#!/usr/bin/env bash

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

set -e

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

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

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

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

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

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

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

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

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

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

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

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

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

# define meta fields
VIASH_META_NAME="parallel_map"
VIASH_META_FUNCTIONALITY_NAME="parallel_map"
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 "parallel_map runner_multiple_input_directories"
  echo ""
  echo "Map wells in batch, using STAR"
  echo "Spliced Transcripts Alignment to a Reference (C) Alexander Dobin"
  echo "https://github.com/alexdobin/STAR"
  echo ""
  echo "Input arguments:"
  echo "    --input_r1"
  echo "        type: file, required parameter, multiple values allowed, file must exist"
  echo "        Input FASTQ files for the forward reads. All FASTQ file names must start"
  echo "        with the prefix '{well_id}_R1', where"
  echo "        'well_id' can be found as the sequence identifier in the barcodes FASTA"
  echo "        file (see 'barcodesFasta' argument)."
  echo "        For each FASTQ file, a matching FASTQ file for the reverse reads must be"
  echo "        provided to the 'input_r2' argument,"
  echo "        meaning that their 'well_id' prefix must match. The number of items"
  echo "        provided for 'input_r1' must be equal"
  echo "        to the number of items for 'input_r2'."
  echo ""
  echo "    --input_r2"
  echo "        type: file, required parameter, multiple values allowed, file must exist"
  echo "        Input FASTQ files for the reverse reads. All FASTQ file names must start"
  echo "        with the prefix '{well_id}_R2', where"
  echo "        'well_id' can be found as the sequence identifier in the barcodes FASTA"
  echo "        file (see 'barcodesFasta' argument)."
  echo "        For each FASTQ file, a matching FASTQ file for the reverse reads must be"
  echo "        provided to the 'input_r1' argument,"
  echo "        meaning that their 'well_id' prefix must match. The number of items"
  echo "        provided for 'input_r1' must be equal"
  echo "        to the number of items for 'input_r2'."
  echo ""
  echo "    --genomeDir"
  echo "        type: file, required parameter, file must exist"
  echo "        Reference genome to match to. Can be generated from genomic FASTA"
  echo "        sequences and a genome annotation"
  echo "        by using STAR with '--runMode genomeGenerate'."
  echo ""
  echo "    --barcodesFasta"
  echo "        type: file, required parameter, file must exist"
  echo "        FASTA file where each entry specifies a unique barcode sequence present"
  echo "        at the start of the forward input reads"
  echo "        (input_r1). The IDs of each barcode (the start of the FASTA headers up"
  echo "        until the first whitespace character) must"
  echo "        match with the start of one input FASTQ pair."
  echo ""
  echo "Barcode arguments:"
  echo "    --umiLength"
  echo "        type: integer, required parameter"
  echo "        Length of the Unique Molecular Identifiers (UMI). The UMI are expected"
  echo "        to be located after the barcodes in the"
  echo "        forwards reads."
  echo ""
  echo "    --limitBAMsortRAM"
  echo "        type: string"
  echo "        default: 10000000000"
  echo ""
  echo "Runtime arguments:"
  echo "    --runThreadN"
  echo "        type: integer"
  echo "        default: 1"
  echo "        Number of threads to use for a single STAR execution."
  echo ""
  echo "Output arguments:"
  echo "    --output"
  echo "        type: file, required parameter, multiple values allowed, output, file"
  echo "must exist"
  echo "        default: ./*"
  echo "        A list of output folders which are the result of using STAR to map each"
  echo "        input FASTQ pair STAR to the reference genome."
  echo "        The order of the items DO NOT match with the order of the entries in the"
  echo "        barcodes FASTA file or the input FASTQ pairs."
  echo ""
  echo "    --joblog"
  echo "        type: file, output, file must exist"
  echo "        default: execution_log.txt"
  echo "        Where to store the log file listing all the jobs."
}

# 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 debian:stable-slim
ENTRYPOINT []
RUN apt-get update && \
  DEBIAN_FRONTEND=noninteractive apt-get install -y procps wget automake make gcc g++ zlib1g-dev parallel file seqkit && \
  rm -rf /var/lib/apt/lists/*

