#!/usr/bin/env bash

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

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="prepare_multiqc_input"
VIASH_META_FUNCTIONALITY_NAME="prepare_multiqc_input"
VIASH_META_EXECUTABLE="$VIASH_META_RESOURCES_DIR/$VIASH_META_NAME"
VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
VIASH_META_TEMP_DIR="$VIASH_TEMP"


# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
  echo "prepare_multiqc_input add_biobase_modules"
  echo ""
  echo "Prepare directory with all the input files for MultiQC."
  echo ""
  echo "Input:"
  echo "    --fail_trimming_multiqc"
  echo "        type: string"
  echo ""
  echo "    --fail_mapping_multiqc"
  echo "        type: string"
  echo ""
  echo "    --fail_strand_multiqc"
  echo "        type: string"
  echo ""
  echo "    --fastqc_raw_multiqc"
  echo "        type: file, multiple values allowed, file must exist"
  echo ""
  echo "    --fastqc_trim_multiqc"
  echo "        type: file, multiple values allowed, file must exist"
  echo ""
  echo "    --trim_log_multiqc"
  echo "        type: file, multiple values allowed, file must exist"
  echo ""
  echo "    --sortmerna_multiqc"
  echo "        type: file, multiple values allowed, file must exist"
  echo ""
  echo "    --star_multiqc"
  echo "        type: file, multiple values allowed, file must exist"
  echo ""
  echo "    --salmon_multiqc"
  echo "        type: file, multiple values allowed, file must exist"
  echo ""
  echo "    --samtools_stats"
  echo "        type: file, multiple values allowed, file must exist"
  echo ""
  echo "    --samtools_flagstat"
  echo "        type: file, multiple values allowed, file must exist"
  echo ""
  echo "    --samtools_idxstats"
  echo "        type: file, multiple values allowed, file must exist"
  echo ""
  echo "    --markduplicates_multiqc"
  echo "        type: file, multiple values allowed, file must exist"
  echo ""
  echo "    --pseudo_multiqc"
  echo "        type: file, multiple values allowed, file must exist"
  echo ""
  echo "    --featurecounts_multiqc"
  echo "        type: file, multiple values allowed, file must exist"
  echo ""
  echo "    --featurecounts_rrna_multiqc"
  echo "        type: file, multiple values allowed, file must exist"
  echo ""
  echo "    --aligner_pca_multiqc"
  echo "        type: file, file must exist"
  echo ""
  echo "    --aligner_clustering_multiqc"
  echo "        type: file, file must exist"
  echo ""
  echo "    --pseudo_aligner_pca_multiqc"
  echo "        type: file, file must exist"
  echo ""
  echo "    --pseudo_aligner_clustering_multiqc"
  echo "        type: file, file must exist"
  echo ""
  echo "    --preseq_multiqc"
  echo "        type: file, multiple values allowed, file must exist"
  echo ""
  echo "    --qualimap_multiqc"
  echo "        type: file, multiple values allowed, file must exist"
  echo ""
  echo "    --dupradar_output_dup_intercept_mqc"
  echo "        type: file, multiple values allowed, file must exist"
  echo ""
  echo "    --dupradar_output_duprate_exp_denscurve_mqc"
  echo "        type: file, multiple values allowed, file must exist"
  echo ""
  echo "    --bamstat_multiqc"
  echo "        type: file, multiple values allowed, file must exist"
  echo ""
  echo "    --inferexperiment_multiqc"
  echo "        type: file, multiple values allowed, file must exist"
  echo ""
  echo "    --innerdistance_multiqc"
  echo "        type: file, multiple values allowed, file must exist"
  echo ""
  echo "    --junctionannotation_multiqc"
  echo "        type: file, multiple values allowed, file must exist"
  echo ""
  echo "    --junctionsaturation_multiqc"
  echo "        type: file, multiple values allowed, file must exist"
  echo ""
  echo "    --readdistribution_multiqc"
  echo "        type: file, multiple values allowed, file must exist"
  echo ""
  echo "    --readduplication_multiqc"
  echo "        type: file, multiple values allowed, file must exist"
  echo ""
  echo "    --tin_multiqc"
  echo "        type: file, multiple values allowed, file must exist"
  echo ""
  echo "    --multiqc_config"
  echo "        type: file, file must exist"
  echo ""
  echo "Ouput:"
  echo "    --output"
  echo "        type: file, output, file must exist"
  echo "        default: multiqc_input"
}

# 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 ubuntu:22.04
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component prepare_multiqc_input"
LABEL org.opencontainers.image.created="2024-09-12T09:35:40Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b0cbbf82c331a079e3d5ad6df5c8b56388349cac"
LABEL org.opencontainers.image.version="add_biobase_modules"

