#!/usr/bin/env bash

# pseudo_alignment_and_quant main
# 
# 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="pseudo_alignment_and_quant"
VIASH_META_FUNCTIONALITY_NAME="pseudo_alignment_and_quant"
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 "pseudo_alignment_and_quant main"
  echo ""
  echo "A viash sub-workflow for pseudo alignment and quantification stage of"
  echo "nf-core/rnaseq pipeline."
  echo ""
  echo "Input:"
  echo "    --id"
  echo "        type: string, required parameter"
  echo "        example: foo"
  echo "        ID of the sample."
  echo ""
  echo "    -i, --fastq_1"
  echo "        type: file, required parameter, file must exist"
  echo "        example: input.fastq.gz"
  echo "        Path to the sample (or read 1 of paired end sample)."
  echo ""
  echo "    --fastq_2"
  echo "        type: file, file must exist"
  echo "        Path to read 2 of the sample."
  echo ""
  echo "    --strandedness"
  echo "        type: string"
  echo "        choices: [ forward, reverse, unstranded ]"
  echo "        Sample strand-specificity. Must be one of unstranded, forward, or"
  echo "        reverse"
  echo ""
  echo "    --gtf"
  echo "        type: file, file must exist"
  echo "        GTF file"
  echo ""
  echo "    --transcript_fasta"
  echo "        type: file, file must exist"
  echo "        Fasta file of the reference transcriptome."
  echo ""
  echo "    --pseudo_aligner"
  echo "        type: string"
  echo "        default: false"
  echo "        choices: [ salmon, kallisto ]"
  echo "        Specifies the pseudo aligner to use - available options are 'salmon'."
  echo "        Runs in addition to '--aligner'."
  echo ""
  echo "    --salmon_index"
  echo "        type: file, file must exist"
  echo "        Salmon index"
  echo ""
  echo "    --kallisto_index"
  echo "        type: file, file must exist"
  echo "        Kallisto index"
  echo ""
  echo "    --lib_type"
  echo "        type: string"
  echo "        default:"
  echo "        Override library type inferred based on strandedness defined in meta"
  echo "        object"
  echo ""
  echo "    --kallisto_quant_fragment_length"
  echo "        type: double"
  echo "        For single-end mode only, the estimated average fragment length to use"
  echo "        for quantification with Kallisto."
  echo ""
  echo "    --kallisto_quant_fragment_length_sd"
  echo "        type: double"
  echo "        For single-end mode only, the estimated standard deviation of the"
  echo "        fragment length for quantification with Kallisto."
  echo ""
  echo "Output:"
  echo "    --pseudo_multiqc"
  echo "        type: file, output, file must exist"
  echo ""
  echo "    --quant_out_dir"
  echo "        type: file, output, file must exist"
  echo "        default: \$id.quant"
  echo ""
  echo "    --salmon_quant_results_file"
  echo "        type: file, output, file must exist"
  echo "        default: \$id.quant.sf"
  echo ""
  echo "    --kallisto_quant_results_file"
  echo "        type: file, output, file must exist"
  echo "        default: \$id.abundance.tsv"
}

