Input folder also reads existing subfolders

[susheelbhanu]

Hi @agudys,

Thanks again for fixing the earlier issues with the output directory. There still exists a potential issue, where all the files and folders in the input folder are being read into the input vir.list. .

For example, my input folder has the following, where the first is a folder containing tmp bins, and the actual file to run would be the dereplicated_bins.fna

all_bins  (folder)
dereplicated_bins.fna

It would help to provide a sanity check of sorts, where the vir.list only reads those with a particular fasta extension such as .fa, .fna, .fasta, .FA, or .FASTA

Thank you!