FoldFlow

Purpose

This repo contains the design for a basic RFdiffusion -> ProteinMPNN -> AlphaFold pipeline in Nextflow.

Pipeline Design

Setup

Once cloned, you will need to make some adjustments to the config files, specifically in nextflow.config

params.rfdiff_editables_dir = '/ibex/user/thariaaa/RFdiffContainer'
params.rfdiff_sif_path = '/ibex/user/thariaaa/RFdiffContainer/RFdiffusion.sif'
...
params.mpnn_editables_dir = '/ibex/user/thariaaa/MPNNContainer'
params.mpnn_sif_path = '/ibex/user/thariaaa/MPNNContainer/ProteinMPNN.sif'
...
params.alphafold_sif_path = '/ibex/user/thariaaa/AlphaFoldContainer/AlphaFold.sif'
params.alphafold_data_dir = '/ibex/reference/KSL/alphafold/2.3.1/'

Each editables_dir, sif_path and data_dir needs to be set according to how you have set up the singularity images as per the setup instructions in:

• RFdiffusion container
• MPNN container
• AlphaFold container

The number of outputs for each stage of the pipeline can also be edited in nextflow.config alongside any naming conventions and the SLURM setup

To change the configuration of any specific model you will need to edit this information in module_configs