking by a"
  echo "        preceding program using the BAM_FDUP flag. This makes sense when unique"
  echo "        molecular"
  echo "        identifiers (UMI) are used."
  echo ""
  echo "    -X, --extra_information"
  echo "        type: boolean_true"
  echo "        To reduce the runtime and file size, by default, the columns"
  echo "        'fusion_transcript',"
  echo "        'peptide_sequence', and 'read_identifiers' are left empty in the file"
  echo "        containing"
  echo "        discarded fusion candidates (see parameter -O). When this flag is set,"
  echo "        this extra"
  echo "        information is reported in the discarded fusions file."
  echo ""
  echo "    -I, --fill_gaps"
  echo "        type: boolean_true"
  echo "        If assembly of the fusion transcript sequence from the supporting reads"
  echo "        is incomplete"
  echo "        (denoted as '...'), fill the gaps using the assembly sequence wherever"
  echo "        possible."
  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 "$1")"
            shift 1
            ;;
        --version)
            echo "arriba main"
            exit
            ;;
        --bam)
            [ -n "$VIASH_PAR_BAM" ] && ViashError Bad arguments for option \'--bam\': \'$VIASH_PAR_BAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_BAM="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --bam. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --bam=*)
            [ -n "$VIASH_PAR_BAM" ] && ViashError Bad arguments for option \'--bam=*\': \'$VIASH_PAR_BAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_BAM=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -x)
            [ -n "$VIASH_PAR_BAM" ] && ViashError Bad arguments for option \'-x\': \'$VIASH_PAR_BAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_BAM="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -x. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --genome)
            [ -n "$VIASH_PAR_GENOME" ] && ViashError Bad arguments for option \'--genome\': \'$VIASH_PAR_GENOME\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_GENOME="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --genome. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --genome=*)
            [ -n "$VIASH_PAR_GENOME" ] && ViashError Bad arguments for option \'--genome=*\': \'$VIASH_PAR_GENOME\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_GENOME=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -a)
            [ -n "$VIASH_PAR_GENOME" ] && ViashError Bad arguments for option \'-a\': \'$VIASH_PAR_GENOME\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_GENOME="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -a. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --gene_annotation)
            [ -n "$VIASH_PAR_GENE_ANNOTATION" ] && ViashError Bad arguments for option \'--gene_annotation\': \'$VIASH_PAR_GENE_ANNOTATION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_GENE_ANNOTATION="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --gene_annotation. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --gene_annotation=*)
            [ -n "$VIASH_PAR_GENE_ANNOTATION" ] && ViashError Bad arguments for option \'--gene_annotation=*\': \'$VIASH_PAR_GENE_ANNOTATION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_GENE_ANNOTATION=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -g)
            [ -n "$VIASH_PAR_GENE_ANNOTATION" ] && ViashError Bad arguments for option \'-g\': \'$VIASH_PAR_GENE_ANNOTATION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_GENE_ANNOTATION="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -g. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --known_fusions)
            [ -n "$VIASH_PAR_KNOWN_FUSIONS" ] && ViashError Bad arguments for option \'--known_fusions\': \'$VIASH_PAR_KNOWN_FUSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_KNOWN_FUSIONS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --known_fusions. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --known_fusions=*)
            [ -n "$VIASH_PAR_KNOWN_FUSIONS" ] && ViashError Bad arguments for option \'--known_fusions=*\': \'$VIASH_PAR_KNOWN_FUSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_KNOWN_FUSIONS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -k)
            [ -n "$VIASH_PAR_KNOWN_FUSIONS" ] && ViashError Bad arguments for option \'-k\': \'$VIASH_PAR_KNOWN_FUSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_KNOWN_FUSIONS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -k. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --blacklist)
            [ -n "$VIASH_PAR_BLACKLIST" ] && ViashError Bad arguments for option \'--blacklist\': \'$VIASH_PAR_BLACKLIST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_BLACKLIST="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --blacklist. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --blacklist=*)
            [ -n "$VIASH_PAR_BLACKLIST" ] && ViashError Bad arguments for option \'--blacklist=*\': \'$VIASH_PAR_BLACKLIST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_BLACKLIST=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -b)
            [ -n "$VIASH_PAR_BLACKLIST" ] && ViashError Bad arguments for option \'-b\': \'$VIASH_PAR_BLACKLIST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_BLACKLIST="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -b. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --structural_variants)
            [ -n "$VIASH_PAR_STRUCTURAL_VARIANTS" ] && ViashError Bad arguments for option \'--structural_variants\': \'$VIASH_PAR_STRUCTURAL_VARIANTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_STRUCTURAL_VARIANTS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --structural_variants. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --structural_variants=*)
            [ -n "$VIASH_PAR_STRUCTURAL_VARIANTS" ] && ViashError Bad arguments for option \'--structural_variants=*\': \'$VIASH_PAR_STRUCTURAL_VARIANTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_STRUCTURAL_VARIANTS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -d)
            [ -n "$VIASH_PAR_STRUCTURAL_VARIANTS" ] && ViashError Bad arguments for option \'-d\': \'$VIASH_PAR_STRUCTURAL_VARIANTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_STRUCTURAL_VARIANTS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -d. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --tags)
            [ -n "$VIASH_PAR_TAGS" ] && ViashError Bad arguments for option \'--tags\': \'$VIASH_PAR_TAGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_TAGS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --tags. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --tags=*)
            [ -n "$VIASH_PAR_TAGS" ] && ViashError Bad arguments for option \'--tags=*\': \'$VIASH_PAR_TAGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_TAGS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -t)
            [ -n "$VIASH_PAR_TAGS" ] && ViashError Bad arguments for option \'-t\': \'$VIASH_PAR_TAGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_TAGS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -t. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --protein_domains)
            [ -n "$VIASH_PAR_PROTEIN_DOMAINS" ] && ViashError Bad arguments for option \'--protein_domains\': \'$VIASH_PAR_PROTEIN_DOMAINS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PROTEIN_DOMAINS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --protein_domains. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --protein_domains=*)
            [ -n "$VIASH_PAR_PROTEIN_DOMAINS" ] && ViashError Bad arguments for option \'--protein_domains=*\': \'$VIASH_PAR_PROTEIN_DOMAINS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PROTEIN_DOMAINS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -p)
            [ -n "$VIASH_PAR_PROTEIN_DOMAINS" ] && ViashError Bad arguments for option \'-p\': \'$VIASH_PAR_PROTEIN_DOMAINS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PROTEIN_DOMAINS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -p. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --fusions)
            [ -n "$VIASH_PAR_FUSIONS" ] && ViashError Bad arguments for option \'--fusions\': \'$VIASH_PAR_FUSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FUSIONS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --fusions. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --fusions=*)
            [ -n "$VIASH_PAR_FUSIONS" ] && ViashError Bad arguments for option \'--fusions=*\': \'$VIASH_PAR_FUSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FUSIONS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -o)
            [ -n "$VIASH_PAR_FUSIONS" ] && ViashError Bad arguments for option \'-o\': \'$VIASH_PAR_FUSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FUSIONS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -o. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --fusions_discarded)
