#!/usr/bin/env bash

# star_align_v273a v4.0.2
# 
# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
# 
# The component may contain files which fall under a different license. The
# authors of this component should specify the license in the header of such
# files, or include a separate license file detailing the licenses of all included
# files.
# 
# Component authors:
#  * Angela Oliveira Pisco (author)
#  * 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="star_align_v273a"
VIASH_META_FUNCTIONALITY_NAME="star_align_v273a"
VIASH_META_EXECUTABLE="$VIASH_META_RESOURCES_DIR/$VIASH_META_NAME"
VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
VIASH_META_TEMP_DIR="$VIASH_TEMP"



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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

  if [[ "$engine_id" == "docker" ]]; then
    cat << 'VIASHDOCKER'
FROM python:3.13-slim
ENTRYPOINT []
RUN apt-get update && \
  DEBIAN_FRONTEND=noninteractive apt-get install -y procps && \
  rm -rf /var/lib/apt/lists/*

ENV STAR_VERSION 2.7.3a
ENV PACKAGES gcc g++ make wget zlib1g-dev unzip
RUN apt-get update && \
  apt-get install -y --no-install-recommends ${PACKAGES} && \
  cd /tmp && \
  wget --no-check-certificate https://github.com/alexdobin/STAR/archive/refs/tags/${STAR_VERSION}.zip && \
  unzip ${STAR_VERSION}.zip && \
  cd STAR-${STAR_VERSION}/source && \
  make STARstatic CXXFLAGS_SIMD=-std=c++11 && \
  cp STAR /usr/local/bin && \
  cd / && \
  rm -rf /tmp/STAR-${STAR_VERSION} /tmp/${STAR_VERSION}.zip && \
  apt-get --purge autoremove -y ${PACKAGES} && \
  apt-get clean

LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt"
LABEL org.opencontainers.image.description="Companion container for running component mapping star_align_v273a"
LABEL org.opencontainers.image.created="2026-02-11T14:34:07Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62"
LABEL org.opencontainers.image.version="v4.0.2"

