Consider changing snakemake input and output variable rules

[taylorreiter]

The names refer both to file contents (peptides) and to file types (tsv). It might be good to pick on convention and stick to it throughout (e.g. peptides & predictions or fasta & tsv)

[taylorreiter]

This should also be made more consistent:

outputs/cleavage
├── deeppeptide
│   ├── peptide_predictions.json
│   ├── peptides.faa
│   └── propeptides.faa
├── nlpprecursor
│   ├── nlpprecursor_peptides.fasta
│   └── nlpprecursor_predictions.tsv
└── preprocessing
    └── noasterisk.faa

The deeppeptide files don't have the word deeppeptide in them while the nlpprecursor ones do, and they use different endings (fasta vs. faa). I propose to keep the deeppeptide outputs the same and change the nlpprecursor ones to peptides.faa and peptide_predictions.tsv.

[taylorreiter]

I went much more explicit adding tool name, file contents, and file type to a lot these.