            [ -n "$VIASH_PAR_FUSIONS_DISCARDED" ] && ViashError Bad arguments for option \'--fusions_discarded\': \'$VIASH_PAR_FUSIONS_DISCARDED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FUSIONS_DISCARDED="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --fusions_discarded. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --fusions_discarded=*)
            [ -n "$VIASH_PAR_FUSIONS_DISCARDED" ] && ViashError Bad arguments for option \'--fusions_discarded=*\': \'$VIASH_PAR_FUSIONS_DISCARDED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FUSIONS_DISCARDED=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -O)
            [ -n "$VIASH_PAR_FUSIONS_DISCARDED" ] && ViashError Bad arguments for option \'-O\': \'$VIASH_PAR_FUSIONS_DISCARDED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FUSIONS_DISCARDED="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -O. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --max_genomic_breakpoint_distance)
            [ -n "$VIASH_PAR_MAX_GENOMIC_BREAKPOINT_DISTANCE" ] && ViashError Bad arguments for option \'--max_genomic_breakpoint_distance\': \'$VIASH_PAR_MAX_GENOMIC_BREAKPOINT_DISTANCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_GENOMIC_BREAKPOINT_DISTANCE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --max_genomic_breakpoint_distance. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --max_genomic_breakpoint_distance=*)
            [ -n "$VIASH_PAR_MAX_GENOMIC_BREAKPOINT_DISTANCE" ] && ViashError Bad arguments for option \'--max_genomic_breakpoint_distance=*\': \'$VIASH_PAR_MAX_GENOMIC_BREAKPOINT_DISTANCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_GENOMIC_BREAKPOINT_DISTANCE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -D)
            [ -n "$VIASH_PAR_MAX_GENOMIC_BREAKPOINT_DISTANCE" ] && ViashError Bad arguments for option \'-D\': \'$VIASH_PAR_MAX_GENOMIC_BREAKPOINT_DISTANCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_GENOMIC_BREAKPOINT_DISTANCE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -D. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --strandedness)
            [ -n "$VIASH_PAR_STRANDEDNESS" ] && ViashError Bad arguments for option \'--strandedness\': \'$VIASH_PAR_STRANDEDNESS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_STRANDEDNESS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --strandedness. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --strandedness=*)
            [ -n "$VIASH_PAR_STRANDEDNESS" ] && ViashError Bad arguments for option \'--strandedness=*\': \'$VIASH_PAR_STRANDEDNESS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_STRANDEDNESS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -s)
            [ -n "$VIASH_PAR_STRANDEDNESS" ] && ViashError Bad arguments for option \'-s\': \'$VIASH_PAR_STRANDEDNESS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_STRANDEDNESS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -s. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --interesting_contigs)
            if [ -z "$VIASH_PAR_INTERESTING_CONTIGS" ]; then
              VIASH_PAR_INTERESTING_CONTIGS="$2"
            else
              VIASH_PAR_INTERESTING_CONTIGS="$VIASH_PAR_INTERESTING_CONTIGS;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --interesting_contigs. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --interesting_contigs=*)
            if [ -z "$VIASH_PAR_INTERESTING_CONTIGS" ]; then
              VIASH_PAR_INTERESTING_CONTIGS=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_INTERESTING_CONTIGS="$VIASH_PAR_INTERESTING_CONTIGS;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        -i)
            if [ -z "$VIASH_PAR_INTERESTING_CONTIGS" ]; then
              VIASH_PAR_INTERESTING_CONTIGS="$2"
            else
              VIASH_PAR_INTERESTING_CONTIGS="$VIASH_PAR_INTERESTING_CONTIGS;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -i. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --viral_contigs)
            if [ -z "$VIASH_PAR_VIRAL_CONTIGS" ]; then
              VIASH_PAR_VIRAL_CONTIGS="$2"
            else
              VIASH_PAR_VIRAL_CONTIGS="$VIASH_PAR_VIRAL_CONTIGS;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --viral_contigs. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --viral_contigs=*)
            if [ -z "$VIASH_PAR_VIRAL_CONTIGS" ]; then
              VIASH_PAR_VIRAL_CONTIGS=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_VIRAL_CONTIGS="$VIASH_PAR_VIRAL_CONTIGS;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        -v)
            if [ -z "$VIASH_PAR_VIRAL_CONTIGS" ]; then
              VIASH_PAR_VIRAL_CONTIGS="$2"
            else
              VIASH_PAR_VIRAL_CONTIGS="$VIASH_PAR_VIRAL_CONTIGS;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -v. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --disable_filters)
            if [ -z "$VIASH_PAR_DISABLE_FILTERS" ]; then
              VIASH_PAR_DISABLE_FILTERS="$2"
            else
              VIASH_PAR_DISABLE_FILTERS="$VIASH_PAR_DISABLE_FILTERS;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --disable_filters. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --disable_filters=*)
            if [ -z "$VIASH_PAR_DISABLE_FILTERS" ]; then
              VIASH_PAR_DISABLE_FILTERS=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_DISABLE_FILTERS="$VIASH_PAR_DISABLE_FILTERS;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        -f)
            if [ -z "$VIASH_PAR_DISABLE_FILTERS" ]; then
              VIASH_PAR_DISABLE_FILTERS="$2"
            else
              VIASH_PAR_DISABLE_FILTERS="$VIASH_PAR_DISABLE_FILTERS;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -f. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --max_e_value)
            [ -n "$VIASH_PAR_MAX_E_VALUE" ] && ViashError Bad arguments for option \'--max_e_value\': \'$VIASH_PAR_MAX_E_VALUE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_E_VALUE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --max_e_value. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --max_e_value=*)
            [ -n "$VIASH_PAR_MAX_E_VALUE" ] && ViashError Bad arguments for option \'--max_e_value=*\': \'$VIASH_PAR_MAX_E_VALUE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_E_VALUE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -E)
            [ -n "$VIASH_PAR_MAX_E_VALUE" ] && ViashError Bad arguments for option \'-E\': \'$VIASH_PAR_MAX_E_VALUE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_E_VALUE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -E. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --min_supporting_reads)
            [ -n "$VIASH_PAR_MIN_SUPPORTING_READS" ] && ViashError Bad arguments for option \'--min_supporting_reads\': \'$VIASH_PAR_MIN_SUPPORTING_READS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MIN_SUPPORTING_READS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --min_supporting_reads. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --min_supporting_reads=*)
            [ -n "$VIASH_PAR_MIN_SUPPORTING_READS" ] && ViashError Bad arguments for option \'--min_supporting_reads=*\': \'$VIASH_PAR_MIN_SUPPORTING_READS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MIN_SUPPORTING_READS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -S)
            [ -n "$VIASH_PAR_MIN_SUPPORTING_READS" ] && ViashError Bad arguments for option \'-S\': \'$VIASH_PAR_MIN_SUPPORTING_READS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MIN_SUPPORTING_READS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -S. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --max_mismappers)
            [ -n "$VIASH_PAR_MAX_MISMAPPERS" ] && ViashError Bad arguments for option \'--max_mismappers\': \'$VIASH_PAR_MAX_MISMAPPERS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_MISMAPPERS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --max_mismappers. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --max_mismappers=*)
            [ -n "$VIASH_PAR_MAX_MISMAPPERS" ] && ViashError Bad arguments for option \'--max_mismappers=*\': \'$VIASH_PAR_MAX_MISMAPPERS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_MISMAPPERS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -m)
            [ -n "$VIASH_PAR_MAX_MISMAPPERS" ] && ViashError Bad arguments for option \'-m\': \'$VIASH_PAR_MAX_MISMAPPERS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_MISMAPPERS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -m. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --max_homolog_identity)
            [ -n "$VIASH_PAR_MAX_HOMOLOG_IDENTITY" ] && ViashError Bad arguments for option \'--max_homolog_identity\': \'$VIASH_PAR_MAX_HOMOLOG_IDENTITY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_HOMOLOG_IDENTITY="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --max_homolog_identity. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --max_homolog_identity=*)
            [ -n "$VIASH_PAR_MAX_HOMOLOG_IDENTITY" ] && ViashError Bad arguments for option \'--max_homolog_identity=*\': \'$VIASH_PAR_MAX_HOMOLOG_IDENTITY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_HOMOLOG_IDENTITY=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -L)
