Patch to enable large file deletion from git history

[cgpu]

Overview

Patch to enable large file deletion from git history. Commits from main were removed by resetting HEAD force pushing

See this draft PR for more info https://github.com/sheynkman-lab/Long-Read-Proteogenomics/pull/134.

Changes

• Adds fa.gz in .gitignore
• set toml file
• metamorpehus rr point to correct docker
• Add folder to initiate peptide novelty script.

Failed tests

The test is failing on the Metamorpheus step. However we choose to merge this as @bj8th is working on fixing this, and the scope of this PR is to restore the state of the repo.