VIASHDOCKER
  fi
}

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

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

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

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

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


# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
  echo "star_align_v273a v4.0.2"
  echo ""
  echo "Align fastq files using STAR."
  echo ""
  echo "Input/Output:"
  echo "    --readFilesIn, --input"
  echo "        type: file, required parameter, multiple values allowed, file must exist"
  echo "        example:"
  echo "mysample_S1_L001_R1_001.fastq.gz;mysample_S1_L001_R2_001.fastq.gz"
  echo "        The FASTQ files to be analyzed. Corresponds to the --readFilesIn in the"
  echo "        STAR command."
  echo ""
  echo "    --genomeDir, --reference"
  echo "        type: file, required parameter, file must exist"
  echo "        example: /path/to/reference"
  echo "        Path to the reference built by star_build_reference. Corresponds to the"
  echo "        --genomeDir in the STAR command."
  echo ""
  echo "    --outFileNamePrefix, --output"
  echo "        type: file, required parameter, output, file must exist"
  echo "        example: /path/to/foo"
  echo "        Path to output directory. Corresponds to the --outFileNamePrefix in the"
  echo "        STAR command."
  echo ""
  echo "Run Parameters:"
  echo "    --runRNGseed"
  echo "        type: integer"
  echo "        example: 777"
  echo "        random number generator seed."
  echo ""
  echo "Genome Parameters:"
  echo "    --genomeLoad"
  echo "        type: string"
  echo "        example: NoSharedMemory"
  echo "        mode of shared memory usage for the genome files. Only used with"
  echo "        --runMode alignReads."
  echo "        - LoadAndKeep     ... load genome into shared and keep it in memory"
  echo "        after run"
  echo "        - LoadAndRemove   ... load genome into shared but remove it after run"
  echo "        - LoadAndExit     ... load genome into shared memory and exit, keeping"
  echo "        the genome in memory for future runs"
  echo "        - Remove          ... do not map anything, just remove loaded genome"
  echo "        from memory"
  echo "        - NoSharedMemory  ... do not use shared memory, each job will have its"
  echo "        own private copy of the genome"
  echo ""
  echo "    --genomeFastaFiles"
  echo "        type: file, multiple values allowed, file must exist"
  echo "        path(s) to the fasta files with the genome sequences, separated by"
  echo "        spaces. These files should be plain text FASTA files, they *cannot* be"
  echo "        zipped."
  echo "        Required for the genome generation (--runMode genomeGenerate). Can also"
  echo "        be used in the mapping (--runMode alignReads) to add extra (new)"
  echo "        sequences to the genome (e.g. spike-ins)."
  echo ""
  echo "    --genomeFileSizes"
  echo "        type: integer, multiple values allowed"
  echo "        example: 0"
  echo "        genome files exact sizes in bytes. Typically, this should not be defined"
  echo "        by the user."
  echo ""
  echo "    --genomeTransformOutput"
  echo "        type: string, multiple values allowed"
  echo "        which output to transform back to original genome"
  echo "        - SAM     ... SAM/BAM alignments"
  echo "        - SJ      ... splice junctions (SJ.out.tab)"
  echo "        - None    ... no transformation of the output"
  echo ""
  echo "    --genomeChrSetMitochondrial"
  echo "        type: string, multiple values allowed"
  echo "        example: chrM;M;MT"
  echo "        names of the mitochondrial chromosomes. Presently only used for STARsolo"
  echo "        statistics output/"
  echo ""
  echo "Splice Junctions Database:"
  echo "    --sjdbFileChrStartEnd"
  echo "        type: string, multiple values allowed"
  echo "        path to the files with genomic coordinates (chr <tab> start <tab> end"
  echo "        <tab> strand) for the splice junction introns. Multiple files can be"
  echo "        supplied and will be concatenated."
  echo ""
  echo "    --sjdbGTFfile"
  echo "        type: file, file must exist"
  echo "        path to the GTF file with annotations"
  echo ""
  echo "    --sjdbGTFchrPrefix"
  echo "        type: string"
  echo "        prefix for chromosome names in a GTF file (e.g. 'chr' for using ENSMEBL"
  echo "        annotations with UCSC genomes)"
  echo ""
  echo "    --sjdbGTFfeatureExon"
  echo "        type: string"
  echo "        example: exon"
  echo "        feature type in GTF file to be used as exons for building transcripts"
  echo ""
  echo "    --sjdbGTFtagExonParentTranscript"
  echo "        type: string"
  echo "        example: transcript_id"
  echo "        GTF attribute name for parent transcript ID (default \"transcript_id\""
  echo "        works for GTF files)"
  echo ""
  echo "    --sjdbGTFtagExonParentGene"
  echo "        type: string"
  echo "        example: gene_id"
  echo "        GTF attribute name for parent gene ID (default \"gene_id\" works for GTF"
  echo "        files)"
  echo ""
  echo "    --sjdbGTFtagExonParentGeneName"
  echo "        type: string, multiple values allowed"
  echo "        example: gene_name"
  echo "        GTF attribute name for parent gene name"
  echo ""
  echo "    --sjdbGTFtagExonParentGeneType"
  echo "        type: string, multiple values allowed"
  echo "        example: gene_type;gene_biotype"
  echo "        GTF attribute name for parent gene type"
  echo ""
  echo "    --sjdbOverhang"
  echo "        type: integer"
  echo "        example: 100"
  echo "        length of the donor/acceptor sequence on each side of the junctions,"
  echo "        ideally = (mate_length - 1)"
  echo ""
  echo "    --sjdbScore"
  echo "        type: integer"
  echo "        example: 2"
  echo "        extra alignment score for alignments that cross database junctions"
  echo ""
  echo "    --sjdbInsertSave"
  echo "        type: string"
  echo "        example: Basic"
  echo "        which files to save when sjdb junctions are inserted on the fly at the"
  echo "        mapping step"
  echo "        - Basic ... only small junction / transcript files"
  echo "        - All   ... all files including big Genome, SA and SAindex - this will"
  echo "        create a complete genome directory"
  echo ""
  echo "Variation parameters:"
  echo "    --varVCFfile"
  echo "        type: string"
  echo "        path to the VCF file that contains variation data. The 10th column"
  echo "        should contain the genotype information, e.g. 0/1"
  echo ""
  echo "Read Parameters:"
  echo "    --readFilesType"
  echo "        type: string"
  echo "        example: Fastx"
  echo "        format of input read files"
  echo "        - Fastx       ... FASTA or FASTQ"
  echo "        - SAM SE      ... SAM or BAM single-end reads; for BAM use"
  echo "        --readFilesCommand samtools view"
  echo "        - SAM PE      ... SAM or BAM paired-end reads; for BAM use"
  echo "        --readFilesCommand samtools view"
  echo ""
  echo "    --readFilesSAMattrKeep"
  echo "        type: string, multiple values allowed"
  echo "        example: All"
  echo "        for --readFilesType SAM SE/PE, which SAM tags to keep in the output BAM,"
  echo "        e.g.: --readFilesSAMtagsKeep RG PL"
  echo "        - All     ... keep all tags"
  echo "        - None    ... do not keep any tags"
  echo ""
  echo "    --readFilesManifest"
  echo "        type: file, file must exist"
  echo "        path to the \"manifest\" file with the names of read files. The manifest"
  echo "        file should contain 3 tab-separated columns:"
  echo "        paired-end reads: read1_file_name \$tab\$ read2_file_name \$tab\$"
  echo "        read_group_line."
  echo "        single-end reads: read1_file_name \$tab\$ -               \$tab\$"
  echo "        read_group_line."
  echo "        Spaces, but not tabs are allowed in file names."
  echo "        If read_group_line does not start with ID:, it can only contain one ID"
  echo "        field, and ID: will be added to it."
  echo "        If read_group_line starts with ID:, it can contain several fields"
  echo "        separated by \$tab\$, and all fields will be be copied verbatim into SAM"
  echo "        @RG header line."
  echo ""
  echo "    --readFilesPrefix"
  echo "        type: string"
  echo "        prefix for the read files names, i.e. it will be added in front of the"
  echo "        strings in --readFilesIn"
  echo ""
  echo "    --readFilesCommand"
  echo "        type: string, multiple values allowed"
  echo "        command line to execute for each of the input file. This command should"
  echo "        generate FASTA or FASTQ text and send it to stdout"
  echo "        For example: zcat - to uncompress .gz files, bzcat - to uncompress .bz2"
  echo "        files, etc."
  echo ""
  echo "    --readMapNumber"
  echo "        type: integer"
  echo "        example: -1"
  echo "        number of reads to map from the beginning of the file"
  echo "        -1: map all reads"
  echo ""
  echo "    --readMatesLengthsIn"
  echo "        type: string"
  echo "        example: NotEqual"
  echo "        Equal/NotEqual - lengths of names,sequences,qualities for both mates are"
  echo "        the same  / not the same. NotEqual is safe in all situations."
  echo ""
  echo "    --readNameSeparator"
  echo "        type: string, multiple values allowed"
  echo "        example: /"
  echo "        character(s) separating the part of the read names that will be trimmed"
  echo "        in output (read name after space is always trimmed)"
  echo ""
  echo "    --readQualityScoreBase"
  echo "        type: integer"
  echo "        example: 33"
  echo "        number to be subtracted from the ASCII code to get Phred quality score"
  echo ""
  echo "Read Clipping:"
  echo "    --clipAdapterType"
  echo "        type: string"
  echo "        example: Hamming"
  echo "        adapter clipping type"
  echo "        - Hamming ... adapter clipping based on Hamming distance, with the"
  echo "        number of mismatches controlled by --clip5pAdapterMMp"
  echo "        - CellRanger4 ... 5p and 3p adapter clipping similar to CellRanger4."
  echo "        Utilizes Opal package by Martin Sosic: https://github.com/Martinsos/opal"
  echo "        - None ... no adapter clipping, all other clip* parameters are"
  echo "        disregarded"
  echo ""
  echo "    --clip3pNbases"
  echo "        type: integer, multiple values allowed"
  echo "        example: 0"
  echo "        number(s) of bases to clip from 3p of each mate. If one value is given,"
  echo "        it will be assumed the same for both mates."
  echo ""
  echo "    --clip3pAdapterSeq"
  echo "        type: string, multiple values allowed"
  echo "        adapter sequences to clip from 3p of each mate.  If one value is given,"
  echo "        it will be assumed the same for both mates."
  echo "        - polyA ... polyA sequence with the length equal to read length"
  echo ""
  echo "    --clip3pAdapterMMp"
  echo "        type: double, multiple values allowed"
  echo "        example: 0.1"
  echo "        max proportion of mismatches for 3p adapter clipping for each mate.  If"
  echo "        one value is given, it will be assumed the same for both mates."
  echo ""
  echo "    --clip3pAfterAdapterNbases"
  echo "        type: integer, multiple values allowed"
  echo "        example: 0"
  echo "        number of bases to clip from 3p of each mate after the adapter clipping."
  echo "        If one value is given, it will be assumed the same for both mates."
  echo ""
  echo "    --clip5pNbases"
  echo "        type: integer, multiple values allowed"
  echo "        example: 0"
  echo "        number(s) of bases to clip from 5p of each mate. If one value is given,"
  echo "        it will be assumed the same for both mates."
  echo ""
  echo "Limits:"
  echo "    --limitGenomeGenerateRAM"
  echo "        type: long"
  echo "        example: 31000000000"
  echo "        maximum available RAM (bytes) for genome generation"
  echo ""
  echo "    --limitIObufferSize"
  echo "        type: long, multiple values allowed"
  echo "        example: 30000000;50000000"
  echo "        max available buffers size (bytes) for input/output, per thread"
  echo ""
  echo "    --limitOutSAMoneReadBytes"
  echo "        type: long"
  echo "        example: 100000"
  echo "        max size of the SAM record (bytes) for one read. Recommended value:"
  echo "        >(2*(LengthMate1+LengthMate2+100)*outFilterMultimapNmax"
  echo ""
  echo "    --limitOutSJoneRead"
  echo "        type: integer"
  echo "        example: 1000"
  echo "        max number of junctions for one read (including all multi-mappers)"
  echo ""
  echo "    --limitOutSJcollapsed"
  echo "        type: integer"
  echo "        example: 1000000"
  echo "        max number of collapsed junctions"
  echo ""
  echo "    --limitBAMsortRAM"
  echo "        type: long"
  echo "        example: 0"
  echo "        maximum available RAM (bytes) for sorting BAM. If =0, it will be set to"
  echo "        the genome index size. 0 value can only be used with --genomeLoad"
  echo "        NoSharedMemory option."
  echo ""
  echo "    --limitSjdbInsertNsj"
  echo "        type: integer"
  echo "        example: 1000000"
  echo "        maximum number of junctions to be inserted to the genome on the fly at"
  echo "        the mapping stage, including those from annotations and those detected"
  echo "        in the 1st step of the 2-pass run"
  echo ""
  echo "    --limitNreadsSoft"
  echo "        type: integer"
  echo "        example: -1"
  echo "        soft limit on the number of reads"
  echo ""
  echo "Output: general:"
  echo "    --outTmpKeep"
  echo "        type: string"
  echo "        whether to keep the temporary files after STAR runs is finished"
  echo "        - None ... remove all temporary files"
  echo "        - All ... keep all files"
  echo ""
  echo "    --outStd"
  echo "        type: string"
  echo "        example: Log"
  echo "        which output will be directed to stdout (standard out)"
  echo "        - Log                    ... log messages"
  echo "        - SAM                    ... alignments in SAM format (which normally"
  echo "        are output to Aligned.out.sam file), normal standard output will go into"
  echo "        Log.std.out"
  echo "        - BAM_Unsorted           ... alignments in BAM format, unsorted."
  echo "        Requires --outSAMtype BAM Unsorted"
  echo "        - BAM_SortedByCoordinate ... alignments in BAM format, sorted by"
  echo "        coordinate. Requires --outSAMtype BAM SortedByCoordinate"
  echo "        - BAM_Quant              ... alignments to transcriptome in BAM format,"
  echo "        unsorted. Requires --quantMode TranscriptomeSAM"
  echo ""
  echo "    --outReadsUnmapped"
  echo "        type: string"
  echo "        output of unmapped and partially mapped (i.e. mapped only one mate of a"
  echo "        paired end read) reads in separate file(s)."
  echo "        - None    ... no output"
  echo "        - Fastx   ... output in separate fasta/fastq files, Unmapped.out.mate1/2"
  echo ""
  echo "    --outQSconversionAdd"
  echo "        type: integer"
  echo "        example: 0"
  echo "        add this number to the quality score (e.g. to convert from Illumina to"
  echo "        Sanger, use -31)"
  echo ""
  echo "    --outMultimapperOrder"
  echo "        type: string"
  echo "        example: Old_2.4"
  echo "        order of multimapping alignments in the output files"
  echo "        - Old_2.4             ... quasi-random order used before 2.5.0"
  echo "        - Random              ... random order of alignments for each"
  echo "        multi-mapper. Read mates (pairs) are always adjacent, all alignment for"
  echo "        each read stay together. This option will become default in the future"
  echo "        releases."
  echo ""
  echo "Output: SAM and BAM:"
  echo "    --outSAMtype"
  echo "        type: string, multiple values allowed"
  echo "        example: SAM"
  echo "        type of SAM/BAM output"
  echo "        1st word:"
  echo "        - BAM  ... output BAM without sorting"
  echo "        - SAM  ... output SAM without sorting"
  echo "        - None ... no SAM/BAM output"
  echo "        2nd, 3rd:"
  echo "        - Unsorted           ... standard unsorted"
  echo "        - SortedByCoordinate ... sorted by coordinate. This option will allocate"
  echo "        extra memory for sorting which can be specified by --limitBAMsortRAM."
  echo ""
  echo "    --outSAMmode"
  echo "        type: string"
  echo "        example: Full"
  echo "        mode of SAM output"
  echo "        - None ... no SAM output"
  echo "        - Full ... full SAM output"
  echo "        - NoQS ... full SAM but without quality scores"
  echo ""
  echo "    --outSAMstrandField"
  echo "        type: string"
  echo "        Cufflinks-like strand field flag"
  echo "        - None        ... not used"
  echo "        - intronMotif ... strand derived from the intron motif. This option"
  echo "        changes the output alignments: reads with inconsistent and/or"
  echo "        non-canonical introns are filtered out."
  echo ""
  echo "    --outSAMattributes"
  echo "        type: string, multiple values allowed"
  echo "        example: Standard"
  echo "        a string of desired SAM attributes, in the order desired for the output"
  echo "        SAM. Tags can be listed in any combination/order."
  echo "        ***Presets:"
  echo "        - None        ... no attributes"
  echo "        - Standard    ... NH HI AS nM"
  echo "        - All         ... NH HI AS nM NM MD jM jI MC ch"
  echo "        ***Alignment:"
  echo "        - NH          ... number of loci the reads maps to: =1 for unique"
  echo "        mappers, >1 for multimappers. Standard SAM tag."
  echo "        - HI          ... multiple alignment index, starts with"
  echo "        --outSAMattrIHstart (=1 by default). Standard SAM tag."
  echo "        - AS          ... local alignment score, +1/-1 for matches/mismateches,"
  echo "        score* penalties for indels and gaps. For PE reads, total score for two"
  echo "        mates. Stadnard SAM tag."
  echo "        - nM          ... number of mismatches. For PE reads, sum over two"
  echo "        mates."
  echo "        - NM          ... edit distance to the reference (number of mismatched +"
  echo "        inserted + deleted bases) for each mate. Standard SAM tag."
  echo "        - MD          ... string encoding mismatched and deleted reference bases"
  echo "        (see standard SAM specifications). Standard SAM tag."
  echo "        - jM          ... intron motifs for all junctions (i.e. N in CIGAR): 0:"
  echo "        non-canonical; 1: GT/AG, 2: CT/AC, 3: GC/AG, 4: CT/GC, 5: AT/AC, 6:"
  echo "        GT/AT. If splice junctions database is used, and a junction is"
  echo "        annotated, 20 is added to its motif value."
  echo "        - jI          ... start and end of introns for all junctions (1-based)."
  echo "        - XS          ... alignment strand according to --outSAMstrandField."
  echo "        - MC          ... mate's CIGAR string. Standard SAM tag."
  echo "        - ch          ... marks all segment of all chimeric alingments for"
  echo "        --chimOutType WithinBAM output."
  echo "        - cN          ... number of bases clipped from the read ends: 5' and 3'"
  echo "        ***Variation:"
  echo "        - vA          ... variant allele"
  echo "        - vG          ... genomic coordinate of the variant overlapped by the"
  echo "        read."
  echo "        - vW          ... 1 - alignment passes WASP filtering; 2,3,4,5,6,7 -"
  echo "        alignment does not pass WASP filtering. Requires --waspOutputMode"
  echo "        SAMtag."
  echo "        ***STARsolo:"
  echo "        - CR CY UR UY ... sequences and quality scores of cell barcodes and UMIs"
  echo "        for the solo* demultiplexing."
  echo "        - GX GN       ... gene ID and gene name for unique-gene reads."
  echo "        - gx gn       ... gene IDs and gene names for unique- and multi-gene"
  echo "        reads."
  echo "        - CB UB       ... error-corrected cell barcodes and UMIs for solo*"
  echo "        demultiplexing. Requires --outSAMtype BAM SortedByCoordinate."
  echo "        - sM          ... assessment of CB and UMI."
  echo "        - sS          ... sequence of the entire barcode (CB,UMI,adapter)."
  echo "        - sQ          ... quality of the entire barcode."
  echo "        ***Unsupported/undocumented:"
  echo "        - ha          ... haplotype (1/2) when mapping to the diploid genome."
  echo "        Requires genome generated with --genomeTransformType Diploid ."
  echo "        - rB          ... alignment block read/genomic coordinates."
  echo "        - vR          ... read coordinate of the variant."
  echo ""
  echo "    --outSAMattrIHstart"
  echo "        type: integer"
  echo "        example: 1"
  echo "        start value for the IH attribute. 0 may be required by some downstream"
  echo "        software, such as Cufflinks or StringTie."
  echo ""
  echo "    --outSAMunmapped"
  echo "        type: string, multiple values allowed"
  echo "        output of unmapped reads in the SAM format"
  echo "        1st word:"
  echo "        - None   ... no output"
  echo "        - Within ... output unmapped reads within the main SAM file (i.e."
  echo "        Aligned.out.sam)"
  echo "        2nd word:"
  echo "        - KeepPairs ... record unmapped mate for each alignment, and, in case of"
  echo "        unsorted output, keep it adjacent to its mapped mate. Only affects"
  echo "        multi-mapping reads."
  echo ""
  echo "    --outSAMorder"
  echo "        type: string"
  echo "        example: Paired"
  echo "        type of sorting for the SAM output"
  echo "        Paired: one mate after the other for all paired alignments"
  echo "        PairedKeepInputOrder: one mate after the other for all paired"
  echo "        alignments, the order is kept the same as in the input FASTQ files"
  echo ""
  echo "    --outSAMprimaryFlag"
  echo "        type: string"
  echo "        example: OneBestScore"
  echo "        which alignments are considered primary - all others will be marked with"
  echo "        0x100 bit in the FLAG"
  echo "        - OneBestScore ... only one alignment with the best score is primary"
  echo "        - AllBestScore ... all alignments with the best score are primary"
  echo ""
  echo "    --outSAMreadID"
  echo "        type: string"
  echo "        example: Standard"
  echo "        read ID record type"
  echo "        - Standard ... first word (until space) from the FASTx read ID line,"
  echo "        removing /1,/2 from the end"
  echo "        - Number   ... read number (index) in the FASTx file"
  echo ""
  echo "    --outSAMmapqUnique"
  echo "        type: integer"
  echo "        example: 255"
  echo "        0 to 255: the MAPQ value for unique mappers"
  echo ""
  echo "    --outSAMflagOR"
  echo "        type: integer"
  echo "        example: 0"
  echo "        0 to 65535: sam FLAG will be bitwise OR'd with this value, i.e."
  echo "        FLAG=FLAG | outSAMflagOR. This is applied after all flags have been set"
  echo "        by STAR, and after outSAMflagAND. Can be used to set specific bits that"
  echo "        are not set otherwise."
  echo ""
  echo "    --outSAMflagAND"
  echo "        type: integer"
  echo "        example: 65535"
  echo "        0 to 65535: sam FLAG will be bitwise AND'd with this value, i.e."
  echo "        FLAG=FLAG & outSAMflagOR. This is applied after all flags have been set"
  echo "        by STAR, but before outSAMflagOR. Can be used to unset specific bits"
  echo "        that are not set otherwise."
  echo ""
  echo "    --outSAMattrRGline"
  echo "        type: string, multiple values allowed"
  echo "        SAM/BAM read group line. The first word contains the read group"
  echo "        identifier and must start with \"ID:\", e.g. --outSAMattrRGline ID:xxx"
  echo "        CN:yy \"DS:z z z\"."
  echo "        xxx will be added as RG tag to each output alignment. Any spaces in the"
  echo "        tag values have to be double quoted."
  echo "        Comma separated RG lines correspons to different (comma separated) input"
  echo "        files in --readFilesIn. Commas have to be surrounded by spaces, e.g."
  echo "        --outSAMattrRGline ID:xxx , ID:zzz \"DS:z z\" , ID:yyy DS:yyyy"
  echo ""
  echo "    --outSAMheaderHD"
  echo "        type: string, multiple values allowed"
  echo "        @HD (header) line of the SAM header"
  echo ""
  echo "    --outSAMheaderPG"
  echo "        type: string, multiple values allowed"
  echo "        extra @PG (software) line of the SAM header (in addition to STAR)"
  echo ""
  echo "    --outSAMheaderCommentFile"
  echo "        type: string"
  echo "        path to the file with @CO (comment) lines of the SAM header"
  echo ""
  echo "    --outSAMfilter"
  echo "        type: string, multiple values allowed"
  echo "        filter the output into main SAM/BAM files"
  echo "        - KeepOnlyAddedReferences ... only keep the reads for which all"
  echo "        alignments are to the extra reference sequences added with"
  echo "        --genomeFastaFiles at the mapping stage."
  echo "        - KeepAllAddedReferences ...  keep all alignments to the extra reference"
  echo "        sequences added with --genomeFastaFiles at the mapping stage."
  echo ""
  echo "    --outSAMmultNmax"
  echo "        type: integer"
  echo "        example: -1"
  echo "        max number of multiple alignments for a read that will be output to the"
  echo "        SAM/BAM files. Note that if this value is not equal to -1, the top"
  echo "        scoring alignment will be output first"
  echo "        - -1 ... all alignments (up to --outFilterMultimapNmax) will be output"
  echo ""
  echo "    --outSAMtlen"
  echo "        type: integer"
  echo "        example: 1"
  echo "        calculation method for the TLEN field in the SAM/BAM files"
  echo "        - 1 ... leftmost base of the (+)strand mate to rightmost base of the"
  echo "        (-)mate. (+)sign for the (+)strand mate"
  echo "        - 2 ... leftmost base of any mate to rightmost base of any mate. (+)sign"
  echo "        for the mate with the leftmost base. This is different from 1 for"
  echo "        overlapping mates with protruding ends"
  echo ""
  echo "    --outBAMcompression"
  echo "        type: integer"
  echo "        example: 1"
  echo "        -1 to 10  BAM compression level, -1=default compression (6?), 0=no"
  echo "        compression, 10=maximum compression"
  echo ""
  echo "    --outBAMsortingThreadN"
  echo "        type: integer"
  echo "        example: 0"
  echo "        >=0: number of threads for BAM sorting. 0 will default to"
  echo "        min(6,--runThreadN)."
  echo ""
  echo "    --outBAMsortingBinsN"
  echo "        type: integer"
  echo "        example: 50"
  echo "        >0:  number of genome bins for coordinate-sorting"
  echo ""
  echo "BAM processing:"
  echo "    --bamRemoveDuplicatesType"
  echo "        type: string"
  echo "        mark duplicates in the BAM file, for now only works with (i) sorted BAM"
  echo "        fed with inputBAMfile, and (ii) for paired-end alignments only"
  echo "        - -                       ... no duplicate removal/marking"
  echo "        - UniqueIdentical         ... mark all multimappers, and duplicate"
  echo "        unique mappers. The coordinates, FLAG, CIGAR must be identical"
  echo "        - UniqueIdenticalNotMulti  ... mark duplicate unique mappers but not"
  echo "        multimappers."
  echo ""
  echo "    --bamRemoveDuplicatesMate2basesN"
  echo "        type: integer"
  echo "        example: 0"
  echo "        number of bases from the 5' of mate 2 to use in collapsing (e.g. for"
  echo "        RAMPAGE)"
  echo ""
  echo "Output Wiggle:"
  echo "    --outWigType"
  echo "        type: string, multiple values allowed"
  echo "        type of signal output, e.g. \"bedGraph\" OR \"bedGraph read1_5p\". Requires"
  echo "        sorted BAM: --outSAMtype BAM SortedByCoordinate ."
  echo "        1st word:"
  echo "        - None       ... no signal output"
  echo "        - bedGraph   ... bedGraph format"
  echo "        - wiggle     ... wiggle format"
  echo "        2nd word:"
  echo "        - read1_5p   ... signal from only 5' of the 1st read, useful for"
  echo "        CAGE/RAMPAGE etc"
  echo "        - read2      ... signal from only 2nd read"
  echo ""
  echo "    --outWigStrand"
  echo "        type: string"
  echo "        example: Stranded"
  echo "        strandedness of wiggle/bedGraph output"
  echo "        - Stranded   ...  separate strands, str1 and str2"
  echo "        - Unstranded ...  collapsed strands"
  echo ""
  echo "    --outWigReferencesPrefix"
  echo "        type: string"
  echo "        prefix matching reference names to include in the output wiggle file,"
  echo "        e.g. \"chr\", default \"-\" - include all references"
  echo ""
  echo "    --outWigNorm"
  echo "        type: string"
  echo "        example: RPM"
  echo "        type of normalization for the signal"
  echo "        - RPM    ... reads per million of mapped reads"
  echo "        - None   ... no normalization, \"raw\" counts"
  echo ""
  echo "Output Filtering:"
  echo "    --outFilterType"
  echo "        type: string"
  echo "        example: Normal"
  echo "        type of filtering"
  echo "        - Normal  ... standard filtering using only current alignment"
  echo "        - BySJout ... keep only those reads that contain junctions that passed"
  echo "        filtering into SJ.out.tab"
  echo ""
  echo "    --outFilterMultimapScoreRange"
  echo "        type: integer"
  echo "        example: 1"
  echo "        the score range below the maximum score for multimapping alignments"
  echo ""
  echo "    --outFilterMultimapNmax"
  echo "        type: integer"
  echo "        example: 10"
  echo "        maximum number of loci the read is allowed to map to. Alignments (all of"
  echo "        them) will be output only if the read maps to no more loci than this"
  echo "        value."
  echo "        Otherwise no alignments will be output, and the read will be counted as"
  echo "        \"mapped to too many loci\" in the Log.final.out ."
  echo ""
  echo "    --outFilterMismatchNmax"
  echo "        type: integer"
  echo "        example: 10"
  echo "        alignment will be output only if it has no more mismatches than this"
  echo "        value."
  echo ""
  echo "    --outFilterMismatchNoverLmax"
  echo "        type: double"
  echo "        example: 0.3"
  echo "        alignment will be output only if its ratio of mismatches to *mapped*"
  echo "        length is less than or equal to this value."
  echo ""
  echo "    --outFilterMismatchNoverReadLmax"
  echo "        type: double"
  echo "        example: 1.0"
  echo "        alignment will be output only if its ratio of mismatches to *read*"
  echo "        length is less than or equal to this value."
  echo ""
  echo "    --outFilterScoreMin"
  echo "        type: integer"
  echo "        example: 0"
  echo "        alignment will be output only if its score is higher than or equal to"
  echo "        this value."
  echo ""
  echo "    --outFilterScoreMinOverLread"
  echo "        type: double"
  echo "        example: 0.66"
  echo "        same as outFilterScoreMin, but normalized to read length (sum of mates'"
  echo "        lengths for paired-end reads)"
  echo ""
  echo "    --outFilterMatchNmin"
  echo "        type: integer"
  echo "        example: 0"
  echo "        alignment will be output only if the number of matched bases is higher"
  echo "        than or equal to this value."
  echo ""
  echo "    --outFilterMatchNminOverLread"
  echo "        type: double"
  echo "        example: 0.66"
  echo "        sam as outFilterMatchNmin, but normalized to the read length (sum of"
  echo "        mates' lengths for paired-end reads)."
  echo ""
  echo "    --outFilterIntronMotifs"
  echo "        type: string"
  echo "        filter alignment using their motifs"
  echo "        - None                           ... no filtering"
  echo "        - RemoveNoncanonical             ... filter out alignments that contain"
  echo "        non-canonical junctions"
  echo "        - RemoveNoncanonicalUnannotated  ... filter out alignments that contain"
  echo "        non-canonical unannotated junctions when using annotated splice"
  echo "        junctions database. The annotated non-canonical junctions will be kept."
  echo ""
  echo "    --outFilterIntronStrands"
  echo "        type: string"
  echo "        example: RemoveInconsistentStrands"
  echo "        filter alignments"
  echo "        - RemoveInconsistentStrands      ... remove alignments that have"
  echo "        junctions with inconsistent strands"
  echo "        - None                           ... no filtering"
  echo ""
  echo "Output splice junctions (SJ.out.tab):"
  echo "    --outSJtype"
  echo "        type: string"
  echo "        example: Standard"
  echo "        type of splice junction output"
  echo "        - Standard    ... standard SJ.out.tab output"
  echo "        - None        ... no splice junction output"
  echo ""
  echo "Output Filtering: Splice Junctions:"
  echo "    --outSJfilterReads"
  echo "        type: string"
  echo "        example: All"
  echo "        which reads to consider for collapsed splice junctions output"
  echo "        - All     ... all reads, unique- and multi-mappers"
  echo "        - Unique  ... uniquely mapping reads only"
  echo ""
  echo "    --outSJfilterOverhangMin"
  echo "        type: integer, multiple values allowed"
  echo "        example: 30;12;12;12"
  echo "        minimum overhang length for splice junctions on both sides for: (1)"
  echo "        non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC"
  echo "        motif, (4) AT/AC and GT/AT motif. -1 means no output for that motif"
  echo "        does not apply to annotated junctions"
  echo ""
  echo "    --outSJfilterCountUniqueMin"
  echo "        type: integer, multiple values allowed"
  echo "        example: 3;1;1;1"
  echo "        minimum uniquely mapping read count per junction for: (1) non-canonical"
  echo "        motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC motif, (4) AT/AC"
  echo "        and GT/AT motif. -1 means no output for that motif"
  echo "        Junctions are output if one of outSJfilterCountUniqueMin OR"
  echo "        outSJfilterCountTotalMin conditions are satisfied"
  echo "        does not apply to annotated junctions"
  echo ""
  echo "    --outSJfilterCountTotalMin"
  echo "        type: integer, multiple values allowed"
  echo "        example: 3;1;1;1"
  echo "        minimum total (multi-mapping+unique) read count per junction for: (1)"
  echo "        non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC"
  echo "        motif, (4) AT/AC and GT/AT motif. -1 means no output for that motif"
  echo "        Junctions are output if one of outSJfilterCountUniqueMin OR"
  echo "        outSJfilterCountTotalMin conditions are satisfied"
  echo "        does not apply to annotated junctions"
  echo ""
  echo "    --outSJfilterDistToOtherSJmin"
  echo "        type: integer, multiple values allowed"
  echo "        example: 10;0;5;10"
  echo "        minimum allowed distance to other junctions' donor/acceptor"
  echo "        does not apply to annotated junctions"
  echo ""
  echo "    --outSJfilterIntronMaxVsReadN"
  echo "        type: integer, multiple values allowed"
  echo "        example: 50000;100000;200000"
  echo "        maximum gap allowed for junctions supported by 1,2,3,,,N reads"
  echo "        i.e. by default junctions supported by 1 read can have gaps <=50000b, by"
  echo "        2 reads: <=100000b, by 3 reads: <=200000. by >=4 reads any gap"
  echo "        <=alignIntronMax"
  echo "        does not apply to annotated junctions"
  echo ""
  echo "Scoring:"
  echo "    --scoreGap"
  echo "        type: integer"
  echo "        example: 0"
  echo "        splice junction penalty (independent on intron motif)"
  echo ""
  echo "    --scoreGapNoncan"
  echo "        type: integer"
  echo "        example: -8"
  echo "        non-canonical junction penalty (in addition to scoreGap)"
  echo ""
  echo "    --scoreGapGCAG"
  echo "        type: integer"
  echo "        example: -4"
  echo "        GC/AG and CT/GC junction penalty (in addition to scoreGap)"
  echo ""
  echo "    --scoreGapATAC"
  echo "        type: integer"
  echo "        example: -8"
  echo "        AT/AC  and GT/AT junction penalty  (in addition to scoreGap)"
  echo ""
  echo "    --scoreGenomicLengthLog2scale"
  echo "        type: integer"
  echo "        example: 0"
  echo "        extra score logarithmically scaled with genomic length of the alignment:"
  echo "        scoreGenomicLengthLog2scale*log2(genomicLength)"
  echo ""
  echo "    --scoreDelOpen"
  echo "        type: integer"
  echo "        example: -2"
  echo "        deletion open penalty"
  echo ""
  echo "    --scoreDelBase"
  echo "        type: integer"
  echo "        example: -2"
  echo "        deletion extension penalty per base (in addition to scoreDelOpen)"
  echo ""
  echo "    --scoreInsOpen"
  echo "        type: integer"
  echo "        example: -2"
  echo "        insertion open penalty"
  echo ""
  echo "    --scoreInsBase"
  echo "        type: integer"
  echo "        example: -2"
  echo "        insertion extension penalty per base (in addition to scoreInsOpen)"
  echo ""
  echo "    --scoreStitchSJshift"
  echo "        type: integer"
  echo "        example: 1"
  echo "        maximum score reduction while searching for SJ boundaries in the"
  echo "        stitching step"
  echo ""
  echo "Alignments and Seeding:"
  echo "    --seedSearchStartLmax"
  echo "        type: integer"
  echo "        example: 50"
  echo "        defines the search start point through the read - the read is split into"
  echo "        pieces no longer than this value"
  echo ""
  echo "    --seedSearchStartLmaxOverLread"
  echo "        type: double"
  echo "        example: 1.0"
  echo "        seedSearchStartLmax normalized to read length (sum of mates' lengths for"
  echo "        paired-end reads)"
  echo ""
  echo "    --seedSearchLmax"
  echo "        type: integer"
  echo "        example: 0"
  echo "        defines the maximum length of the seeds, if =0 seed length is not"
  echo "        limited"
  echo ""
  echo "    --seedMultimapNmax"
  echo "        type: integer"
  echo "        example: 10000"
  echo "        only pieces that map fewer than this value are utilized in the stitching"
  echo "        procedure"
  echo ""
  echo "    --seedPerReadNmax"
  echo "        type: integer"
  echo "        example: 1000"
  echo "        max number of seeds per read"
  echo ""
  echo "    --seedPerWindowNmax"
  echo "        type: integer"
  echo "        example: 50"
  echo "        max number of seeds per window"
  echo ""
  echo "    --seedNoneLociPerWindow"
  echo "        type: integer"
  echo "        example: 10"
  echo "        max number of one seed loci per window"
  echo ""
  echo "    --seedSplitMin"
  echo "        type: integer"
  echo "        example: 12"
  echo "        min length of the seed sequences split by Ns or mate gap"
  echo ""
  echo "    --seedMapMin"
  echo "        type: integer"
  echo "        example: 5"
  echo "        min length of seeds to be mapped"
  echo ""
  echo "    --alignIntronMin"
  echo "        type: integer"
  echo "        example: 21"
  echo "        minimum intron size, genomic gap is considered intron if its"
  echo "        length>=alignIntronMin, otherwise it is considered Deletion"
  echo ""
  echo "    --alignIntronMax"
  echo "        type: integer"
  echo "        example: 0"
  echo "        maximum intron size, if 0, max intron size will be determined by"
  echo "        (2^winBinNbits)*winAnchorDistNbins"
  echo ""
  echo "    --alignMatesGapMax"
  echo "        type: integer"
  echo "        example: 0"
  echo "        maximum gap between two mates, if 0, max intron gap will be determined"
  echo "        by (2^winBinNbits)*winAnchorDistNbins"
  echo ""
  echo "    --alignSJoverhangMin"
  echo "        type: integer"
  echo "        example: 5"
  echo "        minimum overhang (i.e. block size) for spliced alignments"
  echo ""
  echo "    --alignSJstitchMismatchNmax"
  echo "        type: integer, multiple values allowed"
  echo "        example: 0;-1;0;0"
  echo "        maximum number of mismatches for stitching of the splice junctions (-1:"
  echo "        no limit)."
  echo "        (1) non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC"
  echo "        motif, (4) AT/AC and GT/AT motif."
  echo ""
  echo "    --alignSJDBoverhangMin"
  echo "        type: integer"
  echo "        example: 3"
  echo "        minimum overhang (i.e. block size) for annotated (sjdb) spliced"
  echo "        alignments"
  echo ""
  echo "    --alignSplicedMateMapLmin"
  echo "        type: integer"
  echo "        example: 0"
  echo "        minimum mapped length for a read mate that is spliced"
  echo ""
  echo "    --alignSplicedMateMapLminOverLmate"
  echo "        type: double"
  echo "        example: 0.66"
  echo "        alignSplicedMateMapLmin normalized to mate length"
  echo ""
  echo "    --alignWindowsPerReadNmax"
  echo "        type: integer"
  echo "        example: 10000"
  echo "        max number of windows per read"
  echo ""
  echo "    --alignTranscriptsPerWindowNmax"
  echo "        type: integer"
  echo "        example: 100"
  echo "        max number of transcripts per window"
  echo ""
  echo "    --alignTranscriptsPerReadNmax"
  echo "        type: integer"
  echo "        example: 10000"
  echo "        max number of different alignments per read to consider"
  echo ""
  echo "    --alignEndsType"
  echo "        type: string"
  echo "        example: Local"
  echo "        type of read ends alignment"
  echo "        - Local             ... standard local alignment with soft-clipping"
  echo "        allowed"
  echo "        - EndToEnd          ... force end-to-end read alignment, do not"
  echo "        soft-clip"
  echo "        - Extend5pOfRead1   ... fully extend only the 5p of the read1, all other"
  echo "        ends: local alignment"
  echo "        - Extend5pOfReads12 ... fully extend only the 5p of the both read1 and"
  echo "        read2, all other ends: local alignment"
  echo ""
  echo "    --alignEndsProtrude"
  echo "        type: string"
  echo "        example: 0    ConcordantPair"
  echo "        allow protrusion of alignment ends, i.e. start (end) of the +strand mate"
  echo "        downstream of the start (end) of the -strand mate"
  echo "        1st word: int: maximum number of protrusion bases allowed"
  echo "        2nd word: string:"
  echo "        -                     ConcordantPair ... report alignments with non-zero"
  echo "        protrusion as concordant pairs"
  echo "        -                     DiscordantPair ... report alignments with non-zero"
  echo "        protrusion as discordant pairs"
  echo ""
  echo "    --alignSoftClipAtReferenceEnds"
  echo "        type: string"
  echo "        example: Yes"
  echo "        allow the soft-clipping of the alignments past the end of the"
  echo "        chromosomes"
  echo "        - Yes ... allow"
  echo "        - No  ... prohibit, useful for compatibility with Cufflinks"
  echo ""
  echo "    --alignInsertionFlush"
  echo "        type: string"
  echo "        how to flush ambiguous insertion positions"
  echo "        - None    ... insertions are not flushed"
  echo "        - Right   ... insertions are flushed to the right"
  echo ""
  echo "Paired-End reads:"
  echo "    --peOverlapNbasesMin"
  echo "        type: integer"
  echo "        example: 0"
  echo "        minimum number of overlapping bases to trigger mates merging and"
  echo "        realignment. Specify >0 value to switch on the \"merginf of overlapping"
  echo "        mates\" algorithm."
  echo ""
  echo "    --peOverlapMMp"
  echo "        type: double"
  echo "        example: 0.01"
  echo "        maximum proportion of mismatched bases in the overlap area"
  echo ""
  echo "Windows, Anchors, Binning:"
  echo "    --winAnchorMultimapNmax"
  echo "        type: integer"
  echo "        example: 50"
  echo "        max number of loci anchors are allowed to map to"
  echo ""
  echo "    --winBinNbits"
  echo "        type: integer"
  echo "        example: 16"
  echo "        =log2(winBin), where winBin is the size of the bin for the"
  echo "        windows/clustering, each window will occupy an integer number of bins."
  echo ""
  echo "    --winAnchorDistNbins"
  echo "        type: integer"
  echo "        example: 9"
  echo "        max number of bins between two anchors that allows aggregation of"
  echo "        anchors into one window"
  echo ""
  echo "    --winFlankNbins"
  echo "        type: integer"
  echo "        example: 4"
  echo "        log2(winFlank), where win Flank is the size of the left and right"
  echo "        flanking regions for each window"
  echo ""
  echo "    --winReadCoverageRelativeMin"
  echo "        type: double"
  echo "        example: 0.5"
  echo "        minimum relative coverage of the read sequence by the seeds in a window,"
  echo "        for STARlong algorithm only."
  echo ""
  echo "    --winReadCoverageBasesMin"
  echo "        type: integer"
  echo "        example: 0"
  echo "        minimum number of bases covered by the seeds in a window , for STARlong"
  echo "        algorithm only."
  echo ""
  echo "Chimeric Alignments:"
  echo "    --chimOutType"
  echo "        type: string, multiple values allowed"
  echo "        example: Junctions"
  echo "        type of chimeric output"
  echo "        - Junctions       ... Chimeric.out.junction"
  echo "        - SeparateSAMold  ... output old SAM into separate Chimeric.out.sam file"
  echo "        - WithinBAM       ... output into main aligned BAM files (Aligned.*.bam)"
  echo "        - WithinBAM HardClip  ... (default) hard-clipping in the CIGAR for"
  echo "        supplemental chimeric alignments (default if no 2nd word is present)"
  echo "        - WithinBAM SoftClip  ... soft-clipping in the CIGAR for supplemental"
  echo "        chimeric alignments"
  echo ""
  echo "    --chimSegmentMin"
  echo "        type: integer"
  echo "        example: 0"
  echo "        minimum length of chimeric segment length, if ==0, no chimeric output"
  echo ""
  echo "    --chimScoreMin"
  echo "        type: integer"
  echo "        example: 0"
  echo "        minimum total (summed) score of the chimeric segments"
  echo ""
  echo "    --chimScoreDropMax"
  echo "        type: integer"
  echo "        example: 20"
  echo "        max drop (difference) of chimeric score (the sum of scores of all"
  echo "        chimeric segments) from the read length"
  echo ""
  echo "    --chimScoreSeparation"
  echo "        type: integer"
  echo "        example: 10"
  echo "        minimum difference (separation) between the best chimeric score and the"
  echo "        next one"
  echo ""
  echo "    --chimScoreJunctionNonGTAG"
  echo "        type: integer"
  echo "        example: -1"
  echo "        penalty for a non-GT/AG chimeric junction"
  echo ""
  echo "    --chimJunctionOverhangMin"
  echo "        type: integer"
  echo "        example: 20"
  echo "        minimum overhang for a chimeric junction"
  echo ""
  echo "    --chimSegmentReadGapMax"
  echo "        type: integer"
  echo "        example: 0"
  echo "        maximum gap in the read sequence between chimeric segments"
  echo ""
  echo "    --chimFilter"
  echo "        type: string, multiple values allowed"
  echo "        example: banGenomicN"
  echo "        different filters for chimeric alignments"
  echo "        - None ... no filtering"
  echo "        - banGenomicN ... Ns are not allowed in the genome sequence around the"
  echo "        chimeric junction"
  echo ""
  echo "    --chimMainSegmentMultNmax"
  echo "        type: integer"
  echo "        example: 10"
  echo "        maximum number of multi-alignments for the main chimeric segment. =1"
  echo "        will prohibit multimapping main segments."
  echo ""
  echo "    --chimMultimapNmax"
  echo "        type: integer"
  echo "        example: 0"
  echo "        maximum number of chimeric multi-alignments"
  echo "        - 0 ... use the old scheme for chimeric detection which only considered"
  echo "        unique alignments"
  echo ""
  echo "    --chimMultimapScoreRange"
  echo "        type: integer"
  echo "        example: 1"
  echo "        the score range for multi-mapping chimeras below the best chimeric"
  echo "        score. Only works with --chimMultimapNmax > 1"
  echo ""
  echo "    --chimNonchimScoreDropMin"
  echo "        type: integer"
  echo "        example: 20"
  echo "        to trigger chimeric detection, the drop in the best non-chimeric"
  echo "        alignment score with respect to the read length has to be greater than"
  echo "        this value"
  echo ""
  echo "    --chimOutJunctionFormat"
  echo "        type: integer"
  echo "        example: 0"
  echo "        formatting type for the Chimeric.out.junction file"
  echo "        - 0 ... no comment lines/headers"
  echo "        - 1 ... comment lines at the end of the file: command line and Nreads:"
  echo "        total, unique/multi-mapping"
  echo ""
  echo "Quantification of Annotations:"
  echo "    --quantMode"
  echo "        type: string, multiple values allowed"
  echo "        types of quantification requested"
  echo "        - -                ... none"
  echo "        - TranscriptomeSAM ... output SAM/BAM alignments to transcriptome into a"
  echo "        separate file"
  echo "        - GeneCounts       ... count reads per gene"
  echo ""
  echo "    --quantTranscriptomeBAMcompression"
  echo "        type: integer"
  echo "        example: 1"
  echo "        -2 to 10  transcriptome BAM compression level"
  echo "        - -2  ... no BAM output"
  echo "        - -1  ... default compression (6?)"
  echo "        -  0  ... no compression"
  echo "        -  10 ... maximum compression"
  echo ""
  echo "    --quantTranscriptomeBan"
  echo "        type: string"
  echo "        example: IndelSoftclipSingleend"
  echo "        prohibit various alignment type"
  echo "        - IndelSoftclipSingleend  ... prohibit indels, soft clipping and"
  echo "        single-end alignments - compatible with RSEM"
  echo "        - Singleend               ... prohibit single-end alignments"
  echo ""
  echo "2-pass Mapping:"
  echo "    --twopassMode"
  echo "        type: string"
  echo "        2-pass mapping mode."
  echo "        - None        ... 1-pass mapping"
  echo "        - Basic       ... basic 2-pass mapping, with all 1st pass junctions"
  echo "        inserted into the genome indices on the fly"
  echo ""
  echo "    --twopass1readsN"
  echo "        type: integer"
  echo "        example: -1"
  echo "        number of reads to process for the 1st step. Use very large number (or"
  echo "        default -1) to map all reads in the first step."
  echo ""
  echo "WASP parameters:"
  echo "    --waspOutputMode"
  echo "        type: string"
  echo "        WASP allele-specific output type. This is re-implementation of the"
  echo "        original WASP mappability filtering by Bryce van de Geijn, Graham"
  echo "        McVicker, Yoav Gilad & Jonathan K Pritchard. Please cite the original"
  echo "        WASP paper: Nature Methods 12, 1061-1063 (2015),"
  echo "        https://www.nature.com/articles/nmeth.3582 ."
  echo "        - SAMtag      ... add WASP tags to the alignments that pass WASP"
  echo "        filtering"
  echo ""
  echo "STARsolo (single cell RNA-seq) parameters:"
  echo "    --soloType"
  echo "        type: string, multiple values allowed"
  echo "        type of single-cell RNA-seq"
  echo "        - CB_UMI_Simple   ... (a.k.a. Droplet) one UMI and one Cell Barcode of"
  echo "        fixed length in read2, e.g. Drop-seq and 10X Chromium."
  echo "        - CB_UMI_Complex  ... multiple Cell Barcodes of varying length, one UMI"
  echo "        of fixed length and one adapter sequence of fixed length are allowed in"
  echo "        read2 only (e.g. inDrop, ddSeq)."
  echo "        - CB_samTagOut    ... output Cell Barcode as CR and/or CB SAm tag. No"
  echo "        UMI counting. --readFilesIn cDNA_read1 [cDNA_read2 if paired-end]"
  echo "        CellBarcode_read . Requires --outSAMtype BAM Unsorted [and/or"
  echo "        SortedByCoordinate]"
  echo "        - SmartSeq        ... Smart-seq: each cell in a separate FASTQ (paired-"
  echo "        or single-end), barcodes are corresponding read-groups, no UMI"
  echo "        sequences, alignments deduplicated according to alignment start and end"
  echo "        (after extending soft-clipped bases)"
  echo ""
  echo "    --soloCBwhitelist"
  echo "        type: string, multiple values allowed"
  echo "        file(s) with whitelist(s) of cell barcodes. Only --soloType"
  echo "        CB_UMI_Complex allows more than one whitelist file."
  echo "        - None            ... no whitelist: all cell barcodes are allowed"
  echo ""
  echo "    --soloCBstart"
  echo "        type: integer"
  echo "        example: 1"
  echo "        cell barcode start base"
  echo ""
  echo "    --soloCBlen"
  echo "        type: integer"
  echo "        example: 16"
  echo "        cell barcode length"
  echo ""
  echo "    --soloUMIstart"
  echo "        type: integer"
  echo "        example: 17"
  echo "        UMI start base"
  echo ""
  echo "    --soloUMIlen"
  echo "        type: integer"
  echo "        example: 10"
  echo "        UMI length"
  echo ""
  echo "    --soloBarcodeReadLength"
  echo "        type: integer"
  echo "        example: 1"
  echo "        length of the barcode read"
  echo "        - 1   ... equal to sum of soloCBlen+soloUMIlen"
  echo "        - 0   ... not defined, do not check"
  echo ""
  echo "    --soloBarcodeMate"
  echo "        type: integer"
  echo "        example: 0"
  echo "        identifies which read mate contains the barcode (CB+UMI) sequence"
  echo "        - 0   ... barcode sequence is on separate read, which should always be"
  echo "        the last file in the --readFilesIn listed"
  echo "        - 1   ... barcode sequence is a part of mate 1"
  echo "        - 2   ... barcode sequence is a part of mate 2"
  echo ""
  echo "    --soloCBposition"
  echo "        type: string, multiple values allowed"
  echo "        position of Cell Barcode(s) on the barcode read."
  echo "        Presently only works with --soloType CB_UMI_Complex, and barcodes are"
  echo "        assumed to be on Read2."
  echo "        Format for each barcode: startAnchor_startPosition_endAnchor_endPosition"
  echo "        start(end)Anchor defines the Anchor Base for the CB: 0: read start; 1:"
  echo "        read end; 2: adapter start; 3: adapter end"
  echo "        start(end)Position is the 0-based position with of the CB start(end)"
  echo "        with respect to the Anchor Base"
  echo "        String for different barcodes are separated by space."
  echo "        Example: inDrop (Zilionis et al, Nat. Protocols, 2017):"
  echo "        --soloCBposition  0_0_2_-1  3_1_3_8"
  echo ""
  echo "    --soloUMIposition"
  echo "        type: string"
  echo "        position of the UMI on the barcode read, same as soloCBposition"
  echo "        Example: inDrop (Zilionis et al, Nat. Protocols, 2017):"
  echo "        --soloCBposition  3_9_3_14"
  echo ""
  echo "    --soloAdapterSequence"
  echo "        type: string"
  echo "        adapter sequence to anchor barcodes. Only one adapter sequence is"
  echo "        allowed."
  echo ""
  echo "    --soloAdapterMismatchesNmax"
  echo "        type: integer"
  echo "        example: 1"
  echo "        maximum number of mismatches allowed in adapter sequence."
  echo ""
  echo "    --soloCBmatchWLtype"
  echo "        type: string"
  echo "        example: 1MM_multi"
  echo "        matching the Cell Barcodes to the WhiteList"
  echo "        - Exact                           ... only exact matches allowed"
  echo "        - 1MM                             ... only one match in whitelist with 1"
  echo "        mismatched base allowed. Allowed CBs have to have at least one read with"
  echo "        exact match."
  echo "        - 1MM_multi                       ... multiple matches in whitelist with"
  echo "        1 mismatched base allowed, posterior probability calculation is used"
  echo "        choose one of the matches."
  echo "        Allowed CBs have to have at least one read with exact match. This option"
  echo "        matches best with CellRanger 2.2.0"
  echo "        - 1MM_multi_pseudocounts          ... same as 1MM_Multi, but"
  echo "        pseudocounts of 1 are added to all whitelist barcodes."
  echo "        - 1MM_multi_Nbase_pseudocounts    ... same as 1MM_multi_pseudocounts,"
  echo "        multimatching to WL is allowed for CBs with N-bases. This option matches"
  echo "        best with CellRanger >= 3.0.0"
  echo "        - EditDist_2                    ... allow up to edit distance of 3 fpr"
  echo "        each of the barcodes. May include one deletion + one insertion. Only"
  echo "        works with --soloType CB_UMI_Complex. Matches to multiple passlist"
  echo "        barcdoes are not allowed. Similar to ParseBio Split-seq pipeline."
  echo ""
  echo "    --soloInputSAMattrBarcodeSeq"
  echo "        type: string, multiple values allowed"
  echo "        when inputting reads from a SAM file (--readsFileType SAM SE/PE), these"
  echo "        SAM attributes mark the barcode sequence (in proper order)."
  echo "        For instance, for 10X CellRanger or STARsolo BAMs, use"
  echo "        --soloInputSAMattrBarcodeSeq CR UR ."
  echo "        This parameter is required when running STARsolo with input from SAM."
  echo ""
  echo "    --soloInputSAMattrBarcodeQual"
  echo "        type: string, multiple values allowed"
  echo "        when inputting reads from a SAM file (--readsFileType SAM SE/PE), these"
  echo "        SAM attributes mark the barcode qualities (in proper order)."
  echo "        For instance, for 10X CellRanger or STARsolo BAMs, use"
  echo "        --soloInputSAMattrBarcodeQual CY UY ."
  echo "        If this parameter is '-' (default), the quality 'H' will be assigned to"
  echo "        all bases."
  echo ""
  echo "    --soloStrand"
  echo "        type: string"
  echo "        example: Forward"
  echo "        strandedness of the solo libraries:"
  echo "        - Unstranded  ... no strand information"
  echo "        - Forward     ... read strand same as the original RNA molecule"
  echo "        - Reverse     ... read strand opposite to the original RNA molecule"
  echo ""
  echo "    --soloFeatures"
  echo "        type: string, multiple values allowed"
  echo "        example: Gene"
  echo "        genomic features for which the UMI counts per Cell Barcode are collected"
  echo "        - Gene            ... genes: reads match the gene transcript"
  echo "        - SJ              ... splice junctions: reported in SJ.out.tab"
  echo "        - GeneFull        ... full gene (pre-mRNA): count all reads overlapping"
  echo "        genes' exons and introns"
  echo "        - GeneFull_ExonOverIntron ... full gene (pre-mRNA): count all reads"
  echo "        overlapping genes' exons and introns: prioritize 100% overlap with exons"
  echo "        - GeneFull_Ex50pAS        ... full gene (pre-RNA): count all reads"
  echo "        overlapping genes' exons and introns: prioritize >50% overlap with"
  echo "        exons. Do not count reads with 100% exonic overlap in the antisense"
  echo "        direction."
  echo ""
  echo "    --soloMultiMappers"
  echo "        type: string, multiple values allowed"
  echo "        example: Unique"
  echo "        counting method for reads mapping to multiple genes"
  echo "        - Unique     ... count only reads that map to unique genes"
  echo "        - Uniform    ... uniformly distribute multi-genic UMIs to all genes"
  echo "        - Rescue     ... distribute UMIs proportionally to unique+uniform counts"
  echo "        (~ first iteration of EM)"
  echo "        - PropUnique ... distribute UMIs proportionally to unique mappers, if"
  echo "        present, and uniformly if not."
  echo "        - EM         ... multi-gene UMIs are distributed using Expectation"
  echo "        Maximization algorithm"
  echo ""
  echo "    --soloUMIdedup"
  echo "        type: string, multiple values allowed"
  echo "        example: 1MM_All"
  echo "        type of UMI deduplication (collapsing) algorithm"
  echo "        - 1MM_All                     ... all UMIs with 1 mismatch distance to"
  echo "        each other are collapsed (i.e. counted once)."
  echo "        - 1MM_Directional_UMItools    ... follows the \"directional\" method from"
  echo "        the UMI-tools by Smith, Heger and Sudbery (Genome Research 2017)."
  echo "        - 1MM_Directional             ... same as 1MM_Directional_UMItools, but"
  echo "        with more stringent criteria for duplicate UMIs"
  echo "        - Exact                       ... only exactly matching UMIs are"
  echo "        collapsed."
  echo "        - NoDedup                     ... no deduplication of UMIs, count all"
  echo "        reads."
  echo "        - 1MM_CR                      ... CellRanger2-4 algorithm for 1MM UMI"
  echo "        collapsing."
  echo ""
  echo "    --soloUMIfiltering"
  echo "        type: string, multiple values allowed"
  echo "        type of UMI filtering (for reads uniquely mapping to genes)"
  echo "        - -                  ... basic filtering: remove UMIs with N and"
  echo "        homopolymers (similar to CellRanger 2.2.0)."
  echo "        - MultiGeneUMI       ... basic + remove lower-count UMIs that map to"
  echo "        more than one gene."
  echo "        - MultiGeneUMI_All   ... basic + remove all UMIs that map to more than"
  echo "        one gene."
  echo "        - MultiGeneUMI_CR    ... basic + remove lower-count UMIs that map to"
  echo "        more than one gene, matching CellRanger > 3.0.0 ."
  echo "        Only works with --soloUMIdedup 1MM_CR"
  echo ""
  echo "    --soloOutFileNames"
  echo "        type: string, multiple values allowed"
  echo "        example: Solo.out/;features.tsv;barcodes.tsv;matrix.mtx"
  echo "        file names for STARsolo output:"
  echo "        file_name_prefix   gene_names   barcode_sequences"
  echo "        cell_feature_count_matrix"
  echo ""
  echo "    --soloCellFilter"
  echo "        type: string, multiple values allowed"
  echo "        example: CellRanger2.2;3000;0.99;10"
  echo "        cell filtering type and parameters"
  echo "        - None            ... do not output filtered cells"
  echo "        - TopCells        ... only report top cells by UMI count, followed by"
  echo "        the exact number of cells"
  echo "        - CellRanger2.2   ... simple filtering of CellRanger 2.2."
  echo "        Can be followed by numbers: number of expected cells, robust maximum"
  echo "        percentile for UMI count, maximum to minimum ratio for UMI count"
  echo "        The harcoded values are from CellRanger: nExpectedCells=3000;"
  echo "        maxPercentile=0.99;  maxMinRatio=10"
  echo "        - EmptyDrops_CR   ... EmptyDrops filtering in CellRanger flavor. Please"
  echo "        cite the original EmptyDrops paper: A.T.L Lun et al, Genome Biology, 20,"
  echo "        63 (2019):"
  echo "       "
  echo "https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1662-y"
  echo "        Can be followed by 10 numeric parameters:  nExpectedCells"
  echo "        maxPercentile   maxMinRatio   indMin   indMax   umiMin"
  echo "        umiMinFracMedian   candMaxN   FDR   simN"
  echo "        The harcoded values are from CellRanger:             3000"
  echo "        0.99            10    45000    90000      500               0.01"
  echo "        20000  0.01  10000"
  echo ""
  echo "    --soloOutFormatFeaturesGeneField3"
  echo "        type: string, multiple values allowed"
  echo "        example: Gene Expression"
  echo "        field 3 in the Gene features.tsv file. If \"-\", then no 3rd field is"
  echo "        output."
  echo ""
  echo "    --soloCellReadStats"
  echo "        type: string"
  echo "        Output reads statistics for each CB"
  echo "        - Standard    ... standard output"
  echo ""
  echo "Viash built in Computational Requirements:"
  echo "    ---cpus=INT"
  echo "        Number of CPUs to use"
  echo "    ---memory=STRING"
  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
  echo ""
  echo "Viash built in Docker:"
  echo "    ---setup=STRATEGY"
  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
  echo "        Default: ifneedbepullelsecachedbuild"
  echo "    ---dockerfile"
  echo "        Print the dockerfile to stdout."
  echo "    ---docker_run_args=ARG"
  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
  echo "    ---docker_image_id"
  echo "        Print the docker image id to stdout."
  echo "    ---debug"
  echo "        Enter the docker container for debugging purposes."
  echo ""
  echo "Viash built in Engines:"
  echo "    ---engine=ENGINE_ID"
  echo "        Specify the engine to use. Options are: docker, native."
  echo "        Default: docker"
}

