Optimization "create_new_scheme_with_novel.py"

[Nilad]

Hi,

First, thanks for this tools.

In the way to render MentaLiST containerable, can you in the script create_new_scheme_with_novel.py change the files list needed by just the path of the directory database that contains the fasta files.

Like

parser.add_argument("-db", "--pathDB", type=str, help="MLST Fasta Database Directory")

instead of

parser.add_argument("files", nargs="+", help="MLST Fasta files")

And

for f in os.listdir(param.pathDB):
    f_path = os.path.join(param.pathDB, f)

instad of

for f in param.files:

Because for a large database of fasta files... the length of the python command overflow the maximun allowed by docker or singularity.