VIASHDOCKER
  fi
}

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

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

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

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

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

# initialise array
VIASH_POSITIONAL_ARGS=''

while [[ $# -gt 0 ]]; do
    case "$1" in
        -h|--help)
            ViashHelp
            exit
            ;;
        ---v|---verbose)
            let "VIASH_VERBOSITY=VIASH_VERBOSITY+1"
            shift 1
            ;;
        ---verbosity)
            VIASH_VERBOSITY="$2"
            shift 2
            ;;
        ---verbosity=*)
            VIASH_VERBOSITY="$(ViashRemoveFlags "$1")"
            shift 1
            ;;
        --version)
            echo "prepare_multiqc_input add_biobase_modules"
            exit
            ;;
        --fail_trimming_multiqc)
            [ -n "$VIASH_PAR_FAIL_TRIMMING_MULTIQC" ] && ViashError Bad arguments for option \'--fail_trimming_multiqc\': \'$VIASH_PAR_FAIL_TRIMMING_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FAIL_TRIMMING_MULTIQC="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --fail_trimming_multiqc. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --fail_trimming_multiqc=*)
            [ -n "$VIASH_PAR_FAIL_TRIMMING_MULTIQC" ] && ViashError Bad arguments for option \'--fail_trimming_multiqc=*\': \'$VIASH_PAR_FAIL_TRIMMING_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FAIL_TRIMMING_MULTIQC=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --fail_mapping_multiqc)
            [ -n "$VIASH_PAR_FAIL_MAPPING_MULTIQC" ] && ViashError Bad arguments for option \'--fail_mapping_multiqc\': \'$VIASH_PAR_FAIL_MAPPING_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FAIL_MAPPING_MULTIQC="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --fail_mapping_multiqc. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --fail_mapping_multiqc=*)
            [ -n "$VIASH_PAR_FAIL_MAPPING_MULTIQC" ] && ViashError Bad arguments for option \'--fail_mapping_multiqc=*\': \'$VIASH_PAR_FAIL_MAPPING_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FAIL_MAPPING_MULTIQC=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --fail_strand_multiqc)
            [ -n "$VIASH_PAR_FAIL_STRAND_MULTIQC" ] && ViashError Bad arguments for option \'--fail_strand_multiqc\': \'$VIASH_PAR_FAIL_STRAND_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FAIL_STRAND_MULTIQC="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --fail_strand_multiqc. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --fail_strand_multiqc=*)
            [ -n "$VIASH_PAR_FAIL_STRAND_MULTIQC" ] && ViashError Bad arguments for option \'--fail_strand_multiqc=*\': \'$VIASH_PAR_FAIL_STRAND_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FAIL_STRAND_MULTIQC=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --fastqc_raw_multiqc)
            if [ -z "$VIASH_PAR_FASTQC_RAW_MULTIQC" ]; then
              VIASH_PAR_FASTQC_RAW_MULTIQC="$2"
            else
              VIASH_PAR_FASTQC_RAW_MULTIQC="$VIASH_PAR_FASTQC_RAW_MULTIQC,""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --fastqc_raw_multiqc. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --fastqc_raw_multiqc=*)
            if [ -z "$VIASH_PAR_FASTQC_RAW_MULTIQC" ]; then
              VIASH_PAR_FASTQC_RAW_MULTIQC=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_FASTQC_RAW_MULTIQC="$VIASH_PAR_FASTQC_RAW_MULTIQC,"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --fastqc_trim_multiqc)
            if [ -z "$VIASH_PAR_FASTQC_TRIM_MULTIQC" ]; then
              VIASH_PAR_FASTQC_TRIM_MULTIQC="$2"
            else
              VIASH_PAR_FASTQC_TRIM_MULTIQC="$VIASH_PAR_FASTQC_TRIM_MULTIQC,""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --fastqc_trim_multiqc. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --fastqc_trim_multiqc=*)
            if [ -z "$VIASH_PAR_FASTQC_TRIM_MULTIQC" ]; then
              VIASH_PAR_FASTQC_TRIM_MULTIQC=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_FASTQC_TRIM_MULTIQC="$VIASH_PAR_FASTQC_TRIM_MULTIQC,"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --trim_log_multiqc)
            if [ -z "$VIASH_PAR_TRIM_LOG_MULTIQC" ]; then
              VIASH_PAR_TRIM_LOG_MULTIQC="$2"
            else
              VIASH_PAR_TRIM_LOG_MULTIQC="$VIASH_PAR_TRIM_LOG_MULTIQC,""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --trim_log_multiqc. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --trim_log_multiqc=*)
            if [ -z "$VIASH_PAR_TRIM_LOG_MULTIQC" ]; then
              VIASH_PAR_TRIM_LOG_MULTIQC=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_TRIM_LOG_MULTIQC="$VIASH_PAR_TRIM_LOG_MULTIQC,"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --sortmerna_multiqc)
            if [ -z "$VIASH_PAR_SORTMERNA_MULTIQC" ]; then
              VIASH_PAR_SORTMERNA_MULTIQC="$2"
            else
              VIASH_PAR_SORTMERNA_MULTIQC="$VIASH_PAR_SORTMERNA_MULTIQC,""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --sortmerna_multiqc. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --sortmerna_multiqc=*)
            if [ -z "$VIASH_PAR_SORTMERNA_MULTIQC" ]; then
              VIASH_PAR_SORTMERNA_MULTIQC=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_SORTMERNA_MULTIQC="$VIASH_PAR_SORTMERNA_MULTIQC,"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --star_multiqc)
            if [ -z "$VIASH_PAR_STAR_MULTIQC" ]; then
              VIASH_PAR_STAR_MULTIQC="$2"
            else
              VIASH_PAR_STAR_MULTIQC="$VIASH_PAR_STAR_MULTIQC,""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --star_multiqc. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --star_multiqc=*)
            if [ -z "$VIASH_PAR_STAR_MULTIQC" ]; then
              VIASH_PAR_STAR_MULTIQC=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_STAR_MULTIQC="$VIASH_PAR_STAR_MULTIQC,"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --salmon_multiqc)
            if [ -z "$VIASH_PAR_SALMON_MULTIQC" ]; then
              VIASH_PAR_SALMON_MULTIQC="$2"
            else
              VIASH_PAR_SALMON_MULTIQC="$VIASH_PAR_SALMON_MULTIQC,""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --salmon_multiqc. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --salmon_multiqc=*)
            if [ -z "$VIASH_PAR_SALMON_MULTIQC" ]; then
              VIASH_PAR_SALMON_MULTIQC=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_SALMON_MULTIQC="$VIASH_PAR_SALMON_MULTIQC,"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --samtools_stats)
            if [ -z "$VIASH_PAR_SAMTOOLS_STATS" ]; then
              VIASH_PAR_SAMTOOLS_STATS="$2"
            else
              VIASH_PAR_SAMTOOLS_STATS="$VIASH_PAR_SAMTOOLS_STATS,""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --samtools_stats. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --samtools_stats=*)
            if [ -z "$VIASH_PAR_SAMTOOLS_STATS" ]; then
              VIASH_PAR_SAMTOOLS_STATS=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_SAMTOOLS_STATS="$VIASH_PAR_SAMTOOLS_STATS,"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --samtools_flagstat)
            if [ -z "$VIASH_PAR_SAMTOOLS_FLAGSTAT" ]; then
              VIASH_PAR_SAMTOOLS_FLAGSTAT="$2"
            else
              VIASH_PAR_SAMTOOLS_FLAGSTAT="$VIASH_PAR_SAMTOOLS_FLAGSTAT,""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --samtools_flagstat. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --samtools_flagstat=*)
            if [ -z "$VIASH_PAR_SAMTOOLS_FLAGSTAT" ]; then
              VIASH_PAR_SAMTOOLS_FLAGSTAT=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_SAMTOOLS_FLAGSTAT="$VIASH_PAR_SAMTOOLS_FLAGSTAT,"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --samtools_idxstats)
            if [ -z "$VIASH_PAR_SAMTOOLS_IDXSTATS" ]; then
              VIASH_PAR_SAMTOOLS_IDXSTATS="$2"
            else
              VIASH_PAR_SAMTOOLS_IDXSTATS="$VIASH_PAR_SAMTOOLS_IDXSTATS,""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --samtools_idxstats. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --samtools_idxstats=*)
            if [ -z "$VIASH_PAR_SAMTOOLS_IDXSTATS" ]; then
              VIASH_PAR_SAMTOOLS_IDXSTATS=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_SAMTOOLS_IDXSTATS="$VIASH_PAR_SAMTOOLS_IDXSTATS,"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --markduplicates_multiqc)
            if [ -z "$VIASH_PAR_MARKDUPLICATES_MULTIQC" ]; then
              VIASH_PAR_MARKDUPLICATES_MULTIQC="$2"
            else
              VIASH_PAR_MARKDUPLICATES_MULTIQC="$VIASH_PAR_MARKDUPLICATES_MULTIQC,""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --markduplicates_multiqc. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --markduplicates_multiqc=*)
            if [ -z "$VIASH_PAR_MARKDUPLICATES_MULTIQC" ]; then
              VIASH_PAR_MARKDUPLICATES_MULTIQC=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_MARKDUPLICATES_MULTIQC="$VIASH_PAR_MARKDUPLICATES_MULTIQC,"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --pseudo_multiqc)
            if [ -z "$VIASH_PAR_PSEUDO_MULTIQC" ]; then
              VIASH_PAR_PSEUDO_MULTIQC="$2"
            else
              VIASH_PAR_PSEUDO_MULTIQC="$VIASH_PAR_PSEUDO_MULTIQC,""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --pseudo_multiqc. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --pseudo_multiqc=*)
            if [ -z "$VIASH_PAR_PSEUDO_MULTIQC" ]; then
              VIASH_PAR_PSEUDO_MULTIQC=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_PSEUDO_MULTIQC="$VIASH_PAR_PSEUDO_MULTIQC,"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --featurecounts_multiqc)
            if [ -z "$VIASH_PAR_FEATURECOUNTS_MULTIQC" ]; then
              VIASH_PAR_FEATURECOUNTS_MULTIQC="$2"
            else
              VIASH_PAR_FEATURECOUNTS_MULTIQC="$VIASH_PAR_FEATURECOUNTS_MULTIQC,""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --featurecounts_multiqc. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --featurecounts_multiqc=*)
            if [ -z "$VIASH_PAR_FEATURECOUNTS_MULTIQC" ]; then
              VIASH_PAR_FEATURECOUNTS_MULTIQC=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_FEATURECOUNTS_MULTIQC="$VIASH_PAR_FEATURECOUNTS_MULTIQC,"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --featurecounts_rrna_multiqc)
            if [ -z "$VIASH_PAR_FEATURECOUNTS_RRNA_MULTIQC" ]; then
              VIASH_PAR_FEATURECOUNTS_RRNA_MULTIQC="$2"
            else
              VIASH_PAR_FEATURECOUNTS_RRNA_MULTIQC="$VIASH_PAR_FEATURECOUNTS_RRNA_MULTIQC,""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --featurecounts_rrna_multiqc. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --featurecounts_rrna_multiqc=*)
            if [ -z "$VIASH_PAR_FEATURECOUNTS_RRNA_MULTIQC" ]; then
              VIASH_PAR_FEATURECOUNTS_RRNA_MULTIQC=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_FEATURECOUNTS_RRNA_MULTIQC="$VIASH_PAR_FEATURECOUNTS_RRNA_MULTIQC,"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --aligner_pca_multiqc)
            [ -n "$VIASH_PAR_ALIGNER_PCA_MULTIQC" ] && ViashError Bad arguments for option \'--aligner_pca_multiqc\': \'$VIASH_PAR_ALIGNER_PCA_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALIGNER_PCA_MULTIQC="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --aligner_pca_multiqc. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --aligner_pca_multiqc=*)
            [ -n "$VIASH_PAR_ALIGNER_PCA_MULTIQC" ] && ViashError Bad arguments for option \'--aligner_pca_multiqc=*\': \'$VIASH_PAR_ALIGNER_PCA_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALIGNER_PCA_MULTIQC=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --aligner_clustering_multiqc)
