#!/usr/bin/env bash
##############################################################################################################################################################
# Master metaWRAP script that calls on individual modules/pipelines 
##############################################################################################################################################################

VERSION="1.3.2"

help_message () {
        echo""
	echo "MetaWRAP v=$VERSION"
	echo "Usage: metaWRAP [module]"
	echo ""
        echo "	Modules:"
	echo "	read_qc		Raw read QC module (read trimming and contamination removal)"
        echo "	assembly	Assembly module (metagenomic assembly)"
	echo "	kraken		KRAKEN module (taxonomy annotation of reads and assemblies)"
	echo "	kraken2		KRAKEN2 module (taxonomy annotation of reads and assemblies)"
	echo "	blobology	Blobology module (GC vs Abund plots of contigs and bins)"
	echo ""
	echo "	binning		Binning module (metabat, maxbin, or concoct)"
	echo "	bin_refinement	Refinement of bins from binning module"
	echo "	reassemble_bins Reassemble bins using metagenomic reads"
	echo "	quant_bins	Quantify the abundance of each bin across samples"
	echo "	classify_bins	Assign taxonomy to genomic bins"
	echo "	annotate_bins	Functional annotation of draft genomes"
	echo ""
	echo "	--help | -h		show this help message"
	echo "	--version | -v	show metaWRAP version"
	echo "	--show-config	show where the metawrap configuration files are stored"
        echo "";}

config_file=$(which config-metawrap)
source $config_file
if [[ $? -ne 0 ]]; then 
	echo "cannot find config-metawrap file - something went wrong with the installation!"
	exit 1
fi

comm () { ${SOFT}/print_comment.py "$1" "-"; }

########################################################################################################
########################     LOADING IN THE PARAMETERS AND RUNNING MODULE       ########################
########################################################################################################

# setting scripts, pipelines, and databases locations from config file (should be in same folder as main script)

if [ "$1" = assembly ]; then
	echo metawrap assembly ${@:2}
	time ${PIPES}/assembly.sh ${@:2}
elif [ "$1" = phylosift ]; then
        #echo phylosift.sh ${@:2}
        #${PIPES}/phylosift.sh ${@:2}
	echo "The PHYLOSIFT module of metaWRAP is disabled in this version of metaWRAP"
	exit 1
elif [ "$1" = read_qc ]; then
	echo metawrap read_qc ${@:2}
	time ${PIPES}/read_qc.sh ${@:2}
elif [ "$1" = binning ]; then
        echo metawrap binning ${@:2}
        time ${PIPES}/binning.sh ${@:2}
elif [ "$1" = blobology ]; then
        echo metawrap blobology ${@:2}
	time ${PIPES}/blobology.sh ${@:2}
elif [ "$1" = kraken ]; then
        echo metawrap kraken ${@:2}
	time ${PIPES}/kraken.sh ${@:2}
elif [ "$1" = kraken2 ]; then
	echo metawrap kraken2 ${@:2}
	time ${PIPES}/kraken2.sh ${@:2}
elif [ "$1" = all ]; then
	#echo all.sh ${@:2}
        #${PIPES}/all.sh ${@:2}
	echo "ALL module of metaWRAP is disabled in this version of metaWRAP"
	exit 1
elif [ "$1" = bin_refinement ]; then
        echo metawrap bin_refinement ${@:2}
        time ${PIPES}/bin_refinement.sh ${@:2}
elif [ "$1" = reassemble_bins ]; then
	echo metawrap reassemble_bins ${@:2}
	time ${PIPES}/reassemble_bins.sh ${@:2}
elif [ "$1" = quant_bins ]; then 
	echo metawrap quant_bins ${@:2}
	time ${PIPES}/quant_bins.sh ${@:2}
elif [ "$1" = classify_bins ]; then
	echo metawrap classify_bins ${@:2}
	time ${PIPES}/classify_bins.sh ${@:2}
elif [ "$1" = annotate_bins ]; then
        echo metawrap annotate_bins ${@:2}
        time ${PIPES}/annotate_bins.sh ${@:2}
elif [ "$1" = "-h" ] || [ "$1" = "--help" ]; then
	help_message
elif [ "$1" = "-v" ] || [ "$1" = "--version" ]; then
        echo ""
	echo "metaWRAP v=$VERSION"
	echo ""
elif [ "$1" = "--show-config" ]; then
	comm "MetaWRAP script found in $(which metawrap) and config-metawrap file was found in $(which config-metawrap). Please make sure these paths are consistent with each other."
	comm "Here are the contents of config-metawrap:"
	cat $(which config-metawrap)
else
        comm "Please select a proper module of metaWRAP."
        help_message
        exit 1
fi



########################################################################################################
########################               END OF METAWRAP PIPELINE                 ########################
########################################################################################################