Germinal Workflow

Parallel Germinal execution for antibody and nanobody design across multiple GPUs.

Overview

The --method germinal workflow runs Germinal trajectories in parallel across multiple GPUs — ideal for HPC clusters or multi-GPU workstations. Configuration is supplied via a Germinal Hydra YAML file (combined or partial config with Hydra default groups).

Key Differences

Unlike a single long Germinal run that loops until stopping criteria are met, this pipeline:

• Runs a fixed number of trajectories (--germinal_n_traj)
• Splits work into parallel batches (--germinal_batch_size)
• Merges per-batch CSVs and structure folders into a single output tree

If you want a specific number of accepted designs, run a small pilot (--germinal_n_traj 10) to estimate acceptance rate, then scale up.

Command-line Options

See available options with --method germinal and no config:

nextflow run Australian-Protein-Design-Initiative/nf-binder-design \
  --method germinal

Example Usage

#!/bin/bash

DATESTAMP=$(date +%Y%m%d_%H%M%S)
RUN_DIR=/path/to/runs/germinal/test-protenix2

nextflow run /path/to/nf-binder-design-germinal/main.nf \
  --method germinal \
  --germinal_config "${RUN_DIR}/configs/pdl1_vhh_protenix.yaml" \
  --germinal_pdb_dir "${RUN_DIR}/pdbs" \
  --germinal_experiment_name pdl1_vhh \
  --germinal_n_traj 2 \
  --germinal_batch_size 1 \
  --outdir "${RUN_DIR}/results/nf-germinal" \
  -profile local \
  -resume \
  -with-report "results/logs/report_${DATESTAMP}.html" \
  -with-trace "results/logs/trace_${DATESTAMP}.txt"

For SLURM on M3 BDI, use -profile slurm,m3_bdi with --slurm_account=yt41.

Partial configs (e.g. configs/config.yaml with defaults: [run: vhh, target: pdl1, ...]) are supported: the workflow copies built-in Hydra config groups from the container and places your config alongside them.

Key Parameters

Flag	Description
--germinal_config	Germinal Hydra config YAML (required)
--germinal_pdb_dir	Directory with target PDB and optional nb.pdb scaffold (default: ../pdbs relative to config)
--germinal_experiment_name	Output subdirectory name under results/
--germinal_n_traj	Total trajectory attempts across all batches
--germinal_batch_size	Trajectories per parallel batch
--germinal_max_passing_designs	Max accepted designs per batch (default: high)
--germinal_max_hallucinated_trajectories	Max hallucinated trajectories per batch (default: high)
--gpu_devices	GPU devices for local multi-GPU runs, e.g. --gpu_devices=0,1

Output Structure

results/germinal/
├── all_trajectories.csv      # merged across all batches
├── accepted_designs.csv      # merged from per-batch accepted/designs.csv
├── failure_counts.csv
├── config/
│   └── final_config.yaml     # resolved Hydra config (batch 0 only)
├── accepted/
│   └── structures/           # flattened accepted PDBs from all batches
├── trajectories/
│   ├── designs.csv
│   └── structures/
├── redesign_candidates/
│   ├── designs.csv
│   └── structures/
└── batches/
    └── 0/
        └── pdl1_vhh/         # per-batch Germinal output (includes final_config.yaml)

Notes

• The nanobody scaffold (nb.pdb) is copied from the container into pdb_dir if missing.
• target.target_pdb_path in the config should be relative (e.g. pdbs/pdl1.pdb) so paths resolve from the process working directory.
• Stopping criteria per batch: whichever of max_trajectories, max_hallucinated_trajectories, or max_passing_designs is reached first.