Re-add --protein_fastas option

Adds:

--protein_fastas as input option
Renames --peptide_fasta --> --reference_proteome_fasta for clarity and distinction from input protein fastas

PR checklist

[x] PR is to dev rather than master
[x] This comment contains a description of changes (with reason)
[x] If you've fixed a bug or added code that should be tested, add tests!
[ ] If necessary, also make a PR on the nf-core/kmermaid branch on the nf-core/test-datasets repo
[ ] Ensure the test suite passes (nextflow run . -profile test,docker).
[x] Make sure your code lints (nf-core lint .).
[x] Documentation in docs is updated
[x] CHANGELOG.md is updated
[x] README.md is updated