out_dir should be created just before run

[EricDeveaud]

hello,

when piggy is launched with bad option value or non exiting in-dir or .... it currently produce an empty outdir.

just creating the out_dir after all checks will solve this

create out_dr after check roary_dir check threads check nuc_id check len_id check method check dependencies check in_dir contains gff files

regards

Eric

[harry-thorpe]

Hi Eric,

I've sorted this.

Thanks,

Harry