            [ -n "$VIASH_PAR_MAX_HOMOLOG_IDENTITY" ] && ViashError Bad arguments for option \'-L\': \'$VIASH_PAR_MAX_HOMOLOG_IDENTITY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_HOMOLOG_IDENTITY="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -L. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --homopolymer_length)
            [ -n "$VIASH_PAR_HOMOPOLYMER_LENGTH" ] && ViashError Bad arguments for option \'--homopolymer_length\': \'$VIASH_PAR_HOMOPOLYMER_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_HOMOPOLYMER_LENGTH="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --homopolymer_length. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --homopolymer_length=*)
            [ -n "$VIASH_PAR_HOMOPOLYMER_LENGTH" ] && ViashError Bad arguments for option \'--homopolymer_length=*\': \'$VIASH_PAR_HOMOPOLYMER_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_HOMOPOLYMER_LENGTH=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -H)
            [ -n "$VIASH_PAR_HOMOPOLYMER_LENGTH" ] && ViashError Bad arguments for option \'-H\': \'$VIASH_PAR_HOMOPOLYMER_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_HOMOPOLYMER_LENGTH="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -H. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --read_through_distance)
            [ -n "$VIASH_PAR_READ_THROUGH_DISTANCE" ] && ViashError Bad arguments for option \'--read_through_distance\': \'$VIASH_PAR_READ_THROUGH_DISTANCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_READ_THROUGH_DISTANCE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --read_through_distance. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --read_through_distance=*)
            [ -n "$VIASH_PAR_READ_THROUGH_DISTANCE" ] && ViashError Bad arguments for option \'--read_through_distance=*\': \'$VIASH_PAR_READ_THROUGH_DISTANCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_READ_THROUGH_DISTANCE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -R)
            [ -n "$VIASH_PAR_READ_THROUGH_DISTANCE" ] && ViashError Bad arguments for option \'-R\': \'$VIASH_PAR_READ_THROUGH_DISTANCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_READ_THROUGH_DISTANCE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -R. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --min_anchor_length)
            [ -n "$VIASH_PAR_MIN_ANCHOR_LENGTH" ] && ViashError Bad arguments for option \'--min_anchor_length\': \'$VIASH_PAR_MIN_ANCHOR_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MIN_ANCHOR_LENGTH="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --min_anchor_length. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --min_anchor_length=*)
            [ -n "$VIASH_PAR_MIN_ANCHOR_LENGTH" ] && ViashError Bad arguments for option \'--min_anchor_length=*\': \'$VIASH_PAR_MIN_ANCHOR_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MIN_ANCHOR_LENGTH=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -A)
            [ -n "$VIASH_PAR_MIN_ANCHOR_LENGTH" ] && ViashError Bad arguments for option \'-A\': \'$VIASH_PAR_MIN_ANCHOR_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MIN_ANCHOR_LENGTH="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -A. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --many_spliced_events)
            [ -n "$VIASH_PAR_MANY_SPLICED_EVENTS" ] && ViashError Bad arguments for option \'--many_spliced_events\': \'$VIASH_PAR_MANY_SPLICED_EVENTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MANY_SPLICED_EVENTS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --many_spliced_events. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --many_spliced_events=*)
            [ -n "$VIASH_PAR_MANY_SPLICED_EVENTS" ] && ViashError Bad arguments for option \'--many_spliced_events=*\': \'$VIASH_PAR_MANY_SPLICED_EVENTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MANY_SPLICED_EVENTS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -M)
            [ -n "$VIASH_PAR_MANY_SPLICED_EVENTS" ] && ViashError Bad arguments for option \'-M\': \'$VIASH_PAR_MANY_SPLICED_EVENTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MANY_SPLICED_EVENTS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -M. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --max_kmer_content)
            [ -n "$VIASH_PAR_MAX_KMER_CONTENT" ] && ViashError Bad arguments for option \'--max_kmer_content\': \'$VIASH_PAR_MAX_KMER_CONTENT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_KMER_CONTENT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --max_kmer_content. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --max_kmer_content=*)
            [ -n "$VIASH_PAR_MAX_KMER_CONTENT" ] && ViashError Bad arguments for option \'--max_kmer_content=*\': \'$VIASH_PAR_MAX_KMER_CONTENT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_KMER_CONTENT=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -K)
            [ -n "$VIASH_PAR_MAX_KMER_CONTENT" ] && ViashError Bad arguments for option \'-K\': \'$VIASH_PAR_MAX_KMER_CONTENT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_KMER_CONTENT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -K. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --max_mismatch_pvalue)
            [ -n "$VIASH_PAR_MAX_MISMATCH_PVALUE" ] && ViashError Bad arguments for option \'--max_mismatch_pvalue\': \'$VIASH_PAR_MAX_MISMATCH_PVALUE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_MISMATCH_PVALUE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --max_mismatch_pvalue. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --max_mismatch_pvalue=*)
            [ -n "$VIASH_PAR_MAX_MISMATCH_PVALUE" ] && ViashError Bad arguments for option \'--max_mismatch_pvalue=*\': \'$VIASH_PAR_MAX_MISMATCH_PVALUE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_MISMATCH_PVALUE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -V)
            [ -n "$VIASH_PAR_MAX_MISMATCH_PVALUE" ] && ViashError Bad arguments for option \'-V\': \'$VIASH_PAR_MAX_MISMATCH_PVALUE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_MISMATCH_PVALUE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -V. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --fragment_length)
            [ -n "$VIASH_PAR_FRAGMENT_LENGTH" ] && ViashError Bad arguments for option \'--fragment_length\': \'$VIASH_PAR_FRAGMENT_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FRAGMENT_LENGTH="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --fragment_length. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --fragment_length=*)
            [ -n "$VIASH_PAR_FRAGMENT_LENGTH" ] && ViashError Bad arguments for option \'--fragment_length=*\': \'$VIASH_PAR_FRAGMENT_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FRAGMENT_LENGTH=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -F)
            [ -n "$VIASH_PAR_FRAGMENT_LENGTH" ] && ViashError Bad arguments for option \'-F\': \'$VIASH_PAR_FRAGMENT_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FRAGMENT_LENGTH="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -F. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --max_reads)
            [ -n "$VIASH_PAR_MAX_READS" ] && ViashError Bad arguments for option \'--max_reads\': \'$VIASH_PAR_MAX_READS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_READS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --max_reads. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --max_reads=*)
            [ -n "$VIASH_PAR_MAX_READS" ] && ViashError Bad arguments for option \'--max_reads=*\': \'$VIASH_PAR_MAX_READS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_READS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -U)
            [ -n "$VIASH_PAR_MAX_READS" ] && ViashError Bad arguments for option \'-U\': \'$VIASH_PAR_MAX_READS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_READS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -U. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --quantile)
            [ -n "$VIASH_PAR_QUANTILE" ] && ViashError Bad arguments for option \'--quantile\': \'$VIASH_PAR_QUANTILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_QUANTILE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --quantile. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --quantile=*)
            [ -n "$VIASH_PAR_QUANTILE" ] && ViashError Bad arguments for option \'--quantile=*\': \'$VIASH_PAR_QUANTILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_QUANTILE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -Q)
            [ -n "$VIASH_PAR_QUANTILE" ] && ViashError Bad arguments for option \'-Q\': \'$VIASH_PAR_QUANTILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_QUANTILE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -Q. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --exonic_fraction)
            [ -n "$VIASH_PAR_EXONIC_FRACTION" ] && ViashError Bad arguments for option \'--exonic_fraction\': \'$VIASH_PAR_EXONIC_FRACTION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_EXONIC_FRACTION="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --exonic_fraction. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --exonic_fraction=*)
