Check for proper inputs earlier on in the scripts (feature/nice to have)

[JTFouquier]

The SCNIC modules command was running for a while before it threw me this error:

FileNotFoundError: [Errno 2] No such file or directory: 'example_table.biom'

I meant to change my table name but I forgot. A check earlier on for proper input files would be great to save users' time for modules command and possibly other commands. Thank you!