            [ -n "$VIASH_PAR_ALIGNER_CLUSTERING_MULTIQC" ] && ViashError Bad arguments for option \'--aligner_clustering_multiqc\': \'$VIASH_PAR_ALIGNER_CLUSTERING_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALIGNER_CLUSTERING_MULTIQC="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --aligner_clustering_multiqc. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --aligner_clustering_multiqc=*)
            [ -n "$VIASH_PAR_ALIGNER_CLUSTERING_MULTIQC" ] && ViashError Bad arguments for option \'--aligner_clustering_multiqc=*\': \'$VIASH_PAR_ALIGNER_CLUSTERING_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ALIGNER_CLUSTERING_MULTIQC=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --pseudo_aligner_pca_multiqc)
            [ -n "$VIASH_PAR_PSEUDO_ALIGNER_PCA_MULTIQC" ] && ViashError Bad arguments for option \'--pseudo_aligner_pca_multiqc\': \'$VIASH_PAR_PSEUDO_ALIGNER_PCA_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PSEUDO_ALIGNER_PCA_MULTIQC="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --pseudo_aligner_pca_multiqc. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --pseudo_aligner_pca_multiqc=*)
            [ -n "$VIASH_PAR_PSEUDO_ALIGNER_PCA_MULTIQC" ] && ViashError Bad arguments for option \'--pseudo_aligner_pca_multiqc=*\': \'$VIASH_PAR_PSEUDO_ALIGNER_PCA_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PSEUDO_ALIGNER_PCA_MULTIQC=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --pseudo_aligner_clustering_multiqc)
            [ -n "$VIASH_PAR_PSEUDO_ALIGNER_CLUSTERING_MULTIQC" ] && ViashError Bad arguments for option \'--pseudo_aligner_clustering_multiqc\': \'$VIASH_PAR_PSEUDO_ALIGNER_CLUSTERING_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PSEUDO_ALIGNER_CLUSTERING_MULTIQC="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --pseudo_aligner_clustering_multiqc. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --pseudo_aligner_clustering_multiqc=*)
            [ -n "$VIASH_PAR_PSEUDO_ALIGNER_CLUSTERING_MULTIQC" ] && ViashError Bad arguments for option \'--pseudo_aligner_clustering_multiqc=*\': \'$VIASH_PAR_PSEUDO_ALIGNER_CLUSTERING_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PSEUDO_ALIGNER_CLUSTERING_MULTIQC=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --preseq_multiqc)
            if [ -z "$VIASH_PAR_PRESEQ_MULTIQC" ]; then
              VIASH_PAR_PRESEQ_MULTIQC="$2"
            else
              VIASH_PAR_PRESEQ_MULTIQC="$VIASH_PAR_PRESEQ_MULTIQC,""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --preseq_multiqc. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --preseq_multiqc=*)
            if [ -z "$VIASH_PAR_PRESEQ_MULTIQC" ]; then
              VIASH_PAR_PRESEQ_MULTIQC=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_PRESEQ_MULTIQC="$VIASH_PAR_PRESEQ_MULTIQC,"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --qualimap_multiqc)
            if [ -z "$VIASH_PAR_QUALIMAP_MULTIQC" ]; then
              VIASH_PAR_QUALIMAP_MULTIQC="$2"
            else
              VIASH_PAR_QUALIMAP_MULTIQC="$VIASH_PAR_QUALIMAP_MULTIQC,""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --qualimap_multiqc. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --qualimap_multiqc=*)
            if [ -z "$VIASH_PAR_QUALIMAP_MULTIQC" ]; then
              VIASH_PAR_QUALIMAP_MULTIQC=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_QUALIMAP_MULTIQC="$VIASH_PAR_QUALIMAP_MULTIQC,"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --dupradar_output_dup_intercept_mqc)
            if [ -z "$VIASH_PAR_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC" ]; then
              VIASH_PAR_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC="$2"
            else
              VIASH_PAR_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC="$VIASH_PAR_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC,""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --dupradar_output_dup_intercept_mqc. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --dupradar_output_dup_intercept_mqc=*)
            if [ -z "$VIASH_PAR_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC" ]; then
              VIASH_PAR_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC="$VIASH_PAR_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC,"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --dupradar_output_duprate_exp_denscurve_mqc)
            if [ -z "$VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC" ]; then
              VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC="$2"
            else
              VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC="$VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC,""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --dupradar_output_duprate_exp_denscurve_mqc. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --dupradar_output_duprate_exp_denscurve_mqc=*)
            if [ -z "$VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC" ]; then
              VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC="$VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC,"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --bamstat_multiqc)
            if [ -z "$VIASH_PAR_BAMSTAT_MULTIQC" ]; then
              VIASH_PAR_BAMSTAT_MULTIQC="$2"
            else
              VIASH_PAR_BAMSTAT_MULTIQC="$VIASH_PAR_BAMSTAT_MULTIQC,""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --bamstat_multiqc. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --bamstat_multiqc=*)
            if [ -z "$VIASH_PAR_BAMSTAT_MULTIQC" ]; then
              VIASH_PAR_BAMSTAT_MULTIQC=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_BAMSTAT_MULTIQC="$VIASH_PAR_BAMSTAT_MULTIQC,"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --inferexperiment_multiqc)
            if [ -z "$VIASH_PAR_INFEREXPERIMENT_MULTIQC" ]; then
              VIASH_PAR_INFEREXPERIMENT_MULTIQC="$2"
            else
              VIASH_PAR_INFEREXPERIMENT_MULTIQC="$VIASH_PAR_INFEREXPERIMENT_MULTIQC,""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --inferexperiment_multiqc. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --inferexperiment_multiqc=*)
            if [ -z "$VIASH_PAR_INFEREXPERIMENT_MULTIQC" ]; then
              VIASH_PAR_INFEREXPERIMENT_MULTIQC=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_INFEREXPERIMENT_MULTIQC="$VIASH_PAR_INFEREXPERIMENT_MULTIQC,"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --innerdistance_multiqc)
            if [ -z "$VIASH_PAR_INNERDISTANCE_MULTIQC" ]; then
              VIASH_PAR_INNERDISTANCE_MULTIQC="$2"
            else
              VIASH_PAR_INNERDISTANCE_MULTIQC="$VIASH_PAR_INNERDISTANCE_MULTIQC,""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --innerdistance_multiqc. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --innerdistance_multiqc=*)
            if [ -z "$VIASH_PAR_INNERDISTANCE_MULTIQC" ]; then
              VIASH_PAR_INNERDISTANCE_MULTIQC=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_INNERDISTANCE_MULTIQC="$VIASH_PAR_INNERDISTANCE_MULTIQC,"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --junctionannotation_multiqc)
            if [ -z "$VIASH_PAR_JUNCTIONANNOTATION_MULTIQC" ]; then
              VIASH_PAR_JUNCTIONANNOTATION_MULTIQC="$2"
            else
              VIASH_PAR_JUNCTIONANNOTATION_MULTIQC="$VIASH_PAR_JUNCTIONANNOTATION_MULTIQC,""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --junctionannotation_multiqc. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --junctionannotation_multiqc=*)
            if [ -z "$VIASH_PAR_JUNCTIONANNOTATION_MULTIQC" ]; then
              VIASH_PAR_JUNCTIONANNOTATION_MULTIQC=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_JUNCTIONANNOTATION_MULTIQC="$VIASH_PAR_JUNCTIONANNOTATION_MULTIQC,"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --junctionsaturation_multiqc)
            if [ -z "$VIASH_PAR_JUNCTIONSATURATION_MULTIQC" ]; then
              VIASH_PAR_JUNCTIONSATURATION_MULTIQC="$2"
            else
              VIASH_PAR_JUNCTIONSATURATION_MULTIQC="$VIASH_PAR_JUNCTIONSATURATION_MULTIQC,""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --junctionsaturation_multiqc. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --junctionsaturation_multiqc=*)
            if [ -z "$VIASH_PAR_JUNCTIONSATURATION_MULTIQC" ]; then
              VIASH_PAR_JUNCTIONSATURATION_MULTIQC=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_JUNCTIONSATURATION_MULTIQC="$VIASH_PAR_JUNCTIONSATURATION_MULTIQC,"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --readdistribution_multiqc)
            if [ -z "$VIASH_PAR_READDISTRIBUTION_MULTIQC" ]; then
              VIASH_PAR_READDISTRIBUTION_MULTIQC="$2"
            else
              VIASH_PAR_READDISTRIBUTION_MULTIQC="$VIASH_PAR_READDISTRIBUTION_MULTIQC,""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --readdistribution_multiqc. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --readdistribution_multiqc=*)
            if [ -z "$VIASH_PAR_READDISTRIBUTION_MULTIQC" ]; then
              VIASH_PAR_READDISTRIBUTION_MULTIQC=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_READDISTRIBUTION_MULTIQC="$VIASH_PAR_READDISTRIBUTION_MULTIQC,"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --readduplication_multiqc)
            if [ -z "$VIASH_PAR_READDUPLICATION_MULTIQC" ]; then
              VIASH_PAR_READDUPLICATION_MULTIQC="$2"
            else
              VIASH_PAR_READDUPLICATION_MULTIQC="$VIASH_PAR_READDUPLICATION_MULTIQC,""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --readduplication_multiqc. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --readduplication_multiqc=*)
            if [ -z "$VIASH_PAR_READDUPLICATION_MULTIQC" ]; then
              VIASH_PAR_READDUPLICATION_MULTIQC=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_READDUPLICATION_MULTIQC="$VIASH_PAR_READDUPLICATION_MULTIQC,"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --tin_multiqc)
            if [ -z "$VIASH_PAR_TIN_MULTIQC" ]; then
              VIASH_PAR_TIN_MULTIQC="$2"
            else
              VIASH_PAR_TIN_MULTIQC="$VIASH_PAR_TIN_MULTIQC,""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --tin_multiqc. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --tin_multiqc=*)
            if [ -z "$VIASH_PAR_TIN_MULTIQC" ]; then
              VIASH_PAR_TIN_MULTIQC=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_TIN_MULTIQC="$VIASH_PAR_TIN_MULTIQC,"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --multiqc_config)
            [ -n "$VIASH_PAR_MULTIQC_CONFIG" ] && ViashError Bad arguments for option \'--multiqc_config\': \'$VIASH_PAR_MULTIQC_CONFIG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MULTIQC_CONFIG="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --multiqc_config. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --multiqc_config=*)
            [ -n "$VIASH_PAR_MULTIQC_CONFIG" ] && ViashError Bad arguments for option \'--multiqc_config=*\': \'$VIASH_PAR_MULTIQC_CONFIG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MULTIQC_CONFIG=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --output)
            [ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --output. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --output=*)
            [ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output=*\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        ---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/prepare_multiqc_input:add_biobase_modules'
  fi