ARG STAR_V
ENV STAR_SOURCE="https://github.com/alexdobin/STAR/archive/refs/tags/$STAR_V.tar.gz"
ENV STAR_TARGET="/app/star-$STAR_V.tar.gz"
ENV STAR_INSTALL_DIR="/app/STAR-$STAR_V"
ENV STAR_BINARY=STAR
COPY STAR /usr/local/bin/$STAR_BINARY
LABEL org.opencontainers.image.authors="Dries Schaumont, Toni Verbeiren"
LABEL org.opencontainers.image.description="Companion container for running component parallel_map"
LABEL org.opencontainers.image.created="2025-02-11T19:25:23Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="fc48924aa82d885ede794fd8e19a3514206bbd2d"
LABEL org.opencontainers.image.version="runner_multiple_input_directories"

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 "--build-arg 'STAR_V=2.7.6a'"
  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 "$1")"
            shift 1
            ;;
        --version)
            echo "parallel_map runner_multiple_input_directories"
            exit
            ;;
        --input_r1)
            if [ -z "$VIASH_PAR_INPUT_R1" ]; then
              VIASH_PAR_INPUT_R1="$2"
            else
              VIASH_PAR_INPUT_R1="$VIASH_PAR_INPUT_R1;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --input_r1. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --input_r1=*)
            if [ -z "$VIASH_PAR_INPUT_R1" ]; then
              VIASH_PAR_INPUT_R1=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_INPUT_R1="$VIASH_PAR_INPUT_R1;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --input_r2)
            if [ -z "$VIASH_PAR_INPUT_R2" ]; then
              VIASH_PAR_INPUT_R2="$2"
            else
              VIASH_PAR_INPUT_R2="$VIASH_PAR_INPUT_R2;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --input_r2. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --input_r2=*)
            if [ -z "$VIASH_PAR_INPUT_R2" ]; then
              VIASH_PAR_INPUT_R2=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_INPUT_R2="$VIASH_PAR_INPUT_R2;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --genomeDir)
            [ -n "$VIASH_PAR_GENOMEDIR" ] && ViashError Bad arguments for option \'--genomeDir\': \'$VIASH_PAR_GENOMEDIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_GENOMEDIR="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --genomeDir. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --genomeDir=*)
            [ -n "$VIASH_PAR_GENOMEDIR" ] && ViashError Bad arguments for option \'--genomeDir=*\': \'$VIASH_PAR_GENOMEDIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_GENOMEDIR=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --barcodesFasta)
            [ -n "$VIASH_PAR_BARCODESFASTA" ] && ViashError Bad arguments for option \'--barcodesFasta\': \'$VIASH_PAR_BARCODESFASTA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_BARCODESFASTA="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --barcodesFasta. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --barcodesFasta=*)
            [ -n "$VIASH_PAR_BARCODESFASTA" ] && ViashError Bad arguments for option \'--barcodesFasta=*\': \'$VIASH_PAR_BARCODESFASTA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_BARCODESFASTA=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --umiLength)
            [ -n "$VIASH_PAR_UMILENGTH" ] && ViashError Bad arguments for option \'--umiLength\': \'$VIASH_PAR_UMILENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_UMILENGTH="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --umiLength. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --umiLength=*)
            [ -n "$VIASH_PAR_UMILENGTH" ] && ViashError Bad arguments for option \'--umiLength=*\': \'$VIASH_PAR_UMILENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_UMILENGTH=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --limitBAMsortRAM)
            [ -n "$VIASH_PAR_LIMITBAMSORTRAM" ] && ViashError Bad arguments for option \'--limitBAMsortRAM\': \'$VIASH_PAR_LIMITBAMSORTRAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LIMITBAMSORTRAM="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --limitBAMsortRAM. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --limitBAMsortRAM=*)
            [ -n "$VIASH_PAR_LIMITBAMSORTRAM" ] && ViashError Bad arguments for option \'--limitBAMsortRAM=*\': \'$VIASH_PAR_LIMITBAMSORTRAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LIMITBAMSORTRAM=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --runThreadN)
            [ -n "$VIASH_PAR_RUNTHREADN" ] && ViashError Bad arguments for option \'--runThreadN\': \'$VIASH_PAR_RUNTHREADN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_RUNTHREADN="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --runThreadN. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --runThreadN=*)
            [ -n "$VIASH_PAR_RUNTHREADN" ] && ViashError Bad arguments for option \'--runThreadN=*\': \'$VIASH_PAR_RUNTHREADN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_RUNTHREADN=$(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 "$1")
            shift 1
            ;;
        --joblog)
            [ -n "$VIASH_PAR_JOBLOG" ] && ViashError Bad arguments for option \'--joblog\': \'$VIASH_PAR_JOBLOG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_JOBLOG="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --joblog. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --joblog=*)
            [ -n "$VIASH_PAR_JOBLOG" ] && ViashError Bad arguments for option \'--joblog=*\': \'$VIASH_PAR_JOBLOG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_JOBLOG=$(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/htrnaseq/parallel_map:runner_multiple_input_directories'
  fi