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

# 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 "$1")"
            shift 1
            ;;
        --version)
            echo "pseudo_alignment_and_quant main"
            exit
            ;;
        --id)
            [ -n "$VIASH_PAR_ID" ] && ViashError Bad arguments for option \'--id\': \'$VIASH_PAR_ID\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ID="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --id. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --id=*)
            [ -n "$VIASH_PAR_ID" ] && ViashError Bad arguments for option \'--id=*\': \'$VIASH_PAR_ID\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_ID=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --fastq_1)
            [ -n "$VIASH_PAR_FASTQ_1" ] && ViashError Bad arguments for option \'--fastq_1\': \'$VIASH_PAR_FASTQ_1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FASTQ_1="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --fastq_1. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --fastq_1=*)
            [ -n "$VIASH_PAR_FASTQ_1" ] && ViashError Bad arguments for option \'--fastq_1=*\': \'$VIASH_PAR_FASTQ_1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FASTQ_1=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -i)
            [ -n "$VIASH_PAR_FASTQ_1" ] && ViashError Bad arguments for option \'-i\': \'$VIASH_PAR_FASTQ_1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FASTQ_1="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -i. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --fastq_2)
            [ -n "$VIASH_PAR_FASTQ_2" ] && ViashError Bad arguments for option \'--fastq_2\': \'$VIASH_PAR_FASTQ_2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FASTQ_2="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --fastq_2. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --fastq_2=*)
            [ -n "$VIASH_PAR_FASTQ_2" ] && ViashError Bad arguments for option \'--fastq_2=*\': \'$VIASH_PAR_FASTQ_2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_FASTQ_2=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --strandedness)
            [ -n "$VIASH_PAR_STRANDEDNESS" ] && ViashError Bad arguments for option \'--strandedness\': \'$VIASH_PAR_STRANDEDNESS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_STRANDEDNESS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --strandedness. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --strandedness=*)
            [ -n "$VIASH_PAR_STRANDEDNESS" ] && ViashError Bad arguments for option \'--strandedness=*\': \'$VIASH_PAR_STRANDEDNESS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_STRANDEDNESS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --gtf)
            [ -n "$VIASH_PAR_GTF" ] && ViashError Bad arguments for option \'--gtf\': \'$VIASH_PAR_GTF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_GTF="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --gtf. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --gtf=*)
            [ -n "$VIASH_PAR_GTF" ] && ViashError Bad arguments for option \'--gtf=*\': \'$VIASH_PAR_GTF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_GTF=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --transcript_fasta)
            [ -n "$VIASH_PAR_TRANSCRIPT_FASTA" ] && ViashError Bad arguments for option \'--transcript_fasta\': \'$VIASH_PAR_TRANSCRIPT_FASTA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_TRANSCRIPT_FASTA="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --transcript_fasta. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --transcript_fasta=*)
            [ -n "$VIASH_PAR_TRANSCRIPT_FASTA" ] && ViashError Bad arguments for option \'--transcript_fasta=*\': \'$VIASH_PAR_TRANSCRIPT_FASTA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_TRANSCRIPT_FASTA=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --pseudo_aligner)
            [ -n "$VIASH_PAR_PSEUDO_ALIGNER" ] && ViashError Bad arguments for option \'--pseudo_aligner\': \'$VIASH_PAR_PSEUDO_ALIGNER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PSEUDO_ALIGNER="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --pseudo_aligner. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --pseudo_aligner=*)
            [ -n "$VIASH_PAR_PSEUDO_ALIGNER" ] && ViashError Bad arguments for option \'--pseudo_aligner=*\': \'$VIASH_PAR_PSEUDO_ALIGNER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PSEUDO_ALIGNER=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --salmon_index)
            [ -n "$VIASH_PAR_SALMON_INDEX" ] && ViashError Bad arguments for option \'--salmon_index\': \'$VIASH_PAR_SALMON_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SALMON_INDEX="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --salmon_index. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --salmon_index=*)
            [ -n "$VIASH_PAR_SALMON_INDEX" ] && ViashError Bad arguments for option \'--salmon_index=*\': \'$VIASH_PAR_SALMON_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SALMON_INDEX=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --kallisto_index)
            [ -n "$VIASH_PAR_KALLISTO_INDEX" ] && ViashError Bad arguments for option \'--kallisto_index\': \'$VIASH_PAR_KALLISTO_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_KALLISTO_INDEX="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --kallisto_index. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --kallisto_index=*)
            [ -n "$VIASH_PAR_KALLISTO_INDEX" ] && ViashError Bad arguments for option \'--kallisto_index=*\': \'$VIASH_PAR_KALLISTO_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_KALLISTO_INDEX=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --lib_type)