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

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

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

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

# setting computational defaults

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


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

# filling in defaults
if [ -z ${VIASH_PAR_OUTPUT+x} ]; then
  VIASH_PAR_OUTPUT="multiqc_input"
fi

# check whether required files exist
if [ ! -z "$VIASH_PAR_FASTQC_RAW_MULTIQC" ]; then
  IFS=','
  set -f
  for file in $VIASH_PAR_FASTQC_RAW_MULTIQC; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_FASTQC_TRIM_MULTIQC" ]; then
  IFS=','
  set -f
  for file in $VIASH_PAR_FASTQC_TRIM_MULTIQC; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_TRIM_LOG_MULTIQC" ]; then
  IFS=','
  set -f
  for file in $VIASH_PAR_TRIM_LOG_MULTIQC; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_SORTMERNA_MULTIQC" ]; then
  IFS=','
  set -f
  for file in $VIASH_PAR_SORTMERNA_MULTIQC; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_STAR_MULTIQC" ]; then
  IFS=','
  set -f
  for file in $VIASH_PAR_STAR_MULTIQC; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_SALMON_MULTIQC" ]; then
  IFS=','
  set -f
  for file in $VIASH_PAR_SALMON_MULTIQC; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_SAMTOOLS_STATS" ]; then
  IFS=','
  set -f
  for file in $VIASH_PAR_SAMTOOLS_STATS; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_SAMTOOLS_FLAGSTAT" ]; then
  IFS=','
  set -f
  for file in $VIASH_PAR_SAMTOOLS_FLAGSTAT; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_SAMTOOLS_IDXSTATS" ]; then
  IFS=','
  set -f
  for file in $VIASH_PAR_SAMTOOLS_IDXSTATS; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_MARKDUPLICATES_MULTIQC" ]; then
  IFS=','
  set -f
  for file in $VIASH_PAR_MARKDUPLICATES_MULTIQC; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_PSEUDO_MULTIQC" ]; then
  IFS=','
  set -f
  for file in $VIASH_PAR_PSEUDO_MULTIQC; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_FEATURECOUNTS_MULTIQC" ]; then
  IFS=','
  set -f
  for file in $VIASH_PAR_FEATURECOUNTS_MULTIQC; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_FEATURECOUNTS_RRNA_MULTIQC" ]; then
  IFS=','
  set -f
  for file in $VIASH_PAR_FEATURECOUNTS_RRNA_MULTIQC; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_ALIGNER_PCA_MULTIQC" ] && [ ! -e "$VIASH_PAR_ALIGNER_PCA_MULTIQC" ]; then
  ViashError "Input file '$VIASH_PAR_ALIGNER_PCA_MULTIQC' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_ALIGNER_CLUSTERING_MULTIQC" ] && [ ! -e "$VIASH_PAR_ALIGNER_CLUSTERING_MULTIQC" ]; then
  ViashError "Input file '$VIASH_PAR_ALIGNER_CLUSTERING_MULTIQC' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_PSEUDO_ALIGNER_PCA_MULTIQC" ] && [ ! -e "$VIASH_PAR_PSEUDO_ALIGNER_PCA_MULTIQC" ]; then
  ViashError "Input file '$VIASH_PAR_PSEUDO_ALIGNER_PCA_MULTIQC' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_PSEUDO_ALIGNER_CLUSTERING_MULTIQC" ] && [ ! -e "$VIASH_PAR_PSEUDO_ALIGNER_CLUSTERING_MULTIQC" ]; then
  ViashError "Input file '$VIASH_PAR_PSEUDO_ALIGNER_CLUSTERING_MULTIQC' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_PRESEQ_MULTIQC" ]; then
  IFS=','
  set -f
  for file in $VIASH_PAR_PRESEQ_MULTIQC; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_QUALIMAP_MULTIQC" ]; then
  IFS=','
  set -f
  for file in $VIASH_PAR_QUALIMAP_MULTIQC; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC" ]; then
  IFS=','
  set -f
  for file in $VIASH_PAR_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC" ]; then
  IFS=','
  set -f
  for file in $VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_BAMSTAT_MULTIQC" ]; then
  IFS=','
  set -f
  for file in $VIASH_PAR_BAMSTAT_MULTIQC; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_INFEREXPERIMENT_MULTIQC" ]; then
  IFS=','
  set -f
  for file in $VIASH_PAR_INFEREXPERIMENT_MULTIQC; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_INNERDISTANCE_MULTIQC" ]; then
  IFS=','
  set -f
  for file in $VIASH_PAR_INNERDISTANCE_MULTIQC; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_JUNCTIONANNOTATION_MULTIQC" ]; then
  IFS=','
  set -f
  for file in $VIASH_PAR_JUNCTIONANNOTATION_MULTIQC; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_JUNCTIONSATURATION_MULTIQC" ]; then
  IFS=','
  set -f
  for file in $VIASH_PAR_JUNCTIONSATURATION_MULTIQC; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_READDISTRIBUTION_MULTIQC" ]; then
  IFS=','
  set -f
  for file in $VIASH_PAR_READDISTRIBUTION_MULTIQC; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_READDUPLICATION_MULTIQC" ]; then
  IFS=','
  set -f
  for file in $VIASH_PAR_READDUPLICATION_MULTIQC; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_TIN_MULTIQC" ]; then
  IFS=','
  set -f
  for file in $VIASH_PAR_TIN_MULTIQC; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_MULTIQC_CONFIG" ] && [ ! -e "$VIASH_PAR_MULTIQC_CONFIG" ]; then
  ViashError "Input file '$VIASH_PAR_MULTIQC_CONFIG' does not exist."
  exit 1
fi