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

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

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

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

# setting computational defaults

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


# check whether required parameters exist
if [ -z ${VIASH_PAR_INPUT_R1+x} ]; then
  ViashError '--input_r1' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_PAR_INPUT_R2+x} ]; then
  ViashError '--input_r2' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_PAR_GENOMEDIR+x} ]; then
  ViashError '--genomeDir' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_PAR_BARCODESFASTA+x} ]; then
  ViashError '--barcodesFasta' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_PAR_UMILENGTH+x} ]; then
  ViashError '--umiLength' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_PAR_OUTPUT+x} ]; then
  ViashError '--output' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_NAME+x} ]; then
  ViashError 'name' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then
  ViashError 'functionality_name' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_RESOURCES_DIR+x} ]; then
  ViashError 'resources_dir' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_EXECUTABLE+x} ]; then
  ViashError 'executable' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_CONFIG+x} ]; then
  ViashError 'config' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_TEMP_DIR+x} ]; then
  ViashError 'temp_dir' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi

# filling in defaults
if [ -z ${VIASH_PAR_LIMITBAMSORTRAM+x} ]; then
  VIASH_PAR_LIMITBAMSORTRAM="10000000000"
fi
if [ -z ${VIASH_PAR_RUNTHREADN+x} ]; then
  VIASH_PAR_RUNTHREADN="1"
fi
if [ -z ${VIASH_PAR_JOBLOG+x} ]; then
  VIASH_PAR_JOBLOG="execution_log.txt"
fi

# check whether required files exist
if [ ! -z "$VIASH_PAR_INPUT_R1" ]; then
  IFS=';'
  set -f
  for file in $VIASH_PAR_INPUT_R1; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_INPUT_R2" ]; then
  IFS=';'
  set -f
  for file in $VIASH_PAR_INPUT_R2; do
    unset IFS
    if [ ! -e "$file" ]; then
      ViashError "Input file '$file' does not exist."
      exit 1
    fi
  done
  set +f
fi
if [ ! -z "$VIASH_PAR_GENOMEDIR" ] && [ ! -e "$VIASH_PAR_GENOMEDIR" ]; then
  ViashError "Input file '$VIASH_PAR_GENOMEDIR' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_BARCODESFASTA" ] && [ ! -e "$VIASH_PAR_BARCODESFASTA" ]; then
  ViashError "Input file '$VIASH_PAR_BARCODESFASTA' does not exist."
  exit 1
fi

# check whether parameters values are of the right type
if [[ -n "$VIASH_PAR_UMILENGTH" ]]; then
  if ! [[ "$VIASH_PAR_UMILENGTH" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--umiLength' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_RUNTHREADN" ]]; then
  if ! [[ "$VIASH_PAR_RUNTHREADN" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--runThreadN' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_OUTPUT" ]]; then
  if ! [[ "$VIASH_PAR_OUTPUT" =~ \* ]]; then
    ViashError '--output' has to be a path containing a wildcard, e.g. 'output_*.txt'. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_CPUS" ]]; then
  if ! [[ "$VIASH_META_CPUS" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'cpus' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_B" ]]; then
  if ! [[ "$VIASH_META_MEMORY_B" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_b' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_KB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_KB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_kb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_MB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_MB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_mb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_GB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_GB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_gb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_TB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_TB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_tb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_PB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_PB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_pb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_KIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_KIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_kib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_MIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_MIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_mib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_GIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_GIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_gib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_TIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_TIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_tib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_PIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_PIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_pib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi

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

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

if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  # detect volumes from file arguments
  VIASH_CHOWN_VARS=()
if [ ! -z "$VIASH_PAR_INPUT_R1" ]; then
  VIASH_TEST_INPUT_R1=()
  IFS=';'
  for var in $VIASH_PAR_INPUT_R1; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_INPUT_R1+=( "$var" )
  done
  VIASH_PAR_INPUT_R1=$(IFS=';' ; echo "${VIASH_TEST_INPUT_R1[*]}")
fi
if [ ! -z "$VIASH_PAR_INPUT_R2" ]; then
  VIASH_TEST_INPUT_R2=()
  IFS=';'
  for var in $VIASH_PAR_INPUT_R2; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_INPUT_R2+=( "$var" )
  done
  VIASH_PAR_INPUT_R2=$(IFS=';' ; echo "${VIASH_TEST_INPUT_R2[*]}")
fi
if [ ! -z "$VIASH_PAR_GENOMEDIR" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_GENOMEDIR")" )
  VIASH_PAR_GENOMEDIR=$(ViashDockerAutodetectMount "$VIASH_PAR_GENOMEDIR")
fi
if [ ! -z "$VIASH_PAR_BARCODESFASTA" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_BARCODESFASTA")" )
  VIASH_PAR_BARCODESFASTA=$(ViashDockerAutodetectMount "$VIASH_PAR_BARCODESFASTA")
fi
if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
  VIASH_TEST_OUTPUT=()
  IFS=';'
  for var in $VIASH_PAR_OUTPUT; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_OUTPUT+=( "$var" )
    VIASH_CHOWN_VARS+=( "$var" )
  done
  VIASH_PAR_OUTPUT=$(IFS=';' ; echo "${VIASH_TEST_OUTPUT[*]}")
fi
if [ ! -z "$VIASH_PAR_JOBLOG" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_JOBLOG")" )
  VIASH_PAR_JOBLOG=$(ViashDockerAutodetectMount "$VIASH_PAR_JOBLOG")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_JOBLOG" )
fi
if [ ! -z "$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-parallel_map-XXXXXX").sh
function clean_up {
  rm "\$tempscript"
}
function interrupt {
  echo -e "\nCTRL-C Pressed..."
  exit 1
}
trap clean_up EXIT
trap interrupt INT SIGINT
cat > "\$tempscript" << 'VIASHMAIN'
#!/bin/bash

## VIASH START
# The following code has been auto-generated by Viash.
$( if [ ! -z ${VIASH_PAR_INPUT_R1+x} ]; then echo "${VIASH_PAR_INPUT_R1}" | sed "s#'#'\"'\"'#g;s#.*#par_input_r1='&'#" ; else echo "# par_input_r1="; fi )
$( if [ ! -z ${VIASH_PAR_INPUT_R2+x} ]; then echo "${VIASH_PAR_INPUT_R2}" | sed "s#'#'\"'\"'#g;s#.*#par_input_r2='&'#" ; else echo "# par_input_r2="; fi )
$( if [ ! -z ${VIASH_PAR_GENOMEDIR+x} ]; then echo "${VIASH_PAR_GENOMEDIR}" | sed "s#'#'\"'\"'#g;s#.*#par_genomeDir='&'#" ; else echo "# par_genomeDir="; fi )
$( if [ ! -z ${VIASH_PAR_BARCODESFASTA+x} ]; then echo "${VIASH_PAR_BARCODESFASTA}" | sed "s#'#'\"'\"'#g;s#.*#par_barcodesFasta='&'#" ; else echo "# par_barcodesFasta="; fi )
$( if [ ! -z ${VIASH_PAR_UMILENGTH+x} ]; then echo "${VIASH_PAR_UMILENGTH}" | sed "s#'#'\"'\"'#g;s#.*#par_umiLength='&'#" ; else echo "# par_umiLength="; fi )
$( if [ ! -z ${VIASH_PAR_LIMITBAMSORTRAM+x} ]; then echo "${VIASH_PAR_LIMITBAMSORTRAM}" | sed "s#'#'\"'\"'#g;s#.*#par_limitBAMsortRAM='&'#" ; else echo "# par_limitBAMsortRAM="; fi )
$( if [ ! -z ${VIASH_PAR_RUNTHREADN+x} ]; then echo "${VIASH_PAR_RUNTHREADN}" | sed "s#'#'\"'\"'#g;s#.*#par_runThreadN='&'#" ; else echo "# par_runThreadN="; fi )
$( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "${VIASH_PAR_OUTPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_output='&'#" ; else echo "# par_output="; fi )
$( if [ ! -z ${VIASH_PAR_JOBLOG+x} ]; then echo "${VIASH_PAR_JOBLOG}" | sed "s#'#'\"'\"'#g;s#.*#par_joblog='&'#" ; else echo "# par_joblog="; fi )
$( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi )
$( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi )
$( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "${VIASH_META_RESOURCES_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_resources_dir='&'#" ; else echo "# meta_resources_dir="; fi )
$( if [ ! -z ${VIASH_META_EXECUTABLE+x} ]; then echo "${VIASH_META_EXECUTABLE}" | sed "s#'#'\"'\"'#g;s#.*#meta_executable='&'#" ; else echo "# meta_executable="; fi )
$( if [ ! -z ${VIASH_META_CONFIG+x} ]; then echo "${VIASH_META_CONFIG}" | sed "s#'#'\"'\"'#g;s#.*#meta_config='&'#" ; else echo "# meta_config="; fi )
$( if [ ! -z ${VIASH_META_TEMP_DIR+x} ]; then echo "${VIASH_META_TEMP_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_temp_dir='&'#" ; else echo "# meta_temp_dir="; fi )
$( if [ ! -z ${VIASH_META_CPUS+x} ]; then echo "${VIASH_META_CPUS}" | sed "s#'#'\"'\"'#g;s#.*#meta_cpus='&'#" ; else echo "# meta_cpus="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_B+x} ]; then echo "${VIASH_META_MEMORY_B}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_b='&'#" ; else echo "# meta_memory_b="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_KB+x} ]; then echo "${VIASH_META_MEMORY_KB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_kb='&'#" ; else echo "# meta_memory_kb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_MB+x} ]; then echo "${VIASH_META_MEMORY_MB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_mb='&'#" ; else echo "# meta_memory_mb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_GB+x} ]; then echo "${VIASH_META_MEMORY_GB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_gb='&'#" ; else echo "# meta_memory_gb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_TB+x} ]; then echo "${VIASH_META_MEMORY_TB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_tb='&'#" ; else echo "# meta_memory_tb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_PB+x} ]; then echo "${VIASH_META_MEMORY_PB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_pb='&'#" ; else echo "# meta_memory_pb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_KIB+x} ]; then echo "${VIASH_META_MEMORY_KIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_kib='&'#" ; else echo "# meta_memory_kib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_MIB+x} ]; then echo "${VIASH_META_MEMORY_MIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_mib='&'#" ; else echo "# meta_memory_mib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_GIB+x} ]; then echo "${VIASH_META_MEMORY_GIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_gib='&'#" ; else echo "# meta_memory_gib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_TIB+x} ]; then echo "${VIASH_META_MEMORY_TIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_tib='&'#" ; else echo "# meta_memory_tib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_pib='&'#" ; else echo "# meta_memory_pib="; fi )