# initialise array
VIASH_POSITIONAL_ARGS=''

while [[ $# -gt 0 ]]; do
    case "$1" in
        -h|--help)
            ViashHelp
            exit
            ;;
        ---v|---verbose)
            let "VIASH_VERBOSITY=VIASH_VERBOSITY+1"
            shift 1
            ;;
        ---verbosity)
            VIASH_VERBOSITY="$2"
            shift 2
            ;;
        ---verbosity=*)
            VIASH_VERBOSITY="$(ViashRemoveFlags "$1")"
            shift 1
            ;;
        --version)
            echo "star_align_v273a v4.0.2"
            exit
            ;;
        --input)
            if [ -z "$VIASH_PAR_INPUT" ]; then
              VIASH_PAR_INPUT="$2"
            else
              VIASH_PAR_INPUT="$VIASH_PAR_INPUT;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --input. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --input=*)
            if [ -z "$VIASH_PAR_INPUT" ]; then
              VIASH_PAR_INPUT=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_INPUT="$VIASH_PAR_INPUT;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --readFilesIn)
            if [ -z "$VIASH_PAR_INPUT" ]; then
              VIASH_PAR_INPUT="$2"
            else
              VIASH_PAR_INPUT="$VIASH_PAR_INPUT;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --readFilesIn. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --reference)
            [ -n "$VIASH_PAR_REFERENCE" ] && ViashError Bad arguments for option \'--reference\': \'$VIASH_PAR_REFERENCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_REFERENCE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --reference. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --reference=*)
            [ -n "$VIASH_PAR_REFERENCE" ] && ViashError Bad arguments for option \'--reference=*\': \'$VIASH_PAR_REFERENCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_REFERENCE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --genomeDir)
            [ -n "$VIASH_PAR_REFERENCE" ] && ViashError Bad arguments for option \'--genomeDir\': \'$VIASH_PAR_REFERENCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_REFERENCE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --genomeDir. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --output)
            [ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --output. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --output=*)
            [ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output=*\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --outFileNamePrefix)
            [ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--outFileNamePrefix\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outFileNamePrefix. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --runRNGseed)
            [ -n "$VIASH_PAR_RUNRNGSEED" ] && ViashError Bad arguments for option \'--runRNGseed\': \'$VIASH_PAR_RUNRNGSEED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_RUNRNGSEED="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --runRNGseed. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --runRNGseed=*)
            [ -n "$VIASH_PAR_RUNRNGSEED" ] && ViashError Bad arguments for option \'--runRNGseed=*\': \'$VIASH_PAR_RUNRNGSEED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_RUNRNGSEED=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --genomeLoad)
            [ -n "$VIASH_PAR_GENOMELOAD" ] && ViashError Bad arguments for option \'--genomeLoad\': \'$VIASH_PAR_GENOMELOAD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_GENOMELOAD="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --genomeLoad. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --genomeLoad=*)
            [ -n "$VIASH_PAR_GENOMELOAD" ] && ViashError Bad arguments for option \'--genomeLoad=*\': \'$VIASH_PAR_GENOMELOAD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_GENOMELOAD=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --genomeFastaFiles)
            if [ -z "$VIASH_PAR_GENOMEFASTAFILES" ]; then
              VIASH_PAR_GENOMEFASTAFILES="$2"
            else
              VIASH_PAR_GENOMEFASTAFILES="$VIASH_PAR_GENOMEFASTAFILES;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --genomeFastaFiles. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --genomeFastaFiles=*)
            if [ -z "$VIASH_PAR_GENOMEFASTAFILES" ]; then
              VIASH_PAR_GENOMEFASTAFILES=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_GENOMEFASTAFILES="$VIASH_PAR_GENOMEFASTAFILES;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --genomeFileSizes)
            if [ -z "$VIASH_PAR_GENOMEFILESIZES" ]; then
              VIASH_PAR_GENOMEFILESIZES="$2"
            else
              VIASH_PAR_GENOMEFILESIZES="$VIASH_PAR_GENOMEFILESIZES;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --genomeFileSizes. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --genomeFileSizes=*)
            if [ -z "$VIASH_PAR_GENOMEFILESIZES" ]; then
              VIASH_PAR_GENOMEFILESIZES=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_GENOMEFILESIZES="$VIASH_PAR_GENOMEFILESIZES;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --genomeTransformOutput)
            if [ -z "$VIASH_PAR_GENOMETRANSFORMOUTPUT" ]; then
              VIASH_PAR_GENOMETRANSFORMOUTPUT="$2"
            else
              VIASH_PAR_GENOMETRANSFORMOUTPUT="$VIASH_PAR_GENOMETRANSFORMOUTPUT;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --genomeTransformOutput. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --genomeTransformOutput=*)
            if [ -z "$VIASH_PAR_GENOMETRANSFORMOUTPUT" ]; then
              VIASH_PAR_GENOMETRANSFORMOUTPUT=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_GENOMETRANSFORMOUTPUT="$VIASH_PAR_GENOMETRANSFORMOUTPUT;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --genomeChrSetMitochondrial)
            if [ -z "$VIASH_PAR_GENOMECHRSETMITOCHONDRIAL" ]; then
              VIASH_PAR_GENOMECHRSETMITOCHONDRIAL="$2"
            else
              VIASH_PAR_GENOMECHRSETMITOCHONDRIAL="$VIASH_PAR_GENOMECHRSETMITOCHONDRIAL;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --genomeChrSetMitochondrial. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --genomeChrSetMitochondrial=*)
            if [ -z "$VIASH_PAR_GENOMECHRSETMITOCHONDRIAL" ]; then
              VIASH_PAR_GENOMECHRSETMITOCHONDRIAL=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_GENOMECHRSETMITOCHONDRIAL="$VIASH_PAR_GENOMECHRSETMITOCHONDRIAL;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --sjdbFileChrStartEnd)
            if [ -z "$VIASH_PAR_SJDBFILECHRSTARTEND" ]; then
              VIASH_PAR_SJDBFILECHRSTARTEND="$2"
            else
              VIASH_PAR_SJDBFILECHRSTARTEND="$VIASH_PAR_SJDBFILECHRSTARTEND;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --sjdbFileChrStartEnd. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --sjdbFileChrStartEnd=*)
            if [ -z "$VIASH_PAR_SJDBFILECHRSTARTEND" ]; then
              VIASH_PAR_SJDBFILECHRSTARTEND=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_SJDBFILECHRSTARTEND="$VIASH_PAR_SJDBFILECHRSTARTEND;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --sjdbGTFfile)
            [ -n "$VIASH_PAR_SJDBGTFFILE" ] && ViashError Bad arguments for option \'--sjdbGTFfile\': \'$VIASH_PAR_SJDBGTFFILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SJDBGTFFILE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --sjdbGTFfile. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --sjdbGTFfile=*)
            [ -n "$VIASH_PAR_SJDBGTFFILE" ] && ViashError Bad arguments for option \'--sjdbGTFfile=*\': \'$VIASH_PAR_SJDBGTFFILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SJDBGTFFILE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --sjdbGTFchrPrefix)
            [ -n "$VIASH_PAR_SJDBGTFCHRPREFIX" ] && ViashError Bad arguments for option \'--sjdbGTFchrPrefix\': \'$VIASH_PAR_SJDBGTFCHRPREFIX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SJDBGTFCHRPREFIX="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --sjdbGTFchrPrefix. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --sjdbGTFchrPrefix=*)
            [ -n "$VIASH_PAR_SJDBGTFCHRPREFIX" ] && ViashError Bad arguments for option \'--sjdbGTFchrPrefix=*\': \'$VIASH_PAR_SJDBGTFCHRPREFIX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SJDBGTFCHRPREFIX=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --sjdbGTFfeatureExon)
            [ -n "$VIASH_PAR_SJDBGTFFEATUREEXON" ] && ViashError Bad arguments for option \'--sjdbGTFfeatureExon\': \'$VIASH_PAR_SJDBGTFFEATUREEXON\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SJDBGTFFEATUREEXON="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --sjdbGTFfeatureExon. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --sjdbGTFfeatureExon=*)
            [ -n "$VIASH_PAR_SJDBGTFFEATUREEXON" ] && ViashError Bad arguments for option \'--sjdbGTFfeatureExon=*\': \'$VIASH_PAR_SJDBGTFFEATUREEXON\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SJDBGTFFEATUREEXON=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --sjdbGTFtagExonParentTranscript)
            [ -n "$VIASH_PAR_SJDBGTFTAGEXONPARENTTRANSCRIPT" ] && ViashError Bad arguments for option \'--sjdbGTFtagExonParentTranscript\': \'$VIASH_PAR_SJDBGTFTAGEXONPARENTTRANSCRIPT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SJDBGTFTAGEXONPARENTTRANSCRIPT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --sjdbGTFtagExonParentTranscript. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --sjdbGTFtagExonParentTranscript=*)
            [ -n "$VIASH_PAR_SJDBGTFTAGEXONPARENTTRANSCRIPT" ] && ViashError Bad arguments for option \'--sjdbGTFtagExonParentTranscript=*\': \'$VIASH_PAR_SJDBGTFTAGEXONPARENTTRANSCRIPT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SJDBGTFTAGEXONPARENTTRANSCRIPT=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --sjdbGTFtagExonParentGene)
            [ -n "$VIASH_PAR_SJDBGTFTAGEXONPARENTGENE" ] && ViashError Bad arguments for option \'--sjdbGTFtagExonParentGene\': \'$VIASH_PAR_SJDBGTFTAGEXONPARENTGENE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SJDBGTFTAGEXONPARENTGENE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --sjdbGTFtagExonParentGene. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --sjdbGTFtagExonParentGene=*)
            [ -n "$VIASH_PAR_SJDBGTFTAGEXONPARENTGENE" ] && ViashError Bad arguments for option \'--sjdbGTFtagExonParentGene=*\': \'$VIASH_PAR_SJDBGTFTAGEXONPARENTGENE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SJDBGTFTAGEXONPARENTGENE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --sjdbGTFtagExonParentGeneName)
            if [ -z "$VIASH_PAR_SJDBGTFTAGEXONPARENTGENENAME" ]; then
              VIASH_PAR_SJDBGTFTAGEXONPARENTGENENAME="$2"
            else
              VIASH_PAR_SJDBGTFTAGEXONPARENTGENENAME="$VIASH_PAR_SJDBGTFTAGEXONPARENTGENENAME;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --sjdbGTFtagExonParentGeneName. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --sjdbGTFtagExonParentGeneName=*)
            if [ -z "$VIASH_PAR_SJDBGTFTAGEXONPARENTGENENAME" ]; then
              VIASH_PAR_SJDBGTFTAGEXONPARENTGENENAME=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_SJDBGTFTAGEXONPARENTGENENAME="$VIASH_PAR_SJDBGTFTAGEXONPARENTGENENAME;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --sjdbGTFtagExonParentGeneType)
            if [ -z "$VIASH_PAR_SJDBGTFTAGEXONPARENTGENETYPE" ]; then
              VIASH_PAR_SJDBGTFTAGEXONPARENTGENETYPE="$2"
            else
              VIASH_PAR_SJDBGTFTAGEXONPARENTGENETYPE="$VIASH_PAR_SJDBGTFTAGEXONPARENTGENETYPE;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --sjdbGTFtagExonParentGeneType. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --sjdbGTFtagExonParentGeneType=*)
            if [ -z "$VIASH_PAR_SJDBGTFTAGEXONPARENTGENETYPE" ]; then
              VIASH_PAR_SJDBGTFTAGEXONPARENTGENETYPE=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_SJDBGTFTAGEXONPARENTGENETYPE="$VIASH_PAR_SJDBGTFTAGEXONPARENTGENETYPE;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --sjdbOverhang)
            [ -n "$VIASH_PAR_SJDBOVERHANG" ] && ViashError Bad arguments for option \'--sjdbOverhang\': \'$VIASH_PAR_SJDBOVERHANG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SJDBOVERHANG="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --sjdbOverhang. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --sjdbOverhang=*)
            [ -n "$VIASH_PAR_SJDBOVERHANG" ] && ViashError Bad arguments for option \'--sjdbOverhang=*\': \'$VIASH_PAR_SJDBOVERHANG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SJDBOVERHANG=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --sjdbScore)
            [ -n "$VIASH_PAR_SJDBSCORE" ] && ViashError Bad arguments for option \'--sjdbScore\': \'$VIASH_PAR_SJDBSCORE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SJDBSCORE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --sjdbScore. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --sjdbScore=*)
            [ -n "$VIASH_PAR_SJDBSCORE" ] && ViashError Bad arguments for option \'--sjdbScore=*\': \'$VIASH_PAR_SJDBSCORE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SJDBSCORE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --sjdbInsertSave)
            [ -n "$VIASH_PAR_SJDBINSERTSAVE" ] && ViashError Bad arguments for option \'--sjdbInsertSave\': \'$VIASH_PAR_SJDBINSERTSAVE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SJDBINSERTSAVE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --sjdbInsertSave. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --sjdbInsertSave=*)
            [ -n "$VIASH_PAR_SJDBINSERTSAVE" ] && ViashError Bad arguments for option \'--sjdbInsertSave=*\': \'$VIASH_PAR_SJDBINSERTSAVE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SJDBINSERTSAVE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --varVCFfile)
            [ -n "$VIASH_PAR_VARVCFFILE" ] && ViashError Bad arguments for option \'--varVCFfile\': \'$VIASH_PAR_VARVCFFILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_VARVCFFILE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --varVCFfile. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --varVCFfile=*)
            [ -n "$VIASH_PAR_VARVCFFILE" ] && ViashError Bad arguments for option \'--varVCFfile=*\': \'$VIASH_PAR_VARVCFFILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_VARVCFFILE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --readFilesType)
            [ -n "$VIASH_PAR_READFILESTYPE" ] && ViashError Bad arguments for option \'--readFilesType\': \'$VIASH_PAR_READFILESTYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_READFILESTYPE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --readFilesType. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --readFilesType=*)
            [ -n "$VIASH_PAR_READFILESTYPE" ] && ViashError Bad arguments for option \'--readFilesType=*\': \'$VIASH_PAR_READFILESTYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_READFILESTYPE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --readFilesSAMattrKeep)
            if [ -z "$VIASH_PAR_READFILESSAMATTRKEEP" ]; then
              VIASH_PAR_READFILESSAMATTRKEEP="$2"
            else
              VIASH_PAR_READFILESSAMATTRKEEP="$VIASH_PAR_READFILESSAMATTRKEEP;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --readFilesSAMattrKeep. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --readFilesSAMattrKeep=*)
            if [ -z "$VIASH_PAR_READFILESSAMATTRKEEP" ]; then
              VIASH_PAR_READFILESSAMATTRKEEP=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_READFILESSAMATTRKEEP="$VIASH_PAR_READFILESSAMATTRKEEP;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --readFilesManifest)
            [ -n "$VIASH_PAR_READFILESMANIFEST" ] && ViashError Bad arguments for option \'--readFilesManifest\': \'$VIASH_PAR_READFILESMANIFEST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_READFILESMANIFEST="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --readFilesManifest. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --readFilesManifest=*)
            [ -n "$VIASH_PAR_READFILESMANIFEST" ] && ViashError Bad arguments for option \'--readFilesManifest=*\': \'$VIASH_PAR_READFILESMANIFEST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_READFILESMANIFEST=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --readFilesPrefix)
            [ -n "$VIASH_PAR_READFILESPREFIX" ] && ViashError Bad arguments for option \'--readFilesPrefix\': \'$VIASH_PAR_READFILESPREFIX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_READFILESPREFIX="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --readFilesPrefix. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --readFilesPrefix=*)
            [ -n "$VIASH_PAR_READFILESPREFIX" ] && ViashError Bad arguments for option \'--readFilesPrefix=*\': \'$VIASH_PAR_READFILESPREFIX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_READFILESPREFIX=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --readFilesCommand)
            if [ -z "$VIASH_PAR_READFILESCOMMAND" ]; then
              VIASH_PAR_READFILESCOMMAND="$2"
            else
              VIASH_PAR_READFILESCOMMAND="$VIASH_PAR_READFILESCOMMAND;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --readFilesCommand. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --readFilesCommand=*)
            if [ -z "$VIASH_PAR_READFILESCOMMAND" ]; then
              VIASH_PAR_READFILESCOMMAND=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_READFILESCOMMAND="$VIASH_PAR_READFILESCOMMAND;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --readMapNumber)
            [ -n "$VIASH_PAR_READMAPNUMBER" ] && ViashError Bad arguments for option \'--readMapNumber\': \'$VIASH_PAR_READMAPNUMBER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_READMAPNUMBER="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --readMapNumber. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --readMapNumber=*)
            [ -n "$VIASH_PAR_READMAPNUMBER" ] && ViashError Bad arguments for option \'--readMapNumber=*\': \'$VIASH_PAR_READMAPNUMBER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_READMAPNUMBER=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --readMatesLengthsIn)
            [ -n "$VIASH_PAR_READMATESLENGTHSIN" ] && ViashError Bad arguments for option \'--readMatesLengthsIn\': \'$VIASH_PAR_READMATESLENGTHSIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_READMATESLENGTHSIN="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --readMatesLengthsIn. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --readMatesLengthsIn=*)
            [ -n "$VIASH_PAR_READMATESLENGTHSIN" ] && ViashError Bad arguments for option \'--readMatesLengthsIn=*\': \'$VIASH_PAR_READMATESLENGTHSIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_READMATESLENGTHSIN=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --readNameSeparator)
            if [ -z "$VIASH_PAR_READNAMESEPARATOR" ]; then
              VIASH_PAR_READNAMESEPARATOR="$2"
            else
              VIASH_PAR_READNAMESEPARATOR="$VIASH_PAR_READNAMESEPARATOR;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --readNameSeparator. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --readNameSeparator=*)
            if [ -z "$VIASH_PAR_READNAMESEPARATOR" ]; then
              VIASH_PAR_READNAMESEPARATOR=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_READNAMESEPARATOR="$VIASH_PAR_READNAMESEPARATOR;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --readQualityScoreBase)
            [ -n "$VIASH_PAR_READQUALITYSCOREBASE" ] && ViashError Bad arguments for option \'--readQualityScoreBase\': \'$VIASH_PAR_READQUALITYSCOREBASE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_READQUALITYSCOREBASE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --readQualityScoreBase. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --readQualityScoreBase=*)
            [ -n "$VIASH_PAR_READQUALITYSCOREBASE" ] && ViashError Bad arguments for option \'--readQualityScoreBase=*\': \'$VIASH_PAR_READQUALITYSCOREBASE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_READQUALITYSCOREBASE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --clipAdapterType)
            [ -n "$VIASH_PAR_CLIPADAPTERTYPE" ] && ViashError Bad arguments for option \'--clipAdapterType\': \'$VIASH_PAR_CLIPADAPTERTYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CLIPADAPTERTYPE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --clipAdapterType. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --clipAdapterType=*)
            [ -n "$VIASH_PAR_CLIPADAPTERTYPE" ] && ViashError Bad arguments for option \'--clipAdapterType=*\': \'$VIASH_PAR_CLIPADAPTERTYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CLIPADAPTERTYPE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --clip3pNbases)
            if [ -z "$VIASH_PAR_CLIP3PNBASES" ]; then
              VIASH_PAR_CLIP3PNBASES="$2"
            else
              VIASH_PAR_CLIP3PNBASES="$VIASH_PAR_CLIP3PNBASES;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --clip3pNbases. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --clip3pNbases=*)
            if [ -z "$VIASH_PAR_CLIP3PNBASES" ]; then
              VIASH_PAR_CLIP3PNBASES=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_CLIP3PNBASES="$VIASH_PAR_CLIP3PNBASES;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --clip3pAdapterSeq)
            if [ -z "$VIASH_PAR_CLIP3PADAPTERSEQ" ]; then
              VIASH_PAR_CLIP3PADAPTERSEQ="$2"
            else
              VIASH_PAR_CLIP3PADAPTERSEQ="$VIASH_PAR_CLIP3PADAPTERSEQ;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --clip3pAdapterSeq. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --clip3pAdapterSeq=*)
            if [ -z "$VIASH_PAR_CLIP3PADAPTERSEQ" ]; then
              VIASH_PAR_CLIP3PADAPTERSEQ=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_CLIP3PADAPTERSEQ="$VIASH_PAR_CLIP3PADAPTERSEQ;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --clip3pAdapterMMp)
            if [ -z "$VIASH_PAR_CLIP3PADAPTERMMP" ]; then
              VIASH_PAR_CLIP3PADAPTERMMP="$2"
            else
              VIASH_PAR_CLIP3PADAPTERMMP="$VIASH_PAR_CLIP3PADAPTERMMP;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --clip3pAdapterMMp. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --clip3pAdapterMMp=*)
            if [ -z "$VIASH_PAR_CLIP3PADAPTERMMP" ]; then
              VIASH_PAR_CLIP3PADAPTERMMP=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_CLIP3PADAPTERMMP="$VIASH_PAR_CLIP3PADAPTERMMP;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --clip3pAfterAdapterNbases)
            if [ -z "$VIASH_PAR_CLIP3PAFTERADAPTERNBASES" ]; then
              VIASH_PAR_CLIP3PAFTERADAPTERNBASES="$2"
            else
              VIASH_PAR_CLIP3PAFTERADAPTERNBASES="$VIASH_PAR_CLIP3PAFTERADAPTERNBASES;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --clip3pAfterAdapterNbases. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --clip3pAfterAdapterNbases=*)
            if [ -z "$VIASH_PAR_CLIP3PAFTERADAPTERNBASES" ]; then
              VIASH_PAR_CLIP3PAFTERADAPTERNBASES=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_CLIP3PAFTERADAPTERNBASES="$VIASH_PAR_CLIP3PAFTERADAPTERNBASES;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --clip5pNbases)
            if [ -z "$VIASH_PAR_CLIP5PNBASES" ]; then
              VIASH_PAR_CLIP5PNBASES="$2"
            else
              VIASH_PAR_CLIP5PNBASES="$VIASH_PAR_CLIP5PNBASES;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --clip5pNbases. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --clip5pNbases=*)
            if [ -z "$VIASH_PAR_CLIP5PNBASES" ]; then
              VIASH_PAR_CLIP5PNBASES=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_CLIP5PNBASES="$VIASH_PAR_CLIP5PNBASES;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --limitGenomeGenerateRAM)
            [ -n "$VIASH_PAR_LIMITGENOMEGENERATERAM" ] && ViashError Bad arguments for option \'--limitGenomeGenerateRAM\': \'$VIASH_PAR_LIMITGENOMEGENERATERAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LIMITGENOMEGENERATERAM="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --limitGenomeGenerateRAM. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --limitGenomeGenerateRAM=*)
            [ -n "$VIASH_PAR_LIMITGENOMEGENERATERAM" ] && ViashError Bad arguments for option \'--limitGenomeGenerateRAM=*\': \'$VIASH_PAR_LIMITGENOMEGENERATERAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LIMITGENOMEGENERATERAM=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --limitIObufferSize)
            if [ -z "$VIASH_PAR_LIMITIOBUFFERSIZE" ]; then
              VIASH_PAR_LIMITIOBUFFERSIZE="$2"
            else
              VIASH_PAR_LIMITIOBUFFERSIZE="$VIASH_PAR_LIMITIOBUFFERSIZE;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --limitIObufferSize. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --limitIObufferSize=*)
            if [ -z "$VIASH_PAR_LIMITIOBUFFERSIZE" ]; then
              VIASH_PAR_LIMITIOBUFFERSIZE=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_LIMITIOBUFFERSIZE="$VIASH_PAR_LIMITIOBUFFERSIZE;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --limitOutSAMoneReadBytes)
            [ -n "$VIASH_PAR_LIMITOUTSAMONEREADBYTES" ] && ViashError Bad arguments for option \'--limitOutSAMoneReadBytes\': \'$VIASH_PAR_LIMITOUTSAMONEREADBYTES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LIMITOUTSAMONEREADBYTES="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --limitOutSAMoneReadBytes. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --limitOutSAMoneReadBytes=*)
            [ -n "$VIASH_PAR_LIMITOUTSAMONEREADBYTES" ] && ViashError Bad arguments for option \'--limitOutSAMoneReadBytes=*\': \'$VIASH_PAR_LIMITOUTSAMONEREADBYTES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LIMITOUTSAMONEREADBYTES=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --limitOutSJoneRead)
            [ -n "$VIASH_PAR_LIMITOUTSJONEREAD" ] && ViashError Bad arguments for option \'--limitOutSJoneRead\': \'$VIASH_PAR_LIMITOUTSJONEREAD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LIMITOUTSJONEREAD="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --limitOutSJoneRead. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --limitOutSJoneRead=*)
            [ -n "$VIASH_PAR_LIMITOUTSJONEREAD" ] && ViashError Bad arguments for option \'--limitOutSJoneRead=*\': \'$VIASH_PAR_LIMITOUTSJONEREAD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LIMITOUTSJONEREAD=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --limitOutSJcollapsed)
            [ -n "$VIASH_PAR_LIMITOUTSJCOLLAPSED" ] && ViashError Bad arguments for option \'--limitOutSJcollapsed\': \'$VIASH_PAR_LIMITOUTSJCOLLAPSED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LIMITOUTSJCOLLAPSED="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --limitOutSJcollapsed. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --limitOutSJcollapsed=*)
            [ -n "$VIASH_PAR_LIMITOUTSJCOLLAPSED" ] && ViashError Bad arguments for option \'--limitOutSJcollapsed=*\': \'$VIASH_PAR_LIMITOUTSJCOLLAPSED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LIMITOUTSJCOLLAPSED=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --limitBAMsortRAM)
            [ -n "$VIASH_PAR_LIMITBAMSORTRAM" ] && ViashError Bad arguments for option \'--limitBAMsortRAM\': \'$VIASH_PAR_LIMITBAMSORTRAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LIMITBAMSORTRAM="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --limitBAMsortRAM. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --limitBAMsortRAM=*)
            [ -n "$VIASH_PAR_LIMITBAMSORTRAM" ] && ViashError Bad arguments for option \'--limitBAMsortRAM=*\': \'$VIASH_PAR_LIMITBAMSORTRAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LIMITBAMSORTRAM=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --limitSjdbInsertNsj)
            [ -n "$VIASH_PAR_LIMITSJDBINSERTNSJ" ] && ViashError Bad arguments for option \'--limitSjdbInsertNsj\': \'$VIASH_PAR_LIMITSJDBINSERTNSJ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LIMITSJDBINSERTNSJ="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --limitSjdbInsertNsj. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --limitSjdbInsertNsj=*)
            [ -n "$VIASH_PAR_LIMITSJDBINSERTNSJ" ] && ViashError Bad arguments for option \'--limitSjdbInsertNsj=*\': \'$VIASH_PAR_LIMITSJDBINSERTNSJ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LIMITSJDBINSERTNSJ=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --limitNreadsSoft)
            [ -n "$VIASH_PAR_LIMITNREADSSOFT" ] && ViashError Bad arguments for option \'--limitNreadsSoft\': \'$VIASH_PAR_LIMITNREADSSOFT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LIMITNREADSSOFT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --limitNreadsSoft. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --limitNreadsSoft=*)
            [ -n "$VIASH_PAR_LIMITNREADSSOFT" ] && ViashError Bad arguments for option \'--limitNreadsSoft=*\': \'$VIASH_PAR_LIMITNREADSSOFT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LIMITNREADSSOFT=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --outTmpKeep)
            [ -n "$VIASH_PAR_OUTTMPKEEP" ] && ViashError Bad arguments for option \'--outTmpKeep\': \'$VIASH_PAR_OUTTMPKEEP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTTMPKEEP="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outTmpKeep. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outTmpKeep=*)
            [ -n "$VIASH_PAR_OUTTMPKEEP" ] && ViashError Bad arguments for option \'--outTmpKeep=*\': \'$VIASH_PAR_OUTTMPKEEP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTTMPKEEP=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --outStd)
            [ -n "$VIASH_PAR_OUTSTD" ] && ViashError Bad arguments for option \'--outStd\': \'$VIASH_PAR_OUTSTD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTSTD="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outStd. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outStd=*)
            [ -n "$VIASH_PAR_OUTSTD" ] && ViashError Bad arguments for option \'--outStd=*\': \'$VIASH_PAR_OUTSTD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTSTD=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --outReadsUnmapped)
            [ -n "$VIASH_PAR_OUTREADSUNMAPPED" ] && ViashError Bad arguments for option \'--outReadsUnmapped\': \'$VIASH_PAR_OUTREADSUNMAPPED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTREADSUNMAPPED="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outReadsUnmapped. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outReadsUnmapped=*)
            [ -n "$VIASH_PAR_OUTREADSUNMAPPED" ] && ViashError Bad arguments for option \'--outReadsUnmapped=*\': \'$VIASH_PAR_OUTREADSUNMAPPED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTREADSUNMAPPED=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --outQSconversionAdd)
            [ -n "$VIASH_PAR_OUTQSCONVERSIONADD" ] && ViashError Bad arguments for option \'--outQSconversionAdd\': \'$VIASH_PAR_OUTQSCONVERSIONADD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTQSCONVERSIONADD="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outQSconversionAdd. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outQSconversionAdd=*)
            [ -n "$VIASH_PAR_OUTQSCONVERSIONADD" ] && ViashError Bad arguments for option \'--outQSconversionAdd=*\': \'$VIASH_PAR_OUTQSCONVERSIONADD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTQSCONVERSIONADD=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --outMultimapperOrder)
            [ -n "$VIASH_PAR_OUTMULTIMAPPERORDER" ] && ViashError Bad arguments for option \'--outMultimapperOrder\': \'$VIASH_PAR_OUTMULTIMAPPERORDER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTMULTIMAPPERORDER="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outMultimapperOrder. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outMultimapperOrder=*)
            [ -n "$VIASH_PAR_OUTMULTIMAPPERORDER" ] && ViashError Bad arguments for option \'--outMultimapperOrder=*\': \'$VIASH_PAR_OUTMULTIMAPPERORDER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTMULTIMAPPERORDER=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --outSAMtype)
            if [ -z "$VIASH_PAR_OUTSAMTYPE" ]; then
              VIASH_PAR_OUTSAMTYPE="$2"
            else
              VIASH_PAR_OUTSAMTYPE="$VIASH_PAR_OUTSAMTYPE;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outSAMtype. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outSAMtype=*)
            if [ -z "$VIASH_PAR_OUTSAMTYPE" ]; then
              VIASH_PAR_OUTSAMTYPE=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_OUTSAMTYPE="$VIASH_PAR_OUTSAMTYPE;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --outSAMmode)
            [ -n "$VIASH_PAR_OUTSAMMODE" ] && ViashError Bad arguments for option \'--outSAMmode\': \'$VIASH_PAR_OUTSAMMODE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTSAMMODE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outSAMmode. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outSAMmode=*)
            [ -n "$VIASH_PAR_OUTSAMMODE" ] && ViashError Bad arguments for option \'--outSAMmode=*\': \'$VIASH_PAR_OUTSAMMODE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTSAMMODE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --outSAMstrandField)
            [ -n "$VIASH_PAR_OUTSAMSTRANDFIELD" ] && ViashError Bad arguments for option \'--outSAMstrandField\': \'$VIASH_PAR_OUTSAMSTRANDFIELD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTSAMSTRANDFIELD="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outSAMstrandField. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outSAMstrandField=*)
            [ -n "$VIASH_PAR_OUTSAMSTRANDFIELD" ] && ViashError Bad arguments for option \'--outSAMstrandField=*\': \'$VIASH_PAR_OUTSAMSTRANDFIELD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTSAMSTRANDFIELD=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --outSAMattributes)
            if [ -z "$VIASH_PAR_OUTSAMATTRIBUTES" ]; then
              VIASH_PAR_OUTSAMATTRIBUTES="$2"
            else
              VIASH_PAR_OUTSAMATTRIBUTES="$VIASH_PAR_OUTSAMATTRIBUTES;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outSAMattributes. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outSAMattributes=*)
            if [ -z "$VIASH_PAR_OUTSAMATTRIBUTES" ]; then
              VIASH_PAR_OUTSAMATTRIBUTES=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_OUTSAMATTRIBUTES="$VIASH_PAR_OUTSAMATTRIBUTES;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --outSAMattrIHstart)
            [ -n "$VIASH_PAR_OUTSAMATTRIHSTART" ] && ViashError Bad arguments for option \'--outSAMattrIHstart\': \'$VIASH_PAR_OUTSAMATTRIHSTART\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTSAMATTRIHSTART="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outSAMattrIHstart. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outSAMattrIHstart=*)
            [ -n "$VIASH_PAR_OUTSAMATTRIHSTART" ] && ViashError Bad arguments for option \'--outSAMattrIHstart=*\': \'$VIASH_PAR_OUTSAMATTRIHSTART\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTSAMATTRIHSTART=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --outSAMunmapped)
            if [ -z "$VIASH_PAR_OUTSAMUNMAPPED" ]; then
              VIASH_PAR_OUTSAMUNMAPPED="$2"
            else
              VIASH_PAR_OUTSAMUNMAPPED="$VIASH_PAR_OUTSAMUNMAPPED;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outSAMunmapped. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outSAMunmapped=*)
            if [ -z "$VIASH_PAR_OUTSAMUNMAPPED" ]; then
              VIASH_PAR_OUTSAMUNMAPPED=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_OUTSAMUNMAPPED="$VIASH_PAR_OUTSAMUNMAPPED;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --outSAMorder)
            [ -n "$VIASH_PAR_OUTSAMORDER" ] && ViashError Bad arguments for option \'--outSAMorder\': \'$VIASH_PAR_OUTSAMORDER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTSAMORDER="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outSAMorder. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outSAMorder=*)
            [ -n "$VIASH_PAR_OUTSAMORDER" ] && ViashError Bad arguments for option \'--outSAMorder=*\': \'$VIASH_PAR_OUTSAMORDER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTSAMORDER=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --outSAMprimaryFlag)
            [ -n "$VIASH_PAR_OUTSAMPRIMARYFLAG" ] && ViashError Bad arguments for option \'--outSAMprimaryFlag\': \'$VIASH_PAR_OUTSAMPRIMARYFLAG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTSAMPRIMARYFLAG="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outSAMprimaryFlag. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outSAMprimaryFlag=*)
            [ -n "$VIASH_PAR_OUTSAMPRIMARYFLAG" ] && ViashError Bad arguments for option \'--outSAMprimaryFlag=*\': \'$VIASH_PAR_OUTSAMPRIMARYFLAG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTSAMPRIMARYFLAG=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --outSAMreadID)
            [ -n "$VIASH_PAR_OUTSAMREADID" ] && ViashError Bad arguments for option \'--outSAMreadID\': \'$VIASH_PAR_OUTSAMREADID\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTSAMREADID="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outSAMreadID. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outSAMreadID=*)
            [ -n "$VIASH_PAR_OUTSAMREADID" ] && ViashError Bad arguments for option \'--outSAMreadID=*\': \'$VIASH_PAR_OUTSAMREADID\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTSAMREADID=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --outSAMmapqUnique)
            [ -n "$VIASH_PAR_OUTSAMMAPQUNIQUE" ] && ViashError Bad arguments for option \'--outSAMmapqUnique\': \'$VIASH_PAR_OUTSAMMAPQUNIQUE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTSAMMAPQUNIQUE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outSAMmapqUnique. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outSAMmapqUnique=*)
            [ -n "$VIASH_PAR_OUTSAMMAPQUNIQUE" ] && ViashError Bad arguments for option \'--outSAMmapqUnique=*\': \'$VIASH_PAR_OUTSAMMAPQUNIQUE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTSAMMAPQUNIQUE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --outSAMflagOR)
            [ -n "$VIASH_PAR_OUTSAMFLAGOR" ] && ViashError Bad arguments for option \'--outSAMflagOR\': \'$VIASH_PAR_OUTSAMFLAGOR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTSAMFLAGOR="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outSAMflagOR. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outSAMflagOR=*)
            [ -n "$VIASH_PAR_OUTSAMFLAGOR" ] && ViashError Bad arguments for option \'--outSAMflagOR=*\': \'$VIASH_PAR_OUTSAMFLAGOR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTSAMFLAGOR=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --outSAMflagAND)
            [ -n "$VIASH_PAR_OUTSAMFLAGAND" ] && ViashError Bad arguments for option \'--outSAMflagAND\': \'$VIASH_PAR_OUTSAMFLAGAND\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTSAMFLAGAND="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outSAMflagAND. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outSAMflagAND=*)
            [ -n "$VIASH_PAR_OUTSAMFLAGAND" ] && ViashError Bad arguments for option \'--outSAMflagAND=*\': \'$VIASH_PAR_OUTSAMFLAGAND\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTSAMFLAGAND=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --outSAMattrRGline)
            if [ -z "$VIASH_PAR_OUTSAMATTRRGLINE" ]; then
              VIASH_PAR_OUTSAMATTRRGLINE="$2"
            else
              VIASH_PAR_OUTSAMATTRRGLINE="$VIASH_PAR_OUTSAMATTRRGLINE;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outSAMattrRGline. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outSAMattrRGline=*)
            if [ -z "$VIASH_PAR_OUTSAMATTRRGLINE" ]; then
              VIASH_PAR_OUTSAMATTRRGLINE=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_OUTSAMATTRRGLINE="$VIASH_PAR_OUTSAMATTRRGLINE;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --outSAMheaderHD)
            if [ -z "$VIASH_PAR_OUTSAMHEADERHD" ]; then
              VIASH_PAR_OUTSAMHEADERHD="$2"
            else
              VIASH_PAR_OUTSAMHEADERHD="$VIASH_PAR_OUTSAMHEADERHD;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outSAMheaderHD. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outSAMheaderHD=*)