            [ -n "$VIASH_PAR_LIB_TYPE" ] && ViashError Bad arguments for option \'--lib_type\': \'$VIASH_PAR_LIB_TYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LIB_TYPE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --lib_type. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --lib_type=*)
            [ -n "$VIASH_PAR_LIB_TYPE" ] && ViashError Bad arguments for option \'--lib_type=*\': \'$VIASH_PAR_LIB_TYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LIB_TYPE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --kallisto_quant_fragment_length)
            [ -n "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH" ] && ViashError Bad arguments for option \'--kallisto_quant_fragment_length\': \'$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --kallisto_quant_fragment_length. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --kallisto_quant_fragment_length=*)
            [ -n "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH" ] && ViashError Bad arguments for option \'--kallisto_quant_fragment_length=*\': \'$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --kallisto_quant_fragment_length_sd)
            [ -n "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH_SD" ] && ViashError Bad arguments for option \'--kallisto_quant_fragment_length_sd\': \'$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH_SD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH_SD="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --kallisto_quant_fragment_length_sd. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --kallisto_quant_fragment_length_sd=*)
            [ -n "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH_SD" ] && ViashError Bad arguments for option \'--kallisto_quant_fragment_length_sd=*\': \'$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH_SD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH_SD=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --pseudo_multiqc)
            [ -n "$VIASH_PAR_PSEUDO_MULTIQC" ] && ViashError Bad arguments for option \'--pseudo_multiqc\': \'$VIASH_PAR_PSEUDO_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PSEUDO_MULTIQC="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --pseudo_multiqc. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --pseudo_multiqc=*)
            [ -n "$VIASH_PAR_PSEUDO_MULTIQC" ] && ViashError Bad arguments for option \'--pseudo_multiqc=*\': \'$VIASH_PAR_PSEUDO_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_PSEUDO_MULTIQC=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --quant_out_dir)
            [ -n "$VIASH_PAR_QUANT_OUT_DIR" ] && ViashError Bad arguments for option \'--quant_out_dir\': \'$VIASH_PAR_QUANT_OUT_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_QUANT_OUT_DIR="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --quant_out_dir. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --quant_out_dir=*)
            [ -n "$VIASH_PAR_QUANT_OUT_DIR" ] && ViashError Bad arguments for option \'--quant_out_dir=*\': \'$VIASH_PAR_QUANT_OUT_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_QUANT_OUT_DIR=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --salmon_quant_results_file)
            [ -n "$VIASH_PAR_SALMON_QUANT_RESULTS_FILE" ] && ViashError Bad arguments for option \'--salmon_quant_results_file\': \'$VIASH_PAR_SALMON_QUANT_RESULTS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SALMON_QUANT_RESULTS_FILE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --salmon_quant_results_file. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --salmon_quant_results_file=*)
            [ -n "$VIASH_PAR_SALMON_QUANT_RESULTS_FILE" ] && ViashError Bad arguments for option \'--salmon_quant_results_file=*\': \'$VIASH_PAR_SALMON_QUANT_RESULTS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SALMON_QUANT_RESULTS_FILE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --kallisto_quant_results_file)
            [ -n "$VIASH_PAR_KALLISTO_QUANT_RESULTS_FILE" ] && ViashError Bad arguments for option \'--kallisto_quant_results_file\': \'$VIASH_PAR_KALLISTO_QUANT_RESULTS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_KALLISTO_QUANT_RESULTS_FILE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --kallisto_quant_results_file. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --kallisto_quant_results_file=*)
            [ -n "$VIASH_PAR_KALLISTO_QUANT_RESULTS_FILE" ] && ViashError Bad arguments for option \'--kallisto_quant_results_file=*\': \'$VIASH_PAR_KALLISTO_QUANT_RESULTS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_KALLISTO_QUANT_RESULTS_FILE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        ---engine)
            VIASH_ENGINE_ID="$2"
            shift 2
            ;;
        ---engine=*)
            VIASH_ENGINE_ID="$(ViashRemoveFlags "$1")"
            shift 1
            ;;
        ---cpus)
            [ -n "$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   [ "$VIASH_ENGINE_ID" == "native" ]  ; then
  VIASH_ENGINE_TYPE='native'
else
  ViashError "Engine '$VIASH_ENGINE_ID' is not recognized. Options are: native."
  exit 1
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_ID+x} ]; then
  ViashError '--id' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_PAR_FASTQ_1+x} ]; then
  ViashError '--fastq_1' 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_PSEUDO_ALIGNER+x} ]; then
  VIASH_PAR_PSEUDO_ALIGNER="false"
fi
if [ -z ${VIASH_PAR_LIB_TYPE+x} ]; then
  VIASH_PAR_LIB_TYPE=""
fi
if [ -z ${VIASH_PAR_QUANT_OUT_DIR+x} ]; then
  VIASH_PAR_QUANT_OUT_DIR="\$id.quant"
fi
if [ -z ${VIASH_PAR_SALMON_QUANT_RESULTS_FILE+x} ]; then
  VIASH_PAR_SALMON_QUANT_RESULTS_FILE="\$id.quant.sf"
fi
if [ -z ${VIASH_PAR_KALLISTO_QUANT_RESULTS_FILE+x} ]; then
  VIASH_PAR_KALLISTO_QUANT_RESULTS_FILE="\$id.abundance.tsv"
fi