## VIASH END

set -eo pipefail

# Check if wildcard character is present in output folder template
printf "Checking if output folder template (\$par_output) contains a single wildcard character '*'. "
output_glob_character="\${par_output//[^\\*]}"
if [[ "\${#output_glob_character}" -ne "1" ]]; then
  echo "The value for --output must contain exactly one '*' character. Exiting..."
  exit 1
else
  echo "Done, wildcard character found!"
fi

# Split the delimited strings into arrays
IFS=';' read -r -a input_r1 <<< "\$par_input_r1"
IFS=';' read -r -a input_r2 <<< "\$par_input_r2"

# Read barcodes FASTQ
# seqkit will make sure to take the leading non-whitespace as sequence identifier (ID)
# Luckily, this is the same as how cutadapt determines an adapter name from the FASTA header.
readarray -t well_ids < <(seqkit seq --name "\$par_barcodesFasta" )
readarray -t barcodes < <(seqkit seq --seq --upper-case --remove-gaps --gap-letters '^' --validate-seq "\$par_barcodesFasta")

# Function to test for unique values in array
function arrayContainsUniqueValues {
  # Pass the argument by reference
  local -n arr=\$1
  # Create a temporary associative array
  # in order to use its uniqueness of keys
  # 'declare' in a function is automatically local
  declare -A uniq_tmp
  for item in "\${arr[@]}"; do
    uniq_tmp[\$item]=0 # assigning a placeholder
  done
  local unique_array_values=(\${!uniq_tmp[@]})
  if [ "\${#unique_array_values[@]}" -eq "\${#arr[@]}" ]; then
    return
  fi
  false
}
arrayContainsUniqueValues barcodes
is_array_unique_exit_code=\$?
if ! (exit \$is_array_unique_exit_code); then 
  echo "The provided barcodes should be unique!"
  echo "Values: \$par_barcodes"
  exit 1
fi

# Check that the number of values provided for the fastq files are the same.
num_r1_inputs="\${#input_r1[@]}"
num_r2_inputs="\${#input_r2[@]}"

if [ ! "\$num_r1_inputs" -eq "\$num_r2_inputs" ]; then
  echo "The number of values for arguments "\\
        "'input_r1' (\$num_r1_inputs) and 'input_r2' (\$num_r2_inputs) "\\
        "should be the same."
  exit 1
else
  echo "Checked if the same as the number of R1 FASTQ (\$num_r1_inputs) and R2 FASTQ files "\\
       "(\$num_r2_inputs) were provided. Seems OK!"
fi