# check whether parameters values are of the right type
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_FASTQC_RAW_MULTIQC" ]; then
  VIASH_TEST_FASTQC_RAW_MULTIQC=()
  IFS=','
  for var in $VIASH_PAR_FASTQC_RAW_MULTIQC; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_FASTQC_RAW_MULTIQC+=( "$var" )
  done
  VIASH_PAR_FASTQC_RAW_MULTIQC=$(IFS=',' ; echo "${VIASH_TEST_FASTQC_RAW_MULTIQC[*]}")
fi
if [ ! -z "$VIASH_PAR_FASTQC_TRIM_MULTIQC" ]; then
  VIASH_TEST_FASTQC_TRIM_MULTIQC=()
  IFS=','
  for var in $VIASH_PAR_FASTQC_TRIM_MULTIQC; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_FASTQC_TRIM_MULTIQC+=( "$var" )
  done
  VIASH_PAR_FASTQC_TRIM_MULTIQC=$(IFS=',' ; echo "${VIASH_TEST_FASTQC_TRIM_MULTIQC[*]}")
fi
if [ ! -z "$VIASH_PAR_TRIM_LOG_MULTIQC" ]; then
  VIASH_TEST_TRIM_LOG_MULTIQC=()
  IFS=','
  for var in $VIASH_PAR_TRIM_LOG_MULTIQC; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_TRIM_LOG_MULTIQC+=( "$var" )
  done
  VIASH_PAR_TRIM_LOG_MULTIQC=$(IFS=',' ; echo "${VIASH_TEST_TRIM_LOG_MULTIQC[*]}")
fi
if [ ! -z "$VIASH_PAR_SORTMERNA_MULTIQC" ]; then
  VIASH_TEST_SORTMERNA_MULTIQC=()
  IFS=','
  for var in $VIASH_PAR_SORTMERNA_MULTIQC; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_SORTMERNA_MULTIQC+=( "$var" )
  done
  VIASH_PAR_SORTMERNA_MULTIQC=$(IFS=',' ; echo "${VIASH_TEST_SORTMERNA_MULTIQC[*]}")
fi
if [ ! -z "$VIASH_PAR_STAR_MULTIQC" ]; then
  VIASH_TEST_STAR_MULTIQC=()
  IFS=','
  for var in $VIASH_PAR_STAR_MULTIQC; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_STAR_MULTIQC+=( "$var" )
  done
  VIASH_PAR_STAR_MULTIQC=$(IFS=',' ; echo "${VIASH_TEST_STAR_MULTIQC[*]}")
fi
if [ ! -z "$VIASH_PAR_SALMON_MULTIQC" ]; then
  VIASH_TEST_SALMON_MULTIQC=()
  IFS=','
  for var in $VIASH_PAR_SALMON_MULTIQC; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_SALMON_MULTIQC+=( "$var" )
  done
  VIASH_PAR_SALMON_MULTIQC=$(IFS=',' ; echo "${VIASH_TEST_SALMON_MULTIQC[*]}")
fi
if [ ! -z "$VIASH_PAR_SAMTOOLS_STATS" ]; then
  VIASH_TEST_SAMTOOLS_STATS=()
  IFS=','
  for var in $VIASH_PAR_SAMTOOLS_STATS; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_SAMTOOLS_STATS+=( "$var" )
  done
  VIASH_PAR_SAMTOOLS_STATS=$(IFS=',' ; echo "${VIASH_TEST_SAMTOOLS_STATS[*]}")
fi
if [ ! -z "$VIASH_PAR_SAMTOOLS_FLAGSTAT" ]; then
  VIASH_TEST_SAMTOOLS_FLAGSTAT=()
  IFS=','
  for var in $VIASH_PAR_SAMTOOLS_FLAGSTAT; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_SAMTOOLS_FLAGSTAT+=( "$var" )
  done
  VIASH_PAR_SAMTOOLS_FLAGSTAT=$(IFS=',' ; echo "${VIASH_TEST_SAMTOOLS_FLAGSTAT[*]}")
fi
if [ ! -z "$VIASH_PAR_SAMTOOLS_IDXSTATS" ]; then
  VIASH_TEST_SAMTOOLS_IDXSTATS=()
  IFS=','
  for var in $VIASH_PAR_SAMTOOLS_IDXSTATS; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_SAMTOOLS_IDXSTATS+=( "$var" )
  done
  VIASH_PAR_SAMTOOLS_IDXSTATS=$(IFS=',' ; echo "${VIASH_TEST_SAMTOOLS_IDXSTATS[*]}")
fi
if [ ! -z "$VIASH_PAR_MARKDUPLICATES_MULTIQC" ]; then
  VIASH_TEST_MARKDUPLICATES_MULTIQC=()
  IFS=','
  for var in $VIASH_PAR_MARKDUPLICATES_MULTIQC; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_MARKDUPLICATES_MULTIQC+=( "$var" )
  done
  VIASH_PAR_MARKDUPLICATES_MULTIQC=$(IFS=',' ; echo "${VIASH_TEST_MARKDUPLICATES_MULTIQC[*]}")
fi
if [ ! -z "$VIASH_PAR_PSEUDO_MULTIQC" ]; then
  VIASH_TEST_PSEUDO_MULTIQC=()
  IFS=','
  for var in $VIASH_PAR_PSEUDO_MULTIQC; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_PSEUDO_MULTIQC+=( "$var" )
  done
  VIASH_PAR_PSEUDO_MULTIQC=$(IFS=',' ; echo "${VIASH_TEST_PSEUDO_MULTIQC[*]}")
fi
if [ ! -z "$VIASH_PAR_FEATURECOUNTS_MULTIQC" ]; then
  VIASH_TEST_FEATURECOUNTS_MULTIQC=()
  IFS=','
  for var in $VIASH_PAR_FEATURECOUNTS_MULTIQC; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_FEATURECOUNTS_MULTIQC+=( "$var" )
  done
  VIASH_PAR_FEATURECOUNTS_MULTIQC=$(IFS=',' ; echo "${VIASH_TEST_FEATURECOUNTS_MULTIQC[*]}")
fi
if [ ! -z "$VIASH_PAR_FEATURECOUNTS_RRNA_MULTIQC" ]; then
  VIASH_TEST_FEATURECOUNTS_RRNA_MULTIQC=()
  IFS=','
  for var in $VIASH_PAR_FEATURECOUNTS_RRNA_MULTIQC; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_FEATURECOUNTS_RRNA_MULTIQC+=( "$var" )
  done
  VIASH_PAR_FEATURECOUNTS_RRNA_MULTIQC=$(IFS=',' ; echo "${VIASH_TEST_FEATURECOUNTS_RRNA_MULTIQC[*]}")
fi
if [ ! -z "$VIASH_PAR_ALIGNER_PCA_MULTIQC" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_ALIGNER_PCA_MULTIQC")" )
  VIASH_PAR_ALIGNER_PCA_MULTIQC=$(ViashDockerAutodetectMount "$VIASH_PAR_ALIGNER_PCA_MULTIQC")
fi
if [ ! -z "$VIASH_PAR_ALIGNER_CLUSTERING_MULTIQC" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_ALIGNER_CLUSTERING_MULTIQC")" )
  VIASH_PAR_ALIGNER_CLUSTERING_MULTIQC=$(ViashDockerAutodetectMount "$VIASH_PAR_ALIGNER_CLUSTERING_MULTIQC")
fi
if [ ! -z "$VIASH_PAR_PSEUDO_ALIGNER_PCA_MULTIQC" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_PSEUDO_ALIGNER_PCA_MULTIQC")" )
  VIASH_PAR_PSEUDO_ALIGNER_PCA_MULTIQC=$(ViashDockerAutodetectMount "$VIASH_PAR_PSEUDO_ALIGNER_PCA_MULTIQC")
fi
if [ ! -z "$VIASH_PAR_PSEUDO_ALIGNER_CLUSTERING_MULTIQC" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_PSEUDO_ALIGNER_CLUSTERING_MULTIQC")" )
  VIASH_PAR_PSEUDO_ALIGNER_CLUSTERING_MULTIQC=$(ViashDockerAutodetectMount "$VIASH_PAR_PSEUDO_ALIGNER_CLUSTERING_MULTIQC")
fi
if [ ! -z "$VIASH_PAR_PRESEQ_MULTIQC" ]; then
  VIASH_TEST_PRESEQ_MULTIQC=()
  IFS=','
  for var in $VIASH_PAR_PRESEQ_MULTIQC; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_PRESEQ_MULTIQC+=( "$var" )
  done
  VIASH_PAR_PRESEQ_MULTIQC=$(IFS=',' ; echo "${VIASH_TEST_PRESEQ_MULTIQC[*]}")
fi
if [ ! -z "$VIASH_PAR_QUALIMAP_MULTIQC" ]; then
  VIASH_TEST_QUALIMAP_MULTIQC=()
  IFS=','
  for var in $VIASH_PAR_QUALIMAP_MULTIQC; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_QUALIMAP_MULTIQC+=( "$var" )
  done
  VIASH_PAR_QUALIMAP_MULTIQC=$(IFS=',' ; echo "${VIASH_TEST_QUALIMAP_MULTIQC[*]}")
fi
if [ ! -z "$VIASH_PAR_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC" ]; then
  VIASH_TEST_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC=()
  IFS=','
  for var in $VIASH_PAR_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC+=( "$var" )
  done
  VIASH_PAR_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC=$(IFS=',' ; echo "${VIASH_TEST_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC[*]}")
fi
if [ ! -z "$VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC" ]; then
  VIASH_TEST_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC=()
  IFS=','
  for var in $VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC+=( "$var" )
  done
  VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC=$(IFS=',' ; echo "${VIASH_TEST_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC[*]}")
fi
if [ ! -z "$VIASH_PAR_BAMSTAT_MULTIQC" ]; then
  VIASH_TEST_BAMSTAT_MULTIQC=()
  IFS=','
  for var in $VIASH_PAR_BAMSTAT_MULTIQC; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_BAMSTAT_MULTIQC+=( "$var" )
  done
  VIASH_PAR_BAMSTAT_MULTIQC=$(IFS=',' ; echo "${VIASH_TEST_BAMSTAT_MULTIQC[*]}")
fi
if [ ! -z "$VIASH_PAR_INFEREXPERIMENT_MULTIQC" ]; then
  VIASH_TEST_INFEREXPERIMENT_MULTIQC=()
  IFS=','
  for var in $VIASH_PAR_INFEREXPERIMENT_MULTIQC; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_INFEREXPERIMENT_MULTIQC+=( "$var" )
  done
  VIASH_PAR_INFEREXPERIMENT_MULTIQC=$(IFS=',' ; echo "${VIASH_TEST_INFEREXPERIMENT_MULTIQC[*]}")
fi
if [ ! -z "$VIASH_PAR_INNERDISTANCE_MULTIQC" ]; then
  VIASH_TEST_INNERDISTANCE_MULTIQC=()
  IFS=','
  for var in $VIASH_PAR_INNERDISTANCE_MULTIQC; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_INNERDISTANCE_MULTIQC+=( "$var" )
  done
  VIASH_PAR_INNERDISTANCE_MULTIQC=$(IFS=',' ; echo "${VIASH_TEST_INNERDISTANCE_MULTIQC[*]}")
fi
if [ ! -z "$VIASH_PAR_JUNCTIONANNOTATION_MULTIQC" ]; then
  VIASH_TEST_JUNCTIONANNOTATION_MULTIQC=()
  IFS=','
  for var in $VIASH_PAR_JUNCTIONANNOTATION_MULTIQC; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_JUNCTIONANNOTATION_MULTIQC+=( "$var" )
  done
  VIASH_PAR_JUNCTIONANNOTATION_MULTIQC=$(IFS=',' ; echo "${VIASH_TEST_JUNCTIONANNOTATION_MULTIQC[*]}")
fi
if [ ! -z "$VIASH_PAR_JUNCTIONSATURATION_MULTIQC" ]; then
  VIASH_TEST_JUNCTIONSATURATION_MULTIQC=()
  IFS=','
  for var in $VIASH_PAR_JUNCTIONSATURATION_MULTIQC; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_JUNCTIONSATURATION_MULTIQC+=( "$var" )
  done
  VIASH_PAR_JUNCTIONSATURATION_MULTIQC=$(IFS=',' ; echo "${VIASH_TEST_JUNCTIONSATURATION_MULTIQC[*]}")
fi
if [ ! -z "$VIASH_PAR_READDISTRIBUTION_MULTIQC" ]; then
  VIASH_TEST_READDISTRIBUTION_MULTIQC=()
  IFS=','
  for var in $VIASH_PAR_READDISTRIBUTION_MULTIQC; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_READDISTRIBUTION_MULTIQC+=( "$var" )
  done
  VIASH_PAR_READDISTRIBUTION_MULTIQC=$(IFS=',' ; echo "${VIASH_TEST_READDISTRIBUTION_MULTIQC[*]}")
fi
if [ ! -z "$VIASH_PAR_READDUPLICATION_MULTIQC" ]; then
  VIASH_TEST_READDUPLICATION_MULTIQC=()
  IFS=','
  for var in $VIASH_PAR_READDUPLICATION_MULTIQC; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_READDUPLICATION_MULTIQC+=( "$var" )
  done
  VIASH_PAR_READDUPLICATION_MULTIQC=$(IFS=',' ; echo "${VIASH_TEST_READDUPLICATION_MULTIQC[*]}")
fi
if [ ! -z "$VIASH_PAR_TIN_MULTIQC" ]; then
  VIASH_TEST_TIN_MULTIQC=()
  IFS=','
  for var in $VIASH_PAR_TIN_MULTIQC; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_TIN_MULTIQC+=( "$var" )
  done
  VIASH_PAR_TIN_MULTIQC=$(IFS=',' ; echo "${VIASH_TEST_TIN_MULTIQC[*]}")
fi
if [ ! -z "$VIASH_PAR_MULTIQC_CONFIG" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_MULTIQC_CONFIG")" )
  VIASH_PAR_MULTIQC_CONFIG=$(ViashDockerAutodetectMount "$VIASH_PAR_MULTIQC_CONFIG")
fi
if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT")" )
  VIASH_PAR_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT" )
fi
if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_RESOURCES_DIR")" )
  VIASH_META_RESOURCES_DIR=$(ViashDockerAutodetectMount "$VIASH_META_RESOURCES_DIR")
fi
if [ ! -z "$VIASH_META_EXECUTABLE" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_EXECUTABLE")" )
  VIASH_META_EXECUTABLE=$(ViashDockerAutodetectMount "$VIASH_META_EXECUTABLE")
fi
if [ ! -z "$VIASH_META_CONFIG" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_CONFIG")" )
  VIASH_META_CONFIG=$(ViashDockerAutodetectMount "$VIASH_META_CONFIG")
fi
if [ ! -z "$VIASH_META_TEMP_DIR" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_TEMP_DIR")" )
  VIASH_META_TEMP_DIR=$(ViashDockerAutodetectMount "$VIASH_META_TEMP_DIR")
fi
  