            [ -n "$VIASH_PAR_EXONIC_FRACTION" ] && ViashError Bad arguments for option \'--exonic_fraction=*\': \'$VIASH_PAR_EXONIC_FRACTION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_EXONIC_FRACTION=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -e)
            [ -n "$VIASH_PAR_EXONIC_FRACTION" ] && ViashError Bad arguments for option \'-e\': \'$VIASH_PAR_EXONIC_FRACTION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_EXONIC_FRACTION="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -e. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --top_n)
            [ -n "$VIASH_PAR_TOP_N" ] && ViashError Bad arguments for option \'--top_n\': \'$VIASH_PAR_TOP_N\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_TOP_N="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --top_n. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --top_n=*)
            [ -n "$VIASH_PAR_TOP_N" ] && ViashError Bad arguments for option \'--top_n=*\': \'$VIASH_PAR_TOP_N\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_TOP_N=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -T)
            [ -n "$VIASH_PAR_TOP_N" ] && ViashError Bad arguments for option \'-T\': \'$VIASH_PAR_TOP_N\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_TOP_N="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -T. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --covered_fraction)
            [ -n "$VIASH_PAR_COVERED_FRACTION" ] && ViashError Bad arguments for option \'--covered_fraction\': \'$VIASH_PAR_COVERED_FRACTION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_COVERED_FRACTION="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --covered_fraction. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --covered_fraction=*)
            [ -n "$VIASH_PAR_COVERED_FRACTION" ] && ViashError Bad arguments for option \'--covered_fraction=*\': \'$VIASH_PAR_COVERED_FRACTION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_COVERED_FRACTION=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -C)
            [ -n "$VIASH_PAR_COVERED_FRACTION" ] && ViashError Bad arguments for option \'-C\': \'$VIASH_PAR_COVERED_FRACTION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_COVERED_FRACTION="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -C. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --max_itd_length)
            [ -n "$VIASH_PAR_MAX_ITD_LENGTH" ] && ViashError Bad arguments for option \'--max_itd_length\': \'$VIASH_PAR_MAX_ITD_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_ITD_LENGTH="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --max_itd_length. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --max_itd_length=*)
            [ -n "$VIASH_PAR_MAX_ITD_LENGTH" ] && ViashError Bad arguments for option \'--max_itd_length=*\': \'$VIASH_PAR_MAX_ITD_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_ITD_LENGTH=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -l)
            [ -n "$VIASH_PAR_MAX_ITD_LENGTH" ] && ViashError Bad arguments for option \'-l\': \'$VIASH_PAR_MAX_ITD_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_ITD_LENGTH="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -l. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --min_itd_allele_fraction)
            [ -n "$VIASH_PAR_MIN_ITD_ALLELE_FRACTION" ] && ViashError Bad arguments for option \'--min_itd_allele_fraction\': \'$VIASH_PAR_MIN_ITD_ALLELE_FRACTION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MIN_ITD_ALLELE_FRACTION="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --min_itd_allele_fraction. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --min_itd_allele_fraction=*)
            [ -n "$VIASH_PAR_MIN_ITD_ALLELE_FRACTION" ] && ViashError Bad arguments for option \'--min_itd_allele_fraction=*\': \'$VIASH_PAR_MIN_ITD_ALLELE_FRACTION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MIN_ITD_ALLELE_FRACTION=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -z)
            [ -n "$VIASH_PAR_MIN_ITD_ALLELE_FRACTION" ] && ViashError Bad arguments for option \'-z\': \'$VIASH_PAR_MIN_ITD_ALLELE_FRACTION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MIN_ITD_ALLELE_FRACTION="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -z. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --min_itd_supporting_reads)
            [ -n "$VIASH_PAR_MIN_ITD_SUPPORTING_READS" ] && ViashError Bad arguments for option \'--min_itd_supporting_reads\': \'$VIASH_PAR_MIN_ITD_SUPPORTING_READS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MIN_ITD_SUPPORTING_READS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --min_itd_supporting_reads. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --min_itd_supporting_reads=*)
            [ -n "$VIASH_PAR_MIN_ITD_SUPPORTING_READS" ] && ViashError Bad arguments for option \'--min_itd_supporting_reads=*\': \'$VIASH_PAR_MIN_ITD_SUPPORTING_READS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MIN_ITD_SUPPORTING_READS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -Z)
            [ -n "$VIASH_PAR_MIN_ITD_SUPPORTING_READS" ] && ViashError Bad arguments for option \'-Z\': \'$VIASH_PAR_MIN_ITD_SUPPORTING_READS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MIN_ITD_SUPPORTING_READS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -Z. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --skip_duplicate_marking)
            [ -n "$VIASH_PAR_SKIP_DUPLICATE_MARKING" ] && ViashError Bad arguments for option \'--skip_duplicate_marking\': \'$VIASH_PAR_SKIP_DUPLICATE_MARKING\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SKIP_DUPLICATE_MARKING=true
            shift 1
            ;;
        -u)
            [ -n "$VIASH_PAR_SKIP_DUPLICATE_MARKING" ] && ViashError Bad arguments for option \'-u\': \'$VIASH_PAR_SKIP_DUPLICATE_MARKING\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SKIP_DUPLICATE_MARKING=true
            shift 1
            ;;
        --extra_information)
            [ -n "$VIASH_PAR_EXTRA_INFORMATION" ] && ViashError Bad arguments for option \'--extra_information\': \'$VIASH_PAR_EXTRA_INFORMATION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_EXTRA_INFORMATION=true
            shift 1
            ;;
        -X)
            [ -n "$VIASH_PAR_EXTRA_INFORMATION" ] && ViashError Bad arguments for option \'-X\': \'$VIASH_PAR_EXTRA_INFORMATION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_EXTRA_INFORMATION=true
            shift 1
            ;;
        --fill_gaps)
            [ -n "$VIASH_PAR_FILL_GAPS" ] && ViashError Bad arguments for option \'--fill_gaps\': \'$VIASH_PAR_FILL_GAPS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FILL_GAPS=true
            shift 1
            ;;
        -I)
            [ -n "$VIASH_PAR_FILL_GAPS" ] && ViashError Bad arguments for option \'-I\': \'$VIASH_PAR_FILL_GAPS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FILL_GAPS=true
            shift 1
            ;;
        ---engine)
            VIASH_ENGINE_ID="$2"
            shift 2
            ;;
        ---engine=*)
            VIASH_ENGINE_ID="$(ViashRemoveFlags "$1")"
            shift 1
            ;;
        ---setup)
            VIASH_MODE='setup'
            VIASH_SETUP_STRATEGY="$2"
            shift 2
            ;;
        ---setup=*)
            VIASH_MODE='setup'
            VIASH_SETUP_STRATEGY="$(ViashRemoveFlags "$1")"
            shift 1
            ;;
        ---dockerfile)
            VIASH_MODE='dockerfile'
            shift 1
            ;;
        ---docker_run_args)
            VIASH_DOCKER_RUN_ARGS+=("$2")
            shift 2
            ;;
        ---docker_run_args=*)
            VIASH_DOCKER_RUN_ARGS+=("$(ViashRemoveFlags "$1")")
            shift 1
            ;;
        ---docker_image_id)
            VIASH_MODE='docker_image_id'
            shift 1
            ;;
        ---debug)
            VIASH_MODE='debug'
            shift 1
            ;;
        ---cpus)
            [ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_CPUS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to ---cpus. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        ---cpus=*)
            [ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus=*\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_CPUS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        ---memory)
            [ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_MEMORY="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to ---memory. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        ---memory=*)
            [ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory=*\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_MEMORY=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        *)  # positional arg or unknown option
            # since the positional args will be eval'd, can we always quote, instead of using ViashQuote
            VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'"
            [[ $1 == -* ]] && ViashWarning $1 looks like a parameter but is not a defined parameter and will instead be treated as a positional argument. Use "--help" to get more information on the parameters.
            shift # past argument
            ;;
    esac
done

