Perform multicore trimming with fastp (https://github.com/OpenGene/fastp)

def _fastp_trim(fastq_files, adapters, out_dir, data):
    """Perform multicore trimming with fastp (https://github.com/OpenGene/fastp)
    """
    report_file = os.path.join(out_dir, "%s-report.json" % utils.splitext_plus(os.path.basename(fastq_files[0]))[0])
    out_files = [os.path.join(out_dir, "%s-trimmed.fq.gz" % utils.splitext_plus(os.path.basename(x))[0])
                 for x in fastq_files]
    if not utils.file_exists(out_files[0]):
        with file_transaction(data, *[report_file] + out_files) as tx_out:
            tx_report = tx_out[0]
            tx_out_files = tx_out[1:]
            cmd = ["fastp", "--thread", dd.get_num_cores(data)]
            if dd.get_quality_format(data).lower() == "illumina":
                cmd += ["--phred64"]
            for i, (inf, outf) in enumerate(zip(fastq_files, tx_out_files)):
                if i == 0:
                    cmd += ["-i", inf, "-o", outf]
                else:
                    cmd += ["-I", inf, "-O", outf]
            cmd += ["--cut_by_quality3", "--cut_mean_quality", "5",
                    "--length_required", str(dd.get_min_read_length(data)),
                    "--disable_quality_filtering"]
            if "polyx" in dd.get_adapters(data):
                cmd += ["--trim_poly_x", "--poly_x_min_len", "8"]
            if "polyx" in dd.get_adapters(data) or "polyg" in dd.get_adapters(data):
                cmd += ["--trim_poly_g", "--poly_g_min_len", "8"]
            for a in adapters:
                cmd += ["--adapter_sequence", a]
            if not adapters:
                cmd += ["--disable_adapter_trimming"]
            cmd += ["--json", report_file, "--report_title", dd.get_sample_name(data)]
            do.run(cmd, "Trimming with fastp: %s" % dd.get_sample_name(data))
    return out_files, report_file