def main():
    '''
    Organization function
    -setups logging
    -gets inputdata
    -calls plotting function
    '''
    args = get_args()
    try:
        utils.make_output_dir(args.outdir)
        utils.init_logs(args)
        args.format = nanoplotter.check_valid_format(args.format)
        settings = vars(args)
        settings["path"] = path.join(args.outdir, args.prefix)
        sources = {
            "fastq": args.fastq,
            "bam": args.bam,
            "cram": args.cram,
            "fastq_rich": args.fastq_rich,
            "fastq_minimal": args.fastq_minimal,
            "summary": args.summary,
            "fasta": args.fasta,
            "ubam": args.ubam,
        }

        if args.pickle:
            datadf = pickle.load(open(args.pickle, 'rb'))
        else:
            datadf = get_input(
                source=[n for n, s in sources.items() if s][0],
                files=[f for f in sources.values() if f][0],
                threads=args.threads,
                readtype=args.readtype,
                combine="simple",
                barcoded=args.barcoded)
        if args.store:
            pickle.dump(
                obj=datadf,
                file=open(settings["path"] + "NanoPlot-data.pickle", 'wb'))
        if args.raw:
            datadf.to_csv(settings["path"] + "NanoPlot-data.tsv.gz",
                          sep="\t",
                          index=False,
                          compression="gzip")

        settings["statsfile"] = [make_stats(datadf, settings, suffix="")]
        datadf, settings = filter_and_transform_data(datadf, settings)
        if settings["filtered"]:  # Bool set when filter was applied in filter_and_transform_data()
            settings["statsfile"].append(make_stats(datadf, settings, suffix="_post_filtering"))

        if args.barcoded:
            barcodes = list(datadf["barcode"].unique())
            plots = []
            for barc in barcodes:
                logging.info("Processing {}".format(barc))
                settings["path"] = path.join(args.outdir, args.prefix + barc + "_")
                dfbarc = datadf[datadf["barcode"] == barc]
                if len(dfbarc) > 5:
                    settings["title"] = barc
                    plots.extend(
                        make_plots(dfbarc, settings)
                    )
                else:
                    sys.stderr.write("Found barcode {} less than 5x, ignoring...\n".format(barc))
                    logging.info("Found barcode {} less than 5 times, ignoring".format(barc))
        else:
            plots = make_plots(datadf, settings)
        make_report(plots, settings)
        logging.info("Finished!")
    except Exception as e:
        logging.error(e, exc_info=True)
        print("\n\n\nIf you read this then NanoPlot has crashed :-(")
        print("Please try updating NanoPlot and see if that helps...\n")
        print("If not, please report this issue at https://github.com/wdecoster/NanoPlot/issues")
        print("If you could include the log file that would be really helpful.")
        print("Thanks!\n\n\n")
        raise