# Loop over the well IDs and match them to the input FASTQ files
# The FASTQ file names should have the format {well_id}_R(1|2).fastq,
# which is the output format that the cutadapt component uses for demultiplexing.
# sorted_input_r1 and sorted_input_r2 are the input FASTQ files sorted by the order
# of the barcodes in the barcodes array (i.e. the order in the barcodes FASTA file).
declare -a sorted_input_r1=()
declare -a sorted_input_r2=()
for barcode_index in "\${!barcodes[@]}"; do
  barcode="\${barcodes[\$barcode_index]}"
  well_id="\${well_ids[\$barcode_index]}"
  echo "Finding FASTQ files for barcode \${barcode}, well ID '\${well_id}'."
  # The FASTQ files for a particular barcode must match the following regex:
  input_file_regex="^\${well_id}_R[1-2]"
  
  for r1_index in "\${!input_r1[@]}"; do
    r1_file_path=\${input_r1[\$r1_index]}
    r2_file_path=\${input_r2[\$r1_index]}
    # Get the file names from the full path
    r1_file_name=\$(basename -- "\$r1_file_path")
    r2_file_name=\$(basename -- "\$r2_file_path")

    # Check if the file names match the regex
    if [[ \$r1_file_name =~ \$input_file_regex ]]; then
      echo "Matched with \$r1_file_name and \$r2_file_name."
      # If the R1 FASTQ file matched the regex, 
      # the R2 file must have also been matched
      if ! [[ \$r2_file_name =~ \$input_file_regex ]]; then
        echo "File \${r1_file_name} matched with regex \${input_file_regex} "\\
          "but \${r2_file_name} did not! Make sure that the order of "\\
          "the R1 and R2 input files match."
        exit 1
      fi
      # Add the 
      sorted_input_r1+=("\$r1_file_path")
      sorted_input_r2+=("\$r2_file_path")
      # Do not continue looking for more files for this barcode
      # '2' to affect the *outer* loop (which indeed loops barcodes)!
      continue 2
    fi
  done
  echo "Did not find FASTQ files files for well \${well_id}! "\\
    "Make sure that the input files have the correct file name format."
  exit 1
done


# Define the function that will be used to run a single job
function _run() {
  local par_UMIlength="\$1"
  local par_output="\$2"
  local par_genomeDir="\$3"
  local par_limitBAMsortRAM="\$4"
  local par_runThreadN="\$5"
  local barcode="\$6"
  local input_R1="\$7"
  local input_R2="\$8"

  local barcode_length="\${#barcode}"
  local umi_start="\$((\$barcode_length + 1))"

  set -eo pipefail

  echo <<-EOF
    Processing \$barcode
    For the following inputs (lanes):
    "\$star_readFilesIn
	EOF

  echo "Writing barcode '\$barcode' to \$barcode.txt and using it as input".
  # Note that there is no possible conflict between jobs here
  # because the barcodes are unique (and the barcode is part of the name
  # of the file).
  echo "\$barcode" > "\$barcode.txt"

  local dir="\${par_output//\\*/\$barcode}/"
  echo "Setting output for barcode '\$barcode' to '\$dir'."
  mkdir -p "\$dir"

  # check if files are compressed
  local TMPDIR=\$(mktemp -d "\$meta_temp_dir/parallel_map-\$barcode-XXXXXX")
  function clean_up {
    [[ -d "\$TMPDIR" ]] && rm -r "\$TMPDIR"
  }
  trap clean_up RETURN

  # Decompress the input files when needed
  # NOTE: for some reason, using STAR's --readFilesCommand does not always work
  # This might be because STAR creates fifo files (see https://man7.org/linux/man-pages/man7/fifo.7.html)
  # and this requires a filesystem that supports this. Another cause might be that the input files
  # are symlinks. When testing this, using '--readFilesCommand "zcat"' 
  # always produced empty BAM files, but also a succesfull exit code (0) so the problem is not reported.
  # However, the logs showed the following error: "gzip -: unexpected end of file".

  function is_gzipped {
    printf "Checking if input '\$1' (barcode '\$barcode') is gzipped... "
    if file "\$1" | grep -q 'gzip'; then
      echo "Done, detected compressed file."
      return
    fi
    echo "Done, file does not need decompression."
    false
  }
  