# parse positional parameters
eval set -- $VIASH_POSITIONAL_ARGS


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

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

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/arriba: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" 'arriba' 'ps' 'bash'
    exit 0
  fi

  # check if docker image exists
  ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild
  ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'arriba' '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_BAM+x} ]; then
  ViashError '--bam' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_PAR_GENOME+x} ]; then
  ViashError '--genome' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_PAR_GENE_ANNOTATION+x} ]; then
  ViashError '--gene_annotation' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_PAR_FUSIONS+x} ]; then
  ViashError '--fusions' 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_DUPLICATE_MARKING+x} ]; then
  VIASH_PAR_SKIP_DUPLICATE_MARKING="false"
fi
if [ -z ${VIASH_PAR_EXTRA_INFORMATION+x} ]; then
  VIASH_PAR_EXTRA_INFORMATION="false"
fi
if [ -z ${VIASH_PAR_FILL_GAPS+x} ]; then
  VIASH_PAR_FILL_GAPS="false"
fi

# check whether required files exist
if [ ! -z "$VIASH_PAR_BAM" ] && [ ! -e "$VIASH_PAR_BAM" ]; then
  ViashError "Input file '$VIASH_PAR_BAM' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_GENOME" ] && [ ! -e "$VIASH_PAR_GENOME" ]; then
  ViashError "Input file '$VIASH_PAR_GENOME' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_GENE_ANNOTATION" ] && [ ! -e "$VIASH_PAR_GENE_ANNOTATION" ]; then
  ViashError "Input file '$VIASH_PAR_GENE_ANNOTATION' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_KNOWN_FUSIONS" ] && [ ! -e "$VIASH_PAR_KNOWN_FUSIONS" ]; then
  ViashError "Input file '$VIASH_PAR_KNOWN_FUSIONS' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_BLACKLIST" ] && [ ! -e "$VIASH_PAR_BLACKLIST" ]; then
  ViashError "Input file '$VIASH_PAR_BLACKLIST' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_STRUCTURAL_VARIANTS" ] && [ ! -e "$VIASH_PAR_STRUCTURAL_VARIANTS" ]; then
  ViashError "Input file '$VIASH_PAR_STRUCTURAL_VARIANTS' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_TAGS" ] && [ ! -e "$VIASH_PAR_TAGS" ]; then
  ViashError "Input file '$VIASH_PAR_TAGS' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_PROTEIN_DOMAINS" ] && [ ! -e "$VIASH_PAR_PROTEIN_DOMAINS" ]; then
  ViashError "Input file '$VIASH_PAR_PROTEIN_DOMAINS' does not exist."
  exit 1
fi

# check whether parameters values are of the right type
if [[ -n "$VIASH_PAR_MAX_GENOMIC_BREAKPOINT_DISTANCE" ]]; then
  if ! [[ "$VIASH_PAR_MAX_GENOMIC_BREAKPOINT_DISTANCE" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--max_genomic_breakpoint_distance' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_MAX_E_VALUE" ]]; then
  if ! [[ "$VIASH_PAR_MAX_E_VALUE" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--max_e_value' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_MIN_SUPPORTING_READS" ]]; then
  if ! [[ "$VIASH_PAR_MIN_SUPPORTING_READS" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--min_supporting_reads' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_MAX_MISMAPPERS" ]]; then
  if ! [[ "$VIASH_PAR_MAX_MISMAPPERS" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--max_mismappers' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_MAX_HOMOLOG_IDENTITY" ]]; then
  if ! [[ "$VIASH_PAR_MAX_HOMOLOG_IDENTITY" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--max_homolog_identity' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_HOMOPOLYMER_LENGTH" ]]; then
  if ! [[ "$VIASH_PAR_HOMOPOLYMER_LENGTH" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--homopolymer_length' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_READ_THROUGH_DISTANCE" ]]; then
  if ! [[ "$VIASH_PAR_READ_THROUGH_DISTANCE" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--read_through_distance' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_MIN_ANCHOR_LENGTH" ]]; then
  if ! [[ "$VIASH_PAR_MIN_ANCHOR_LENGTH" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--min_anchor_length' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_MANY_SPLICED_EVENTS" ]]; then
  if ! [[ "$VIASH_PAR_MANY_SPLICED_EVENTS" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--many_spliced_events' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_MAX_KMER_CONTENT" ]]; then
  if ! [[ "$VIASH_PAR_MAX_KMER_CONTENT" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--max_kmer_content' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_MAX_MISMATCH_PVALUE" ]]; then
  if ! [[ "$VIASH_PAR_MAX_MISMATCH_PVALUE" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--max_mismatch_pvalue' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_FRAGMENT_LENGTH" ]]; then
  if ! [[ "$VIASH_PAR_FRAGMENT_LENGTH" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--fragment_length' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_MAX_READS" ]]; then
  if ! [[ "$VIASH_PAR_MAX_READS" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--max_reads' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_QUANTILE" ]]; then
  if ! [[ "$VIASH_PAR_QUANTILE" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--quantile' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_EXONIC_FRACTION" ]]; then
  if ! [[ "$VIASH_PAR_EXONIC_FRACTION" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--exonic_fraction' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_TOP_N" ]]; then
  if ! [[ "$VIASH_PAR_TOP_N" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--top_n' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_COVERED_FRACTION" ]]; then
  if ! [[ "$VIASH_PAR_COVERED_FRACTION" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--covered_fraction' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_MAX_ITD_LENGTH" ]]; then
  if ! [[ "$VIASH_PAR_MAX_ITD_LENGTH" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--max_itd_length' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_MIN_ITD_ALLELE_FRACTION" ]]; then
  if ! [[ "$VIASH_PAR_MIN_ITD_ALLELE_FRACTION" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--min_itd_allele_fraction' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_MIN_ITD_SUPPORTING_READS" ]]; then
  if ! [[ "$VIASH_PAR_MIN_ITD_SUPPORTING_READS" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--min_itd_supporting_reads' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SKIP_DUPLICATE_MARKING" ]]; then
  if ! [[ "$VIASH_PAR_SKIP_DUPLICATE_MARKING" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--skip_duplicate_marking' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_EXTRA_INFORMATION" ]]; then
  if ! [[ "$VIASH_PAR_EXTRA_INFORMATION" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--extra_information' has to be a boolean_true. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_FILL_GAPS" ]]; then
  if ! [[ "$VIASH_PAR_FILL_GAPS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--fill_gaps' 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 "$VIASH_PAR_STRANDEDNESS" ]; then
  VIASH_PAR_STRANDEDNESS_CHOICES=("auto;yes;no;reverse")
  IFS=';'
  set -f
  if ! [[ ";${VIASH_PAR_STRANDEDNESS_CHOICES[*]};" =~ ";$VIASH_PAR_STRANDEDNESS;" ]]; then
    ViashError '--strandedness' specified value of \'$VIASH_PAR_STRANDEDNESS\' 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_DISABLE_FILTERS" ]; then
  VIASH_PAR_DISABLE_FILTERS_CHOICES=("homologs;low_entropy;isoforms;top_expressed_viral_contigs;viral_contigs;uninteresting_contigs;non_coding_neighbors;mismatches;duplicates;no_genomic_support;genomic_support;intronic;end_to_end;relative_support;low_coverage_viral_contigs;merge_adjacent;mismappers;multimappers;same_gene;long_gap;internal_tandem_duplication;small_insert_size;read_through;inconsistently_clipped;intragenic_exonic;marginal_read_through;spliced;hairpin;blacklist;min_support;select_best;in_vitro;short_anchor;known_fusions;no_coverage;homopolymer;many_spliced")
  IFS=';'
  set -f
  for val in $VIASH_PAR_DISABLE_FILTERS; do
    if ! [[ ";${VIASH_PAR_DISABLE_FILTERS_CHOICES[*]};" =~ ";${val};" ]]; then
      ViashError '--disable_filters' specified value of \'${val}\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
      exit 1
    fi
  done
  set +f
  unset IFS
fi

