Linear epitope prediction using AlphaFold3

Setup

Swap the path in envs/env.yaml to the project root to your cloned path:

...
  - pip:
    # swap me for git URL
    - /path/to/cloned/repo
...

Install the nextflow and project environments:

# project environment
conda env create --name <name> --file envs/env.yaml
# nf-core/nextflow env 
conda env create --name <name> --file envs/nf-core.yaml

If running on Gemini, ensure that Alphafold MSAs will use your scratch as a tmp directory (some MSA intermediate files are larger than /tmp on compute nodes)

vim ~/.nextflow/config

params.msa_tmpdir = "/scratch/<username>/tmp"