            if [ -z "$VIASH_PAR_OUTSAMHEADERHD" ]; then
              VIASH_PAR_OUTSAMHEADERHD=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_OUTSAMHEADERHD="$VIASH_PAR_OUTSAMHEADERHD;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --outSAMheaderPG)
            if [ -z "$VIASH_PAR_OUTSAMHEADERPG" ]; then
              VIASH_PAR_OUTSAMHEADERPG="$2"
            else
              VIASH_PAR_OUTSAMHEADERPG="$VIASH_PAR_OUTSAMHEADERPG;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outSAMheaderPG. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outSAMheaderPG=*)
            if [ -z "$VIASH_PAR_OUTSAMHEADERPG" ]; then
              VIASH_PAR_OUTSAMHEADERPG=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_OUTSAMHEADERPG="$VIASH_PAR_OUTSAMHEADERPG;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --outSAMheaderCommentFile)
            [ -n "$VIASH_PAR_OUTSAMHEADERCOMMENTFILE" ] && ViashError Bad arguments for option \'--outSAMheaderCommentFile\': \'$VIASH_PAR_OUTSAMHEADERCOMMENTFILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTSAMHEADERCOMMENTFILE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outSAMheaderCommentFile. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outSAMheaderCommentFile=*)
            [ -n "$VIASH_PAR_OUTSAMHEADERCOMMENTFILE" ] && ViashError Bad arguments for option \'--outSAMheaderCommentFile=*\': \'$VIASH_PAR_OUTSAMHEADERCOMMENTFILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTSAMHEADERCOMMENTFILE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --outSAMfilter)
            if [ -z "$VIASH_PAR_OUTSAMFILTER" ]; then
              VIASH_PAR_OUTSAMFILTER="$2"
            else
              VIASH_PAR_OUTSAMFILTER="$VIASH_PAR_OUTSAMFILTER;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outSAMfilter. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outSAMfilter=*)
            if [ -z "$VIASH_PAR_OUTSAMFILTER" ]; then
              VIASH_PAR_OUTSAMFILTER=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_OUTSAMFILTER="$VIASH_PAR_OUTSAMFILTER;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --outSAMmultNmax)
            [ -n "$VIASH_PAR_OUTSAMMULTNMAX" ] && ViashError Bad arguments for option \'--outSAMmultNmax\': \'$VIASH_PAR_OUTSAMMULTNMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTSAMMULTNMAX="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outSAMmultNmax. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outSAMmultNmax=*)
            [ -n "$VIASH_PAR_OUTSAMMULTNMAX" ] && ViashError Bad arguments for option \'--outSAMmultNmax=*\': \'$VIASH_PAR_OUTSAMMULTNMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTSAMMULTNMAX=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --outSAMtlen)
            [ -n "$VIASH_PAR_OUTSAMTLEN" ] && ViashError Bad arguments for option \'--outSAMtlen\': \'$VIASH_PAR_OUTSAMTLEN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTSAMTLEN="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outSAMtlen. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outSAMtlen=*)
            [ -n "$VIASH_PAR_OUTSAMTLEN" ] && ViashError Bad arguments for option \'--outSAMtlen=*\': \'$VIASH_PAR_OUTSAMTLEN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTSAMTLEN=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --outBAMcompression)
            [ -n "$VIASH_PAR_OUTBAMCOMPRESSION" ] && ViashError Bad arguments for option \'--outBAMcompression\': \'$VIASH_PAR_OUTBAMCOMPRESSION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTBAMCOMPRESSION="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outBAMcompression. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outBAMcompression=*)
            [ -n "$VIASH_PAR_OUTBAMCOMPRESSION" ] && ViashError Bad arguments for option \'--outBAMcompression=*\': \'$VIASH_PAR_OUTBAMCOMPRESSION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTBAMCOMPRESSION=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --outBAMsortingThreadN)
            [ -n "$VIASH_PAR_OUTBAMSORTINGTHREADN" ] && ViashError Bad arguments for option \'--outBAMsortingThreadN\': \'$VIASH_PAR_OUTBAMSORTINGTHREADN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTBAMSORTINGTHREADN="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outBAMsortingThreadN. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outBAMsortingThreadN=*)
            [ -n "$VIASH_PAR_OUTBAMSORTINGTHREADN" ] && ViashError Bad arguments for option \'--outBAMsortingThreadN=*\': \'$VIASH_PAR_OUTBAMSORTINGTHREADN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTBAMSORTINGTHREADN=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --outBAMsortingBinsN)
            [ -n "$VIASH_PAR_OUTBAMSORTINGBINSN" ] && ViashError Bad arguments for option \'--outBAMsortingBinsN\': \'$VIASH_PAR_OUTBAMSORTINGBINSN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTBAMSORTINGBINSN="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outBAMsortingBinsN. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outBAMsortingBinsN=*)
            [ -n "$VIASH_PAR_OUTBAMSORTINGBINSN" ] && ViashError Bad arguments for option \'--outBAMsortingBinsN=*\': \'$VIASH_PAR_OUTBAMSORTINGBINSN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTBAMSORTINGBINSN=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --bamRemoveDuplicatesType)
            [ -n "$VIASH_PAR_BAMREMOVEDUPLICATESTYPE" ] && ViashError Bad arguments for option \'--bamRemoveDuplicatesType\': \'$VIASH_PAR_BAMREMOVEDUPLICATESTYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_BAMREMOVEDUPLICATESTYPE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --bamRemoveDuplicatesType. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --bamRemoveDuplicatesType=*)
            [ -n "$VIASH_PAR_BAMREMOVEDUPLICATESTYPE" ] && ViashError Bad arguments for option \'--bamRemoveDuplicatesType=*\': \'$VIASH_PAR_BAMREMOVEDUPLICATESTYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_BAMREMOVEDUPLICATESTYPE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --bamRemoveDuplicatesMate2basesN)
            [ -n "$VIASH_PAR_BAMREMOVEDUPLICATESMATE2BASESN" ] && ViashError Bad arguments for option \'--bamRemoveDuplicatesMate2basesN\': \'$VIASH_PAR_BAMREMOVEDUPLICATESMATE2BASESN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_BAMREMOVEDUPLICATESMATE2BASESN="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --bamRemoveDuplicatesMate2basesN. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --bamRemoveDuplicatesMate2basesN=*)
            [ -n "$VIASH_PAR_BAMREMOVEDUPLICATESMATE2BASESN" ] && ViashError Bad arguments for option \'--bamRemoveDuplicatesMate2basesN=*\': \'$VIASH_PAR_BAMREMOVEDUPLICATESMATE2BASESN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_BAMREMOVEDUPLICATESMATE2BASESN=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --outWigType)
            if [ -z "$VIASH_PAR_OUTWIGTYPE" ]; then
              VIASH_PAR_OUTWIGTYPE="$2"
            else
              VIASH_PAR_OUTWIGTYPE="$VIASH_PAR_OUTWIGTYPE;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outWigType. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outWigType=*)
            if [ -z "$VIASH_PAR_OUTWIGTYPE" ]; then
              VIASH_PAR_OUTWIGTYPE=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_OUTWIGTYPE="$VIASH_PAR_OUTWIGTYPE;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --outWigStrand)
            [ -n "$VIASH_PAR_OUTWIGSTRAND" ] && ViashError Bad arguments for option \'--outWigStrand\': \'$VIASH_PAR_OUTWIGSTRAND\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTWIGSTRAND="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outWigStrand. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outWigStrand=*)
            [ -n "$VIASH_PAR_OUTWIGSTRAND" ] && ViashError Bad arguments for option \'--outWigStrand=*\': \'$VIASH_PAR_OUTWIGSTRAND\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTWIGSTRAND=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --outWigReferencesPrefix)
            [ -n "$VIASH_PAR_OUTWIGREFERENCESPREFIX" ] && ViashError Bad arguments for option \'--outWigReferencesPrefix\': \'$VIASH_PAR_OUTWIGREFERENCESPREFIX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTWIGREFERENCESPREFIX="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outWigReferencesPrefix. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outWigReferencesPrefix=*)
            [ -n "$VIASH_PAR_OUTWIGREFERENCESPREFIX" ] && ViashError Bad arguments for option \'--outWigReferencesPrefix=*\': \'$VIASH_PAR_OUTWIGREFERENCESPREFIX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTWIGREFERENCESPREFIX=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --outWigNorm)
            [ -n "$VIASH_PAR_OUTWIGNORM" ] && ViashError Bad arguments for option \'--outWigNorm\': \'$VIASH_PAR_OUTWIGNORM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTWIGNORM="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outWigNorm. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outWigNorm=*)
            [ -n "$VIASH_PAR_OUTWIGNORM" ] && ViashError Bad arguments for option \'--outWigNorm=*\': \'$VIASH_PAR_OUTWIGNORM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTWIGNORM=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --outFilterType)
            [ -n "$VIASH_PAR_OUTFILTERTYPE" ] && ViashError Bad arguments for option \'--outFilterType\': \'$VIASH_PAR_OUTFILTERTYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTFILTERTYPE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outFilterType. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outFilterType=*)
            [ -n "$VIASH_PAR_OUTFILTERTYPE" ] && ViashError Bad arguments for option \'--outFilterType=*\': \'$VIASH_PAR_OUTFILTERTYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTFILTERTYPE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --outFilterMultimapScoreRange)
            [ -n "$VIASH_PAR_OUTFILTERMULTIMAPSCORERANGE" ] && ViashError Bad arguments for option \'--outFilterMultimapScoreRange\': \'$VIASH_PAR_OUTFILTERMULTIMAPSCORERANGE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTFILTERMULTIMAPSCORERANGE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outFilterMultimapScoreRange. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outFilterMultimapScoreRange=*)
            [ -n "$VIASH_PAR_OUTFILTERMULTIMAPSCORERANGE" ] && ViashError Bad arguments for option \'--outFilterMultimapScoreRange=*\': \'$VIASH_PAR_OUTFILTERMULTIMAPSCORERANGE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTFILTERMULTIMAPSCORERANGE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --outFilterMultimapNmax)
            [ -n "$VIASH_PAR_OUTFILTERMULTIMAPNMAX" ] && ViashError Bad arguments for option \'--outFilterMultimapNmax\': \'$VIASH_PAR_OUTFILTERMULTIMAPNMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTFILTERMULTIMAPNMAX="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outFilterMultimapNmax. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outFilterMultimapNmax=*)
            [ -n "$VIASH_PAR_OUTFILTERMULTIMAPNMAX" ] && ViashError Bad arguments for option \'--outFilterMultimapNmax=*\': \'$VIASH_PAR_OUTFILTERMULTIMAPNMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTFILTERMULTIMAPNMAX=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --outFilterMismatchNmax)
            [ -n "$VIASH_PAR_OUTFILTERMISMATCHNMAX" ] && ViashError Bad arguments for option \'--outFilterMismatchNmax\': \'$VIASH_PAR_OUTFILTERMISMATCHNMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTFILTERMISMATCHNMAX="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outFilterMismatchNmax. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outFilterMismatchNmax=*)
            [ -n "$VIASH_PAR_OUTFILTERMISMATCHNMAX" ] && ViashError Bad arguments for option \'--outFilterMismatchNmax=*\': \'$VIASH_PAR_OUTFILTERMISMATCHNMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTFILTERMISMATCHNMAX=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --outFilterMismatchNoverLmax)
            [ -n "$VIASH_PAR_OUTFILTERMISMATCHNOVERLMAX" ] && ViashError Bad arguments for option \'--outFilterMismatchNoverLmax\': \'$VIASH_PAR_OUTFILTERMISMATCHNOVERLMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTFILTERMISMATCHNOVERLMAX="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outFilterMismatchNoverLmax. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outFilterMismatchNoverLmax=*)
            [ -n "$VIASH_PAR_OUTFILTERMISMATCHNOVERLMAX" ] && ViashError Bad arguments for option \'--outFilterMismatchNoverLmax=*\': \'$VIASH_PAR_OUTFILTERMISMATCHNOVERLMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTFILTERMISMATCHNOVERLMAX=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --outFilterMismatchNoverReadLmax)
            [ -n "$VIASH_PAR_OUTFILTERMISMATCHNOVERREADLMAX" ] && ViashError Bad arguments for option \'--outFilterMismatchNoverReadLmax\': \'$VIASH_PAR_OUTFILTERMISMATCHNOVERREADLMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTFILTERMISMATCHNOVERREADLMAX="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outFilterMismatchNoverReadLmax. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outFilterMismatchNoverReadLmax=*)
            [ -n "$VIASH_PAR_OUTFILTERMISMATCHNOVERREADLMAX" ] && ViashError Bad arguments for option \'--outFilterMismatchNoverReadLmax=*\': \'$VIASH_PAR_OUTFILTERMISMATCHNOVERREADLMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTFILTERMISMATCHNOVERREADLMAX=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --outFilterScoreMin)
            [ -n "$VIASH_PAR_OUTFILTERSCOREMIN" ] && ViashError Bad arguments for option \'--outFilterScoreMin\': \'$VIASH_PAR_OUTFILTERSCOREMIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTFILTERSCOREMIN="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outFilterScoreMin. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outFilterScoreMin=*)
            [ -n "$VIASH_PAR_OUTFILTERSCOREMIN" ] && ViashError Bad arguments for option \'--outFilterScoreMin=*\': \'$VIASH_PAR_OUTFILTERSCOREMIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTFILTERSCOREMIN=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --outFilterScoreMinOverLread)
            [ -n "$VIASH_PAR_OUTFILTERSCOREMINOVERLREAD" ] && ViashError Bad arguments for option \'--outFilterScoreMinOverLread\': \'$VIASH_PAR_OUTFILTERSCOREMINOVERLREAD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTFILTERSCOREMINOVERLREAD="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outFilterScoreMinOverLread. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outFilterScoreMinOverLread=*)
            [ -n "$VIASH_PAR_OUTFILTERSCOREMINOVERLREAD" ] && ViashError Bad arguments for option \'--outFilterScoreMinOverLread=*\': \'$VIASH_PAR_OUTFILTERSCOREMINOVERLREAD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTFILTERSCOREMINOVERLREAD=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --outFilterMatchNmin)
            [ -n "$VIASH_PAR_OUTFILTERMATCHNMIN" ] && ViashError Bad arguments for option \'--outFilterMatchNmin\': \'$VIASH_PAR_OUTFILTERMATCHNMIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTFILTERMATCHNMIN="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outFilterMatchNmin. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outFilterMatchNmin=*)
            [ -n "$VIASH_PAR_OUTFILTERMATCHNMIN" ] && ViashError Bad arguments for option \'--outFilterMatchNmin=*\': \'$VIASH_PAR_OUTFILTERMATCHNMIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTFILTERMATCHNMIN=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --outFilterMatchNminOverLread)
            [ -n "$VIASH_PAR_OUTFILTERMATCHNMINOVERLREAD" ] && ViashError Bad arguments for option \'--outFilterMatchNminOverLread\': \'$VIASH_PAR_OUTFILTERMATCHNMINOVERLREAD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTFILTERMATCHNMINOVERLREAD="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outFilterMatchNminOverLread. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outFilterMatchNminOverLread=*)
            [ -n "$VIASH_PAR_OUTFILTERMATCHNMINOVERLREAD" ] && ViashError Bad arguments for option \'--outFilterMatchNminOverLread=*\': \'$VIASH_PAR_OUTFILTERMATCHNMINOVERLREAD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTFILTERMATCHNMINOVERLREAD=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --outFilterIntronMotifs)
            [ -n "$VIASH_PAR_OUTFILTERINTRONMOTIFS" ] && ViashError Bad arguments for option \'--outFilterIntronMotifs\': \'$VIASH_PAR_OUTFILTERINTRONMOTIFS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTFILTERINTRONMOTIFS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outFilterIntronMotifs. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outFilterIntronMotifs=*)
            [ -n "$VIASH_PAR_OUTFILTERINTRONMOTIFS" ] && ViashError Bad arguments for option \'--outFilterIntronMotifs=*\': \'$VIASH_PAR_OUTFILTERINTRONMOTIFS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTFILTERINTRONMOTIFS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --outFilterIntronStrands)
            [ -n "$VIASH_PAR_OUTFILTERINTRONSTRANDS" ] && ViashError Bad arguments for option \'--outFilterIntronStrands\': \'$VIASH_PAR_OUTFILTERINTRONSTRANDS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTFILTERINTRONSTRANDS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outFilterIntronStrands. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outFilterIntronStrands=*)
            [ -n "$VIASH_PAR_OUTFILTERINTRONSTRANDS" ] && ViashError Bad arguments for option \'--outFilterIntronStrands=*\': \'$VIASH_PAR_OUTFILTERINTRONSTRANDS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTFILTERINTRONSTRANDS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --outSJtype)
            [ -n "$VIASH_PAR_OUTSJTYPE" ] && ViashError Bad arguments for option \'--outSJtype\': \'$VIASH_PAR_OUTSJTYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTSJTYPE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outSJtype. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outSJtype=*)
            [ -n "$VIASH_PAR_OUTSJTYPE" ] && ViashError Bad arguments for option \'--outSJtype=*\': \'$VIASH_PAR_OUTSJTYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTSJTYPE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --outSJfilterReads)
            [ -n "$VIASH_PAR_OUTSJFILTERREADS" ] && ViashError Bad arguments for option \'--outSJfilterReads\': \'$VIASH_PAR_OUTSJFILTERREADS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTSJFILTERREADS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outSJfilterReads. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outSJfilterReads=*)
            [ -n "$VIASH_PAR_OUTSJFILTERREADS" ] && ViashError Bad arguments for option \'--outSJfilterReads=*\': \'$VIASH_PAR_OUTSJFILTERREADS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTSJFILTERREADS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --outSJfilterOverhangMin)
            if [ -z "$VIASH_PAR_OUTSJFILTEROVERHANGMIN" ]; then
              VIASH_PAR_OUTSJFILTEROVERHANGMIN="$2"
            else
              VIASH_PAR_OUTSJFILTEROVERHANGMIN="$VIASH_PAR_OUTSJFILTEROVERHANGMIN;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outSJfilterOverhangMin. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outSJfilterOverhangMin=*)
            if [ -z "$VIASH_PAR_OUTSJFILTEROVERHANGMIN" ]; then
              VIASH_PAR_OUTSJFILTEROVERHANGMIN=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_OUTSJFILTEROVERHANGMIN="$VIASH_PAR_OUTSJFILTEROVERHANGMIN;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --outSJfilterCountUniqueMin)
            if [ -z "$VIASH_PAR_OUTSJFILTERCOUNTUNIQUEMIN" ]; then
              VIASH_PAR_OUTSJFILTERCOUNTUNIQUEMIN="$2"
            else
              VIASH_PAR_OUTSJFILTERCOUNTUNIQUEMIN="$VIASH_PAR_OUTSJFILTERCOUNTUNIQUEMIN;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outSJfilterCountUniqueMin. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outSJfilterCountUniqueMin=*)
            if [ -z "$VIASH_PAR_OUTSJFILTERCOUNTUNIQUEMIN" ]; then
              VIASH_PAR_OUTSJFILTERCOUNTUNIQUEMIN=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_OUTSJFILTERCOUNTUNIQUEMIN="$VIASH_PAR_OUTSJFILTERCOUNTUNIQUEMIN;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --outSJfilterCountTotalMin)
            if [ -z "$VIASH_PAR_OUTSJFILTERCOUNTTOTALMIN" ]; then
              VIASH_PAR_OUTSJFILTERCOUNTTOTALMIN="$2"
            else
              VIASH_PAR_OUTSJFILTERCOUNTTOTALMIN="$VIASH_PAR_OUTSJFILTERCOUNTTOTALMIN;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outSJfilterCountTotalMin. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outSJfilterCountTotalMin=*)
            if [ -z "$VIASH_PAR_OUTSJFILTERCOUNTTOTALMIN" ]; then
              VIASH_PAR_OUTSJFILTERCOUNTTOTALMIN=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_OUTSJFILTERCOUNTTOTALMIN="$VIASH_PAR_OUTSJFILTERCOUNTTOTALMIN;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --outSJfilterDistToOtherSJmin)
            if [ -z "$VIASH_PAR_OUTSJFILTERDISTTOOTHERSJMIN" ]; then
              VIASH_PAR_OUTSJFILTERDISTTOOTHERSJMIN="$2"
            else
              VIASH_PAR_OUTSJFILTERDISTTOOTHERSJMIN="$VIASH_PAR_OUTSJFILTERDISTTOOTHERSJMIN;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outSJfilterDistToOtherSJmin. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outSJfilterDistToOtherSJmin=*)
            if [ -z "$VIASH_PAR_OUTSJFILTERDISTTOOTHERSJMIN" ]; then
              VIASH_PAR_OUTSJFILTERDISTTOOTHERSJMIN=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_OUTSJFILTERDISTTOOTHERSJMIN="$VIASH_PAR_OUTSJFILTERDISTTOOTHERSJMIN;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --outSJfilterIntronMaxVsReadN)
            if [ -z "$VIASH_PAR_OUTSJFILTERINTRONMAXVSREADN" ]; then
              VIASH_PAR_OUTSJFILTERINTRONMAXVSREADN="$2"
            else
              VIASH_PAR_OUTSJFILTERINTRONMAXVSREADN="$VIASH_PAR_OUTSJFILTERINTRONMAXVSREADN;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --outSJfilterIntronMaxVsReadN. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --outSJfilterIntronMaxVsReadN=*)
            if [ -z "$VIASH_PAR_OUTSJFILTERINTRONMAXVSREADN" ]; then
              VIASH_PAR_OUTSJFILTERINTRONMAXVSREADN=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_OUTSJFILTERINTRONMAXVSREADN="$VIASH_PAR_OUTSJFILTERINTRONMAXVSREADN;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --scoreGap)
            [ -n "$VIASH_PAR_SCOREGAP" ] && ViashError Bad arguments for option \'--scoreGap\': \'$VIASH_PAR_SCOREGAP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SCOREGAP="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --scoreGap. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --scoreGap=*)
            [ -n "$VIASH_PAR_SCOREGAP" ] && ViashError Bad arguments for option \'--scoreGap=*\': \'$VIASH_PAR_SCOREGAP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SCOREGAP=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --scoreGapNoncan)
            [ -n "$VIASH_PAR_SCOREGAPNONCAN" ] && ViashError Bad arguments for option \'--scoreGapNoncan\': \'$VIASH_PAR_SCOREGAPNONCAN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SCOREGAPNONCAN="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --scoreGapNoncan. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --scoreGapNoncan=*)
            [ -n "$VIASH_PAR_SCOREGAPNONCAN" ] && ViashError Bad arguments for option \'--scoreGapNoncan=*\': \'$VIASH_PAR_SCOREGAPNONCAN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SCOREGAPNONCAN=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --scoreGapGCAG)
            [ -n "$VIASH_PAR_SCOREGAPGCAG" ] && ViashError Bad arguments for option \'--scoreGapGCAG\': \'$VIASH_PAR_SCOREGAPGCAG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SCOREGAPGCAG="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --scoreGapGCAG. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --scoreGapGCAG=*)
            [ -n "$VIASH_PAR_SCOREGAPGCAG" ] && ViashError Bad arguments for option \'--scoreGapGCAG=*\': \'$VIASH_PAR_SCOREGAPGCAG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SCOREGAPGCAG=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --scoreGapATAC)
            [ -n "$VIASH_PAR_SCOREGAPATAC" ] && ViashError Bad arguments for option \'--scoreGapATAC\': \'$VIASH_PAR_SCOREGAPATAC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SCOREGAPATAC="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --scoreGapATAC. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --scoreGapATAC=*)
            [ -n "$VIASH_PAR_SCOREGAPATAC" ] && ViashError Bad arguments for option \'--scoreGapATAC=*\': \'$VIASH_PAR_SCOREGAPATAC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SCOREGAPATAC=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --scoreGenomicLengthLog2scale)
            [ -n "$VIASH_PAR_SCOREGENOMICLENGTHLOG2SCALE" ] && ViashError Bad arguments for option \'--scoreGenomicLengthLog2scale\': \'$VIASH_PAR_SCOREGENOMICLENGTHLOG2SCALE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SCOREGENOMICLENGTHLOG2SCALE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --scoreGenomicLengthLog2scale. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --scoreGenomicLengthLog2scale=*)
            [ -n "$VIASH_PAR_SCOREGENOMICLENGTHLOG2SCALE" ] && ViashError Bad arguments for option \'--scoreGenomicLengthLog2scale=*\': \'$VIASH_PAR_SCOREGENOMICLENGTHLOG2SCALE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SCOREGENOMICLENGTHLOG2SCALE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --scoreDelOpen)
            [ -n "$VIASH_PAR_SCOREDELOPEN" ] && ViashError Bad arguments for option \'--scoreDelOpen\': \'$VIASH_PAR_SCOREDELOPEN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SCOREDELOPEN="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --scoreDelOpen. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --scoreDelOpen=*)
            [ -n "$VIASH_PAR_SCOREDELOPEN" ] && ViashError Bad arguments for option \'--scoreDelOpen=*\': \'$VIASH_PAR_SCOREDELOPEN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SCOREDELOPEN=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --scoreDelBase)
            [ -n "$VIASH_PAR_SCOREDELBASE" ] && ViashError Bad arguments for option \'--scoreDelBase\': \'$VIASH_PAR_SCOREDELBASE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SCOREDELBASE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --scoreDelBase. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --scoreDelBase=*)
            [ -n "$VIASH_PAR_SCOREDELBASE" ] && ViashError Bad arguments for option \'--scoreDelBase=*\': \'$VIASH_PAR_SCOREDELBASE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SCOREDELBASE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --scoreInsOpen)
            [ -n "$VIASH_PAR_SCOREINSOPEN" ] && ViashError Bad arguments for option \'--scoreInsOpen\': \'$VIASH_PAR_SCOREINSOPEN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SCOREINSOPEN="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --scoreInsOpen. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --scoreInsOpen=*)
            [ -n "$VIASH_PAR_SCOREINSOPEN" ] && ViashError Bad arguments for option \'--scoreInsOpen=*\': \'$VIASH_PAR_SCOREINSOPEN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SCOREINSOPEN=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --scoreInsBase)
            [ -n "$VIASH_PAR_SCOREINSBASE" ] && ViashError Bad arguments for option \'--scoreInsBase\': \'$VIASH_PAR_SCOREINSBASE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SCOREINSBASE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --scoreInsBase. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --scoreInsBase=*)
            [ -n "$VIASH_PAR_SCOREINSBASE" ] && ViashError Bad arguments for option \'--scoreInsBase=*\': \'$VIASH_PAR_SCOREINSBASE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SCOREINSBASE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --scoreStitchSJshift)
            [ -n "$VIASH_PAR_SCORESTITCHSJSHIFT" ] && ViashError Bad arguments for option \'--scoreStitchSJshift\': \'$VIASH_PAR_SCORESTITCHSJSHIFT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SCORESTITCHSJSHIFT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --scoreStitchSJshift. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --scoreStitchSJshift=*)
            [ -n "$VIASH_PAR_SCORESTITCHSJSHIFT" ] && ViashError Bad arguments for option \'--scoreStitchSJshift=*\': \'$VIASH_PAR_SCORESTITCHSJSHIFT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SCORESTITCHSJSHIFT=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --seedSearchStartLmax)
            [ -n "$VIASH_PAR_SEEDSEARCHSTARTLMAX" ] && ViashError Bad arguments for option \'--seedSearchStartLmax\': \'$VIASH_PAR_SEEDSEARCHSTARTLMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SEEDSEARCHSTARTLMAX="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --seedSearchStartLmax. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --seedSearchStartLmax=*)
            [ -n "$VIASH_PAR_SEEDSEARCHSTARTLMAX" ] && ViashError Bad arguments for option \'--seedSearchStartLmax=*\': \'$VIASH_PAR_SEEDSEARCHSTARTLMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SEEDSEARCHSTARTLMAX=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --seedSearchStartLmaxOverLread)
            [ -n "$VIASH_PAR_SEEDSEARCHSTARTLMAXOVERLREAD" ] && ViashError Bad arguments for option \'--seedSearchStartLmaxOverLread\': \'$VIASH_PAR_SEEDSEARCHSTARTLMAXOVERLREAD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SEEDSEARCHSTARTLMAXOVERLREAD="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --seedSearchStartLmaxOverLread. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --seedSearchStartLmaxOverLread=*)
            [ -n "$VIASH_PAR_SEEDSEARCHSTARTLMAXOVERLREAD" ] && ViashError Bad arguments for option \'--seedSearchStartLmaxOverLread=*\': \'$VIASH_PAR_SEEDSEARCHSTARTLMAXOVERLREAD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SEEDSEARCHSTARTLMAXOVERLREAD=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --seedSearchLmax)
            [ -n "$VIASH_PAR_SEEDSEARCHLMAX" ] && ViashError Bad arguments for option \'--seedSearchLmax\': \'$VIASH_PAR_SEEDSEARCHLMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SEEDSEARCHLMAX="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --seedSearchLmax. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --seedSearchLmax=*)
            [ -n "$VIASH_PAR_SEEDSEARCHLMAX" ] && ViashError Bad arguments for option \'--seedSearchLmax=*\': \'$VIASH_PAR_SEEDSEARCHLMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SEEDSEARCHLMAX=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --seedMultimapNmax)
            [ -n "$VIASH_PAR_SEEDMULTIMAPNMAX" ] && ViashError Bad arguments for option \'--seedMultimapNmax\': \'$VIASH_PAR_SEEDMULTIMAPNMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SEEDMULTIMAPNMAX="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --seedMultimapNmax. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --seedMultimapNmax=*)
            [ -n "$VIASH_PAR_SEEDMULTIMAPNMAX" ] && ViashError Bad arguments for option \'--seedMultimapNmax=*\': \'$VIASH_PAR_SEEDMULTIMAPNMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SEEDMULTIMAPNMAX=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --seedPerReadNmax)
            [ -n "$VIASH_PAR_SEEDPERREADNMAX" ] && ViashError Bad arguments for option \'--seedPerReadNmax\': \'$VIASH_PAR_SEEDPERREADNMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SEEDPERREADNMAX="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --seedPerReadNmax. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --seedPerReadNmax=*)
            [ -n "$VIASH_PAR_SEEDPERREADNMAX" ] && ViashError Bad arguments for option \'--seedPerReadNmax=*\': \'$VIASH_PAR_SEEDPERREADNMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SEEDPERREADNMAX=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --seedPerWindowNmax)
            [ -n "$VIASH_PAR_SEEDPERWINDOWNMAX" ] && ViashError Bad arguments for option \'--seedPerWindowNmax\': \'$VIASH_PAR_SEEDPERWINDOWNMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SEEDPERWINDOWNMAX="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --seedPerWindowNmax. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --seedPerWindowNmax=*)
            [ -n "$VIASH_PAR_SEEDPERWINDOWNMAX" ] && ViashError Bad arguments for option \'--seedPerWindowNmax=*\': \'$VIASH_PAR_SEEDPERWINDOWNMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SEEDPERWINDOWNMAX=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --seedNoneLociPerWindow)
            [ -n "$VIASH_PAR_SEEDNONELOCIPERWINDOW" ] && ViashError Bad arguments for option \'--seedNoneLociPerWindow\': \'$VIASH_PAR_SEEDNONELOCIPERWINDOW\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SEEDNONELOCIPERWINDOW="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --seedNoneLociPerWindow. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --seedNoneLociPerWindow=*)
            [ -n "$VIASH_PAR_SEEDNONELOCIPERWINDOW" ] && ViashError Bad arguments for option \'--seedNoneLociPerWindow=*\': \'$VIASH_PAR_SEEDNONELOCIPERWINDOW\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SEEDNONELOCIPERWINDOW=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --seedSplitMin)
            [ -n "$VIASH_PAR_SEEDSPLITMIN" ] && ViashError Bad arguments for option \'--seedSplitMin\': \'$VIASH_PAR_SEEDSPLITMIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SEEDSPLITMIN="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --seedSplitMin. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --seedSplitMin=*)
            [ -n "$VIASH_PAR_SEEDSPLITMIN" ] && ViashError Bad arguments for option \'--seedSplitMin=*\': \'$VIASH_PAR_SEEDSPLITMIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SEEDSPLITMIN=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --seedMapMin)
            [ -n "$VIASH_PAR_SEEDMAPMIN" ] && ViashError Bad arguments for option \'--seedMapMin\': \'$VIASH_PAR_SEEDMAPMIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SEEDMAPMIN="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --seedMapMin. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --seedMapMin=*)
            [ -n "$VIASH_PAR_SEEDMAPMIN" ] && ViashError Bad arguments for option \'--seedMapMin=*\': \'$VIASH_PAR_SEEDMAPMIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SEEDMAPMIN=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --alignIntronMin)
            [ -n "$VIASH_PAR_ALIGNINTRONMIN" ] && ViashError Bad arguments for option \'--alignIntronMin\': \'$VIASH_PAR_ALIGNINTRONMIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALIGNINTRONMIN="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --alignIntronMin. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --alignIntronMin=*)
            [ -n "$VIASH_PAR_ALIGNINTRONMIN" ] && ViashError Bad arguments for option \'--alignIntronMin=*\': \'$VIASH_PAR_ALIGNINTRONMIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALIGNINTRONMIN=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --alignIntronMax)
            [ -n "$VIASH_PAR_ALIGNINTRONMAX" ] && ViashError Bad arguments for option \'--alignIntronMax\': \'$VIASH_PAR_ALIGNINTRONMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALIGNINTRONMAX="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --alignIntronMax. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --alignIntronMax=*)
            [ -n "$VIASH_PAR_ALIGNINTRONMAX" ] && ViashError Bad arguments for option \'--alignIntronMax=*\': \'$VIASH_PAR_ALIGNINTRONMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALIGNINTRONMAX=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --alignMatesGapMax)
            [ -n "$VIASH_PAR_ALIGNMATESGAPMAX" ] && ViashError Bad arguments for option \'--alignMatesGapMax\': \'$VIASH_PAR_ALIGNMATESGAPMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALIGNMATESGAPMAX="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --alignMatesGapMax. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --alignMatesGapMax=*)
            [ -n "$VIASH_PAR_ALIGNMATESGAPMAX" ] && ViashError Bad arguments for option \'--alignMatesGapMax=*\': \'$VIASH_PAR_ALIGNMATESGAPMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALIGNMATESGAPMAX=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --alignSJoverhangMin)
            [ -n "$VIASH_PAR_ALIGNSJOVERHANGMIN" ] && ViashError Bad arguments for option \'--alignSJoverhangMin\': \'$VIASH_PAR_ALIGNSJOVERHANGMIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALIGNSJOVERHANGMIN="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --alignSJoverhangMin. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --alignSJoverhangMin=*)
            [ -n "$VIASH_PAR_ALIGNSJOVERHANGMIN" ] && ViashError Bad arguments for option \'--alignSJoverhangMin=*\': \'$VIASH_PAR_ALIGNSJOVERHANGMIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALIGNSJOVERHANGMIN=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --alignSJstitchMismatchNmax)
            if [ -z "$VIASH_PAR_ALIGNSJSTITCHMISMATCHNMAX" ]; then
              VIASH_PAR_ALIGNSJSTITCHMISMATCHNMAX="$2"
            else
              VIASH_PAR_ALIGNSJSTITCHMISMATCHNMAX="$VIASH_PAR_ALIGNSJSTITCHMISMATCHNMAX;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --alignSJstitchMismatchNmax. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --alignSJstitchMismatchNmax=*)
            if [ -z "$VIASH_PAR_ALIGNSJSTITCHMISMATCHNMAX" ]; then
              VIASH_PAR_ALIGNSJSTITCHMISMATCHNMAX=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_ALIGNSJSTITCHMISMATCHNMAX="$VIASH_PAR_ALIGNSJSTITCHMISMATCHNMAX;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --alignSJDBoverhangMin)
            [ -n "$VIASH_PAR_ALIGNSJDBOVERHANGMIN" ] && ViashError Bad arguments for option \'--alignSJDBoverhangMin\': \'$VIASH_PAR_ALIGNSJDBOVERHANGMIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALIGNSJDBOVERHANGMIN="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --alignSJDBoverhangMin. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --alignSJDBoverhangMin=*)
            [ -n "$VIASH_PAR_ALIGNSJDBOVERHANGMIN" ] && ViashError Bad arguments for option \'--alignSJDBoverhangMin=*\': \'$VIASH_PAR_ALIGNSJDBOVERHANGMIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALIGNSJDBOVERHANGMIN=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --alignSplicedMateMapLmin)
            [ -n "$VIASH_PAR_ALIGNSPLICEDMATEMAPLMIN" ] && ViashError Bad arguments for option \'--alignSplicedMateMapLmin\': \'$VIASH_PAR_ALIGNSPLICEDMATEMAPLMIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALIGNSPLICEDMATEMAPLMIN="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --alignSplicedMateMapLmin. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --alignSplicedMateMapLmin=*)
            [ -n "$VIASH_PAR_ALIGNSPLICEDMATEMAPLMIN" ] && ViashError Bad arguments for option \'--alignSplicedMateMapLmin=*\': \'$VIASH_PAR_ALIGNSPLICEDMATEMAPLMIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALIGNSPLICEDMATEMAPLMIN=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --alignSplicedMateMapLminOverLmate)
            [ -n "$VIASH_PAR_ALIGNSPLICEDMATEMAPLMINOVERLMATE" ] && ViashError Bad arguments for option \'--alignSplicedMateMapLminOverLmate\': \'$VIASH_PAR_ALIGNSPLICEDMATEMAPLMINOVERLMATE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALIGNSPLICEDMATEMAPLMINOVERLMATE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --alignSplicedMateMapLminOverLmate. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --alignSplicedMateMapLminOverLmate=*)
            [ -n "$VIASH_PAR_ALIGNSPLICEDMATEMAPLMINOVERLMATE" ] && ViashError Bad arguments for option \'--alignSplicedMateMapLminOverLmate=*\': \'$VIASH_PAR_ALIGNSPLICEDMATEMAPLMINOVERLMATE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALIGNSPLICEDMATEMAPLMINOVERLMATE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --alignWindowsPerReadNmax)
            [ -n "$VIASH_PAR_ALIGNWINDOWSPERREADNMAX" ] && ViashError Bad arguments for option \'--alignWindowsPerReadNmax\': \'$VIASH_PAR_ALIGNWINDOWSPERREADNMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALIGNWINDOWSPERREADNMAX="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --alignWindowsPerReadNmax. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --alignWindowsPerReadNmax=*)