# create parent directories of output files, if so desired
if [ ! -z "$VIASH_PAR_FUSIONS" ] && [ ! -d "$(dirname "$VIASH_PAR_FUSIONS")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_FUSIONS")"
fi
if [ ! -z "$VIASH_PAR_FUSIONS_DISCARDED" ] && [ ! -d "$(dirname "$VIASH_PAR_FUSIONS_DISCARDED")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_FUSIONS_DISCARDED")"
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_BAM" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_BAM")" )
  VIASH_PAR_BAM=$(ViashDockerAutodetectMount "$VIASH_PAR_BAM")
fi
if [ ! -z "$VIASH_PAR_GENOME" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_GENOME")" )
  VIASH_PAR_GENOME=$(ViashDockerAutodetectMount "$VIASH_PAR_GENOME")
fi
if [ ! -z "$VIASH_PAR_GENE_ANNOTATION" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_GENE_ANNOTATION")" )
  VIASH_PAR_GENE_ANNOTATION=$(ViashDockerAutodetectMount "$VIASH_PAR_GENE_ANNOTATION")
fi
if [ ! -z "$VIASH_PAR_KNOWN_FUSIONS" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_KNOWN_FUSIONS")" )
  VIASH_PAR_KNOWN_FUSIONS=$(ViashDockerAutodetectMount "$VIASH_PAR_KNOWN_FUSIONS")
fi
if [ ! -z "$VIASH_PAR_BLACKLIST" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_BLACKLIST")" )
  VIASH_PAR_BLACKLIST=$(ViashDockerAutodetectMount "$VIASH_PAR_BLACKLIST")
fi
if [ ! -z "$VIASH_PAR_STRUCTURAL_VARIANTS" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_STRUCTURAL_VARIANTS")" )
  VIASH_PAR_STRUCTURAL_VARIANTS=$(ViashDockerAutodetectMount "$VIASH_PAR_STRUCTURAL_VARIANTS")
fi
if [ ! -z "$VIASH_PAR_TAGS" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_TAGS")" )
  VIASH_PAR_TAGS=$(ViashDockerAutodetectMount "$VIASH_PAR_TAGS")
fi
if [ ! -z "$VIASH_PAR_PROTEIN_DOMAINS" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_PROTEIN_DOMAINS")" )
  VIASH_PAR_PROTEIN_DOMAINS=$(ViashDockerAutodetectMount "$VIASH_PAR_PROTEIN_DOMAINS")
fi
if [ ! -z "$VIASH_PAR_FUSIONS" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_FUSIONS")" )
  VIASH_PAR_FUSIONS=$(ViashDockerAutodetectMount "$VIASH_PAR_FUSIONS")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_FUSIONS" )
fi
if [ ! -z "$VIASH_PAR_FUSIONS_DISCARDED" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_FUSIONS_DISCARDED")" )
  VIASH_PAR_FUSIONS_DISCARDED=$(ViashDockerAutodetectMount "$VIASH_PAR_FUSIONS_DISCARDED")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_FUSIONS_DISCARDED" )
fi
if [ ! -z "$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-arriba-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 ${VIASH_PAR_BAM+x} ]; then echo "${VIASH_PAR_BAM}" | sed "s#'#'\"'\"'#g;s#.*#par_bam='&'#" ; else echo "# par_bam="; fi )
$( if [ ! -z ${VIASH_PAR_GENOME+x} ]; then echo "${VIASH_PAR_GENOME}" | sed "s#'#'\"'\"'#g;s#.*#par_genome='&'#" ; else echo "# par_genome="; fi )
$( if [ ! -z ${VIASH_PAR_GENE_ANNOTATION+x} ]; then echo "${VIASH_PAR_GENE_ANNOTATION}" | sed "s#'#'\"'\"'#g;s#.*#par_gene_annotation='&'#" ; else echo "# par_gene_annotation="; fi )
$( if [ ! -z ${VIASH_PAR_KNOWN_FUSIONS+x} ]; then echo "${VIASH_PAR_KNOWN_FUSIONS}" | sed "s#'#'\"'\"'#g;s#.*#par_known_fusions='&'#" ; else echo "# par_known_fusions="; fi )
$( if [ ! -z ${VIASH_PAR_BLACKLIST+x} ]; then echo "${VIASH_PAR_BLACKLIST}" | sed "s#'#'\"'\"'#g;s#.*#par_blacklist='&'#" ; else echo "# par_blacklist="; fi )
$( if [ ! -z ${VIASH_PAR_STRUCTURAL_VARIANTS+x} ]; then echo "${VIASH_PAR_STRUCTURAL_VARIANTS}" | sed "s#'#'\"'\"'#g;s#.*#par_structural_variants='&'#" ; else echo "# par_structural_variants="; fi )
$( if [ ! -z ${VIASH_PAR_TAGS+x} ]; then echo "${VIASH_PAR_TAGS}" | sed "s#'#'\"'\"'#g;s#.*#par_tags='&'#" ; else echo "# par_tags="; fi )
$( if [ ! -z ${VIASH_PAR_PROTEIN_DOMAINS+x} ]; then echo "${VIASH_PAR_PROTEIN_DOMAINS}" | sed "s#'#'\"'\"'#g;s#.*#par_protein_domains='&'#" ; else echo "# par_protein_domains="; fi )
$( if [ ! -z ${VIASH_PAR_FUSIONS+x} ]; then echo "${VIASH_PAR_FUSIONS}" | sed "s#'#'\"'\"'#g;s#.*#par_fusions='&'#" ; else echo "# par_fusions="; fi )
$( if [ ! -z ${VIASH_PAR_FUSIONS_DISCARDED+x} ]; then echo "${VIASH_PAR_FUSIONS_DISCARDED}" | sed "s#'#'\"'\"'#g;s#.*#par_fusions_discarded='&'#" ; else echo "# par_fusions_discarded="; fi )
$( if [ ! -z ${VIASH_PAR_MAX_GENOMIC_BREAKPOINT_DISTANCE+x} ]; then echo "${VIASH_PAR_MAX_GENOMIC_BREAKPOINT_DISTANCE}" | sed "s#'#'\"'\"'#g;s#.*#par_max_genomic_breakpoint_distance='&'#" ; else echo "# par_max_genomic_breakpoint_distance="; fi )
$( if [ ! -z ${VIASH_PAR_STRANDEDNESS+x} ]; then echo "${VIASH_PAR_STRANDEDNESS}" | sed "s#'#'\"'\"'#g;s#.*#par_strandedness='&'#" ; else echo "# par_strandedness="; fi )
$( if [ ! -z ${VIASH_PAR_INTERESTING_CONTIGS+x} ]; then echo "${VIASH_PAR_INTERESTING_CONTIGS}" | sed "s#'#'\"'\"'#g;s#.*#par_interesting_contigs='&'#" ; else echo "# par_interesting_contigs="; fi )