  # Resolve symbolic links to actual file paths
  input_R1=\$(realpath \$input_R1)
  input_R2=\$(realpath \$input_R2)

  if is_gzipped \$input_R1; then
    local compressed_file_name_r1="\$(basename -- \$input_R1)"
    local uncompressed_file_r1="\$TMPDIR/\${compressed_file_name_r1%.gz}"
    printf "Unpacking input to \$uncompressed_file_r1... "
    zcat "\$input_R1" > "\$uncompressed_file_r1"
    echo "Decompression done."
  else
    local uncompressed_file_r1="\$input_R1"
  fi

  if is_gzipped \$input_R2; then
    local compressed_file_name_r2="\$(basename -- \$input_R2)"
    local uncompressed_file_r2="\$TMPDIR/\${compressed_file_name_r2%.gz}"
    printf "Unpacking input to \$uncompressed_file_r2... "
    zcat "\$input_R2" > "\$uncompressed_file_r2"
    echo "Decompression done."
  else
    local uncompressed_file_r2="\$input_R2"
  fi

  local n_input_lines_r1=\$(wc -l < "\$uncompressed_file_r1")
  local n_input_lines_r2=\$(wc -l < "\$uncompressed_file_r2")

  printf "Checking if length of input file mates match. "
  if (( \$n_input_lines_r1 != n_input_lines_r2 )); then
    echo "The length of file \$input_R1 (\$n_input_lines_r1) does not match with \$input_R2 (\$n_input_lines_r2)"
    return 1
  else
    echo "Seems OK, \$n_input_lines_r1 input lines."
  fi
  echo "Starting STAR for barcode '\$barcode'"
  # soloType 'Droplet' is the same as 'CB_UMI_Simple': one UMI and one cell barcode of fixed length. 
  # By default in this mode, STAR will look for the cell barcode and the UMI int the last files specified with --readFilesIn
  # So we need to specify R2 first and R1 second, because R1 contains the barcode and UMI.
  # Also, you might be tempted to use '--soloBarcodeMate 1' to alter this behavior, but this requires the clipping
  # the barcode from this mate by specifying --clip5pNbases and/or --clip3pNbases, which we do not want to do.
  STAR \\
    --readFilesIn "\$uncompressed_file_r2" "\$uncompressed_file_r1" \\
    --soloType Droplet \\
    --quantMode GeneCounts \\
    --genomeLoad LoadAndKeep \\
    --limitBAMsortRAM "\$par_limitBAMsortRAM" \\
    --runThreadN "\$par_runThreadN" \\
    --outFilterMultimapNmax 1 \\
    --outSAMtype BAM SortedByCoordinate \\
    --soloCBstart 1 \\
    --readFilesType "Fastx" \\
    --soloCBlen "\$barcode_length" \\
    --soloUMIstart "\$umi_start" \\
    --soloUMIlen "\$par_UMIlength" \\
    --soloBarcodeReadLength 0 \\
    --soloStrand Unstranded \\
    --soloFeatures Gene \\
    --genomeDir "\$par_genomeDir" \\
    --outReadsUnmapped Fastx \\
    --outSAMunmapped Within \\
    --outSAMattributes NH HI nM AS CR UR CB UB GX GN \\
    --soloCBwhitelist "\$barcode.txt" \\
    --outFileNamePrefix "\$dir" \\
    --outTmpDir "\$TMPDIR/STARtemp/"

  printf "Done running STAR. "
  # Check if the number of processed reads is equal to the number of input reads
  local n_input_reads=\$((\$n_input_lines_r1 / 4))
  local nr_output_reads=\$(grep -Po "Number\\ of\\ input\\ reads \\\\|\\W*\\K\\d+" "\$dir/Log.final.out")
  if (( \$nr_output_reads != \$n_input_reads )); then
    echo "Not all input reads were processed for barcode \$barcode."
    return 1
  else
    echo "Processed \$nr_output_reads reads for barcode \$barcode".
  fi

  printf "Making sure that the output has the proper permissions."
  find "\$dir" -type d -exec chmod o+x {} \\;
  chmod -R o+r "\$dir"
  echo "Done"
}

# Export the function - requires bash
export -f _run

# Load reference genome
echo "Loading reference genome"
STAR --genomeLoad LoadAndExit --genomeDir "\$par_genomeDir"

# Run the concurrent jobs using GNU parallel

# Make sure that parallel uses the correct shell
export PARALLEL_SHELL="/bin/bash"

# Some notes:
#   --halt now,fail=1: instruct parallel to exit when a job has failed and kill remaining running jobs.
#   
# ::: is a special syntax for GNU parallel to delineate inputs
# If multiple ::: are given, each group will be treated as an input source, and all combinations of input
# sources will be generated. E.g. ::: 1 2 ::: a b c will result in the combinations (1,a) (1,b) (1,c) (2,a) (2,b) (2,c)
# The delimiter :::+ (note the extra '+') links the argument to the previous argument, and one argument from each of the input
# sources will be read.
parallel_cmd=("parallel" "--jobs" "80%" "--verbose" "--memfree" "2G"
              "--tmpdir" "\$meta_temp_dir"
              "--retry-failed" "--retries" "4" "--halt" "soon,fail=1"
              "--joblog" "\$par_joblog" "_run" "{}")