            [ -n "$VIASH_PAR_ALIGNWINDOWSPERREADNMAX" ] && ViashError Bad arguments for option \'--alignWindowsPerReadNmax=*\': \'$VIASH_PAR_ALIGNWINDOWSPERREADNMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALIGNWINDOWSPERREADNMAX=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --alignTranscriptsPerWindowNmax)
            [ -n "$VIASH_PAR_ALIGNTRANSCRIPTSPERWINDOWNMAX" ] && ViashError Bad arguments for option \'--alignTranscriptsPerWindowNmax\': \'$VIASH_PAR_ALIGNTRANSCRIPTSPERWINDOWNMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALIGNTRANSCRIPTSPERWINDOWNMAX="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --alignTranscriptsPerWindowNmax. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --alignTranscriptsPerWindowNmax=*)
            [ -n "$VIASH_PAR_ALIGNTRANSCRIPTSPERWINDOWNMAX" ] && ViashError Bad arguments for option \'--alignTranscriptsPerWindowNmax=*\': \'$VIASH_PAR_ALIGNTRANSCRIPTSPERWINDOWNMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALIGNTRANSCRIPTSPERWINDOWNMAX=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --alignTranscriptsPerReadNmax)
            [ -n "$VIASH_PAR_ALIGNTRANSCRIPTSPERREADNMAX" ] && ViashError Bad arguments for option \'--alignTranscriptsPerReadNmax\': \'$VIASH_PAR_ALIGNTRANSCRIPTSPERREADNMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALIGNTRANSCRIPTSPERREADNMAX="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --alignTranscriptsPerReadNmax. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --alignTranscriptsPerReadNmax=*)
            [ -n "$VIASH_PAR_ALIGNTRANSCRIPTSPERREADNMAX" ] && ViashError Bad arguments for option \'--alignTranscriptsPerReadNmax=*\': \'$VIASH_PAR_ALIGNTRANSCRIPTSPERREADNMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALIGNTRANSCRIPTSPERREADNMAX=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --alignEndsType)
            [ -n "$VIASH_PAR_ALIGNENDSTYPE" ] && ViashError Bad arguments for option \'--alignEndsType\': \'$VIASH_PAR_ALIGNENDSTYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALIGNENDSTYPE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --alignEndsType. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --alignEndsType=*)
            [ -n "$VIASH_PAR_ALIGNENDSTYPE" ] && ViashError Bad arguments for option \'--alignEndsType=*\': \'$VIASH_PAR_ALIGNENDSTYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALIGNENDSTYPE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --alignEndsProtrude)
            [ -n "$VIASH_PAR_ALIGNENDSPROTRUDE" ] && ViashError Bad arguments for option \'--alignEndsProtrude\': \'$VIASH_PAR_ALIGNENDSPROTRUDE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALIGNENDSPROTRUDE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --alignEndsProtrude. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --alignEndsProtrude=*)
            [ -n "$VIASH_PAR_ALIGNENDSPROTRUDE" ] && ViashError Bad arguments for option \'--alignEndsProtrude=*\': \'$VIASH_PAR_ALIGNENDSPROTRUDE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALIGNENDSPROTRUDE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --alignSoftClipAtReferenceEnds)
            [ -n "$VIASH_PAR_ALIGNSOFTCLIPATREFERENCEENDS" ] && ViashError Bad arguments for option \'--alignSoftClipAtReferenceEnds\': \'$VIASH_PAR_ALIGNSOFTCLIPATREFERENCEENDS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALIGNSOFTCLIPATREFERENCEENDS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --alignSoftClipAtReferenceEnds. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --alignSoftClipAtReferenceEnds=*)
            [ -n "$VIASH_PAR_ALIGNSOFTCLIPATREFERENCEENDS" ] && ViashError Bad arguments for option \'--alignSoftClipAtReferenceEnds=*\': \'$VIASH_PAR_ALIGNSOFTCLIPATREFERENCEENDS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALIGNSOFTCLIPATREFERENCEENDS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --alignInsertionFlush)
            [ -n "$VIASH_PAR_ALIGNINSERTIONFLUSH" ] && ViashError Bad arguments for option \'--alignInsertionFlush\': \'$VIASH_PAR_ALIGNINSERTIONFLUSH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALIGNINSERTIONFLUSH="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --alignInsertionFlush. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --alignInsertionFlush=*)
            [ -n "$VIASH_PAR_ALIGNINSERTIONFLUSH" ] && ViashError Bad arguments for option \'--alignInsertionFlush=*\': \'$VIASH_PAR_ALIGNINSERTIONFLUSH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALIGNINSERTIONFLUSH=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --peOverlapNbasesMin)
            [ -n "$VIASH_PAR_PEOVERLAPNBASESMIN" ] && ViashError Bad arguments for option \'--peOverlapNbasesMin\': \'$VIASH_PAR_PEOVERLAPNBASESMIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PEOVERLAPNBASESMIN="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --peOverlapNbasesMin. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --peOverlapNbasesMin=*)
            [ -n "$VIASH_PAR_PEOVERLAPNBASESMIN" ] && ViashError Bad arguments for option \'--peOverlapNbasesMin=*\': \'$VIASH_PAR_PEOVERLAPNBASESMIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PEOVERLAPNBASESMIN=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --peOverlapMMp)
            [ -n "$VIASH_PAR_PEOVERLAPMMP" ] && ViashError Bad arguments for option \'--peOverlapMMp\': \'$VIASH_PAR_PEOVERLAPMMP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PEOVERLAPMMP="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --peOverlapMMp. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --peOverlapMMp=*)
            [ -n "$VIASH_PAR_PEOVERLAPMMP" ] && ViashError Bad arguments for option \'--peOverlapMMp=*\': \'$VIASH_PAR_PEOVERLAPMMP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PEOVERLAPMMP=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --winAnchorMultimapNmax)
            [ -n "$VIASH_PAR_WINANCHORMULTIMAPNMAX" ] && ViashError Bad arguments for option \'--winAnchorMultimapNmax\': \'$VIASH_PAR_WINANCHORMULTIMAPNMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_WINANCHORMULTIMAPNMAX="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --winAnchorMultimapNmax. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --winAnchorMultimapNmax=*)
            [ -n "$VIASH_PAR_WINANCHORMULTIMAPNMAX" ] && ViashError Bad arguments for option \'--winAnchorMultimapNmax=*\': \'$VIASH_PAR_WINANCHORMULTIMAPNMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_WINANCHORMULTIMAPNMAX=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --winBinNbits)
            [ -n "$VIASH_PAR_WINBINNBITS" ] && ViashError Bad arguments for option \'--winBinNbits\': \'$VIASH_PAR_WINBINNBITS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_WINBINNBITS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --winBinNbits. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --winBinNbits=*)
            [ -n "$VIASH_PAR_WINBINNBITS" ] && ViashError Bad arguments for option \'--winBinNbits=*\': \'$VIASH_PAR_WINBINNBITS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_WINBINNBITS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --winAnchorDistNbins)
            [ -n "$VIASH_PAR_WINANCHORDISTNBINS" ] && ViashError Bad arguments for option \'--winAnchorDistNbins\': \'$VIASH_PAR_WINANCHORDISTNBINS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_WINANCHORDISTNBINS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --winAnchorDistNbins. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --winAnchorDistNbins=*)
            [ -n "$VIASH_PAR_WINANCHORDISTNBINS" ] && ViashError Bad arguments for option \'--winAnchorDistNbins=*\': \'$VIASH_PAR_WINANCHORDISTNBINS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_WINANCHORDISTNBINS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --winFlankNbins)
            [ -n "$VIASH_PAR_WINFLANKNBINS" ] && ViashError Bad arguments for option \'--winFlankNbins\': \'$VIASH_PAR_WINFLANKNBINS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_WINFLANKNBINS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --winFlankNbins. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --winFlankNbins=*)
            [ -n "$VIASH_PAR_WINFLANKNBINS" ] && ViashError Bad arguments for option \'--winFlankNbins=*\': \'$VIASH_PAR_WINFLANKNBINS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_WINFLANKNBINS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --winReadCoverageRelativeMin)
            [ -n "$VIASH_PAR_WINREADCOVERAGERELATIVEMIN" ] && ViashError Bad arguments for option \'--winReadCoverageRelativeMin\': \'$VIASH_PAR_WINREADCOVERAGERELATIVEMIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_WINREADCOVERAGERELATIVEMIN="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --winReadCoverageRelativeMin. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --winReadCoverageRelativeMin=*)
            [ -n "$VIASH_PAR_WINREADCOVERAGERELATIVEMIN" ] && ViashError Bad arguments for option \'--winReadCoverageRelativeMin=*\': \'$VIASH_PAR_WINREADCOVERAGERELATIVEMIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_WINREADCOVERAGERELATIVEMIN=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --winReadCoverageBasesMin)
            [ -n "$VIASH_PAR_WINREADCOVERAGEBASESMIN" ] && ViashError Bad arguments for option \'--winReadCoverageBasesMin\': \'$VIASH_PAR_WINREADCOVERAGEBASESMIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_WINREADCOVERAGEBASESMIN="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --winReadCoverageBasesMin. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --winReadCoverageBasesMin=*)
            [ -n "$VIASH_PAR_WINREADCOVERAGEBASESMIN" ] && ViashError Bad arguments for option \'--winReadCoverageBasesMin=*\': \'$VIASH_PAR_WINREADCOVERAGEBASESMIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_WINREADCOVERAGEBASESMIN=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --chimOutType)
            if [ -z "$VIASH_PAR_CHIMOUTTYPE" ]; then
              VIASH_PAR_CHIMOUTTYPE="$2"
            else
              VIASH_PAR_CHIMOUTTYPE="$VIASH_PAR_CHIMOUTTYPE;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --chimOutType. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --chimOutType=*)
            if [ -z "$VIASH_PAR_CHIMOUTTYPE" ]; then
              VIASH_PAR_CHIMOUTTYPE=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_CHIMOUTTYPE="$VIASH_PAR_CHIMOUTTYPE;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --chimSegmentMin)
            [ -n "$VIASH_PAR_CHIMSEGMENTMIN" ] && ViashError Bad arguments for option \'--chimSegmentMin\': \'$VIASH_PAR_CHIMSEGMENTMIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CHIMSEGMENTMIN="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --chimSegmentMin. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --chimSegmentMin=*)
            [ -n "$VIASH_PAR_CHIMSEGMENTMIN" ] && ViashError Bad arguments for option \'--chimSegmentMin=*\': \'$VIASH_PAR_CHIMSEGMENTMIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CHIMSEGMENTMIN=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --chimScoreMin)
            [ -n "$VIASH_PAR_CHIMSCOREMIN" ] && ViashError Bad arguments for option \'--chimScoreMin\': \'$VIASH_PAR_CHIMSCOREMIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CHIMSCOREMIN="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --chimScoreMin. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --chimScoreMin=*)
            [ -n "$VIASH_PAR_CHIMSCOREMIN" ] && ViashError Bad arguments for option \'--chimScoreMin=*\': \'$VIASH_PAR_CHIMSCOREMIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CHIMSCOREMIN=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --chimScoreDropMax)
            [ -n "$VIASH_PAR_CHIMSCOREDROPMAX" ] && ViashError Bad arguments for option \'--chimScoreDropMax\': \'$VIASH_PAR_CHIMSCOREDROPMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CHIMSCOREDROPMAX="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --chimScoreDropMax. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --chimScoreDropMax=*)
            [ -n "$VIASH_PAR_CHIMSCOREDROPMAX" ] && ViashError Bad arguments for option \'--chimScoreDropMax=*\': \'$VIASH_PAR_CHIMSCOREDROPMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CHIMSCOREDROPMAX=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --chimScoreSeparation)
            [ -n "$VIASH_PAR_CHIMSCORESEPARATION" ] && ViashError Bad arguments for option \'--chimScoreSeparation\': \'$VIASH_PAR_CHIMSCORESEPARATION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CHIMSCORESEPARATION="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --chimScoreSeparation. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --chimScoreSeparation=*)
            [ -n "$VIASH_PAR_CHIMSCORESEPARATION" ] && ViashError Bad arguments for option \'--chimScoreSeparation=*\': \'$VIASH_PAR_CHIMSCORESEPARATION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CHIMSCORESEPARATION=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --chimScoreJunctionNonGTAG)
            [ -n "$VIASH_PAR_CHIMSCOREJUNCTIONNONGTAG" ] && ViashError Bad arguments for option \'--chimScoreJunctionNonGTAG\': \'$VIASH_PAR_CHIMSCOREJUNCTIONNONGTAG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CHIMSCOREJUNCTIONNONGTAG="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --chimScoreJunctionNonGTAG. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --chimScoreJunctionNonGTAG=*)
            [ -n "$VIASH_PAR_CHIMSCOREJUNCTIONNONGTAG" ] && ViashError Bad arguments for option \'--chimScoreJunctionNonGTAG=*\': \'$VIASH_PAR_CHIMSCOREJUNCTIONNONGTAG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CHIMSCOREJUNCTIONNONGTAG=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --chimJunctionOverhangMin)
            [ -n "$VIASH_PAR_CHIMJUNCTIONOVERHANGMIN" ] && ViashError Bad arguments for option \'--chimJunctionOverhangMin\': \'$VIASH_PAR_CHIMJUNCTIONOVERHANGMIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CHIMJUNCTIONOVERHANGMIN="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --chimJunctionOverhangMin. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --chimJunctionOverhangMin=*)
            [ -n "$VIASH_PAR_CHIMJUNCTIONOVERHANGMIN" ] && ViashError Bad arguments for option \'--chimJunctionOverhangMin=*\': \'$VIASH_PAR_CHIMJUNCTIONOVERHANGMIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CHIMJUNCTIONOVERHANGMIN=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --chimSegmentReadGapMax)
            [ -n "$VIASH_PAR_CHIMSEGMENTREADGAPMAX" ] && ViashError Bad arguments for option \'--chimSegmentReadGapMax\': \'$VIASH_PAR_CHIMSEGMENTREADGAPMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CHIMSEGMENTREADGAPMAX="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --chimSegmentReadGapMax. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --chimSegmentReadGapMax=*)
            [ -n "$VIASH_PAR_CHIMSEGMENTREADGAPMAX" ] && ViashError Bad arguments for option \'--chimSegmentReadGapMax=*\': \'$VIASH_PAR_CHIMSEGMENTREADGAPMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CHIMSEGMENTREADGAPMAX=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --chimFilter)
            if [ -z "$VIASH_PAR_CHIMFILTER" ]; then
              VIASH_PAR_CHIMFILTER="$2"
            else
              VIASH_PAR_CHIMFILTER="$VIASH_PAR_CHIMFILTER;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --chimFilter. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --chimFilter=*)
            if [ -z "$VIASH_PAR_CHIMFILTER" ]; then
              VIASH_PAR_CHIMFILTER=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_CHIMFILTER="$VIASH_PAR_CHIMFILTER;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --chimMainSegmentMultNmax)
            [ -n "$VIASH_PAR_CHIMMAINSEGMENTMULTNMAX" ] && ViashError Bad arguments for option \'--chimMainSegmentMultNmax\': \'$VIASH_PAR_CHIMMAINSEGMENTMULTNMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CHIMMAINSEGMENTMULTNMAX="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --chimMainSegmentMultNmax. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --chimMainSegmentMultNmax=*)
            [ -n "$VIASH_PAR_CHIMMAINSEGMENTMULTNMAX" ] && ViashError Bad arguments for option \'--chimMainSegmentMultNmax=*\': \'$VIASH_PAR_CHIMMAINSEGMENTMULTNMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CHIMMAINSEGMENTMULTNMAX=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --chimMultimapNmax)
            [ -n "$VIASH_PAR_CHIMMULTIMAPNMAX" ] && ViashError Bad arguments for option \'--chimMultimapNmax\': \'$VIASH_PAR_CHIMMULTIMAPNMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CHIMMULTIMAPNMAX="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --chimMultimapNmax. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --chimMultimapNmax=*)
            [ -n "$VIASH_PAR_CHIMMULTIMAPNMAX" ] && ViashError Bad arguments for option \'--chimMultimapNmax=*\': \'$VIASH_PAR_CHIMMULTIMAPNMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CHIMMULTIMAPNMAX=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --chimMultimapScoreRange)
            [ -n "$VIASH_PAR_CHIMMULTIMAPSCORERANGE" ] && ViashError Bad arguments for option \'--chimMultimapScoreRange\': \'$VIASH_PAR_CHIMMULTIMAPSCORERANGE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CHIMMULTIMAPSCORERANGE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --chimMultimapScoreRange. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --chimMultimapScoreRange=*)
            [ -n "$VIASH_PAR_CHIMMULTIMAPSCORERANGE" ] && ViashError Bad arguments for option \'--chimMultimapScoreRange=*\': \'$VIASH_PAR_CHIMMULTIMAPSCORERANGE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CHIMMULTIMAPSCORERANGE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --chimNonchimScoreDropMin)
            [ -n "$VIASH_PAR_CHIMNONCHIMSCOREDROPMIN" ] && ViashError Bad arguments for option \'--chimNonchimScoreDropMin\': \'$VIASH_PAR_CHIMNONCHIMSCOREDROPMIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CHIMNONCHIMSCOREDROPMIN="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --chimNonchimScoreDropMin. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --chimNonchimScoreDropMin=*)
            [ -n "$VIASH_PAR_CHIMNONCHIMSCOREDROPMIN" ] && ViashError Bad arguments for option \'--chimNonchimScoreDropMin=*\': \'$VIASH_PAR_CHIMNONCHIMSCOREDROPMIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CHIMNONCHIMSCOREDROPMIN=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --chimOutJunctionFormat)
            [ -n "$VIASH_PAR_CHIMOUTJUNCTIONFORMAT" ] && ViashError Bad arguments for option \'--chimOutJunctionFormat\': \'$VIASH_PAR_CHIMOUTJUNCTIONFORMAT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CHIMOUTJUNCTIONFORMAT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --chimOutJunctionFormat. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --chimOutJunctionFormat=*)
            [ -n "$VIASH_PAR_CHIMOUTJUNCTIONFORMAT" ] && ViashError Bad arguments for option \'--chimOutJunctionFormat=*\': \'$VIASH_PAR_CHIMOUTJUNCTIONFORMAT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_CHIMOUTJUNCTIONFORMAT=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --quantMode)
            if [ -z "$VIASH_PAR_QUANTMODE" ]; then
              VIASH_PAR_QUANTMODE="$2"
            else
              VIASH_PAR_QUANTMODE="$VIASH_PAR_QUANTMODE;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --quantMode. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --quantMode=*)
            if [ -z "$VIASH_PAR_QUANTMODE" ]; then
              VIASH_PAR_QUANTMODE=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_QUANTMODE="$VIASH_PAR_QUANTMODE;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --quantTranscriptomeBAMcompression)
            [ -n "$VIASH_PAR_QUANTTRANSCRIPTOMEBAMCOMPRESSION" ] && ViashError Bad arguments for option \'--quantTranscriptomeBAMcompression\': \'$VIASH_PAR_QUANTTRANSCRIPTOMEBAMCOMPRESSION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_QUANTTRANSCRIPTOMEBAMCOMPRESSION="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --quantTranscriptomeBAMcompression. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --quantTranscriptomeBAMcompression=*)
            [ -n "$VIASH_PAR_QUANTTRANSCRIPTOMEBAMCOMPRESSION" ] && ViashError Bad arguments for option \'--quantTranscriptomeBAMcompression=*\': \'$VIASH_PAR_QUANTTRANSCRIPTOMEBAMCOMPRESSION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_QUANTTRANSCRIPTOMEBAMCOMPRESSION=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --quantTranscriptomeBan)
            [ -n "$VIASH_PAR_QUANTTRANSCRIPTOMEBAN" ] && ViashError Bad arguments for option \'--quantTranscriptomeBan\': \'$VIASH_PAR_QUANTTRANSCRIPTOMEBAN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_QUANTTRANSCRIPTOMEBAN="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --quantTranscriptomeBan. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --quantTranscriptomeBan=*)
            [ -n "$VIASH_PAR_QUANTTRANSCRIPTOMEBAN" ] && ViashError Bad arguments for option \'--quantTranscriptomeBan=*\': \'$VIASH_PAR_QUANTTRANSCRIPTOMEBAN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_QUANTTRANSCRIPTOMEBAN=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --twopassMode)
            [ -n "$VIASH_PAR_TWOPASSMODE" ] && ViashError Bad arguments for option \'--twopassMode\': \'$VIASH_PAR_TWOPASSMODE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_TWOPASSMODE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --twopassMode. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --twopassMode=*)
            [ -n "$VIASH_PAR_TWOPASSMODE" ] && ViashError Bad arguments for option \'--twopassMode=*\': \'$VIASH_PAR_TWOPASSMODE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_TWOPASSMODE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --twopass1readsN)
            [ -n "$VIASH_PAR_TWOPASS1READSN" ] && ViashError Bad arguments for option \'--twopass1readsN\': \'$VIASH_PAR_TWOPASS1READSN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_TWOPASS1READSN="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --twopass1readsN. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --twopass1readsN=*)
            [ -n "$VIASH_PAR_TWOPASS1READSN" ] && ViashError Bad arguments for option \'--twopass1readsN=*\': \'$VIASH_PAR_TWOPASS1READSN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_TWOPASS1READSN=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --waspOutputMode)
            [ -n "$VIASH_PAR_WASPOUTPUTMODE" ] && ViashError Bad arguments for option \'--waspOutputMode\': \'$VIASH_PAR_WASPOUTPUTMODE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_WASPOUTPUTMODE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --waspOutputMode. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --waspOutputMode=*)
            [ -n "$VIASH_PAR_WASPOUTPUTMODE" ] && ViashError Bad arguments for option \'--waspOutputMode=*\': \'$VIASH_PAR_WASPOUTPUTMODE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_WASPOUTPUTMODE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --soloType)
            if [ -z "$VIASH_PAR_SOLOTYPE" ]; then
              VIASH_PAR_SOLOTYPE="$2"
            else
              VIASH_PAR_SOLOTYPE="$VIASH_PAR_SOLOTYPE;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --soloType. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --soloType=*)
            if [ -z "$VIASH_PAR_SOLOTYPE" ]; then
              VIASH_PAR_SOLOTYPE=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_SOLOTYPE="$VIASH_PAR_SOLOTYPE;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --soloCBwhitelist)
            if [ -z "$VIASH_PAR_SOLOCBWHITELIST" ]; then
              VIASH_PAR_SOLOCBWHITELIST="$2"
            else
              VIASH_PAR_SOLOCBWHITELIST="$VIASH_PAR_SOLOCBWHITELIST;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --soloCBwhitelist. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --soloCBwhitelist=*)
            if [ -z "$VIASH_PAR_SOLOCBWHITELIST" ]; then
              VIASH_PAR_SOLOCBWHITELIST=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_SOLOCBWHITELIST="$VIASH_PAR_SOLOCBWHITELIST;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --soloCBstart)
            [ -n "$VIASH_PAR_SOLOCBSTART" ] && ViashError Bad arguments for option \'--soloCBstart\': \'$VIASH_PAR_SOLOCBSTART\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SOLOCBSTART="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --soloCBstart. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --soloCBstart=*)
            [ -n "$VIASH_PAR_SOLOCBSTART" ] && ViashError Bad arguments for option \'--soloCBstart=*\': \'$VIASH_PAR_SOLOCBSTART\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SOLOCBSTART=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --soloCBlen)
            [ -n "$VIASH_PAR_SOLOCBLEN" ] && ViashError Bad arguments for option \'--soloCBlen\': \'$VIASH_PAR_SOLOCBLEN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SOLOCBLEN="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --soloCBlen. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --soloCBlen=*)
            [ -n "$VIASH_PAR_SOLOCBLEN" ] && ViashError Bad arguments for option \'--soloCBlen=*\': \'$VIASH_PAR_SOLOCBLEN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SOLOCBLEN=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --soloUMIstart)
            [ -n "$VIASH_PAR_SOLOUMISTART" ] && ViashError Bad arguments for option \'--soloUMIstart\': \'$VIASH_PAR_SOLOUMISTART\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SOLOUMISTART="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --soloUMIstart. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --soloUMIstart=*)
            [ -n "$VIASH_PAR_SOLOUMISTART" ] && ViashError Bad arguments for option \'--soloUMIstart=*\': \'$VIASH_PAR_SOLOUMISTART\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SOLOUMISTART=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --soloUMIlen)
            [ -n "$VIASH_PAR_SOLOUMILEN" ] && ViashError Bad arguments for option \'--soloUMIlen\': \'$VIASH_PAR_SOLOUMILEN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SOLOUMILEN="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --soloUMIlen. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --soloUMIlen=*)
            [ -n "$VIASH_PAR_SOLOUMILEN" ] && ViashError Bad arguments for option \'--soloUMIlen=*\': \'$VIASH_PAR_SOLOUMILEN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SOLOUMILEN=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --soloBarcodeReadLength)
            [ -n "$VIASH_PAR_SOLOBARCODEREADLENGTH" ] && ViashError Bad arguments for option \'--soloBarcodeReadLength\': \'$VIASH_PAR_SOLOBARCODEREADLENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SOLOBARCODEREADLENGTH="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --soloBarcodeReadLength. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --soloBarcodeReadLength=*)
            [ -n "$VIASH_PAR_SOLOBARCODEREADLENGTH" ] && ViashError Bad arguments for option \'--soloBarcodeReadLength=*\': \'$VIASH_PAR_SOLOBARCODEREADLENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SOLOBARCODEREADLENGTH=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --soloBarcodeMate)
            [ -n "$VIASH_PAR_SOLOBARCODEMATE" ] && ViashError Bad arguments for option \'--soloBarcodeMate\': \'$VIASH_PAR_SOLOBARCODEMATE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SOLOBARCODEMATE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --soloBarcodeMate. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --soloBarcodeMate=*)
            [ -n "$VIASH_PAR_SOLOBARCODEMATE" ] && ViashError Bad arguments for option \'--soloBarcodeMate=*\': \'$VIASH_PAR_SOLOBARCODEMATE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SOLOBARCODEMATE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --soloCBposition)
            if [ -z "$VIASH_PAR_SOLOCBPOSITION" ]; then
              VIASH_PAR_SOLOCBPOSITION="$2"
            else
              VIASH_PAR_SOLOCBPOSITION="$VIASH_PAR_SOLOCBPOSITION;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --soloCBposition. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --soloCBposition=*)
            if [ -z "$VIASH_PAR_SOLOCBPOSITION" ]; then
              VIASH_PAR_SOLOCBPOSITION=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_SOLOCBPOSITION="$VIASH_PAR_SOLOCBPOSITION;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --soloUMIposition)
            [ -n "$VIASH_PAR_SOLOUMIPOSITION" ] && ViashError Bad arguments for option \'--soloUMIposition\': \'$VIASH_PAR_SOLOUMIPOSITION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SOLOUMIPOSITION="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --soloUMIposition. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --soloUMIposition=*)
            [ -n "$VIASH_PAR_SOLOUMIPOSITION" ] && ViashError Bad arguments for option \'--soloUMIposition=*\': \'$VIASH_PAR_SOLOUMIPOSITION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SOLOUMIPOSITION=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --soloAdapterSequence)
            [ -n "$VIASH_PAR_SOLOADAPTERSEQUENCE" ] && ViashError Bad arguments for option \'--soloAdapterSequence\': \'$VIASH_PAR_SOLOADAPTERSEQUENCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SOLOADAPTERSEQUENCE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --soloAdapterSequence. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --soloAdapterSequence=*)
            [ -n "$VIASH_PAR_SOLOADAPTERSEQUENCE" ] && ViashError Bad arguments for option \'--soloAdapterSequence=*\': \'$VIASH_PAR_SOLOADAPTERSEQUENCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SOLOADAPTERSEQUENCE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --soloAdapterMismatchesNmax)
            [ -n "$VIASH_PAR_SOLOADAPTERMISMATCHESNMAX" ] && ViashError Bad arguments for option \'--soloAdapterMismatchesNmax\': \'$VIASH_PAR_SOLOADAPTERMISMATCHESNMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SOLOADAPTERMISMATCHESNMAX="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --soloAdapterMismatchesNmax. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --soloAdapterMismatchesNmax=*)
            [ -n "$VIASH_PAR_SOLOADAPTERMISMATCHESNMAX" ] && ViashError Bad arguments for option \'--soloAdapterMismatchesNmax=*\': \'$VIASH_PAR_SOLOADAPTERMISMATCHESNMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SOLOADAPTERMISMATCHESNMAX=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --soloCBmatchWLtype)
            [ -n "$VIASH_PAR_SOLOCBMATCHWLTYPE" ] && ViashError Bad arguments for option \'--soloCBmatchWLtype\': \'$VIASH_PAR_SOLOCBMATCHWLTYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SOLOCBMATCHWLTYPE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --soloCBmatchWLtype. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --soloCBmatchWLtype=*)
            [ -n "$VIASH_PAR_SOLOCBMATCHWLTYPE" ] && ViashError Bad arguments for option \'--soloCBmatchWLtype=*\': \'$VIASH_PAR_SOLOCBMATCHWLTYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SOLOCBMATCHWLTYPE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --soloInputSAMattrBarcodeSeq)
            if [ -z "$VIASH_PAR_SOLOINPUTSAMATTRBARCODESEQ" ]; then
              VIASH_PAR_SOLOINPUTSAMATTRBARCODESEQ="$2"
            else
              VIASH_PAR_SOLOINPUTSAMATTRBARCODESEQ="$VIASH_PAR_SOLOINPUTSAMATTRBARCODESEQ;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --soloInputSAMattrBarcodeSeq. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --soloInputSAMattrBarcodeSeq=*)
            if [ -z "$VIASH_PAR_SOLOINPUTSAMATTRBARCODESEQ" ]; then
              VIASH_PAR_SOLOINPUTSAMATTRBARCODESEQ=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_SOLOINPUTSAMATTRBARCODESEQ="$VIASH_PAR_SOLOINPUTSAMATTRBARCODESEQ;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --soloInputSAMattrBarcodeQual)
            if [ -z "$VIASH_PAR_SOLOINPUTSAMATTRBARCODEQUAL" ]; then
              VIASH_PAR_SOLOINPUTSAMATTRBARCODEQUAL="$2"
            else
              VIASH_PAR_SOLOINPUTSAMATTRBARCODEQUAL="$VIASH_PAR_SOLOINPUTSAMATTRBARCODEQUAL;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --soloInputSAMattrBarcodeQual. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --soloInputSAMattrBarcodeQual=*)
            if [ -z "$VIASH_PAR_SOLOINPUTSAMATTRBARCODEQUAL" ]; then
              VIASH_PAR_SOLOINPUTSAMATTRBARCODEQUAL=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_SOLOINPUTSAMATTRBARCODEQUAL="$VIASH_PAR_SOLOINPUTSAMATTRBARCODEQUAL;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --soloStrand)
            [ -n "$VIASH_PAR_SOLOSTRAND" ] && ViashError Bad arguments for option \'--soloStrand\': \'$VIASH_PAR_SOLOSTRAND\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SOLOSTRAND="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --soloStrand. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --soloStrand=*)
            [ -n "$VIASH_PAR_SOLOSTRAND" ] && ViashError Bad arguments for option \'--soloStrand=*\': \'$VIASH_PAR_SOLOSTRAND\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SOLOSTRAND=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --soloFeatures)
            if [ -z "$VIASH_PAR_SOLOFEATURES" ]; then
              VIASH_PAR_SOLOFEATURES="$2"
            else
              VIASH_PAR_SOLOFEATURES="$VIASH_PAR_SOLOFEATURES;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --soloFeatures. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --soloFeatures=*)
            if [ -z "$VIASH_PAR_SOLOFEATURES" ]; then
              VIASH_PAR_SOLOFEATURES=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_SOLOFEATURES="$VIASH_PAR_SOLOFEATURES;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --soloMultiMappers)
            if [ -z "$VIASH_PAR_SOLOMULTIMAPPERS" ]; then
              VIASH_PAR_SOLOMULTIMAPPERS="$2"
            else
              VIASH_PAR_SOLOMULTIMAPPERS="$VIASH_PAR_SOLOMULTIMAPPERS;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --soloMultiMappers. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --soloMultiMappers=*)
            if [ -z "$VIASH_PAR_SOLOMULTIMAPPERS" ]; then
              VIASH_PAR_SOLOMULTIMAPPERS=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_SOLOMULTIMAPPERS="$VIASH_PAR_SOLOMULTIMAPPERS;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --soloUMIdedup)
            if [ -z "$VIASH_PAR_SOLOUMIDEDUP" ]; then
              VIASH_PAR_SOLOUMIDEDUP="$2"
            else
              VIASH_PAR_SOLOUMIDEDUP="$VIASH_PAR_SOLOUMIDEDUP;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --soloUMIdedup. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --soloUMIdedup=*)
            if [ -z "$VIASH_PAR_SOLOUMIDEDUP" ]; then
              VIASH_PAR_SOLOUMIDEDUP=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_SOLOUMIDEDUP="$VIASH_PAR_SOLOUMIDEDUP;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --soloUMIfiltering)
            if [ -z "$VIASH_PAR_SOLOUMIFILTERING" ]; then
              VIASH_PAR_SOLOUMIFILTERING="$2"
            else
              VIASH_PAR_SOLOUMIFILTERING="$VIASH_PAR_SOLOUMIFILTERING;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --soloUMIfiltering. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --soloUMIfiltering=*)
            if [ -z "$VIASH_PAR_SOLOUMIFILTERING" ]; then
              VIASH_PAR_SOLOUMIFILTERING=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_SOLOUMIFILTERING="$VIASH_PAR_SOLOUMIFILTERING;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --soloOutFileNames)
            if [ -z "$VIASH_PAR_SOLOOUTFILENAMES" ]; then
              VIASH_PAR_SOLOOUTFILENAMES="$2"
            else
              VIASH_PAR_SOLOOUTFILENAMES="$VIASH_PAR_SOLOOUTFILENAMES;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --soloOutFileNames. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --soloOutFileNames=*)
            if [ -z "$VIASH_PAR_SOLOOUTFILENAMES" ]; then
              VIASH_PAR_SOLOOUTFILENAMES=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_SOLOOUTFILENAMES="$VIASH_PAR_SOLOOUTFILENAMES;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --soloCellFilter)
            if [ -z "$VIASH_PAR_SOLOCELLFILTER" ]; then
              VIASH_PAR_SOLOCELLFILTER="$2"
            else
              VIASH_PAR_SOLOCELLFILTER="$VIASH_PAR_SOLOCELLFILTER;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --soloCellFilter. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --soloCellFilter=*)
            if [ -z "$VIASH_PAR_SOLOCELLFILTER" ]; then
              VIASH_PAR_SOLOCELLFILTER=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_SOLOCELLFILTER="$VIASH_PAR_SOLOCELLFILTER;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --soloOutFormatFeaturesGeneField3)
            if [ -z "$VIASH_PAR_SOLOOUTFORMATFEATURESGENEFIELD3" ]; then
              VIASH_PAR_SOLOOUTFORMATFEATURESGENEFIELD3="$2"
            else
              VIASH_PAR_SOLOOUTFORMATFEATURESGENEFIELD3="$VIASH_PAR_SOLOOUTFORMATFEATURESGENEFIELD3;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --soloOutFormatFeaturesGeneField3. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --soloOutFormatFeaturesGeneField3=*)
            if [ -z "$VIASH_PAR_SOLOOUTFORMATFEATURESGENEFIELD3" ]; then
              VIASH_PAR_SOLOOUTFORMATFEATURESGENEFIELD3=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_SOLOOUTFORMATFEATURESGENEFIELD3="$VIASH_PAR_SOLOOUTFORMATFEATURESGENEFIELD3;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --soloCellReadStats)
            [ -n "$VIASH_PAR_SOLOCELLREADSTATS" ] && ViashError Bad arguments for option \'--soloCellReadStats\': \'$VIASH_PAR_SOLOCELLREADSTATS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SOLOCELLREADSTATS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --soloCellReadStats. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --soloCellReadStats=*)
            [ -n "$VIASH_PAR_SOLOCELLREADSTATS" ] && ViashError Bad arguments for option \'--soloCellReadStats=*\': \'$VIASH_PAR_SOLOCELLREADSTATS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SOLOCELLREADSTATS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        ---engine)
            VIASH_ENGINE_ID="$2"
            shift 2
            ;;
        ---engine=*)
            VIASH_ENGINE_ID="$(ViashRemoveFlags "$1")"
            shift 1
            ;;
        ---setup)
            VIASH_MODE='setup'
            VIASH_SETUP_STRATEGY="$2"
            shift 2
            ;;
        ---setup=*)
            VIASH_MODE='setup'
            VIASH_SETUP_STRATEGY="$(ViashRemoveFlags "$1")"
            shift 1
            ;;
        ---dockerfile)
            VIASH_MODE='dockerfile'
            shift 1
            ;;
        ---docker_run_args)
            VIASH_DOCKER_RUN_ARGS+=("$2")
            shift 2
            ;;
        ---docker_run_args=*)
            VIASH_DOCKER_RUN_ARGS+=("$(ViashRemoveFlags "$1")")
            shift 1
            ;;
        ---docker_image_id)
            VIASH_MODE='docker_image_id'
            shift 1
            ;;
        ---debug)
            VIASH_MODE='debug'
            shift 1
            ;;
        ---cpus)
            [ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_CPUS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to ---cpus. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        ---cpus=*)
            [ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus=*\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_CPUS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        ---memory)
            [ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_MEMORY="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to ---memory. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        ---memory=*)
            [ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory=*\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_MEMORY=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        *)  # positional arg or unknown option
            # since the positional args will be eval'd, can we always quote, instead of using ViashQuote
            VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'"
            [[ $1 == -* ]] && ViashWarning $1 looks like a parameter but is not a defined parameter and will instead be treated as a positional argument. Use "--help" to get more information on the parameters.
            shift # past argument
            ;;
    esac
done