  # get unique mounts
  VIASH_UNIQUE_MOUNTS=($(for val in "${VIASH_DIRECTORY_MOUNTS[@]}"; do echo "$val"; done | sort -u))
fi

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

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

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


# set dependency paths


ViashDebug "Running command: $(echo $VIASH_CMD)"
cat << VIASHEOF | eval $VIASH_CMD
set -e
tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-prepare_multiqc_input-XXXXXX").sh
function clean_up {
  rm "\$tempscript"
}
function interrupt {
  echo -e "\nCTRL-C Pressed..."
  exit 1
}
trap clean_up EXIT
trap interrupt INT SIGINT
cat > "\$tempscript" << 'VIASHMAIN'
## VIASH START
# The following code has been auto-generated by Viash.
$( if [ ! -z ${VIASH_PAR_FAIL_TRIMMING_MULTIQC+x} ]; then echo "${VIASH_PAR_FAIL_TRIMMING_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_fail_trimming_multiqc='&'#" ; else echo "# par_fail_trimming_multiqc="; fi )
$( if [ ! -z ${VIASH_PAR_FAIL_MAPPING_MULTIQC+x} ]; then echo "${VIASH_PAR_FAIL_MAPPING_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_fail_mapping_multiqc='&'#" ; else echo "# par_fail_mapping_multiqc="; fi )
$( if [ ! -z ${VIASH_PAR_FAIL_STRAND_MULTIQC+x} ]; then echo "${VIASH_PAR_FAIL_STRAND_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_fail_strand_multiqc='&'#" ; else echo "# par_fail_strand_multiqc="; fi )
$( if [ ! -z ${VIASH_PAR_FASTQC_RAW_MULTIQC+x} ]; then echo "${VIASH_PAR_FASTQC_RAW_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_fastqc_raw_multiqc='&'#" ; else echo "# par_fastqc_raw_multiqc="; fi )
$( if [ ! -z ${VIASH_PAR_FASTQC_TRIM_MULTIQC+x} ]; then echo "${VIASH_PAR_FASTQC_TRIM_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_fastqc_trim_multiqc='&'#" ; else echo "# par_fastqc_trim_multiqc="; fi )
$( if [ ! -z ${VIASH_PAR_TRIM_LOG_MULTIQC+x} ]; then echo "${VIASH_PAR_TRIM_LOG_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_trim_log_multiqc='&'#" ; else echo "# par_trim_log_multiqc="; fi )
$( if [ ! -z ${VIASH_PAR_SORTMERNA_MULTIQC+x} ]; then echo "${VIASH_PAR_SORTMERNA_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_sortmerna_multiqc='&'#" ; else echo "# par_sortmerna_multiqc="; fi )
$( if [ ! -z ${VIASH_PAR_STAR_MULTIQC+x} ]; then echo "${VIASH_PAR_STAR_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_star_multiqc='&'#" ; else echo "# par_star_multiqc="; fi )
$( if [ ! -z ${VIASH_PAR_SALMON_MULTIQC+x} ]; then echo "${VIASH_PAR_SALMON_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_salmon_multiqc='&'#" ; else echo "# par_salmon_multiqc="; fi )
$( if [ ! -z ${VIASH_PAR_SAMTOOLS_STATS+x} ]; then echo "${VIASH_PAR_SAMTOOLS_STATS}" | sed "s#'#'\"'\"'#g;s#.*#par_samtools_stats='&'#" ; else echo "# par_samtools_stats="; fi )
$( if [ ! -z ${VIASH_PAR_SAMTOOLS_FLAGSTAT+x} ]; then echo "${VIASH_PAR_SAMTOOLS_FLAGSTAT}" | sed "s#'#'\"'\"'#g;s#.*#par_samtools_flagstat='&'#" ; else echo "# par_samtools_flagstat="; fi )
$( if [ ! -z ${VIASH_PAR_SAMTOOLS_IDXSTATS+x} ]; then echo "${VIASH_PAR_SAMTOOLS_IDXSTATS}" | sed "s#'#'\"'\"'#g;s#.*#par_samtools_idxstats='&'#" ; else echo "# par_samtools_idxstats="; fi )
$( if [ ! -z ${VIASH_PAR_MARKDUPLICATES_MULTIQC+x} ]; then echo "${VIASH_PAR_MARKDUPLICATES_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_markduplicates_multiqc='&'#" ; else echo "# par_markduplicates_multiqc="; fi )
$( if [ ! -z ${VIASH_PAR_PSEUDO_MULTIQC+x} ]; then echo "${VIASH_PAR_PSEUDO_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_pseudo_multiqc='&'#" ; else echo "# par_pseudo_multiqc="; fi )
$( if [ ! -z ${VIASH_PAR_FEATURECOUNTS_MULTIQC+x} ]; then echo "${VIASH_PAR_FEATURECOUNTS_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_featurecounts_multiqc='&'#" ; else echo "# par_featurecounts_multiqc="; fi )
$( if [ ! -z ${VIASH_PAR_FEATURECOUNTS_RRNA_MULTIQC+x} ]; then echo "${VIASH_PAR_FEATURECOUNTS_RRNA_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_featurecounts_rrna_multiqc='&'#" ; else echo "# par_featurecounts_rrna_multiqc="; fi )
$( if [ ! -z ${VIASH_PAR_ALIGNER_PCA_MULTIQC+x} ]; then echo "${VIASH_PAR_ALIGNER_PCA_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_aligner_pca_multiqc='&'#" ; else echo "# par_aligner_pca_multiqc="; fi )
$( if [ ! -z ${VIASH_PAR_ALIGNER_CLUSTERING_MULTIQC+x} ]; then echo "${VIASH_PAR_ALIGNER_CLUSTERING_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_aligner_clustering_multiqc='&'#" ; else echo "# par_aligner_clustering_multiqc="; fi )
$( if [ ! -z ${VIASH_PAR_PSEUDO_ALIGNER_PCA_MULTIQC+x} ]; then echo "${VIASH_PAR_PSEUDO_ALIGNER_PCA_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_pseudo_aligner_pca_multiqc='&'#" ; else echo "# par_pseudo_aligner_pca_multiqc="; fi )
$( if [ ! -z ${VIASH_PAR_PSEUDO_ALIGNER_CLUSTERING_MULTIQC+x} ]; then echo "${VIASH_PAR_PSEUDO_ALIGNER_CLUSTERING_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_pseudo_aligner_clustering_multiqc='&'#" ; else echo "# par_pseudo_aligner_clustering_multiqc="; fi )
$( if [ ! -z ${VIASH_PAR_PRESEQ_MULTIQC+x} ]; then echo "${VIASH_PAR_PRESEQ_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_preseq_multiqc='&'#" ; else echo "# par_preseq_multiqc="; fi )
$( if [ ! -z ${VIASH_PAR_QUALIMAP_MULTIQC+x} ]; then echo "${VIASH_PAR_QUALIMAP_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_qualimap_multiqc='&'#" ; else echo "# par_qualimap_multiqc="; fi )
$( if [ ! -z ${VIASH_PAR_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC+x} ]; then echo "${VIASH_PAR_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC}" | sed "s#'#'\"'\"'#g;s#.*#par_dupradar_output_dup_intercept_mqc='&'#" ; else echo "# par_dupradar_output_dup_intercept_mqc="; fi )
$( if [ ! -z ${VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC+x} ]; then echo "${VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC}" | sed "s#'#'\"'\"'#g;s#.*#par_dupradar_output_duprate_exp_denscurve_mqc='&'#" ; else echo "# par_dupradar_output_duprate_exp_denscurve_mqc="; fi )
$( if [ ! -z ${VIASH_PAR_BAMSTAT_MULTIQC+x} ]; then echo "${VIASH_PAR_BAMSTAT_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_bamstat_multiqc='&'#" ; else echo "# par_bamstat_multiqc="; fi )
$( if [ ! -z ${VIASH_PAR_INFEREXPERIMENT_MULTIQC+x} ]; then echo "${VIASH_PAR_INFEREXPERIMENT_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_inferexperiment_multiqc='&'#" ; else echo "# par_inferexperiment_multiqc="; fi )
$( if [ ! -z ${VIASH_PAR_INNERDISTANCE_MULTIQC+x} ]; then echo "${VIASH_PAR_INNERDISTANCE_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_innerdistance_multiqc='&'#" ; else echo "# par_innerdistance_multiqc="; fi )
$( if [ ! -z ${VIASH_PAR_JUNCTIONANNOTATION_MULTIQC+x} ]; then echo "${VIASH_PAR_JUNCTIONANNOTATION_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_junctionannotation_multiqc='&'#" ; else echo "# par_junctionannotation_multiqc="; fi )
$( if [ ! -z ${VIASH_PAR_JUNCTIONSATURATION_MULTIQC+x} ]; then echo "${VIASH_PAR_JUNCTIONSATURATION_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_junctionsaturation_multiqc='&'#" ; else echo "# par_junctionsaturation_multiqc="; fi )
$( if [ ! -z ${VIASH_PAR_READDISTRIBUTION_MULTIQC+x} ]; then echo "${VIASH_PAR_READDISTRIBUTION_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_readdistribution_multiqc='&'#" ; else echo "# par_readdistribution_multiqc="; fi )
$( if [ ! -z ${VIASH_PAR_READDUPLICATION_MULTIQC+x} ]; then echo "${VIASH_PAR_READDUPLICATION_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_readduplication_multiqc='&'#" ; else echo "# par_readduplication_multiqc="; fi )
$( if [ ! -z ${VIASH_PAR_TIN_MULTIQC+x} ]; then echo "${VIASH_PAR_TIN_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_tin_multiqc='&'#" ; else echo "# par_tin_multiqc="; fi )
$( if [ ! -z ${VIASH_PAR_MULTIQC_CONFIG+x} ]; then echo "${VIASH_PAR_MULTIQC_CONFIG}" | sed "s#'#'\"'\"'#g;s#.*#par_multiqc_config='&'#" ; else echo "# par_multiqc_config="; fi )
$( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "${VIASH_PAR_OUTPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_output='&'#" ; else echo "# par_output="; fi )
$( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi )
$( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi )
$( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "${VIASH_META_RESOURCES_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_resources_dir='&'#" ; else echo "# meta_resources_dir="; fi )
$( if [ ! -z ${VIASH_META_EXECUTABLE+x} ]; then echo "${VIASH_META_EXECUTABLE}" | sed "s#'#'\"'\"'#g;s#.*#meta_executable='&'#" ; else echo "# meta_executable="; fi )
$( if [ ! -z ${VIASH_META_CONFIG+x} ]; then echo "${VIASH_META_CONFIG}" | sed "s#'#'\"'\"'#g;s#.*#meta_config='&'#" ; else echo "# meta_config="; fi )
$( if [ ! -z ${VIASH_META_TEMP_DIR+x} ]; then echo "${VIASH_META_TEMP_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_temp_dir='&'#" ; else echo "# meta_temp_dir="; fi )
$( if [ ! -z ${VIASH_META_CPUS+x} ]; then echo "${VIASH_META_CPUS}" | sed "s#'#'\"'\"'#g;s#.*#meta_cpus='&'#" ; else echo "# meta_cpus="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_B+x} ]; then echo "${VIASH_META_MEMORY_B}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_b='&'#" ; else echo "# meta_memory_b="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_KB+x} ]; then echo "${VIASH_META_MEMORY_KB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_kb='&'#" ; else echo "# meta_memory_kb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_MB+x} ]; then echo "${VIASH_META_MEMORY_MB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_mb='&'#" ; else echo "# meta_memory_mb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_GB+x} ]; then echo "${VIASH_META_MEMORY_GB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_gb='&'#" ; else echo "# meta_memory_gb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_TB+x} ]; then echo "${VIASH_META_MEMORY_TB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_tb='&'#" ; else echo "# meta_memory_tb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_PB+x} ]; then echo "${VIASH_META_MEMORY_PB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_pb='&'#" ; else echo "# meta_memory_pb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_KIB+x} ]; then echo "${VIASH_META_MEMORY_KIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_kib='&'#" ; else echo "# meta_memory_kib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_MIB+x} ]; then echo "${VIASH_META_MEMORY_MIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_mib='&'#" ; else echo "# meta_memory_mib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_GIB+x} ]; then echo "${VIASH_META_MEMORY_GIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_gib='&'#" ; else echo "# meta_memory_gib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_TIB+x} ]; then echo "${VIASH_META_MEMORY_TIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_tib='&'#" ; else echo "# meta_memory_tib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_pib='&'#" ; else echo "# meta_memory_pib="; fi )

## VIASH END
#!/bin/bash

set -eo pipefail

mkdir -p \$par_output

echo \$par_fail_trimming_multiqc > \$par_output/fail_trimming_mqc.tsv
echo \$par_fail_mapping_multiqc > \$par_output/fail_mapping_mqc.tsv
echo \$par_fail_strand_multiqc > \$par_output/fail_strand_mqc.tsv

IFS="," read -ra fastqc_raw_multiqc <<< \$par_fastqc_raw_multiqc && for file in "\${fastqc_raw_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done

IFS="," read -ra fastqc_trim_multiqc <<< \$par_fastqc_trim_multiqc && for file in "\${fastqc_trim_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done

IFS="," read -ra trim_log_multiqc <<< \$par_trim_log_multiqc && for file in "\${trim_log_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done

IFS="," read -ra sortmerna_multiqc <<< \$par_sortmerna_multiqc && for file in "\${sortmerna_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done

IFS="," read -ra star_multiqc <<< \$par_star_multiqc && for file in "\${star_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done

# IFS="," read -ra hisat2_multiqc <<< \$par_hisat2_multiqc && for file in "\${hisat2_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done

IFS="," read -ra rsem_multiqc <<< \$par_rsem_multiqc && for file in "\${rsem_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done

IFS="," read -ra salmon_multiqc <<< \$par_salmon_multiqc && for file in "\${salmon_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done

IFS="," read -ra samtools_stats <<< \$par_samtools_stats && for file in "\${samtools_stats[@]}"; do [ -e "\$file" ] && cp -r "\$file" \$par_output/; done

IFS="," read -ra samtools_flagstat <<< \$par_samtools_flagstat && for file in "\${samtools_flagstat[@]}"; do [ -e "\$file" ] && cp -r "\$file" \$par_output/; done

IFS="," read -ra samtools_idxstats <<< \$par_samtools_idxstats && for file in "\${samtools_idxstats[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done

IFS="," read -ra markduplicates_multiqc <<< \$par_markduplicates_multiqc && for file in "\${markduplicates_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done

IFS="," read -ra pseudo_multiqc <<< \$par_pseudo_multiqc && for file in "\${pseudo_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done


IFS="," read -ra featurecounts_multiqc <<< \$par_featurecounts_multiqc && for file in "\${featurecounts_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done

IFS="," read -ra featurecounts_rrna_multiqc <<< \$par_featurecounts_rrna_multiqc&& for file in "\${featurecounts_rrna_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done

[ -e "\$par_aligner_pca_multiqc" ] && cp -r "\$par_aligner_pca_multiqc" "\$par_output/"