# Arguments for which there is one value, so these will not create extra jobs
parallel_cmd+=(":::" "\$par_umiLength" ":::" "\$par_output" ":::" "\$par_genomeDir" ":::" "\$par_limitBAMsortRAM" ":::" "\$par_runThreadN")

# Argument which in fact will cause extra jobs to be spawned, per job one item from each argument will be selected
# Thus, these argument lists should have the same length.
parallel_cmd+=(":::" "\${barcodes[@]}" ":::+" "\${sorted_input_r1[@]}" ":::+" "\${sorted_input_r2[@]}")

set +eo pipefail
"\${parallel_cmd[@]}"
exit_code=\$?
set -eo pipefail

echo "GNU parallel finished!"

# Unload reference
printf "Unloading reference genome. "
STAR --genomeLoad Remove --genomeDir "\$par_genomeDir"
echo "Done!"

# Exit code from GNU parallel:
# If fail=1 is used, the exit status will be the exit status of the failing job.
echo "Checking exit code"
if ((exit_code>0)); then
  # Note that the ending HERE must be indented with TAB characters (not spaces)
  # in order to remove leading indentation
  MESSAGE=\$(
    cat <<-HERE
    ==================================================================

    !!! An error occurred for one of the jobs.
    Exit code of the failing job: \$exit_code.

    %s

    ==================================================================

		HERE
  )
  printf "\$MESSAGE" "\$(<\$par_joblog)"
  exit 1
else
  cat <<-HERE
  ==================================================================

  Mapping went fine (exit code '\$exit_code'), zero errors occurred

  ==================================================================
	HERE

fi
VIASHMAIN
bash "\$tempscript" &
wait "\$!"

VIASHEOF


if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  # strip viash automount from file paths
  
  if [ ! -z "$VIASH_PAR_INPUT_R1" ]; then
    unset VIASH_TEST_INPUT_R1
    IFS=';'
    for var in $VIASH_PAR_INPUT_R1; do
      unset IFS
      if [ -z "$VIASH_TEST_INPUT_R1" ]; then
      VIASH_TEST_INPUT_R1="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_INPUT_R1="$VIASH_TEST_INPUT_R1;""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_INPUT_R1="$VIASH_TEST_INPUT_R1"
  fi
  if [ ! -z "$VIASH_PAR_INPUT_R2" ]; then
    unset VIASH_TEST_INPUT_R2
    IFS=';'
    for var in $VIASH_PAR_INPUT_R2; do
      unset IFS
      if [ -z "$VIASH_TEST_INPUT_R2" ]; then
      VIASH_TEST_INPUT_R2="$(ViashDockerStripAutomount "$var")"
    else
      VIASH_TEST_INPUT_R2="$VIASH_TEST_INPUT_R2;""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_INPUT_R2="$VIASH_TEST_INPUT_R2"
  fi
  if [ ! -z "$VIASH_PAR_GENOMEDIR" ]; then
    VIASH_PAR_GENOMEDIR=$(ViashDockerStripAutomount "$VIASH_PAR_GENOMEDIR")
  fi
  if [ ! -z "$VIASH_PAR_BARCODESFASTA" ]; then
    VIASH_PAR_BARCODESFASTA=$(ViashDockerStripAutomount "$VIASH_PAR_BARCODESFASTA")
  fi
  if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
    VIASH_PAR_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT")
  fi
  if [ ! -z "$VIASH_PAR_JOBLOG" ]; then
    VIASH_PAR_JOBLOG=$(ViashDockerStripAutomount "$VIASH_PAR_JOBLOG")
  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 "$VIASH_PAR_OUTPUT" ] && ! compgen -G "$VIASH_PAR_OUTPUT" > /dev/null; then
  ViashError "Output file '$VIASH_PAR_OUTPUT' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_JOBLOG" ] && [ ! -e "$VIASH_PAR_JOBLOG" ]; then
  ViashError "Output file '$VIASH_PAR_JOBLOG' does not exist."
  exit 1
fi


exit 0