# parse positional parameters
eval set -- $VIASH_POSITIONAL_ARGS


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

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

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/star_align_v273a:v4.0.2'
  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" 'bash'
    exit 0
  fi

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

# setting computational defaults

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


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

# check whether required files exist
if [ ! -z "$VIASH_PAR_INPUT" ]; then
  IFS=';'
  set -f
  for file in $VIASH_PAR_INPUT; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_REFERENCE" ] && [ ! -e "$VIASH_PAR_REFERENCE" ]; then
  ViashError "Input file '$VIASH_PAR_REFERENCE' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_GENOMEFASTAFILES" ]; then
  IFS=';'
  set -f
  for file in $VIASH_PAR_GENOMEFASTAFILES; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_SJDBGTFFILE" ] && [ ! -e "$VIASH_PAR_SJDBGTFFILE" ]; then
  ViashError "Input file '$VIASH_PAR_SJDBGTFFILE' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_READFILESMANIFEST" ] && [ ! -e "$VIASH_PAR_READFILESMANIFEST" ]; then
  ViashError "Input file '$VIASH_PAR_READFILESMANIFEST' does not exist."
  exit 1
fi

# check whether parameters values are of the right type
if [[ -n "$VIASH_PAR_RUNRNGSEED" ]]; then
  if ! [[ "$VIASH_PAR_RUNRNGSEED" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--runRNGseed' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [ -n "$VIASH_PAR_GENOMEFILESIZES" ]; then
  IFS=';'
  set -f
  for val in $VIASH_PAR_GENOMEFILESIZES; do
    if ! [[ "${val}" =~ ^[-+]?[0-9]+$ ]]; then
      ViashError '--genomeFileSizes' has to be an integer. Use "--help" to get more information on the parameters.
      exit 1
    fi
  done
  set +f
  unset IFS
fi

if [[ -n "$VIASH_PAR_SJDBOVERHANG" ]]; then
  if ! [[ "$VIASH_PAR_SJDBOVERHANG" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--sjdbOverhang' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SJDBSCORE" ]]; then
  if ! [[ "$VIASH_PAR_SJDBSCORE" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--sjdbScore' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_READMAPNUMBER" ]]; then
  if ! [[ "$VIASH_PAR_READMAPNUMBER" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--readMapNumber' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_READQUALITYSCOREBASE" ]]; then
  if ! [[ "$VIASH_PAR_READQUALITYSCOREBASE" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--readQualityScoreBase' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [ -n "$VIASH_PAR_CLIP3PNBASES" ]; then
  IFS=';'
  set -f
  for val in $VIASH_PAR_CLIP3PNBASES; do
    if ! [[ "${val}" =~ ^[-+]?[0-9]+$ ]]; then
      ViashError '--clip3pNbases' has to be an integer. Use "--help" to get more information on the parameters.
      exit 1
    fi
  done
  set +f
  unset IFS
fi

if [ -n "$VIASH_PAR_CLIP3PADAPTERMMP" ]; then
  IFS=';'
  set -f
  for val in $VIASH_PAR_CLIP3PADAPTERMMP; do
    if ! [[ "${val}" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
      ViashError '--clip3pAdapterMMp' has to be a double. Use "--help" to get more information on the parameters.
      exit 1
    fi
  done
  set +f
  unset IFS
fi

if [ -n "$VIASH_PAR_CLIP3PAFTERADAPTERNBASES" ]; then
  IFS=';'
  set -f
  for val in $VIASH_PAR_CLIP3PAFTERADAPTERNBASES; do
    if ! [[ "${val}" =~ ^[-+]?[0-9]+$ ]]; then
      ViashError '--clip3pAfterAdapterNbases' has to be an integer. Use "--help" to get more information on the parameters.
      exit 1
    fi
  done
  set +f
  unset IFS
fi

if [ -n "$VIASH_PAR_CLIP5PNBASES" ]; then
  IFS=';'
  set -f
  for val in $VIASH_PAR_CLIP5PNBASES; do
    if ! [[ "${val}" =~ ^[-+]?[0-9]+$ ]]; then
      ViashError '--clip5pNbases' has to be an integer. Use "--help" to get more information on the parameters.
      exit 1
    fi
  done
  set +f
  unset IFS
fi

if [[ -n "$VIASH_PAR_LIMITGENOMEGENERATERAM" ]]; then
  if ! [[ "$VIASH_PAR_LIMITGENOMEGENERATERAM" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--limitGenomeGenerateRAM' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [ -n "$VIASH_PAR_LIMITIOBUFFERSIZE" ]; then
  IFS=';'
  set -f
  for val in $VIASH_PAR_LIMITIOBUFFERSIZE; do
    if ! [[ "${val}" =~ ^[-+]?[0-9]+$ ]]; then
      ViashError '--limitIObufferSize' has to be a long. Use "--help" to get more information on the parameters.
      exit 1
    fi
  done
  set +f
  unset IFS
fi

if [[ -n "$VIASH_PAR_LIMITOUTSAMONEREADBYTES" ]]; then
  if ! [[ "$VIASH_PAR_LIMITOUTSAMONEREADBYTES" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--limitOutSAMoneReadBytes' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_LIMITOUTSJONEREAD" ]]; then
  if ! [[ "$VIASH_PAR_LIMITOUTSJONEREAD" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--limitOutSJoneRead' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_LIMITOUTSJCOLLAPSED" ]]; then
  if ! [[ "$VIASH_PAR_LIMITOUTSJCOLLAPSED" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--limitOutSJcollapsed' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_LIMITBAMSORTRAM" ]]; then
  if ! [[ "$VIASH_PAR_LIMITBAMSORTRAM" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--limitBAMsortRAM' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_LIMITSJDBINSERTNSJ" ]]; then
  if ! [[ "$VIASH_PAR_LIMITSJDBINSERTNSJ" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--limitSjdbInsertNsj' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_LIMITNREADSSOFT" ]]; then
  if ! [[ "$VIASH_PAR_LIMITNREADSSOFT" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--limitNreadsSoft' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_OUTQSCONVERSIONADD" ]]; then
  if ! [[ "$VIASH_PAR_OUTQSCONVERSIONADD" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--outQSconversionAdd' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_OUTSAMATTRIHSTART" ]]; then
  if ! [[ "$VIASH_PAR_OUTSAMATTRIHSTART" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--outSAMattrIHstart' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_OUTSAMMAPQUNIQUE" ]]; then
  if ! [[ "$VIASH_PAR_OUTSAMMAPQUNIQUE" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--outSAMmapqUnique' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_OUTSAMFLAGOR" ]]; then
  if ! [[ "$VIASH_PAR_OUTSAMFLAGOR" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--outSAMflagOR' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_OUTSAMFLAGAND" ]]; then
  if ! [[ "$VIASH_PAR_OUTSAMFLAGAND" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--outSAMflagAND' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_OUTSAMMULTNMAX" ]]; then
  if ! [[ "$VIASH_PAR_OUTSAMMULTNMAX" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--outSAMmultNmax' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_OUTSAMTLEN" ]]; then
  if ! [[ "$VIASH_PAR_OUTSAMTLEN" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--outSAMtlen' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_OUTBAMCOMPRESSION" ]]; then
  if ! [[ "$VIASH_PAR_OUTBAMCOMPRESSION" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--outBAMcompression' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_OUTBAMSORTINGTHREADN" ]]; then
  if ! [[ "$VIASH_PAR_OUTBAMSORTINGTHREADN" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--outBAMsortingThreadN' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_OUTBAMSORTINGBINSN" ]]; then
  if ! [[ "$VIASH_PAR_OUTBAMSORTINGBINSN" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--outBAMsortingBinsN' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_BAMREMOVEDUPLICATESMATE2BASESN" ]]; then
  if ! [[ "$VIASH_PAR_BAMREMOVEDUPLICATESMATE2BASESN" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--bamRemoveDuplicatesMate2basesN' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_OUTFILTERMULTIMAPSCORERANGE" ]]; then
  if ! [[ "$VIASH_PAR_OUTFILTERMULTIMAPSCORERANGE" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--outFilterMultimapScoreRange' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_OUTFILTERMULTIMAPNMAX" ]]; then
  if ! [[ "$VIASH_PAR_OUTFILTERMULTIMAPNMAX" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--outFilterMultimapNmax' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_OUTFILTERMISMATCHNMAX" ]]; then
  if ! [[ "$VIASH_PAR_OUTFILTERMISMATCHNMAX" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--outFilterMismatchNmax' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_OUTFILTERMISMATCHNOVERLMAX" ]]; then
  if ! [[ "$VIASH_PAR_OUTFILTERMISMATCHNOVERLMAX" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--outFilterMismatchNoverLmax' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_OUTFILTERMISMATCHNOVERREADLMAX" ]]; then
  if ! [[ "$VIASH_PAR_OUTFILTERMISMATCHNOVERREADLMAX" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--outFilterMismatchNoverReadLmax' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_OUTFILTERSCOREMIN" ]]; then
  if ! [[ "$VIASH_PAR_OUTFILTERSCOREMIN" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--outFilterScoreMin' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_OUTFILTERSCOREMINOVERLREAD" ]]; then
  if ! [[ "$VIASH_PAR_OUTFILTERSCOREMINOVERLREAD" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--outFilterScoreMinOverLread' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_OUTFILTERMATCHNMIN" ]]; then
  if ! [[ "$VIASH_PAR_OUTFILTERMATCHNMIN" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--outFilterMatchNmin' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_OUTFILTERMATCHNMINOVERLREAD" ]]; then
  if ! [[ "$VIASH_PAR_OUTFILTERMATCHNMINOVERLREAD" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--outFilterMatchNminOverLread' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [ -n "$VIASH_PAR_OUTSJFILTEROVERHANGMIN" ]; then
  IFS=';'
  set -f
  for val in $VIASH_PAR_OUTSJFILTEROVERHANGMIN; do
    if ! [[ "${val}" =~ ^[-+]?[0-9]+$ ]]; then
      ViashError '--outSJfilterOverhangMin' has to be an integer. Use "--help" to get more information on the parameters.
      exit 1
    fi
  done
  set +f
  unset IFS
fi

if [ -n "$VIASH_PAR_OUTSJFILTERCOUNTUNIQUEMIN" ]; then
  IFS=';'
  set -f
  for val in $VIASH_PAR_OUTSJFILTERCOUNTUNIQUEMIN; do
    if ! [[ "${val}" =~ ^[-+]?[0-9]+$ ]]; then
      ViashError '--outSJfilterCountUniqueMin' has to be an integer. Use "--help" to get more information on the parameters.
      exit 1
    fi
  done
  set +f
  unset IFS
fi

if [ -n "$VIASH_PAR_OUTSJFILTERCOUNTTOTALMIN" ]; then
  IFS=';'
  set -f
  for val in $VIASH_PAR_OUTSJFILTERCOUNTTOTALMIN; do
    if ! [[ "${val}" =~ ^[-+]?[0-9]+$ ]]; then
      ViashError '--outSJfilterCountTotalMin' has to be an integer. Use "--help" to get more information on the parameters.
      exit 1
    fi
  done
  set +f
  unset IFS
fi