# check whether required files exist
if [ ! -z "$VIASH_PAR_FASTQ_1" ] && [ ! -e "$VIASH_PAR_FASTQ_1" ]; then
  ViashError "Input file '$VIASH_PAR_FASTQ_1' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_FASTQ_2" ] && [ ! -e "$VIASH_PAR_FASTQ_2" ]; then
  ViashError "Input file '$VIASH_PAR_FASTQ_2' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_GTF" ] && [ ! -e "$VIASH_PAR_GTF" ]; then
  ViashError "Input file '$VIASH_PAR_GTF' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_TRANSCRIPT_FASTA" ] && [ ! -e "$VIASH_PAR_TRANSCRIPT_FASTA" ]; then
  ViashError "Input file '$VIASH_PAR_TRANSCRIPT_FASTA' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_SALMON_INDEX" ] && [ ! -e "$VIASH_PAR_SALMON_INDEX" ]; then
  ViashError "Input file '$VIASH_PAR_SALMON_INDEX' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_KALLISTO_INDEX" ] && [ ! -e "$VIASH_PAR_KALLISTO_INDEX" ]; then
  ViashError "Input file '$VIASH_PAR_KALLISTO_INDEX' does not exist."
  exit 1
fi

# check whether parameters values are of the right type
if [[ -n "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH" ]]; then
  if ! [[ "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--kallisto_quant_fragment_length' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH_SD" ]]; then
  if ! [[ "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH_SD" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--kallisto_quant_fragment_length_sd' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_CPUS" ]]; then
  if ! [[ "$VIASH_META_CPUS" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'cpus' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_B" ]]; then
  if ! [[ "$VIASH_META_MEMORY_B" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_b' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_KB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_KB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_kb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_MB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_MB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_mb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_GB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_GB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_gb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_TB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_TB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_tb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_PB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_PB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_pb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_KIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_KIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_kib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_MIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_MIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_mib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_GIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_GIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_gib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_TIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_TIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_tib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_PIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_PIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_pib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi

# check whether value is belongs to a set of choices
if [ ! -z "$VIASH_PAR_STRANDEDNESS" ]; then
  VIASH_PAR_STRANDEDNESS_CHOICES=("forward;reverse;unstranded")
  IFS=';'
  set -f
  if ! [[ ";${VIASH_PAR_STRANDEDNESS_CHOICES[*]};" =~ ";$VIASH_PAR_STRANDEDNESS;" ]]; then
    ViashError '--strandedness' specified value of \'$VIASH_PAR_STRANDEDNESS\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
    exit 1
  fi
  set +f
  unset IFS
fi

if [ ! -z "$VIASH_PAR_PSEUDO_ALIGNER" ]; then
  VIASH_PAR_PSEUDO_ALIGNER_CHOICES=("salmon;kallisto")
  IFS=';'
  set -f
  if ! [[ ";${VIASH_PAR_PSEUDO_ALIGNER_CHOICES[*]};" =~ ";$VIASH_PAR_PSEUDO_ALIGNER;" ]]; then
    ViashError '--pseudo_aligner' specified value of \'$VIASH_PAR_PSEUDO_ALIGNER\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
    exit 1
  fi
  set +f
  unset IFS
fi

