INNER CODE UNIT · Python

check_remove_mode

nf-core/eager · bin/extract_map_reads.py:130

def check_remove_mode(mode):
    if mode.lower() not in ["replace", "remove"]:
        logging.info(f"Mode must be {' or '.join(mode)}")
    return mode.lower()


if __name__ == "__main__":
    BAM, IN_FWD, MERGED, IN_REV, OUT_FWD, OUT_REV, MODE, PROC = _get_args()

    logging.basicConfig(level=logging.INFO, format="%(message)s")

    if OUT_FWD == None:
        out_fwd = os.path.join(os.getcwd(), Path(IN_FWD).stem + ".r1.fq.gz")
    else:
        out_fwd = OUT_FWD

    if out_fwd.endswith(".gz"):
        write_mode = "wb"

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