if [ -n "$VIASH_PAR_OUTSJFILTERDISTTOOTHERSJMIN" ]; then
  IFS=';'
  set -f
  for val in $VIASH_PAR_OUTSJFILTERDISTTOOTHERSJMIN; do
    if ! [[ "${val}" =~ ^[-+]?[0-9]+$ ]]; then
      ViashError '--outSJfilterDistToOtherSJmin' has to be an integer. Use "--help" to get more information on the parameters.
      exit 1
    fi
  done
  set +f
  unset IFS
fi

if [ -n "$VIASH_PAR_OUTSJFILTERINTRONMAXVSREADN" ]; then
  IFS=';'
  set -f
  for val in $VIASH_PAR_OUTSJFILTERINTRONMAXVSREADN; do
    if ! [[ "${val}" =~ ^[-+]?[0-9]+$ ]]; then
      ViashError '--outSJfilterIntronMaxVsReadN' has to be an integer. Use "--help" to get more information on the parameters.
      exit 1
    fi
  done
  set +f
  unset IFS
fi

if [[ -n "$VIASH_PAR_SCOREGAP" ]]; then
  if ! [[ "$VIASH_PAR_SCOREGAP" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--scoreGap' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SCOREGAPNONCAN" ]]; then
  if ! [[ "$VIASH_PAR_SCOREGAPNONCAN" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--scoreGapNoncan' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SCOREGAPGCAG" ]]; then
  if ! [[ "$VIASH_PAR_SCOREGAPGCAG" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--scoreGapGCAG' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SCOREGAPATAC" ]]; then
  if ! [[ "$VIASH_PAR_SCOREGAPATAC" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--scoreGapATAC' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SCOREGENOMICLENGTHLOG2SCALE" ]]; then
  if ! [[ "$VIASH_PAR_SCOREGENOMICLENGTHLOG2SCALE" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--scoreGenomicLengthLog2scale' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SCOREDELOPEN" ]]; then
  if ! [[ "$VIASH_PAR_SCOREDELOPEN" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--scoreDelOpen' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SCOREDELBASE" ]]; then
  if ! [[ "$VIASH_PAR_SCOREDELBASE" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--scoreDelBase' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SCOREINSOPEN" ]]; then
  if ! [[ "$VIASH_PAR_SCOREINSOPEN" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--scoreInsOpen' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SCOREINSBASE" ]]; then
  if ! [[ "$VIASH_PAR_SCOREINSBASE" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--scoreInsBase' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SCORESTITCHSJSHIFT" ]]; then
  if ! [[ "$VIASH_PAR_SCORESTITCHSJSHIFT" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--scoreStitchSJshift' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SEEDSEARCHSTARTLMAX" ]]; then
  if ! [[ "$VIASH_PAR_SEEDSEARCHSTARTLMAX" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--seedSearchStartLmax' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SEEDSEARCHSTARTLMAXOVERLREAD" ]]; then
  if ! [[ "$VIASH_PAR_SEEDSEARCHSTARTLMAXOVERLREAD" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--seedSearchStartLmaxOverLread' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SEEDSEARCHLMAX" ]]; then
  if ! [[ "$VIASH_PAR_SEEDSEARCHLMAX" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--seedSearchLmax' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SEEDMULTIMAPNMAX" ]]; then
  if ! [[ "$VIASH_PAR_SEEDMULTIMAPNMAX" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--seedMultimapNmax' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SEEDPERREADNMAX" ]]; then
  if ! [[ "$VIASH_PAR_SEEDPERREADNMAX" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--seedPerReadNmax' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SEEDPERWINDOWNMAX" ]]; then
  if ! [[ "$VIASH_PAR_SEEDPERWINDOWNMAX" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--seedPerWindowNmax' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SEEDNONELOCIPERWINDOW" ]]; then
  if ! [[ "$VIASH_PAR_SEEDNONELOCIPERWINDOW" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--seedNoneLociPerWindow' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SEEDSPLITMIN" ]]; then
  if ! [[ "$VIASH_PAR_SEEDSPLITMIN" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--seedSplitMin' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SEEDMAPMIN" ]]; then
  if ! [[ "$VIASH_PAR_SEEDMAPMIN" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--seedMapMin' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_ALIGNINTRONMIN" ]]; then
  if ! [[ "$VIASH_PAR_ALIGNINTRONMIN" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--alignIntronMin' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_ALIGNINTRONMAX" ]]; then
  if ! [[ "$VIASH_PAR_ALIGNINTRONMAX" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--alignIntronMax' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_ALIGNMATESGAPMAX" ]]; then
  if ! [[ "$VIASH_PAR_ALIGNMATESGAPMAX" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--alignMatesGapMax' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_ALIGNSJOVERHANGMIN" ]]; then
  if ! [[ "$VIASH_PAR_ALIGNSJOVERHANGMIN" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--alignSJoverhangMin' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [ -n "$VIASH_PAR_ALIGNSJSTITCHMISMATCHNMAX" ]; then
  IFS=';'
  set -f
  for val in $VIASH_PAR_ALIGNSJSTITCHMISMATCHNMAX; do
    if ! [[ "${val}" =~ ^[-+]?[0-9]+$ ]]; then
      ViashError '--alignSJstitchMismatchNmax' has to be an integer. Use "--help" to get more information on the parameters.
      exit 1
    fi
  done
  set +f
  unset IFS
fi

if [[ -n "$VIASH_PAR_ALIGNSJDBOVERHANGMIN" ]]; then
  if ! [[ "$VIASH_PAR_ALIGNSJDBOVERHANGMIN" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--alignSJDBoverhangMin' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_ALIGNSPLICEDMATEMAPLMIN" ]]; then
  if ! [[ "$VIASH_PAR_ALIGNSPLICEDMATEMAPLMIN" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--alignSplicedMateMapLmin' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_ALIGNSPLICEDMATEMAPLMINOVERLMATE" ]]; then
  if ! [[ "$VIASH_PAR_ALIGNSPLICEDMATEMAPLMINOVERLMATE" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--alignSplicedMateMapLminOverLmate' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_ALIGNWINDOWSPERREADNMAX" ]]; then
  if ! [[ "$VIASH_PAR_ALIGNWINDOWSPERREADNMAX" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--alignWindowsPerReadNmax' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_ALIGNTRANSCRIPTSPERWINDOWNMAX" ]]; then
  if ! [[ "$VIASH_PAR_ALIGNTRANSCRIPTSPERWINDOWNMAX" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--alignTranscriptsPerWindowNmax' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_ALIGNTRANSCRIPTSPERREADNMAX" ]]; then
  if ! [[ "$VIASH_PAR_ALIGNTRANSCRIPTSPERREADNMAX" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--alignTranscriptsPerReadNmax' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_PEOVERLAPNBASESMIN" ]]; then
  if ! [[ "$VIASH_PAR_PEOVERLAPNBASESMIN" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--peOverlapNbasesMin' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_PEOVERLAPMMP" ]]; then
  if ! [[ "$VIASH_PAR_PEOVERLAPMMP" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--peOverlapMMp' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_WINANCHORMULTIMAPNMAX" ]]; then
  if ! [[ "$VIASH_PAR_WINANCHORMULTIMAPNMAX" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--winAnchorMultimapNmax' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_WINBINNBITS" ]]; then
  if ! [[ "$VIASH_PAR_WINBINNBITS" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--winBinNbits' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_WINANCHORDISTNBINS" ]]; then
  if ! [[ "$VIASH_PAR_WINANCHORDISTNBINS" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--winAnchorDistNbins' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_WINFLANKNBINS" ]]; then
  if ! [[ "$VIASH_PAR_WINFLANKNBINS" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--winFlankNbins' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_WINREADCOVERAGERELATIVEMIN" ]]; then
  if ! [[ "$VIASH_PAR_WINREADCOVERAGERELATIVEMIN" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--winReadCoverageRelativeMin' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_WINREADCOVERAGEBASESMIN" ]]; then
  if ! [[ "$VIASH_PAR_WINREADCOVERAGEBASESMIN" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--winReadCoverageBasesMin' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_CHIMSEGMENTMIN" ]]; then
  if ! [[ "$VIASH_PAR_CHIMSEGMENTMIN" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--chimSegmentMin' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_CHIMSCOREMIN" ]]; then
  if ! [[ "$VIASH_PAR_CHIMSCOREMIN" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--chimScoreMin' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_CHIMSCOREDROPMAX" ]]; then
  if ! [[ "$VIASH_PAR_CHIMSCOREDROPMAX" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--chimScoreDropMax' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_CHIMSCORESEPARATION" ]]; then
  if ! [[ "$VIASH_PAR_CHIMSCORESEPARATION" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--chimScoreSeparation' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_CHIMSCOREJUNCTIONNONGTAG" ]]; then
  if ! [[ "$VIASH_PAR_CHIMSCOREJUNCTIONNONGTAG" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--chimScoreJunctionNonGTAG' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_CHIMJUNCTIONOVERHANGMIN" ]]; then
  if ! [[ "$VIASH_PAR_CHIMJUNCTIONOVERHANGMIN" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--chimJunctionOverhangMin' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_CHIMSEGMENTREADGAPMAX" ]]; then
  if ! [[ "$VIASH_PAR_CHIMSEGMENTREADGAPMAX" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--chimSegmentReadGapMax' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_CHIMMAINSEGMENTMULTNMAX" ]]; then
  if ! [[ "$VIASH_PAR_CHIMMAINSEGMENTMULTNMAX" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--chimMainSegmentMultNmax' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_CHIMMULTIMAPNMAX" ]]; then
  if ! [[ "$VIASH_PAR_CHIMMULTIMAPNMAX" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--chimMultimapNmax' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_CHIMMULTIMAPSCORERANGE" ]]; then
  if ! [[ "$VIASH_PAR_CHIMMULTIMAPSCORERANGE" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--chimMultimapScoreRange' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_CHIMNONCHIMSCOREDROPMIN" ]]; then
  if ! [[ "$VIASH_PAR_CHIMNONCHIMSCOREDROPMIN" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--chimNonchimScoreDropMin' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_CHIMOUTJUNCTIONFORMAT" ]]; then
  if ! [[ "$VIASH_PAR_CHIMOUTJUNCTIONFORMAT" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--chimOutJunctionFormat' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_QUANTTRANSCRIPTOMEBAMCOMPRESSION" ]]; then
  if ! [[ "$VIASH_PAR_QUANTTRANSCRIPTOMEBAMCOMPRESSION" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--quantTranscriptomeBAMcompression' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_TWOPASS1READSN" ]]; then
  if ! [[ "$VIASH_PAR_TWOPASS1READSN" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--twopass1readsN' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SOLOCBSTART" ]]; then
  if ! [[ "$VIASH_PAR_SOLOCBSTART" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--soloCBstart' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SOLOCBLEN" ]]; then
  if ! [[ "$VIASH_PAR_SOLOCBLEN" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--soloCBlen' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SOLOUMISTART" ]]; then
  if ! [[ "$VIASH_PAR_SOLOUMISTART" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--soloUMIstart' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SOLOUMILEN" ]]; then
  if ! [[ "$VIASH_PAR_SOLOUMILEN" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--soloUMIlen' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SOLOBARCODEREADLENGTH" ]]; then
  if ! [[ "$VIASH_PAR_SOLOBARCODEREADLENGTH" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--soloBarcodeReadLength' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SOLOBARCODEMATE" ]]; then
  if ! [[ "$VIASH_PAR_SOLOBARCODEMATE" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--soloBarcodeMate' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_SOLOADAPTERMISMATCHESNMAX" ]]; then
  if ! [[ "$VIASH_PAR_SOLOADAPTERMISMATCHESNMAX" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--soloAdapterMismatchesNmax' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_CPUS" ]]; then
  if ! [[ "$VIASH_META_CPUS" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'cpus' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_B" ]]; then
  if ! [[ "$VIASH_META_MEMORY_B" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_b' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_KB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_KB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_kb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_MB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_MB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_mb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_GB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_GB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_gb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_TB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_TB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_tb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_PB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_PB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_pb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_KIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_KIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_kib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_MIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_MIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_mib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_GIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_GIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_gib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_TIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_TIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_tib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_PIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_PIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_pib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi

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

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

if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  # detect volumes from file arguments
  VIASH_CHOWN_VARS=()
if [ ! -z "$VIASH_PAR_INPUT" ]; then
  VIASH_TEST_INPUT=()
  IFS=';'
  for var in $VIASH_PAR_INPUT; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_INPUT+=( "$var" )
  done
  VIASH_PAR_INPUT=$(IFS=';' ; echo "${VIASH_TEST_INPUT[*]}")
fi
if [ ! -z "$VIASH_PAR_REFERENCE" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_REFERENCE")" )
  VIASH_PAR_REFERENCE=$(ViashDockerAutodetectMount "$VIASH_PAR_REFERENCE")
fi
if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT")" )
  VIASH_PAR_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT" )
fi
if [ ! -z "$VIASH_PAR_GENOMEFASTAFILES" ]; then
  VIASH_TEST_GENOMEFASTAFILES=()
  IFS=';'
  for var in $VIASH_PAR_GENOMEFASTAFILES; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_GENOMEFASTAFILES+=( "$var" )
  done
  VIASH_PAR_GENOMEFASTAFILES=$(IFS=';' ; echo "${VIASH_TEST_GENOMEFASTAFILES[*]}")
fi
if [ ! -z "$VIASH_PAR_SJDBGTFFILE" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_SJDBGTFFILE")" )
  VIASH_PAR_SJDBGTFFILE=$(ViashDockerAutodetectMount "$VIASH_PAR_SJDBGTFFILE")
fi
if [ ! -z "$VIASH_PAR_READFILESMANIFEST" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_READFILESMANIFEST")" )
  VIASH_PAR_READFILESMANIFEST=$(ViashDockerAutodetectMount "$VIASH_PAR_READFILESMANIFEST")
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-star_align_v273a-XXXXXX").py
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'
import re
import tempfile
import subprocess
from pathlib import Path
import tarfile
import gzip
import shutil