[ -e "\$par_aligner_clustering_multiqc" ] && cp -r \$par_aligner_clustering_multiqc "\$par_output/"

[ -e "\$par_pseudo_aligner_pca_multiqc" ] && cp -r \$par_pseudo_aligner_pca_multiqc "\$par_output/"

[ -e "\$par_pseudo_aligner_clustering_multiqc" ] && cp -r \$par_pseudo_aligner_clustering_multiqc "\$par_output/"

IFS="," read -ra preseq_multiqc <<< \$par_preseq_multiqc && for file in "\${preseq_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done

IFS="," read -ra qualimap_multiqc <<< \$par_qualimap_multiqc && for file in "\${qualimap_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done

IFS="," read -ra dupradar_output_dup_intercept_mqc <<< \$par_dupradar_output_dup_intercept_mqc && for file in "\${dupradar_output_dup_intercept_mqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done

IFS="," read -ra dupradar_output_duprate_exp_denscurve_mqc <<< \$par_dupradar_output_duprate_exp_denscurve_mqc && for file in "\${dupradar_output_duprate_exp_denscurve_mqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done

IFS="," read -ra bamstat_multiqc <<< \$par_bamstat_multiqc && for file in "\${bamstat_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done

IFS="," read -ra inferexperiment_multiqc <<< \$par_inferexperiment_multiqc && for file in "\${inferexperiment_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done

IFS="," read -ra innerdistance_multiqc <<< \$par_innerdistance_multiqc && for file in "\${innerdistance_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done

IFS="," read -ra junctionannotation_multiqc <<< \$par_junctionannotation_multiqc && for file in "\${junctionannotation_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done

IFS="," read -ra junctionsaturation_multiqc <<< \$par_junctionsaturation_multiqc && for file in "\${junctionsaturation_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done

IFS="," read -ra readdistribution_multiqc <<< \$par_readdistribution_multiqc && for file in "\${readdistribution_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done

IFS="," read -ra readduplication_multiqc <<< \$par_readduplication_multiqc && for file in "\${readduplication_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done

IFS="," read -ra tin_multiqc <<< \$par_tin_multiqc && for file in "\${tin_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done

[ -e "\$par_multiqc_config" ] && cp -r \$par_multiqc_config "\$par_output/"
VIASHMAIN
bash "\$tempscript" &
wait "\$!"

VIASHEOF


if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  # strip viash automount from file paths
  