$( if [ ! -z ${VIASH_PAR_VIRAL_CONTIGS+x} ]; then echo "${VIASH_PAR_VIRAL_CONTIGS}" | sed "s#'#'\"'\"'#g;s#.*#par_viral_contigs='&'#" ; else echo "# par_viral_contigs="; fi )
$( if [ ! -z ${VIASH_PAR_DISABLE_FILTERS+x} ]; then echo "${VIASH_PAR_DISABLE_FILTERS}" | sed "s#'#'\"'\"'#g;s#.*#par_disable_filters='&'#" ; else echo "# par_disable_filters="; fi )
$( if [ ! -z ${VIASH_PAR_MAX_E_VALUE+x} ]; then echo "${VIASH_PAR_MAX_E_VALUE}" | sed "s#'#'\"'\"'#g;s#.*#par_max_e_value='&'#" ; else echo "# par_max_e_value="; fi )
$( if [ ! -z ${VIASH_PAR_MIN_SUPPORTING_READS+x} ]; then echo "${VIASH_PAR_MIN_SUPPORTING_READS}" | sed "s#'#'\"'\"'#g;s#.*#par_min_supporting_reads='&'#" ; else echo "# par_min_supporting_reads="; fi )
$( if [ ! -z ${VIASH_PAR_MAX_MISMAPPERS+x} ]; then echo "${VIASH_PAR_MAX_MISMAPPERS}" | sed "s#'#'\"'\"'#g;s#.*#par_max_mismappers='&'#" ; else echo "# par_max_mismappers="; fi )
$( if [ ! -z ${VIASH_PAR_MAX_HOMOLOG_IDENTITY+x} ]; then echo "${VIASH_PAR_MAX_HOMOLOG_IDENTITY}" | sed "s#'#'\"'\"'#g;s#.*#par_max_homolog_identity='&'#" ; else echo "# par_max_homolog_identity="; fi )
$( if [ ! -z ${VIASH_PAR_HOMOPOLYMER_LENGTH+x} ]; then echo "${VIASH_PAR_HOMOPOLYMER_LENGTH}" | sed "s#'#'\"'\"'#g;s#.*#par_homopolymer_length='&'#" ; else echo "# par_homopolymer_length="; fi )
$( if [ ! -z ${VIASH_PAR_READ_THROUGH_DISTANCE+x} ]; then echo "${VIASH_PAR_READ_THROUGH_DISTANCE}" | sed "s#'#'\"'\"'#g;s#.*#par_read_through_distance='&'#" ; else echo "# par_read_through_distance="; fi )
$( if [ ! -z ${VIASH_PAR_MIN_ANCHOR_LENGTH+x} ]; then echo "${VIASH_PAR_MIN_ANCHOR_LENGTH}" | sed "s#'#'\"'\"'#g;s#.*#par_min_anchor_length='&'#" ; else echo "# par_min_anchor_length="; fi )
$( if [ ! -z ${VIASH_PAR_MANY_SPLICED_EVENTS+x} ]; then echo "${VIASH_PAR_MANY_SPLICED_EVENTS}" | sed "s#'#'\"'\"'#g;s#.*#par_many_spliced_events='&'#" ; else echo "# par_many_spliced_events="; fi )
$( if [ ! -z ${VIASH_PAR_MAX_KMER_CONTENT+x} ]; then echo "${VIASH_PAR_MAX_KMER_CONTENT}" | sed "s#'#'\"'\"'#g;s#.*#par_max_kmer_content='&'#" ; else echo "# par_max_kmer_content="; fi )
$( if [ ! -z ${VIASH_PAR_MAX_MISMATCH_PVALUE+x} ]; then echo "${VIASH_PAR_MAX_MISMATCH_PVALUE}" | sed "s#'#'\"'\"'#g;s#.*#par_max_mismatch_pvalue='&'#" ; else echo "# par_max_mismatch_pvalue="; fi )
$( if [ ! -z ${VIASH_PAR_FRAGMENT_LENGTH+x} ]; then echo "${VIASH_PAR_FRAGMENT_LENGTH}" | sed "s#'#'\"'\"'#g;s#.*#par_fragment_length='&'#" ; else echo "# par_fragment_length="; fi )
$( if [ ! -z ${VIASH_PAR_MAX_READS+x} ]; then echo "${VIASH_PAR_MAX_READS}" | sed "s#'#'\"'\"'#g;s#.*#par_max_reads='&'#" ; else echo "# par_max_reads="; fi )
$( if [ ! -z ${VIASH_PAR_QUANTILE+x} ]; then echo "${VIASH_PAR_QUANTILE}" | sed "s#'#'\"'\"'#g;s#.*#par_quantile='&'#" ; else echo "# par_quantile="; fi )
$( if [ ! -z ${VIASH_PAR_EXONIC_FRACTION+x} ]; then echo "${VIASH_PAR_EXONIC_FRACTION}" | sed "s#'#'\"'\"'#g;s#.*#par_exonic_fraction='&'#" ; else echo "# par_exonic_fraction="; fi )
$( if [ ! -z ${VIASH_PAR_TOP_N+x} ]; then echo "${VIASH_PAR_TOP_N}" | sed "s#'#'\"'\"'#g;s#.*#par_top_n='&'#" ; else echo "# par_top_n="; fi )
$( if [ ! -z ${VIASH_PAR_COVERED_FRACTION+x} ]; then echo "${VIASH_PAR_COVERED_FRACTION}" | sed "s#'#'\"'\"'#g;s#.*#par_covered_fraction='&'#" ; else echo "# par_covered_fraction="; fi )
$( if [ ! -z ${VIASH_PAR_MAX_ITD_LENGTH+x} ]; then echo "${VIASH_PAR_MAX_ITD_LENGTH}" | sed "s#'#'\"'\"'#g;s#.*#par_max_itd_length='&'#" ; else echo "# par_max_itd_length="; fi )
$( if [ ! -z ${VIASH_PAR_MIN_ITD_ALLELE_FRACTION+x} ]; then echo "${VIASH_PAR_MIN_ITD_ALLELE_FRACTION}" | sed "s#'#'\"'\"'#g;s#.*#par_min_itd_allele_fraction='&'#" ; else echo "# par_min_itd_allele_fraction="; fi )
$( if [ ! -z ${VIASH_PAR_MIN_ITD_SUPPORTING_READS+x} ]; then echo "${VIASH_PAR_MIN_ITD_SUPPORTING_READS}" | sed "s#'#'\"'\"'#g;s#.*#par_min_itd_supporting_reads='&'#" ; else echo "# par_min_itd_supporting_reads="; fi )
$( if [ ! -z ${VIASH_PAR_SKIP_DUPLICATE_MARKING+x} ]; then echo "${VIASH_PAR_SKIP_DUPLICATE_MARKING}" | sed "s#'#'\"'\"'#g;s#.*#par_skip_duplicate_marking='&'#" ; else echo "# par_skip_duplicate_marking="; fi )
$( if [ ! -z ${VIASH_PAR_EXTRA_INFORMATION+x} ]; then echo "${VIASH_PAR_EXTRA_INFORMATION}" | sed "s#'#'\"'\"'#g;s#.*#par_extra_information='&'#" ; else echo "# par_extra_information="; fi )
$( if [ ! -z ${VIASH_PAR_FILL_GAPS+x} ]; then echo "${VIASH_PAR_FILL_GAPS}" | sed "s#'#'\"'\"'#g;s#.*#par_fill_gaps='&'#" ; else echo "# par_fill_gaps="; 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 boolean flags that are "false"
[[ "\$par_skip_duplicate_marking" == "false" ]] && unset par_skip_duplicate_marking
[[ "\$par_extra_information" == "false" ]] && unset par_extra_information
[[ "\$par_fill_gaps" == "false" ]] && unset par_fill_gaps