## VIASH START
# The following code has been auto-generated by Viash.
par = {
  'input': $( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "r'${VIASH_PAR_INPUT//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'reference': $( if [ ! -z ${VIASH_PAR_REFERENCE+x} ]; then echo "r'${VIASH_PAR_REFERENCE//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'output': $( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "r'${VIASH_PAR_OUTPUT//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'runRNGseed': $( if [ ! -z ${VIASH_PAR_RUNRNGSEED+x} ]; then echo "int(r'${VIASH_PAR_RUNRNGSEED//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'genomeLoad': $( if [ ! -z ${VIASH_PAR_GENOMELOAD+x} ]; then echo "r'${VIASH_PAR_GENOMELOAD//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'genomeFastaFiles': $( if [ ! -z ${VIASH_PAR_GENOMEFASTAFILES+x} ]; then echo "r'${VIASH_PAR_GENOMEFASTAFILES//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'genomeFileSizes': $( if [ ! -z ${VIASH_PAR_GENOMEFILESIZES+x} ]; then echo "list(map(int, r'${VIASH_PAR_GENOMEFILESIZES//\'/\'\"\'\"r\'}'.split(';')))"; else echo None; fi ),
  'genomeTransformOutput': $( if [ ! -z ${VIASH_PAR_GENOMETRANSFORMOUTPUT+x} ]; then echo "r'${VIASH_PAR_GENOMETRANSFORMOUTPUT//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'genomeChrSetMitochondrial': $( if [ ! -z ${VIASH_PAR_GENOMECHRSETMITOCHONDRIAL+x} ]; then echo "r'${VIASH_PAR_GENOMECHRSETMITOCHONDRIAL//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'sjdbFileChrStartEnd': $( if [ ! -z ${VIASH_PAR_SJDBFILECHRSTARTEND+x} ]; then echo "r'${VIASH_PAR_SJDBFILECHRSTARTEND//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'sjdbGTFfile': $( if [ ! -z ${VIASH_PAR_SJDBGTFFILE+x} ]; then echo "r'${VIASH_PAR_SJDBGTFFILE//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'sjdbGTFchrPrefix': $( if [ ! -z ${VIASH_PAR_SJDBGTFCHRPREFIX+x} ]; then echo "r'${VIASH_PAR_SJDBGTFCHRPREFIX//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'sjdbGTFfeatureExon': $( if [ ! -z ${VIASH_PAR_SJDBGTFFEATUREEXON+x} ]; then echo "r'${VIASH_PAR_SJDBGTFFEATUREEXON//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'sjdbGTFtagExonParentTranscript': $( if [ ! -z ${VIASH_PAR_SJDBGTFTAGEXONPARENTTRANSCRIPT+x} ]; then echo "r'${VIASH_PAR_SJDBGTFTAGEXONPARENTTRANSCRIPT//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'sjdbGTFtagExonParentGene': $( if [ ! -z ${VIASH_PAR_SJDBGTFTAGEXONPARENTGENE+x} ]; then echo "r'${VIASH_PAR_SJDBGTFTAGEXONPARENTGENE//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'sjdbGTFtagExonParentGeneName': $( if [ ! -z ${VIASH_PAR_SJDBGTFTAGEXONPARENTGENENAME+x} ]; then echo "r'${VIASH_PAR_SJDBGTFTAGEXONPARENTGENENAME//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'sjdbGTFtagExonParentGeneType': $( if [ ! -z ${VIASH_PAR_SJDBGTFTAGEXONPARENTGENETYPE+x} ]; then echo "r'${VIASH_PAR_SJDBGTFTAGEXONPARENTGENETYPE//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'sjdbOverhang': $( if [ ! -z ${VIASH_PAR_SJDBOVERHANG+x} ]; then echo "int(r'${VIASH_PAR_SJDBOVERHANG//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'sjdbScore': $( if [ ! -z ${VIASH_PAR_SJDBSCORE+x} ]; then echo "int(r'${VIASH_PAR_SJDBSCORE//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'sjdbInsertSave': $( if [ ! -z ${VIASH_PAR_SJDBINSERTSAVE+x} ]; then echo "r'${VIASH_PAR_SJDBINSERTSAVE//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'varVCFfile': $( if [ ! -z ${VIASH_PAR_VARVCFFILE+x} ]; then echo "r'${VIASH_PAR_VARVCFFILE//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'readFilesType': $( if [ ! -z ${VIASH_PAR_READFILESTYPE+x} ]; then echo "r'${VIASH_PAR_READFILESTYPE//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'readFilesSAMattrKeep': $( if [ ! -z ${VIASH_PAR_READFILESSAMATTRKEEP+x} ]; then echo "r'${VIASH_PAR_READFILESSAMATTRKEEP//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'readFilesManifest': $( if [ ! -z ${VIASH_PAR_READFILESMANIFEST+x} ]; then echo "r'${VIASH_PAR_READFILESMANIFEST//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'readFilesPrefix': $( if [ ! -z ${VIASH_PAR_READFILESPREFIX+x} ]; then echo "r'${VIASH_PAR_READFILESPREFIX//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'readFilesCommand': $( if [ ! -z ${VIASH_PAR_READFILESCOMMAND+x} ]; then echo "r'${VIASH_PAR_READFILESCOMMAND//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'readMapNumber': $( if [ ! -z ${VIASH_PAR_READMAPNUMBER+x} ]; then echo "int(r'${VIASH_PAR_READMAPNUMBER//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'readMatesLengthsIn': $( if [ ! -z ${VIASH_PAR_READMATESLENGTHSIN+x} ]; then echo "r'${VIASH_PAR_READMATESLENGTHSIN//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'readNameSeparator': $( if [ ! -z ${VIASH_PAR_READNAMESEPARATOR+x} ]; then echo "r'${VIASH_PAR_READNAMESEPARATOR//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'readQualityScoreBase': $( if [ ! -z ${VIASH_PAR_READQUALITYSCOREBASE+x} ]; then echo "int(r'${VIASH_PAR_READQUALITYSCOREBASE//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'clipAdapterType': $( if [ ! -z ${VIASH_PAR_CLIPADAPTERTYPE+x} ]; then echo "r'${VIASH_PAR_CLIPADAPTERTYPE//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'clip3pNbases': $( if [ ! -z ${VIASH_PAR_CLIP3PNBASES+x} ]; then echo "list(map(int, r'${VIASH_PAR_CLIP3PNBASES//\'/\'\"\'\"r\'}'.split(';')))"; else echo None; fi ),
  'clip3pAdapterSeq': $( if [ ! -z ${VIASH_PAR_CLIP3PADAPTERSEQ+x} ]; then echo "r'${VIASH_PAR_CLIP3PADAPTERSEQ//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'clip3pAdapterMMp': $( if [ ! -z ${VIASH_PAR_CLIP3PADAPTERMMP+x} ]; then echo "list(map(float, r'${VIASH_PAR_CLIP3PADAPTERMMP//\'/\'\"\'\"r\'}'.split(';')))"; else echo None; fi ),
  'clip3pAfterAdapterNbases': $( if [ ! -z ${VIASH_PAR_CLIP3PAFTERADAPTERNBASES+x} ]; then echo "list(map(int, r'${VIASH_PAR_CLIP3PAFTERADAPTERNBASES//\'/\'\"\'\"r\'}'.split(';')))"; else echo None; fi ),
  'clip5pNbases': $( if [ ! -z ${VIASH_PAR_CLIP5PNBASES+x} ]; then echo "list(map(int, r'${VIASH_PAR_CLIP5PNBASES//\'/\'\"\'\"r\'}'.split(';')))"; else echo None; fi ),
  'limitGenomeGenerateRAM': $( if [ ! -z ${VIASH_PAR_LIMITGENOMEGENERATERAM+x} ]; then echo "int(r'${VIASH_PAR_LIMITGENOMEGENERATERAM//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'limitIObufferSize': $( if [ ! -z ${VIASH_PAR_LIMITIOBUFFERSIZE+x} ]; then echo "list(map(int, r'${VIASH_PAR_LIMITIOBUFFERSIZE//\'/\'\"\'\"r\'}'.split(';')))"; else echo None; fi ),
  'limitOutSAMoneReadBytes': $( if [ ! -z ${VIASH_PAR_LIMITOUTSAMONEREADBYTES+x} ]; then echo "int(r'${VIASH_PAR_LIMITOUTSAMONEREADBYTES//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'limitOutSJoneRead': $( if [ ! -z ${VIASH_PAR_LIMITOUTSJONEREAD+x} ]; then echo "int(r'${VIASH_PAR_LIMITOUTSJONEREAD//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'limitOutSJcollapsed': $( if [ ! -z ${VIASH_PAR_LIMITOUTSJCOLLAPSED+x} ]; then echo "int(r'${VIASH_PAR_LIMITOUTSJCOLLAPSED//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'limitBAMsortRAM': $( if [ ! -z ${VIASH_PAR_LIMITBAMSORTRAM+x} ]; then echo "int(r'${VIASH_PAR_LIMITBAMSORTRAM//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'limitSjdbInsertNsj': $( if [ ! -z ${VIASH_PAR_LIMITSJDBINSERTNSJ+x} ]; then echo "int(r'${VIASH_PAR_LIMITSJDBINSERTNSJ//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'limitNreadsSoft': $( if [ ! -z ${VIASH_PAR_LIMITNREADSSOFT+x} ]; then echo "int(r'${VIASH_PAR_LIMITNREADSSOFT//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'outTmpKeep': $( if [ ! -z ${VIASH_PAR_OUTTMPKEEP+x} ]; then echo "r'${VIASH_PAR_OUTTMPKEEP//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'outStd': $( if [ ! -z ${VIASH_PAR_OUTSTD+x} ]; then echo "r'${VIASH_PAR_OUTSTD//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'outReadsUnmapped': $( if [ ! -z ${VIASH_PAR_OUTREADSUNMAPPED+x} ]; then echo "r'${VIASH_PAR_OUTREADSUNMAPPED//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'outQSconversionAdd': $( if [ ! -z ${VIASH_PAR_OUTQSCONVERSIONADD+x} ]; then echo "int(r'${VIASH_PAR_OUTQSCONVERSIONADD//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'outMultimapperOrder': $( if [ ! -z ${VIASH_PAR_OUTMULTIMAPPERORDER+x} ]; then echo "r'${VIASH_PAR_OUTMULTIMAPPERORDER//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'outSAMtype': $( if [ ! -z ${VIASH_PAR_OUTSAMTYPE+x} ]; then echo "r'${VIASH_PAR_OUTSAMTYPE//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'outSAMmode': $( if [ ! -z ${VIASH_PAR_OUTSAMMODE+x} ]; then echo "r'${VIASH_PAR_OUTSAMMODE//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'outSAMstrandField': $( if [ ! -z ${VIASH_PAR_OUTSAMSTRANDFIELD+x} ]; then echo "r'${VIASH_PAR_OUTSAMSTRANDFIELD//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'outSAMattributes': $( if [ ! -z ${VIASH_PAR_OUTSAMATTRIBUTES+x} ]; then echo "r'${VIASH_PAR_OUTSAMATTRIBUTES//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'outSAMattrIHstart': $( if [ ! -z ${VIASH_PAR_OUTSAMATTRIHSTART+x} ]; then echo "int(r'${VIASH_PAR_OUTSAMATTRIHSTART//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'outSAMunmapped': $( if [ ! -z ${VIASH_PAR_OUTSAMUNMAPPED+x} ]; then echo "r'${VIASH_PAR_OUTSAMUNMAPPED//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'outSAMorder': $( if [ ! -z ${VIASH_PAR_OUTSAMORDER+x} ]; then echo "r'${VIASH_PAR_OUTSAMORDER//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'outSAMprimaryFlag': $( if [ ! -z ${VIASH_PAR_OUTSAMPRIMARYFLAG+x} ]; then echo "r'${VIASH_PAR_OUTSAMPRIMARYFLAG//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'outSAMreadID': $( if [ ! -z ${VIASH_PAR_OUTSAMREADID+x} ]; then echo "r'${VIASH_PAR_OUTSAMREADID//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'outSAMmapqUnique': $( if [ ! -z ${VIASH_PAR_OUTSAMMAPQUNIQUE+x} ]; then echo "int(r'${VIASH_PAR_OUTSAMMAPQUNIQUE//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'outSAMflagOR': $( if [ ! -z ${VIASH_PAR_OUTSAMFLAGOR+x} ]; then echo "int(r'${VIASH_PAR_OUTSAMFLAGOR//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'outSAMflagAND': $( if [ ! -z ${VIASH_PAR_OUTSAMFLAGAND+x} ]; then echo "int(r'${VIASH_PAR_OUTSAMFLAGAND//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'outSAMattrRGline': $( if [ ! -z ${VIASH_PAR_OUTSAMATTRRGLINE+x} ]; then echo "r'${VIASH_PAR_OUTSAMATTRRGLINE//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'outSAMheaderHD': $( if [ ! -z ${VIASH_PAR_OUTSAMHEADERHD+x} ]; then echo "r'${VIASH_PAR_OUTSAMHEADERHD//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'outSAMheaderPG': $( if [ ! -z ${VIASH_PAR_OUTSAMHEADERPG+x} ]; then echo "r'${VIASH_PAR_OUTSAMHEADERPG//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'outSAMheaderCommentFile': $( if [ ! -z ${VIASH_PAR_OUTSAMHEADERCOMMENTFILE+x} ]; then echo "r'${VIASH_PAR_OUTSAMHEADERCOMMENTFILE//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'outSAMfilter': $( if [ ! -z ${VIASH_PAR_OUTSAMFILTER+x} ]; then echo "r'${VIASH_PAR_OUTSAMFILTER//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'outSAMmultNmax': $( if [ ! -z ${VIASH_PAR_OUTSAMMULTNMAX+x} ]; then echo "int(r'${VIASH_PAR_OUTSAMMULTNMAX//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'outSAMtlen': $( if [ ! -z ${VIASH_PAR_OUTSAMTLEN+x} ]; then echo "int(r'${VIASH_PAR_OUTSAMTLEN//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'outBAMcompression': $( if [ ! -z ${VIASH_PAR_OUTBAMCOMPRESSION+x} ]; then echo "int(r'${VIASH_PAR_OUTBAMCOMPRESSION//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'outBAMsortingThreadN': $( if [ ! -z ${VIASH_PAR_OUTBAMSORTINGTHREADN+x} ]; then echo "int(r'${VIASH_PAR_OUTBAMSORTINGTHREADN//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'outBAMsortingBinsN': $( if [ ! -z ${VIASH_PAR_OUTBAMSORTINGBINSN+x} ]; then echo "int(r'${VIASH_PAR_OUTBAMSORTINGBINSN//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'bamRemoveDuplicatesType': $( if [ ! -z ${VIASH_PAR_BAMREMOVEDUPLICATESTYPE+x} ]; then echo "r'${VIASH_PAR_BAMREMOVEDUPLICATESTYPE//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'bamRemoveDuplicatesMate2basesN': $( if [ ! -z ${VIASH_PAR_BAMREMOVEDUPLICATESMATE2BASESN+x} ]; then echo "int(r'${VIASH_PAR_BAMREMOVEDUPLICATESMATE2BASESN//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'outWigType': $( if [ ! -z ${VIASH_PAR_OUTWIGTYPE+x} ]; then echo "r'${VIASH_PAR_OUTWIGTYPE//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'outWigStrand': $( if [ ! -z ${VIASH_PAR_OUTWIGSTRAND+x} ]; then echo "r'${VIASH_PAR_OUTWIGSTRAND//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'outWigReferencesPrefix': $( if [ ! -z ${VIASH_PAR_OUTWIGREFERENCESPREFIX+x} ]; then echo "r'${VIASH_PAR_OUTWIGREFERENCESPREFIX//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'outWigNorm': $( if [ ! -z ${VIASH_PAR_OUTWIGNORM+x} ]; then echo "r'${VIASH_PAR_OUTWIGNORM//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'outFilterType': $( if [ ! -z ${VIASH_PAR_OUTFILTERTYPE+x} ]; then echo "r'${VIASH_PAR_OUTFILTERTYPE//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'outFilterMultimapScoreRange': $( if [ ! -z ${VIASH_PAR_OUTFILTERMULTIMAPSCORERANGE+x} ]; then echo "int(r'${VIASH_PAR_OUTFILTERMULTIMAPSCORERANGE//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'outFilterMultimapNmax': $( if [ ! -z ${VIASH_PAR_OUTFILTERMULTIMAPNMAX+x} ]; then echo "int(r'${VIASH_PAR_OUTFILTERMULTIMAPNMAX//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'outFilterMismatchNmax': $( if [ ! -z ${VIASH_PAR_OUTFILTERMISMATCHNMAX+x} ]; then echo "int(r'${VIASH_PAR_OUTFILTERMISMATCHNMAX//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'outFilterMismatchNoverLmax': $( if [ ! -z ${VIASH_PAR_OUTFILTERMISMATCHNOVERLMAX+x} ]; then echo "float(r'${VIASH_PAR_OUTFILTERMISMATCHNOVERLMAX//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'outFilterMismatchNoverReadLmax': $( if [ ! -z ${VIASH_PAR_OUTFILTERMISMATCHNOVERREADLMAX+x} ]; then echo "float(r'${VIASH_PAR_OUTFILTERMISMATCHNOVERREADLMAX//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'outFilterScoreMin': $( if [ ! -z ${VIASH_PAR_OUTFILTERSCOREMIN+x} ]; then echo "int(r'${VIASH_PAR_OUTFILTERSCOREMIN//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'outFilterScoreMinOverLread': $( if [ ! -z ${VIASH_PAR_OUTFILTERSCOREMINOVERLREAD+x} ]; then echo "float(r'${VIASH_PAR_OUTFILTERSCOREMINOVERLREAD//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'outFilterMatchNmin': $( if [ ! -z ${VIASH_PAR_OUTFILTERMATCHNMIN+x} ]; then echo "int(r'${VIASH_PAR_OUTFILTERMATCHNMIN//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'outFilterMatchNminOverLread': $( if [ ! -z ${VIASH_PAR_OUTFILTERMATCHNMINOVERLREAD+x} ]; then echo "float(r'${VIASH_PAR_OUTFILTERMATCHNMINOVERLREAD//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'outFilterIntronMotifs': $( if [ ! -z ${VIASH_PAR_OUTFILTERINTRONMOTIFS+x} ]; then echo "r'${VIASH_PAR_OUTFILTERINTRONMOTIFS//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'outFilterIntronStrands': $( if [ ! -z ${VIASH_PAR_OUTFILTERINTRONSTRANDS+x} ]; then echo "r'${VIASH_PAR_OUTFILTERINTRONSTRANDS//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'outSJtype': $( if [ ! -z ${VIASH_PAR_OUTSJTYPE+x} ]; then echo "r'${VIASH_PAR_OUTSJTYPE//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'outSJfilterReads': $( if [ ! -z ${VIASH_PAR_OUTSJFILTERREADS+x} ]; then echo "r'${VIASH_PAR_OUTSJFILTERREADS//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'outSJfilterOverhangMin': $( if [ ! -z ${VIASH_PAR_OUTSJFILTEROVERHANGMIN+x} ]; then echo "list(map(int, r'${VIASH_PAR_OUTSJFILTEROVERHANGMIN//\'/\'\"\'\"r\'}'.split(';')))"; else echo None; fi ),
  'outSJfilterCountUniqueMin': $( if [ ! -z ${VIASH_PAR_OUTSJFILTERCOUNTUNIQUEMIN+x} ]; then echo "list(map(int, r'${VIASH_PAR_OUTSJFILTERCOUNTUNIQUEMIN//\'/\'\"\'\"r\'}'.split(';')))"; else echo None; fi ),
  'outSJfilterCountTotalMin': $( if [ ! -z ${VIASH_PAR_OUTSJFILTERCOUNTTOTALMIN+x} ]; then echo "list(map(int, r'${VIASH_PAR_OUTSJFILTERCOUNTTOTALMIN//\'/\'\"\'\"r\'}'.split(';')))"; else echo None; fi ),
  'outSJfilterDistToOtherSJmin': $( if [ ! -z ${VIASH_PAR_OUTSJFILTERDISTTOOTHERSJMIN+x} ]; then echo "list(map(int, r'${VIASH_PAR_OUTSJFILTERDISTTOOTHERSJMIN//\'/\'\"\'\"r\'}'.split(';')))"; else echo None; fi ),
  'outSJfilterIntronMaxVsReadN': $( if [ ! -z ${VIASH_PAR_OUTSJFILTERINTRONMAXVSREADN+x} ]; then echo "list(map(int, r'${VIASH_PAR_OUTSJFILTERINTRONMAXVSREADN//\'/\'\"\'\"r\'}'.split(';')))"; else echo None; fi ),
  'scoreGap': $( if [ ! -z ${VIASH_PAR_SCOREGAP+x} ]; then echo "int(r'${VIASH_PAR_SCOREGAP//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'scoreGapNoncan': $( if [ ! -z ${VIASH_PAR_SCOREGAPNONCAN+x} ]; then echo "int(r'${VIASH_PAR_SCOREGAPNONCAN//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'scoreGapGCAG': $( if [ ! -z ${VIASH_PAR_SCOREGAPGCAG+x} ]; then echo "int(r'${VIASH_PAR_SCOREGAPGCAG//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'scoreGapATAC': $( if [ ! -z ${VIASH_PAR_SCOREGAPATAC+x} ]; then echo "int(r'${VIASH_PAR_SCOREGAPATAC//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'scoreGenomicLengthLog2scale': $( if [ ! -z ${VIASH_PAR_SCOREGENOMICLENGTHLOG2SCALE+x} ]; then echo "int(r'${VIASH_PAR_SCOREGENOMICLENGTHLOG2SCALE//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'scoreDelOpen': $( if [ ! -z ${VIASH_PAR_SCOREDELOPEN+x} ]; then echo "int(r'${VIASH_PAR_SCOREDELOPEN//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'scoreDelBase': $( if [ ! -z ${VIASH_PAR_SCOREDELBASE+x} ]; then echo "int(r'${VIASH_PAR_SCOREDELBASE//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'scoreInsOpen': $( if [ ! -z ${VIASH_PAR_SCOREINSOPEN+x} ]; then echo "int(r'${VIASH_PAR_SCOREINSOPEN//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'scoreInsBase': $( if [ ! -z ${VIASH_PAR_SCOREINSBASE+x} ]; then echo "int(r'${VIASH_PAR_SCOREINSBASE//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'scoreStitchSJshift': $( if [ ! -z ${VIASH_PAR_SCORESTITCHSJSHIFT+x} ]; then echo "int(r'${VIASH_PAR_SCORESTITCHSJSHIFT//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'seedSearchStartLmax': $( if [ ! -z ${VIASH_PAR_SEEDSEARCHSTARTLMAX+x} ]; then echo "int(r'${VIASH_PAR_SEEDSEARCHSTARTLMAX//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'seedSearchStartLmaxOverLread': $( if [ ! -z ${VIASH_PAR_SEEDSEARCHSTARTLMAXOVERLREAD+x} ]; then echo "float(r'${VIASH_PAR_SEEDSEARCHSTARTLMAXOVERLREAD//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'seedSearchLmax': $( if [ ! -z ${VIASH_PAR_SEEDSEARCHLMAX+x} ]; then echo "int(r'${VIASH_PAR_SEEDSEARCHLMAX//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'seedMultimapNmax': $( if [ ! -z ${VIASH_PAR_SEEDMULTIMAPNMAX+x} ]; then echo "int(r'${VIASH_PAR_SEEDMULTIMAPNMAX//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'seedPerReadNmax': $( if [ ! -z ${VIASH_PAR_SEEDPERREADNMAX+x} ]; then echo "int(r'${VIASH_PAR_SEEDPERREADNMAX//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'seedPerWindowNmax': $( if [ ! -z ${VIASH_PAR_SEEDPERWINDOWNMAX+x} ]; then echo "int(r'${VIASH_PAR_SEEDPERWINDOWNMAX//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'seedNoneLociPerWindow': $( if [ ! -z ${VIASH_PAR_SEEDNONELOCIPERWINDOW+x} ]; then echo "int(r'${VIASH_PAR_SEEDNONELOCIPERWINDOW//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'seedSplitMin': $( if [ ! -z ${VIASH_PAR_SEEDSPLITMIN+x} ]; then echo "int(r'${VIASH_PAR_SEEDSPLITMIN//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'seedMapMin': $( if [ ! -z ${VIASH_PAR_SEEDMAPMIN+x} ]; then echo "int(r'${VIASH_PAR_SEEDMAPMIN//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'alignIntronMin': $( if [ ! -z ${VIASH_PAR_ALIGNINTRONMIN+x} ]; then echo "int(r'${VIASH_PAR_ALIGNINTRONMIN//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'alignIntronMax': $( if [ ! -z ${VIASH_PAR_ALIGNINTRONMAX+x} ]; then echo "int(r'${VIASH_PAR_ALIGNINTRONMAX//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'alignMatesGapMax': $( if [ ! -z ${VIASH_PAR_ALIGNMATESGAPMAX+x} ]; then echo "int(r'${VIASH_PAR_ALIGNMATESGAPMAX//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'alignSJoverhangMin': $( if [ ! -z ${VIASH_PAR_ALIGNSJOVERHANGMIN+x} ]; then echo "int(r'${VIASH_PAR_ALIGNSJOVERHANGMIN//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'alignSJstitchMismatchNmax': $( if [ ! -z ${VIASH_PAR_ALIGNSJSTITCHMISMATCHNMAX+x} ]; then echo "list(map(int, r'${VIASH_PAR_ALIGNSJSTITCHMISMATCHNMAX//\'/\'\"\'\"r\'}'.split(';')))"; else echo None; fi ),
  'alignSJDBoverhangMin': $( if [ ! -z ${VIASH_PAR_ALIGNSJDBOVERHANGMIN+x} ]; then echo "int(r'${VIASH_PAR_ALIGNSJDBOVERHANGMIN//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'alignSplicedMateMapLmin': $( if [ ! -z ${VIASH_PAR_ALIGNSPLICEDMATEMAPLMIN+x} ]; then echo "int(r'${VIASH_PAR_ALIGNSPLICEDMATEMAPLMIN//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'alignSplicedMateMapLminOverLmate': $( if [ ! -z ${VIASH_PAR_ALIGNSPLICEDMATEMAPLMINOVERLMATE+x} ]; then echo "float(r'${VIASH_PAR_ALIGNSPLICEDMATEMAPLMINOVERLMATE//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'alignWindowsPerReadNmax': $( if [ ! -z ${VIASH_PAR_ALIGNWINDOWSPERREADNMAX+x} ]; then echo "int(r'${VIASH_PAR_ALIGNWINDOWSPERREADNMAX//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'alignTranscriptsPerWindowNmax': $( if [ ! -z ${VIASH_PAR_ALIGNTRANSCRIPTSPERWINDOWNMAX+x} ]; then echo "int(r'${VIASH_PAR_ALIGNTRANSCRIPTSPERWINDOWNMAX//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'alignTranscriptsPerReadNmax': $( if [ ! -z ${VIASH_PAR_ALIGNTRANSCRIPTSPERREADNMAX+x} ]; then echo "int(r'${VIASH_PAR_ALIGNTRANSCRIPTSPERREADNMAX//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'alignEndsType': $( if [ ! -z ${VIASH_PAR_ALIGNENDSTYPE+x} ]; then echo "r'${VIASH_PAR_ALIGNENDSTYPE//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'alignEndsProtrude': $( if [ ! -z ${VIASH_PAR_ALIGNENDSPROTRUDE+x} ]; then echo "r'${VIASH_PAR_ALIGNENDSPROTRUDE//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'alignSoftClipAtReferenceEnds': $( if [ ! -z ${VIASH_PAR_ALIGNSOFTCLIPATREFERENCEENDS+x} ]; then echo "r'${VIASH_PAR_ALIGNSOFTCLIPATREFERENCEENDS//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'alignInsertionFlush': $( if [ ! -z ${VIASH_PAR_ALIGNINSERTIONFLUSH+x} ]; then echo "r'${VIASH_PAR_ALIGNINSERTIONFLUSH//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'peOverlapNbasesMin': $( if [ ! -z ${VIASH_PAR_PEOVERLAPNBASESMIN+x} ]; then echo "int(r'${VIASH_PAR_PEOVERLAPNBASESMIN//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'peOverlapMMp': $( if [ ! -z ${VIASH_PAR_PEOVERLAPMMP+x} ]; then echo "float(r'${VIASH_PAR_PEOVERLAPMMP//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'winAnchorMultimapNmax': $( if [ ! -z ${VIASH_PAR_WINANCHORMULTIMAPNMAX+x} ]; then echo "int(r'${VIASH_PAR_WINANCHORMULTIMAPNMAX//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'winBinNbits': $( if [ ! -z ${VIASH_PAR_WINBINNBITS+x} ]; then echo "int(r'${VIASH_PAR_WINBINNBITS//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'winAnchorDistNbins': $( if [ ! -z ${VIASH_PAR_WINANCHORDISTNBINS+x} ]; then echo "int(r'${VIASH_PAR_WINANCHORDISTNBINS//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'winFlankNbins': $( if [ ! -z ${VIASH_PAR_WINFLANKNBINS+x} ]; then echo "int(r'${VIASH_PAR_WINFLANKNBINS//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'winReadCoverageRelativeMin': $( if [ ! -z ${VIASH_PAR_WINREADCOVERAGERELATIVEMIN+x} ]; then echo "float(r'${VIASH_PAR_WINREADCOVERAGERELATIVEMIN//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'winReadCoverageBasesMin': $( if [ ! -z ${VIASH_PAR_WINREADCOVERAGEBASESMIN+x} ]; then echo "int(r'${VIASH_PAR_WINREADCOVERAGEBASESMIN//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'chimOutType': $( if [ ! -z ${VIASH_PAR_CHIMOUTTYPE+x} ]; then echo "r'${VIASH_PAR_CHIMOUTTYPE//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'chimSegmentMin': $( if [ ! -z ${VIASH_PAR_CHIMSEGMENTMIN+x} ]; then echo "int(r'${VIASH_PAR_CHIMSEGMENTMIN//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'chimScoreMin': $( if [ ! -z ${VIASH_PAR_CHIMSCOREMIN+x} ]; then echo "int(r'${VIASH_PAR_CHIMSCOREMIN//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'chimScoreDropMax': $( if [ ! -z ${VIASH_PAR_CHIMSCOREDROPMAX+x} ]; then echo "int(r'${VIASH_PAR_CHIMSCOREDROPMAX//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'chimScoreSeparation': $( if [ ! -z ${VIASH_PAR_CHIMSCORESEPARATION+x} ]; then echo "int(r'${VIASH_PAR_CHIMSCORESEPARATION//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'chimScoreJunctionNonGTAG': $( if [ ! -z ${VIASH_PAR_CHIMSCOREJUNCTIONNONGTAG+x} ]; then echo "int(r'${VIASH_PAR_CHIMSCOREJUNCTIONNONGTAG//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'chimJunctionOverhangMin': $( if [ ! -z ${VIASH_PAR_CHIMJUNCTIONOVERHANGMIN+x} ]; then echo "int(r'${VIASH_PAR_CHIMJUNCTIONOVERHANGMIN//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'chimSegmentReadGapMax': $( if [ ! -z ${VIASH_PAR_CHIMSEGMENTREADGAPMAX+x} ]; then echo "int(r'${VIASH_PAR_CHIMSEGMENTREADGAPMAX//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'chimFilter': $( if [ ! -z ${VIASH_PAR_CHIMFILTER+x} ]; then echo "r'${VIASH_PAR_CHIMFILTER//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'chimMainSegmentMultNmax': $( if [ ! -z ${VIASH_PAR_CHIMMAINSEGMENTMULTNMAX+x} ]; then echo "int(r'${VIASH_PAR_CHIMMAINSEGMENTMULTNMAX//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'chimMultimapNmax': $( if [ ! -z ${VIASH_PAR_CHIMMULTIMAPNMAX+x} ]; then echo "int(r'${VIASH_PAR_CHIMMULTIMAPNMAX//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'chimMultimapScoreRange': $( if [ ! -z ${VIASH_PAR_CHIMMULTIMAPSCORERANGE+x} ]; then echo "int(r'${VIASH_PAR_CHIMMULTIMAPSCORERANGE//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'chimNonchimScoreDropMin': $( if [ ! -z ${VIASH_PAR_CHIMNONCHIMSCOREDROPMIN+x} ]; then echo "int(r'${VIASH_PAR_CHIMNONCHIMSCOREDROPMIN//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'chimOutJunctionFormat': $( if [ ! -z ${VIASH_PAR_CHIMOUTJUNCTIONFORMAT+x} ]; then echo "int(r'${VIASH_PAR_CHIMOUTJUNCTIONFORMAT//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'quantMode': $( if [ ! -z ${VIASH_PAR_QUANTMODE+x} ]; then echo "r'${VIASH_PAR_QUANTMODE//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'quantTranscriptomeBAMcompression': $( if [ ! -z ${VIASH_PAR_QUANTTRANSCRIPTOMEBAMCOMPRESSION+x} ]; then echo "int(r'${VIASH_PAR_QUANTTRANSCRIPTOMEBAMCOMPRESSION//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'quantTranscriptomeBan': $( if [ ! -z ${VIASH_PAR_QUANTTRANSCRIPTOMEBAN+x} ]; then echo "r'${VIASH_PAR_QUANTTRANSCRIPTOMEBAN//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'twopassMode': $( if [ ! -z ${VIASH_PAR_TWOPASSMODE+x} ]; then echo "r'${VIASH_PAR_TWOPASSMODE//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'twopass1readsN': $( if [ ! -z ${VIASH_PAR_TWOPASS1READSN+x} ]; then echo "int(r'${VIASH_PAR_TWOPASS1READSN//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'waspOutputMode': $( if [ ! -z ${VIASH_PAR_WASPOUTPUTMODE+x} ]; then echo "r'${VIASH_PAR_WASPOUTPUTMODE//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'soloType': $( if [ ! -z ${VIASH_PAR_SOLOTYPE+x} ]; then echo "r'${VIASH_PAR_SOLOTYPE//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'soloCBwhitelist': $( if [ ! -z ${VIASH_PAR_SOLOCBWHITELIST+x} ]; then echo "r'${VIASH_PAR_SOLOCBWHITELIST//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'soloCBstart': $( if [ ! -z ${VIASH_PAR_SOLOCBSTART+x} ]; then echo "int(r'${VIASH_PAR_SOLOCBSTART//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'soloCBlen': $( if [ ! -z ${VIASH_PAR_SOLOCBLEN+x} ]; then echo "int(r'${VIASH_PAR_SOLOCBLEN//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'soloUMIstart': $( if [ ! -z ${VIASH_PAR_SOLOUMISTART+x} ]; then echo "int(r'${VIASH_PAR_SOLOUMISTART//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'soloUMIlen': $( if [ ! -z ${VIASH_PAR_SOLOUMILEN+x} ]; then echo "int(r'${VIASH_PAR_SOLOUMILEN//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'soloBarcodeReadLength': $( if [ ! -z ${VIASH_PAR_SOLOBARCODEREADLENGTH+x} ]; then echo "int(r'${VIASH_PAR_SOLOBARCODEREADLENGTH//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'soloBarcodeMate': $( if [ ! -z ${VIASH_PAR_SOLOBARCODEMATE+x} ]; then echo "int(r'${VIASH_PAR_SOLOBARCODEMATE//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'soloCBposition': $( if [ ! -z ${VIASH_PAR_SOLOCBPOSITION+x} ]; then echo "r'${VIASH_PAR_SOLOCBPOSITION//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'soloUMIposition': $( if [ ! -z ${VIASH_PAR_SOLOUMIPOSITION+x} ]; then echo "r'${VIASH_PAR_SOLOUMIPOSITION//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'soloAdapterSequence': $( if [ ! -z ${VIASH_PAR_SOLOADAPTERSEQUENCE+x} ]; then echo "r'${VIASH_PAR_SOLOADAPTERSEQUENCE//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'soloAdapterMismatchesNmax': $( if [ ! -z ${VIASH_PAR_SOLOADAPTERMISMATCHESNMAX+x} ]; then echo "int(r'${VIASH_PAR_SOLOADAPTERMISMATCHESNMAX//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'soloCBmatchWLtype': $( if [ ! -z ${VIASH_PAR_SOLOCBMATCHWLTYPE+x} ]; then echo "r'${VIASH_PAR_SOLOCBMATCHWLTYPE//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'soloInputSAMattrBarcodeSeq': $( if [ ! -z ${VIASH_PAR_SOLOINPUTSAMATTRBARCODESEQ+x} ]; then echo "r'${VIASH_PAR_SOLOINPUTSAMATTRBARCODESEQ//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'soloInputSAMattrBarcodeQual': $( if [ ! -z ${VIASH_PAR_SOLOINPUTSAMATTRBARCODEQUAL+x} ]; then echo "r'${VIASH_PAR_SOLOINPUTSAMATTRBARCODEQUAL//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'soloStrand': $( if [ ! -z ${VIASH_PAR_SOLOSTRAND+x} ]; then echo "r'${VIASH_PAR_SOLOSTRAND//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'soloFeatures': $( if [ ! -z ${VIASH_PAR_SOLOFEATURES+x} ]; then echo "r'${VIASH_PAR_SOLOFEATURES//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'soloMultiMappers': $( if [ ! -z ${VIASH_PAR_SOLOMULTIMAPPERS+x} ]; then echo "r'${VIASH_PAR_SOLOMULTIMAPPERS//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'soloUMIdedup': $( if [ ! -z ${VIASH_PAR_SOLOUMIDEDUP+x} ]; then echo "r'${VIASH_PAR_SOLOUMIDEDUP//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'soloUMIfiltering': $( if [ ! -z ${VIASH_PAR_SOLOUMIFILTERING+x} ]; then echo "r'${VIASH_PAR_SOLOUMIFILTERING//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'soloOutFileNames': $( if [ ! -z ${VIASH_PAR_SOLOOUTFILENAMES+x} ]; then echo "r'${VIASH_PAR_SOLOOUTFILENAMES//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'soloCellFilter': $( if [ ! -z ${VIASH_PAR_SOLOCELLFILTER+x} ]; then echo "r'${VIASH_PAR_SOLOCELLFILTER//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'soloOutFormatFeaturesGeneField3': $( if [ ! -z ${VIASH_PAR_SOLOOUTFORMATFEATURESGENEFIELD3+x} ]; then echo "r'${VIASH_PAR_SOLOOUTFORMATFEATURESGENEFIELD3//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'soloCellReadStats': $( if [ ! -z ${VIASH_PAR_SOLOCELLREADSTATS+x} ]; then echo "r'${VIASH_PAR_SOLOCELLREADSTATS//\'/\'\"\'\"r\'}'"; else echo None; fi )
}
meta = {
  'name': $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "r'${VIASH_META_NAME//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'functionality_name': $( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "r'${VIASH_META_FUNCTIONALITY_NAME//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'resources_dir': $( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "r'${VIASH_META_RESOURCES_DIR//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'executable': $( if [ ! -z ${VIASH_META_EXECUTABLE+x} ]; then echo "r'${VIASH_META_EXECUTABLE//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'config': $( if [ ! -z ${VIASH_META_CONFIG+x} ]; then echo "r'${VIASH_META_CONFIG//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'temp_dir': $( if [ ! -z ${VIASH_META_TEMP_DIR+x} ]; then echo "r'${VIASH_META_TEMP_DIR//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'cpus': $( if [ ! -z ${VIASH_META_CPUS+x} ]; then echo "int(r'${VIASH_META_CPUS//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_b': $( if [ ! -z ${VIASH_META_MEMORY_B+x} ]; then echo "int(r'${VIASH_META_MEMORY_B//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_kb': $( if [ ! -z ${VIASH_META_MEMORY_KB+x} ]; then echo "int(r'${VIASH_META_MEMORY_KB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_mb': $( if [ ! -z ${VIASH_META_MEMORY_MB+x} ]; then echo "int(r'${VIASH_META_MEMORY_MB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_gb': $( if [ ! -z ${VIASH_META_MEMORY_GB+x} ]; then echo "int(r'${VIASH_META_MEMORY_GB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_tb': $( if [ ! -z ${VIASH_META_MEMORY_TB+x} ]; then echo "int(r'${VIASH_META_MEMORY_TB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_pb': $( if [ ! -z ${VIASH_META_MEMORY_PB+x} ]; then echo "int(r'${VIASH_META_MEMORY_PB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_kib': $( if [ ! -z ${VIASH_META_MEMORY_KIB+x} ]; then echo "int(r'${VIASH_META_MEMORY_KIB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_mib': $( if [ ! -z ${VIASH_META_MEMORY_MIB+x} ]; then echo "int(r'${VIASH_META_MEMORY_MIB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_gib': $( if [ ! -z ${VIASH_META_MEMORY_GIB+x} ]; then echo "int(r'${VIASH_META_MEMORY_GIB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_tib': $( if [ ! -z ${VIASH_META_MEMORY_TIB+x} ]; then echo "int(r'${VIASH_META_MEMORY_TIB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_pib': $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "int(r'${VIASH_META_MEMORY_PIB//\'/\'\"\'\"r\'}')"; else echo None; fi )
}
dep = {
  
}

## VIASH END

########################
### Helper functions ###
########################

# regex for matching R[12] fastq(gz) files
# examples:
# - TSP10_Fat_MAT_SS2_B134171_B115063_Immune_A1_L003_R1.fastq.gz
# - tinygex_S1_L001_I1_001.fastq.gz
fastqgz_regex = r"(.+)_(R\\d+)(_\\d+)?\\.fastq(\\.gz)?"


# helper function for cheching whether something is a gzip
def is_gz_file(path: Path) -> bool:
    with open(path, "rb") as file:
        return file.read(2) == b"\\x1f\\x8b"


# look for fastq files in a directory
def search_fastqs(path: Path) -> list[Path]:
    if path.is_dir():
        print(
            f"Input '{path}' is a directory, traversing to see if we can detect any FASTQ files.",
            flush=True,
        )
        value_paths = [
            file for file in path.iterdir() if re.match(fastqgz_regex, file.name)
        ]
        return value_paths
    else:
        return [path]


# if {par_value} is a Path, extract it to a temp_dir_path and return the resulting path
def extract_if_need_be(par_value: Path, temp_dir_path: Path) -> Path:
    if par_value.is_file() and tarfile.is_tarfile(par_value):
        # Remove two extensions (if they exist)
        extaction_dir_name = Path(par_value.stem).stem
        unpacked_path = temp_dir_path / extaction_dir_name
        print(f"  Tar detected; extracting {par_value} to {unpacked_path}", flush=True)

        with tarfile.open(par_value, "r") as open_tar:
            members = open_tar.getmembers()
            root_dirs = [
                member
                for member in members
                if member.isdir() and member.name != "." and "/" not in member.name
            ]
            # if there is only one root_dir (and there are files in that directory)
            # strip that directory name from the destination folder
            if len(root_dirs) == 1:
                for mem in members:
                    mem.path = Path(*Path(mem.path).parts[1:])
            members_to_move = [mem for mem in members if mem.path != Path(".")]
            open_tar.extractall(unpacked_path, members=members_to_move)
        return unpacked_path

    elif par_value.is_file() and is_gz_file(par_value):
        # Remove extension (if it exists)
        extaction_file_name = Path(par_value.stem)
        unpacked_path = temp_dir_path / extaction_file_name
        print(f"  Gzip detected; extracting {par_value} to {unpacked_path}", flush=True)

        with gzip.open(par_value, "rb") as f_in:
            with open(unpacked_path, "wb") as f_out:
                shutil.copyfileobj(f_in, f_out)
        return unpacked_path

    else:
        return par_value


########################
###    Main code     ###
########################

# rename keys and convert path strings to Path
# note: only list file arguments here. if non-file arguments also need to be renamed,
# the \`processPar()\` generator needs to be adapted
to_rename = {
    "input": "readFilesIn",
    "reference": "genomeDir",
    "output": "outFileNamePrefix",
}


def process_par(orig_par, to_rename):
    for key, value in orig_par.items():
        # rename the key in par based on the \`to_rename\` dict
        if key in to_rename.keys():
            new_key = to_rename[key]

            # also turn value into a Path
            if isinstance(value, list):
                new_value = [Path(val) for val in value]
            else:
                new_value = Path(value)
        else:
            new_key = key
            new_value = value
        yield new_key, new_value


par = dict(process_par(par, to_rename))

# create output dir if need be
par["outFileNamePrefix"].mkdir(parents=True, exist_ok=True)

with tempfile.TemporaryDirectory(
    prefix="star-", dir=meta["temp_dir"], ignore_cleanup_errors=True
) as temp_dir:
    print(">> Check whether input files are directories", flush=True)
    new_read_files_in = []
    for path in par["readFilesIn"]:
        new_read_files_in.extend(search_fastqs(path))
    par["readFilesIn"] = new_read_files_in
    print("", flush=True)

    # checking for compressed files, ungzip files if need be
    temp_dir_path = Path(temp_dir)
    for par_name in ["genomeDir", "readFilesIn"]:
        par_values = par[par_name]
        if par_values:
            # turn value into list
            is_multiple = isinstance(par_values, list)
            if not is_multiple:
                par_values = [par_values]

            # output list
            new_values = []
            for par_value in par_values:
                print(
                    f">> Check compression of --{par_name} with value: {par_value}",
                    flush=True,
                )
                new_value = extract_if_need_be(par_value, temp_dir_path)
                new_values.append(new_value)

            # unlist if need be
            if not is_multiple:
                new_values = new_values[0]

            # replace value
            par[par_name] = new_values
    # end ungzipping
    print("", flush=True)

    print("Grouping R1/R2 input files into pairs", flush=True)
    input_grouped = {}
    for path in par["readFilesIn"]:
        key = re.search(fastqgz_regex, path.name).group(2)
        if key not in input_grouped:
            input_grouped[key] = []
        input_grouped[key].append(str(path))
    par["readFilesIn"] = [",".join(val) for val in input_grouped.values()]
    print("", flush=True)

    print(">> Constructing command", flush=True)
    par["runMode"] = "alignReads"
    par["outTmpDir"] = temp_dir_path / "run"
    if "cpus" in meta and meta["cpus"]:
        par["runThreadN"] = meta["cpus"]
    # make sure there is a trailing /
    par["outFileNamePrefix"] = f"{par['outFileNamePrefix']}/"

    cmd_args = ["STAR"]
    for name, value in par.items():
        if value is not None:
            if isinstance(value, list):
                cmd_args.extend(["--" + name] + [str(x) for x in value])
            else:
                cmd_args.extend(["--" + name, str(value)])
    print("", flush=True)

    print(">> Running STAR with command:", flush=True)
    print("+ " + " ".join([str(x) for x in cmd_args]), flush=True)
    print("", flush=True)

    subprocess.run(cmd_args, check=True)
VIASHMAIN
python -B "\$tempscript" &
wait "\$!"

VIASHEOF


if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  # strip viash automount from file paths
  
  if [ ! -z "$VIASH_PAR_INPUT" ]; then
    unset VIASH_TEST_INPUT
    IFS=';'
    for var in $VIASH_PAR_INPUT; do
      unset IFS
      if [ -z "$VIASH_TEST_INPUT" ]; then
      VIASH_TEST_INPUT="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_INPUT="$VIASH_TEST_INPUT;""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_INPUT="$VIASH_TEST_INPUT"
  fi
  if [ ! -z "$VIASH_PAR_REFERENCE" ]; then
    VIASH_PAR_REFERENCE=$(ViashDockerStripAutomount "$VIASH_PAR_REFERENCE")
  fi
  if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
    VIASH_PAR_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT")
  fi
  if [ ! -z "$VIASH_PAR_GENOMEFASTAFILES" ]; then
    unset VIASH_TEST_GENOMEFASTAFILES
    IFS=';'
    for var in $VIASH_PAR_GENOMEFASTAFILES; do
      unset IFS
      if [ -z "$VIASH_TEST_GENOMEFASTAFILES" ]; then
      VIASH_TEST_GENOMEFASTAFILES="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_GENOMEFASTAFILES="$VIASH_TEST_GENOMEFASTAFILES;""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_GENOMEFASTAFILES="$VIASH_TEST_GENOMEFASTAFILES"
  fi
  if [ ! -z "$VIASH_PAR_SJDBGTFFILE" ]; then
    VIASH_PAR_SJDBGTFFILE=$(ViashDockerStripAutomount "$VIASH_PAR_SJDBGTFFILE")
  fi
  if [ ! -z "$VIASH_PAR_READFILESMANIFEST" ]; then
    VIASH_PAR_READFILESMANIFEST=$(ViashDockerStripAutomount "$VIASH_PAR_READFILESMANIFEST")
  fi
  if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
    VIASH_META_RESOURCES_DIR=$(ViashDockerStripAutomount "$VIASH_META_RESOURCES_DIR")
  fi
  if [ ! -z "$VIASH_META_EXECUTABLE" ]; then
    VIASH_META_EXECUTABLE=$(ViashDockerStripAutomount "$VIASH_META_EXECUTABLE")
  fi
  if [ ! -z "$VIASH_META_CONFIG" ]; then
    VIASH_META_CONFIG=$(ViashDockerStripAutomount "$VIASH_META_CONFIG")
  fi
  if [ ! -z "$VIASH_META_TEMP_DIR" ]; then
    VIASH_META_TEMP_DIR=$(ViashDockerStripAutomount "$VIASH_META_TEMP_DIR")
  fi
fi


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


exit 0