  if [ ! -z "$VIASH_PAR_FASTQC_RAW_MULTIQC" ]; then
    unset VIASH_TEST_FASTQC_RAW_MULTIQC
    IFS=','
    for var in $VIASH_PAR_FASTQC_RAW_MULTIQC; do
      unset IFS
      if [ -z "$VIASH_TEST_FASTQC_RAW_MULTIQC" ]; then
      VIASH_TEST_FASTQC_RAW_MULTIQC="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_FASTQC_RAW_MULTIQC="$VIASH_TEST_FASTQC_RAW_MULTIQC,""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_FASTQC_RAW_MULTIQC="$VIASH_TEST_FASTQC_RAW_MULTIQC"
  fi
  if [ ! -z "$VIASH_PAR_FASTQC_TRIM_MULTIQC" ]; then
    unset VIASH_TEST_FASTQC_TRIM_MULTIQC
    IFS=','
    for var in $VIASH_PAR_FASTQC_TRIM_MULTIQC; do
      unset IFS
      if [ -z "$VIASH_TEST_FASTQC_TRIM_MULTIQC" ]; then
      VIASH_TEST_FASTQC_TRIM_MULTIQC="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_FASTQC_TRIM_MULTIQC="$VIASH_TEST_FASTQC_TRIM_MULTIQC,""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_FASTQC_TRIM_MULTIQC="$VIASH_TEST_FASTQC_TRIM_MULTIQC"
  fi
  if [ ! -z "$VIASH_PAR_TRIM_LOG_MULTIQC" ]; then
    unset VIASH_TEST_TRIM_LOG_MULTIQC
    IFS=','
    for var in $VIASH_PAR_TRIM_LOG_MULTIQC; do
      unset IFS
      if [ -z "$VIASH_TEST_TRIM_LOG_MULTIQC" ]; then
      VIASH_TEST_TRIM_LOG_MULTIQC="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_TRIM_LOG_MULTIQC="$VIASH_TEST_TRIM_LOG_MULTIQC,""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_TRIM_LOG_MULTIQC="$VIASH_TEST_TRIM_LOG_MULTIQC"
  fi
  if [ ! -z "$VIASH_PAR_SORTMERNA_MULTIQC" ]; then
    unset VIASH_TEST_SORTMERNA_MULTIQC
    IFS=','
    for var in $VIASH_PAR_SORTMERNA_MULTIQC; do
      unset IFS
      if [ -z "$VIASH_TEST_SORTMERNA_MULTIQC" ]; then
      VIASH_TEST_SORTMERNA_MULTIQC="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_SORTMERNA_MULTIQC="$VIASH_TEST_SORTMERNA_MULTIQC,""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_SORTMERNA_MULTIQC="$VIASH_TEST_SORTMERNA_MULTIQC"
  fi
  if [ ! -z "$VIASH_PAR_STAR_MULTIQC" ]; then
    unset VIASH_TEST_STAR_MULTIQC
    IFS=','
    for var in $VIASH_PAR_STAR_MULTIQC; do
      unset IFS
      if [ -z "$VIASH_TEST_STAR_MULTIQC" ]; then
      VIASH_TEST_STAR_MULTIQC="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_STAR_MULTIQC="$VIASH_TEST_STAR_MULTIQC,""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_STAR_MULTIQC="$VIASH_TEST_STAR_MULTIQC"
  fi
  if [ ! -z "$VIASH_PAR_SALMON_MULTIQC" ]; then
    unset VIASH_TEST_SALMON_MULTIQC
    IFS=','
    for var in $VIASH_PAR_SALMON_MULTIQC; do
      unset IFS
      if [ -z "$VIASH_TEST_SALMON_MULTIQC" ]; then
      VIASH_TEST_SALMON_MULTIQC="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_SALMON_MULTIQC="$VIASH_TEST_SALMON_MULTIQC,""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_SALMON_MULTIQC="$VIASH_TEST_SALMON_MULTIQC"
  fi
  if [ ! -z "$VIASH_PAR_SAMTOOLS_STATS" ]; then
    unset VIASH_TEST_SAMTOOLS_STATS
    IFS=','
    for var in $VIASH_PAR_SAMTOOLS_STATS; do
      unset IFS
      if [ -z "$VIASH_TEST_SAMTOOLS_STATS" ]; then
      VIASH_TEST_SAMTOOLS_STATS="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_SAMTOOLS_STATS="$VIASH_TEST_SAMTOOLS_STATS,""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_SAMTOOLS_STATS="$VIASH_TEST_SAMTOOLS_STATS"
  fi
  if [ ! -z "$VIASH_PAR_SAMTOOLS_FLAGSTAT" ]; then
    unset VIASH_TEST_SAMTOOLS_FLAGSTAT
    IFS=','
    for var in $VIASH_PAR_SAMTOOLS_FLAGSTAT; do
      unset IFS
      if [ -z "$VIASH_TEST_SAMTOOLS_FLAGSTAT" ]; then
      VIASH_TEST_SAMTOOLS_FLAGSTAT="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_SAMTOOLS_FLAGSTAT="$VIASH_TEST_SAMTOOLS_FLAGSTAT,""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_SAMTOOLS_FLAGSTAT="$VIASH_TEST_SAMTOOLS_FLAGSTAT"
  fi
  if [ ! -z "$VIASH_PAR_SAMTOOLS_IDXSTATS" ]; then
    unset VIASH_TEST_SAMTOOLS_IDXSTATS
    IFS=','
    for var in $VIASH_PAR_SAMTOOLS_IDXSTATS; do
      unset IFS
      if [ -z "$VIASH_TEST_SAMTOOLS_IDXSTATS" ]; then
      VIASH_TEST_SAMTOOLS_IDXSTATS="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_SAMTOOLS_IDXSTATS="$VIASH_TEST_SAMTOOLS_IDXSTATS,""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_SAMTOOLS_IDXSTATS="$VIASH_TEST_SAMTOOLS_IDXSTATS"
  fi
  if [ ! -z "$VIASH_PAR_MARKDUPLICATES_MULTIQC" ]; then
    unset VIASH_TEST_MARKDUPLICATES_MULTIQC
    IFS=','
    for var in $VIASH_PAR_MARKDUPLICATES_MULTIQC; do
      unset IFS
      if [ -z "$VIASH_TEST_MARKDUPLICATES_MULTIQC" ]; then
      VIASH_TEST_MARKDUPLICATES_MULTIQC="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_MARKDUPLICATES_MULTIQC="$VIASH_TEST_MARKDUPLICATES_MULTIQC,""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_MARKDUPLICATES_MULTIQC="$VIASH_TEST_MARKDUPLICATES_MULTIQC"
  fi
  if [ ! -z "$VIASH_PAR_PSEUDO_MULTIQC" ]; then
    unset VIASH_TEST_PSEUDO_MULTIQC
    IFS=','
    for var in $VIASH_PAR_PSEUDO_MULTIQC; do
      unset IFS
      if [ -z "$VIASH_TEST_PSEUDO_MULTIQC" ]; then
      VIASH_TEST_PSEUDO_MULTIQC="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_PSEUDO_MULTIQC="$VIASH_TEST_PSEUDO_MULTIQC,""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_PSEUDO_MULTIQC="$VIASH_TEST_PSEUDO_MULTIQC"
  fi
  if [ ! -z "$VIASH_PAR_FEATURECOUNTS_MULTIQC" ]; then
    unset VIASH_TEST_FEATURECOUNTS_MULTIQC
    IFS=','
    for var in $VIASH_PAR_FEATURECOUNTS_MULTIQC; do
      unset IFS
      if [ -z "$VIASH_TEST_FEATURECOUNTS_MULTIQC" ]; then
      VIASH_TEST_FEATURECOUNTS_MULTIQC="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_FEATURECOUNTS_MULTIQC="$VIASH_TEST_FEATURECOUNTS_MULTIQC,""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_FEATURECOUNTS_MULTIQC="$VIASH_TEST_FEATURECOUNTS_MULTIQC"
  fi
  if [ ! -z "$VIASH_PAR_FEATURECOUNTS_RRNA_MULTIQC" ]; then
    unset VIASH_TEST_FEATURECOUNTS_RRNA_MULTIQC
    IFS=','
    for var in $VIASH_PAR_FEATURECOUNTS_RRNA_MULTIQC; do
      unset IFS
      if [ -z "$VIASH_TEST_FEATURECOUNTS_RRNA_MULTIQC" ]; then
      VIASH_TEST_FEATURECOUNTS_RRNA_MULTIQC="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_FEATURECOUNTS_RRNA_MULTIQC="$VIASH_TEST_FEATURECOUNTS_RRNA_MULTIQC,""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_FEATURECOUNTS_RRNA_MULTIQC="$VIASH_TEST_FEATURECOUNTS_RRNA_MULTIQC"
  fi
  if [ ! -z "$VIASH_PAR_ALIGNER_PCA_MULTIQC" ]; then
    VIASH_PAR_ALIGNER_PCA_MULTIQC=$(ViashDockerStripAutomount "$VIASH_PAR_ALIGNER_PCA_MULTIQC")
  fi
  if [ ! -z "$VIASH_PAR_ALIGNER_CLUSTERING_MULTIQC" ]; then
    VIASH_PAR_ALIGNER_CLUSTERING_MULTIQC=$(ViashDockerStripAutomount "$VIASH_PAR_ALIGNER_CLUSTERING_MULTIQC")
  fi
  if [ ! -z "$VIASH_PAR_PSEUDO_ALIGNER_PCA_MULTIQC" ]; then
    VIASH_PAR_PSEUDO_ALIGNER_PCA_MULTIQC=$(ViashDockerStripAutomount "$VIASH_PAR_PSEUDO_ALIGNER_PCA_MULTIQC")
  fi
  if [ ! -z "$VIASH_PAR_PSEUDO_ALIGNER_CLUSTERING_MULTIQC" ]; then
    VIASH_PAR_PSEUDO_ALIGNER_CLUSTERING_MULTIQC=$(ViashDockerStripAutomount "$VIASH_PAR_PSEUDO_ALIGNER_CLUSTERING_MULTIQC")
  fi
  if [ ! -z "$VIASH_PAR_PRESEQ_MULTIQC" ]; then
    unset VIASH_TEST_PRESEQ_MULTIQC
    IFS=','
    for var in $VIASH_PAR_PRESEQ_MULTIQC; do
      unset IFS
      if [ -z "$VIASH_TEST_PRESEQ_MULTIQC" ]; then
      VIASH_TEST_PRESEQ_MULTIQC="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_PRESEQ_MULTIQC="$VIASH_TEST_PRESEQ_MULTIQC,""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_PRESEQ_MULTIQC="$VIASH_TEST_PRESEQ_MULTIQC"
  fi
  if [ ! -z "$VIASH_PAR_QUALIMAP_MULTIQC" ]; then
    unset VIASH_TEST_QUALIMAP_MULTIQC
    IFS=','
    for var in $VIASH_PAR_QUALIMAP_MULTIQC; do
      unset IFS
      if [ -z "$VIASH_TEST_QUALIMAP_MULTIQC" ]; then
      VIASH_TEST_QUALIMAP_MULTIQC="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_QUALIMAP_MULTIQC="$VIASH_TEST_QUALIMAP_MULTIQC,""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_QUALIMAP_MULTIQC="$VIASH_TEST_QUALIMAP_MULTIQC"
  fi
  if [ ! -z "$VIASH_PAR_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC" ]; then
    unset VIASH_TEST_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC
    IFS=','
    for var in $VIASH_PAR_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC; do
      unset IFS
      if [ -z "$VIASH_TEST_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC" ]; then
      VIASH_TEST_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC="$VIASH_TEST_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC,""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC="$VIASH_TEST_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC"
  fi
  if [ ! -z "$VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC" ]; then
    unset VIASH_TEST_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC
    IFS=','
    for var in $VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC; do
      unset IFS
      if [ -z "$VIASH_TEST_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC" ]; then
      VIASH_TEST_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC="$VIASH_TEST_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC,""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC="$VIASH_TEST_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC"
  fi
  if [ ! -z "$VIASH_PAR_BAMSTAT_MULTIQC" ]; then
    unset VIASH_TEST_BAMSTAT_MULTIQC
    IFS=','
    for var in $VIASH_PAR_BAMSTAT_MULTIQC; do
      unset IFS
      if [ -z "$VIASH_TEST_BAMSTAT_MULTIQC" ]; then
      VIASH_TEST_BAMSTAT_MULTIQC="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_BAMSTAT_MULTIQC="$VIASH_TEST_BAMSTAT_MULTIQC,""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_BAMSTAT_MULTIQC="$VIASH_TEST_BAMSTAT_MULTIQC"
  fi
  if [ ! -z "$VIASH_PAR_INFEREXPERIMENT_MULTIQC" ]; then
    unset VIASH_TEST_INFEREXPERIMENT_MULTIQC
    IFS=','
    for var in $VIASH_PAR_INFEREXPERIMENT_MULTIQC; do
      unset IFS
      if [ -z "$VIASH_TEST_INFEREXPERIMENT_MULTIQC" ]; then
      VIASH_TEST_INFEREXPERIMENT_MULTIQC="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_INFEREXPERIMENT_MULTIQC="$VIASH_TEST_INFEREXPERIMENT_MULTIQC,""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_INFEREXPERIMENT_MULTIQC="$VIASH_TEST_INFEREXPERIMENT_MULTIQC"
  fi
  if [ ! -z "$VIASH_PAR_INNERDISTANCE_MULTIQC" ]; then
    unset VIASH_TEST_INNERDISTANCE_MULTIQC
    IFS=','
    for var in $VIASH_PAR_INNERDISTANCE_MULTIQC; do
      unset IFS
      if [ -z "$VIASH_TEST_INNERDISTANCE_MULTIQC" ]; then
      VIASH_TEST_INNERDISTANCE_MULTIQC="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_INNERDISTANCE_MULTIQC="$VIASH_TEST_INNERDISTANCE_MULTIQC,""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_INNERDISTANCE_MULTIQC="$VIASH_TEST_INNERDISTANCE_MULTIQC"
  fi
  if [ ! -z "$VIASH_PAR_JUNCTIONANNOTATION_MULTIQC" ]; then
    unset VIASH_TEST_JUNCTIONANNOTATION_MULTIQC
    IFS=','
    for var in $VIASH_PAR_JUNCTIONANNOTATION_MULTIQC; do
      unset IFS
      if [ -z "$VIASH_TEST_JUNCTIONANNOTATION_MULTIQC" ]; then
      VIASH_TEST_JUNCTIONANNOTATION_MULTIQC="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_JUNCTIONANNOTATION_MULTIQC="$VIASH_TEST_JUNCTIONANNOTATION_MULTIQC,""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_JUNCTIONANNOTATION_MULTIQC="$VIASH_TEST_JUNCTIONANNOTATION_MULTIQC"
  fi
  if [ ! -z "$VIASH_PAR_JUNCTIONSATURATION_MULTIQC" ]; then
    unset VIASH_TEST_JUNCTIONSATURATION_MULTIQC
    IFS=','
    for var in $VIASH_PAR_JUNCTIONSATURATION_MULTIQC; do
      unset IFS
      if [ -z "$VIASH_TEST_JUNCTIONSATURATION_MULTIQC" ]; then
      VIASH_TEST_JUNCTIONSATURATION_MULTIQC="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_JUNCTIONSATURATION_MULTIQC="$VIASH_TEST_JUNCTIONSATURATION_MULTIQC,""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_JUNCTIONSATURATION_MULTIQC="$VIASH_TEST_JUNCTIONSATURATION_MULTIQC"
  fi
  if [ ! -z "$VIASH_PAR_READDISTRIBUTION_MULTIQC" ]; then
    unset VIASH_TEST_READDISTRIBUTION_MULTIQC
    IFS=','
    for var in $VIASH_PAR_READDISTRIBUTION_MULTIQC; do
      unset IFS
      if [ -z "$VIASH_TEST_READDISTRIBUTION_MULTIQC" ]; then
      VIASH_TEST_READDISTRIBUTION_MULTIQC="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_READDISTRIBUTION_MULTIQC="$VIASH_TEST_READDISTRIBUTION_MULTIQC,""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_READDISTRIBUTION_MULTIQC="$VIASH_TEST_READDISTRIBUTION_MULTIQC"
  fi
  if [ ! -z "$VIASH_PAR_READDUPLICATION_MULTIQC" ]; then
    unset VIASH_TEST_READDUPLICATION_MULTIQC
    IFS=','
    for var in $VIASH_PAR_READDUPLICATION_MULTIQC; do
      unset IFS
      if [ -z "$VIASH_TEST_READDUPLICATION_MULTIQC" ]; then
      VIASH_TEST_READDUPLICATION_MULTIQC="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_READDUPLICATION_MULTIQC="$VIASH_TEST_READDUPLICATION_MULTIQC,""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_READDUPLICATION_MULTIQC="$VIASH_TEST_READDUPLICATION_MULTIQC"
  fi
  if [ ! -z "$VIASH_PAR_TIN_MULTIQC" ]; then
    unset VIASH_TEST_TIN_MULTIQC
    IFS=','
    for var in $VIASH_PAR_TIN_MULTIQC; do
      unset IFS
      if [ -z "$VIASH_TEST_TIN_MULTIQC" ]; then
      VIASH_TEST_TIN_MULTIQC="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_TIN_MULTIQC="$VIASH_TEST_TIN_MULTIQC,""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_TIN_MULTIQC="$VIASH_TEST_TIN_MULTIQC"
  fi
  if [ ! -z "$VIASH_PAR_MULTIQC_CONFIG" ]; then
    VIASH_PAR_MULTIQC_CONFIG=$(ViashDockerStripAutomount "$VIASH_PAR_MULTIQC_CONFIG")
  fi
  if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
    VIASH_PAR_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT")
  fi
  if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
    VIASH_META_RESOURCES_DIR=$(ViashDockerStripAutomount "$VIASH_META_RESOURCES_DIR")
  fi
  if [ ! -z "$VIASH_META_EXECUTABLE" ]; then
    VIASH_META_EXECUTABLE=$(ViashDockerStripAutomount "$VIASH_META_EXECUTABLE")
  fi
  if [ ! -z "$VIASH_META_CONFIG" ]; then
    VIASH_META_CONFIG=$(ViashDockerStripAutomount "$VIASH_META_CONFIG")
  fi
  if [ ! -z "$VIASH_META_TEMP_DIR" ]; then
    VIASH_META_TEMP_DIR=$(ViashDockerStripAutomount "$VIASH_META_TEMP_DIR")
  fi
fi


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


exit 0