# process multi-value parameters: replace ';' with ',' for arriba compatibility
if [[ -n "\${par_interesting_contigs:-}" ]]; then
  par_interesting_contigs=\$(echo "\$par_interesting_contigs" | tr ';' ',')
fi
if [[ -n "\${par_viral_contigs:-}" ]]; then
  par_viral_contigs=\$(echo "\$par_viral_contigs" | tr ';' ',')
fi
if [[ -n "\${par_disable_filters:-}" ]]; then
  par_disable_filters=\$(echo "\$par_disable_filters" | tr ';' ',')
fi

# build command arguments array
cmd_args=(
  # required arguments
  -x "\$par_bam"
  -a "\$par_genome" 
  -g "\$par_gene_annotation"
  -o "\$par_fusions"
  
  # optional input files
  \${par_known_fusions:+-k "\$par_known_fusions"}
  \${par_blacklist:+-b "\$par_blacklist"}
  \${par_structural_variants:+-d "\$par_structural_variants"}
  \${par_tags:+-t "\$par_tags"}
  \${par_protein_domains:+-p "\$par_protein_domains"}
  
  # optional output files
  \${par_fusions_discarded:+-O "\$par_fusions_discarded"}
  
  # filter and analysis options
  \${par_max_genomic_breakpoint_distance:+-D "\$par_max_genomic_breakpoint_distance"}
  \${par_strandedness:+-s "\$par_strandedness"}
  \${par_interesting_contigs:+-i "\$par_interesting_contigs"}
  \${par_viral_contigs:+-v "\$par_viral_contigs"}
  \${par_disable_filters:+-f "\$par_disable_filters"}
  
  # statistical thresholds
  \${par_max_e_value:+-E "\$par_max_e_value"}
  \${par_min_supporting_reads:+-S "\$par_min_supporting_reads"}
  \${par_max_mismappers:+-m "\$par_max_mismappers"}
  \${par_max_homolog_identity:+-L "\$par_max_homolog_identity"}
  \${par_homopolymer_length:+-H "\$par_homopolymer_length"}
  \${par_read_through_distance:+-R "\$par_read_through_distance"}
  \${par_min_anchor_length:+-A "\$par_min_anchor_length"}
  \${par_many_spliced_events:+-M "\$par_many_spliced_events"}
  \${par_max_kmer_content:+-K "\$par_max_kmer_content"}
  \${par_max_mismatch_pvalue:+-V "\$par_max_mismatch_pvalue"}
  \${par_fragment_length:+-F "\$par_fragment_length"}
  \${par_max_reads:+-U "\$par_max_reads"}
  \${par_quantile:+-Q "\$par_quantile"}
  \${par_exonic_fraction:+-e "\$par_exonic_fraction"}
  \${par_top_n:+-T "\$par_top_n"}
  \${par_covered_fraction:+-C "\$par_covered_fraction"}
  
  # internal tandem duplication options
  \${par_max_itd_length:+-l "\$par_max_itd_length"}
  \${par_min_itd_allele_fraction:+-z "\$par_min_itd_allele_fraction"}
  \${par_min_itd_supporting_reads:+-Z "\$par_min_itd_supporting_reads"}
  
  # boolean flags
  \${par_skip_duplicate_marking:+-u}
  \${par_extra_information:+-X}
  \${par_fill_gaps:+-I}
)

# execute arriba
arriba "\${cmd_args[@]}"
VIASHMAIN
bash "\$tempscript" &
wait "\$!"

VIASHEOF


if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  # strip viash automount from file paths
  
  if [ ! -z "$VIASH_PAR_BAM" ]; then
    VIASH_PAR_BAM=$(ViashDockerStripAutomount "$VIASH_PAR_BAM")
  fi
  if [ ! -z "$VIASH_PAR_GENOME" ]; then
    VIASH_PAR_GENOME=$(ViashDockerStripAutomount "$VIASH_PAR_GENOME")
  fi
  if [ ! -z "$VIASH_PAR_GENE_ANNOTATION" ]; then
    VIASH_PAR_GENE_ANNOTATION=$(ViashDockerStripAutomount "$VIASH_PAR_GENE_ANNOTATION")
  fi
  if [ ! -z "$VIASH_PAR_KNOWN_FUSIONS" ]; then
    VIASH_PAR_KNOWN_FUSIONS=$(ViashDockerStripAutomount "$VIASH_PAR_KNOWN_FUSIONS")
  fi
  if [ ! -z "$VIASH_PAR_BLACKLIST" ]; then
    VIASH_PAR_BLACKLIST=$(ViashDockerStripAutomount "$VIASH_PAR_BLACKLIST")
  fi
  if [ ! -z "$VIASH_PAR_STRUCTURAL_VARIANTS" ]; then
    VIASH_PAR_STRUCTURAL_VARIANTS=$(ViashDockerStripAutomount "$VIASH_PAR_STRUCTURAL_VARIANTS")
  fi
  if [ ! -z "$VIASH_PAR_TAGS" ]; then
    VIASH_PAR_TAGS=$(ViashDockerStripAutomount "$VIASH_PAR_TAGS")
  fi
  if [ ! -z "$VIASH_PAR_PROTEIN_DOMAINS" ]; then
    VIASH_PAR_PROTEIN_DOMAINS=$(ViashDockerStripAutomount "$VIASH_PAR_PROTEIN_DOMAINS")
  fi
  if [ ! -z "$VIASH_PAR_FUSIONS" ]; then
    VIASH_PAR_FUSIONS=$(ViashDockerStripAutomount "$VIASH_PAR_FUSIONS")
  fi
  if [ ! -z "$VIASH_PAR_FUSIONS_DISCARDED" ]; then
    VIASH_PAR_FUSIONS_DISCARDED=$(ViashDockerStripAutomount "$VIASH_PAR_FUSIONS_DISCARDED")
  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 "$VIASH_PAR_FUSIONS" ] && [ ! -e "$VIASH_PAR_FUSIONS" ]; then
  ViashError "Output file '$VIASH_PAR_FUSIONS' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_FUSIONS_DISCARDED" ] && [ ! -e "$VIASH_PAR_FUSIONS_DISCARDED" ]; then
  ViashError "Output file '$VIASH_PAR_FUSIONS_DISCARDED' does not exist."
  exit 1
fi


exit 0
