#!/usr/bin/env bash

# arriba v0.2.0
# 
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
# 
# The component may contain files which fall under a different license. The
# authors of this component should specify the license in the header of such
# files, or include a separate license file detailing the licenses of all included
# files.
# 
# Component authors:
#  * 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"


# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
  echo "arriba v0.2.0"
  echo ""
  echo "Detect gene fusions from RNA-Seq data"
  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). Arriba extracts candidate reads from this file."
  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."
}

# 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:2.4.0--h0033a41_2
ENTRYPOINT []
RUN arriba -h | grep 'Version:' 2>&1 |  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="2024-09-13T12:35:20Z"
LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba"
LABEL org.opencontainers.image.revision="7e530218844c373048bc33de58f021b6460642e5"
LABEL org.opencontainers.image.version="v0.2.0"

VIASHDOCKER
  fi
}

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

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

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

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

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

# initialise array
VIASH_POSITIONAL_ARGS=''

while [[ $# -gt 0 ]]; do
    case "$1" in
        -h|--help)
            ViashHelp
            exit
            ;;
        ---v|---verbose)
            let "VIASH_VERBOSITY=VIASH_VERBOSITY+1"
            shift 1
            ;;
        ---verbosity)
            VIASH_VERBOSITY="$2"
            shift 2
            ;;
        ---verbosity=*)
            VIASH_VERBOSITY="$(ViashRemoveFlags "$1")"
            shift 1
            ;;
        --version)
            echo "arriba v0.2.0"
            exit
            ;;
        --bam)
            [ -n "$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:v0.2.0'
  fi

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

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

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

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

# setting computational defaults
if [ -z ${VIASH_META_CPUS+x} ]; then
  VIASH_META_CPUS="1"
fi

# 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

# unset flags
[[ "\$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

# replace ';' with ','
par_interesting_contigs=\$(echo \$par_interesting_contigs | tr ';' ',')
par_viral_contigs=\$(echo \$par_viral_contigs | tr ';' ',')
par_disable_filters=\$(echo \$par_disable_filters | tr ';' ',')

# run arriba
arriba \\
  -x "\$par_bam" \\
  -a "\$par_genome" \\
  -g "\$par_gene_annotation" \\
  -o "\$par_fusions" \\
  \${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}"} \\
  \${par_fusions_discarded:+-O "\${par_fusions_discarded}"} \\
  \${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}"} \\
  \${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}"} \\
  \${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}"} \\
  \${par_skip_duplicate_marking:+-u} \\
  \${par_extra_information:+-X} \\
  \${par_fill_gaps:+-I}
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