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


# set dependency paths
VIASH_DEP_SALMON_SALMON_QUANT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/main.nf"
VIASH_DEP_KALLISTO_KALLISTO_QUANT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/kallisto/kallisto_quant/main.nf"

ViashDebug "Running command: $(echo $VIASH_CMD)"
cat << VIASHEOF | eval $VIASH_CMD
set -e
tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-pseudo_alignment_and_quant-XXXXXX").nf
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.

//// VIASH END
workflow run_wf {
  take:
    input_ch

  main:
    output_ch = input_ch
    
      | map { id, state ->
        def input = state.fastq_2 ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ]
        def paired = input.size() == 2
        [ id, state + [ paired: paired, input: input ] ]
      }


      // Infer lib-type for salmon quant
      | map { id, state -> 
        def lib_type = (state.paired) ? 
          (
            (state.strandedness == "forward") ? 
              "ISF" : 
              (
                (state.strandedness == "reverse") ? "ISR" : "IU"
              )
          ) 
          : (
            (state.strandedness == "forward") ? 
              "SF" : 
              (
                (state.strandedness == "reverse") ? "SR" : "U"
              )
          ) 
        [ id, state + [lib_type: lib_type] ]
      }
      
      // Count reads from BAM alignments using Salmon
      | salmon_quant.run ( 
        runIf: { id, state -> state.pseudo_aligner == 'salmon' },
        fromState: { id, state ->
          def unmated_reads = !state.paired ? state.fastq_1 : null
          def mates1 = state.paired ? state.fastq_1 : null
          def mates2 = state.paired ? state.fastq_2 : null
          [ unmated_reads: unmated_reads,
            mates1: mates1, 
            mates2: mates2, 
            gene_map: state.gtf, 
            index: state.salmon_index,
            lib_type: state.lib_type ]
        },
        toState: [ 
          "quant_out_dir": "output",
          "salmon_quant_results_file": "quant_results" 
        ],
        directives: [ label: [ "midmem", "highcpu" ] ]
      )

      | map { id, state -> 
        def mod_state = (state.pseudo_aligner == 'salmon') ? state + [pseudo_multiqc: state.quant_out_dir] : state
        [ id, mod_state ]
      }

      | kallisto_quant.run ( 
        runIf: { id, state -> state.pseudo_aligner == 'kallisto'},
        fromState: { id, state -> 
          def fr_stranded = state.strandedness == 'forward'
          def rf_stranded = state.strandedness == 'reverse'
          [
            input: state.input,
            index: state.kallisto_index,
            fragment_length: state.kallisto_quant_fragment_length,
            sd: state.kallisto_quant_fragment_length_sd,
            single: !state.paired,
            fr_stranded: fr_stranded,
            rf_stranded: rf_stranded,
          ]
        },
        args: [log: "kallisto_quant.log"],
        toState: { id, output_state, state -> 
          def neKeys = [
            "quant_out_dir": output_state["output_dir"],
            "kallisto_quant_results_file": output_state["output_dir"] + "/abundance.tsv",
            "pseudo_multiqc": output_state["log"]
          ]
          def new_state = state + newKeys
          return new_state
        },
        directives: [ label: [ "midmem", "highcpu" ] ]
      )

      | map { id, state -> 
        def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() }
        [ id, mod_state ]
      }

      | setState (
        [ "pseudo_multiqc": "quant_results", 
          "quant_out_dir": "quant_out_dir",
          "salmon_quant_results_file": "salmon_quant_results_file",
          "kallisto_quant_results_file": "kallisto_quant_results_file"
        ]
      )

  emit:
    output_ch
}
VIASHMAIN
nextflow run . -main-script "\$tempscript" &
wait "\$!"

VIASHEOF


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


exit 0
