RUN

#!/bin/bash -e

wd=$(pwd)
source ./paths
source ./funcs

usage() {
    echo ""
}


main() {
    OUTPUTDIR="/n/scratch3/users/a/ak586/microtrawler"
    for i in "$@"; do
    case $i in
        -o|--outputdir)
        OUTPUTDIR="$2"
        shift
        shift
        ;;
        -s|--step)
        STEP="$2"
        shift
        shift
        ;;
        -h|--help)
        usage
        exit
        ;;
        *)
        ;;
    esac
    done
    
    mkdir -p $OUTPUTDIR
    newl
    log " " " " "Running Microtrawler pipeline"
    log "Analysis Directory" "$OUTPUTDIR"
    newl

    #log "Downloading up-to-date culture reference databases" "" "Step 0"
    #dbjobnums=$(./0_dl-db -o "$OUTPUTDIR/0_databases")
    #dbjobnums=${dbjobnums%?}
    #log "Download database jobs submitted" "$dbjobnums"
    #newl

    #log "Downloading assembled sequences for isolates" "" "Step 1"
    #if [ ! -z $dbjobnums ]; then
        #seqjobnums=$(./1_dl-seqs -i "$OUTPUTDIR/0_databases" -o "$OUTPUTDIR/1_sequences" --dependency $dbjobnums)
    #else
        #seqjobnums=$(./1_dl-seqs -i "$OUTPUTDIR/0_databases" -o "$OUTPUTDIR/1_sequences")
    #fi
    #seqjobnums=${seqjobnums%?}
    #log "Download sequence jobs submitted" "$seqjobnums"
    #newl

    log "Searching for antibiotic resistance" "" "Step 2"
    if [ ! -z $seqjobnums ]; then
        rgijobnums=$(./2_analyze-seqs -i "$OUTPUTDIR/1_sequences" -o "$OUTPUTDIR/2_analyze-seqs" --dependency $seqjobnums -c 50)
    else
        rgijobnums=$(./2_analyze-seqs -i "$OUTPUTDIR/1_sequences" -o "$OUTPUTDIR/2_analyze-seqs" -c 50)
    fi
    rgijobnums=${rgijobnums%?}
    log "Antibiotic resistance jobs submitted" "$rgijobnums"
    newl

    log "Performing meta-analysis" "" "Step 3"
    ./3_analyze-resistance -i "$OUTPUTDIR/2_analyze-seqs" -o "$OUTPUTDIR/3_analysis-resistance" -d "$OUTPUTDIR/0_databases" -f "$OUTPUTDIR/1_sequences"
    log "Complete" "" "Step 3"
    newl
}

main "$@"