make changes so protein only input files can be used

PR checklist

[x] Tag the issue(s) or milestones this PR fixes (e.g. Fixes #123, Resolves #456).
[x] Describe the changes you've made.
[x] Describe any tests you have conducted to confirm that your changes behave as expected.
[x] If you've added new software dependencies, make sure that those dependencies are included in the appropriate conda environments.
[x] If you've added new functionality, make sure that the documentation is updated accordingly.
[x] If you encountered bugs or features that you won't address, but should be addressed eventually, create new issues for them.

PR description

This PR makes a new snakefile to run peptide prediction and annotation when the user only has proteins as input. It mostly copies the snakefile to a new file (I recognize this is and that refactoring would be better) and removes all of the nucleotide-specific stuff. it also changes a few of the scripts so that they can run without nucleotide information.

i know it would be much better to re-factor this, but with our timeline I think this is ok for now -- if this becomes widely used, I think we can go back and refactor properly for this use case.

Tests to confirm behavior

I ran this code on protein-only input and got meaningful/accurate/correctly formatted results back.

Issues

note I have not opened any issues for this yet because it isn't clear to me what they should include...I can open issues tho if you think it would be useful for anything!

Arcadia-Science / peptigate