Skip to content

CLAUDE.md

Latest commit

 

History

History
82 lines (61 loc) · 2.88 KB

CLAUDE.md

File metadata and controls

82 lines (61 loc) · 2.88 KB

Protein Engineering Workflows

Project Overview

CWL workflows combining BV-BRC protein structure prediction tools (Boltz-2, Chai-1) with stability analysis (stabiliNNator) for protein engineering applications.

Repository: https://github.com/CEPI-dxkb/ProteinEngineeringWorkflows

Key Components

CWL Tools (cwl/tools/) - 9 total

Direct Command Tools

  • boltz.cwl - Boltz-2 structure prediction (boltz predict)
  • chai.cwl - Chai-1 structure prediction (chai-lab)
  • stabilinnator.cwl - Combined stability analysis (dynamic command selection)
  • prolinnator.cwl - Proline mutation analysis (prolinnator)
  • disulfinnate.cwl - Disulfide bond analysis (disulfinnate)

BV-BRC App Script Tools

  • app-boltz.cwl - Uses App-Boltz.pl
  • app-chai.cwl - Uses App-ChaiLab.pl
  • app-prolinnator.cwl - Uses App-StabiliNNator.pl (proline mode)
  • app-disulfinnate.cwl - Uses App-StabiliNNator.pl (disulfide mode)

CWL Workflows (cwl/workflows/) - 6 total

Type Boltz Chai-1
Simple (dynamic) protein_stability_pipeline.cwl protein_stability_with_chai.cwl
Explicit (parallel) protein_stability_explicit.cwl protein_stability_explicit_chai.cwl
App scripts protein_stability_app.cwl protein_stability_app_chai.cwl

Docker Images

  • dxkb/boltz-bvbrc:latest-gpu - Boltz-2 with GPU support
  • dxkb/chai-bvbrc:latest-gpu - Chai-1 with GPU support
  • dxkb/stabilinnator-bvbrc:latest-gpu - stabiliNNator with GPU support

Development Notes

Running Workflows

# Simple pipeline (Boltz)
cwltool cwl/workflows/protein_stability_pipeline.cwl examples/crambin_job.yml

# Explicit parallel analysis (Chai-1)
cwltool cwl/workflows/protein_stability_explicit_chai.cwl examples/crambin_fasta_job.yml

# BV-BRC App script workflow
cwltool cwl/workflows/protein_stability_app.cwl examples/crambin_job.yml

# With Toil (for HPC)
toil-cwl-runner cwl/workflows/protein_stability_pipeline.cwl examples/crambin_job.yml

Testing

./tests/test_pipeline.sh --quick  # Fast CWL validation (21 tests)
./tests/test_pipeline.sh          # Full test with real predictions

CI/CD

GitHub Actions workflow validates all CWL files on push/PR to main.

File Format Notes

  • Boltz prefers YAML input format for complex molecules (constraints, ligands)
  • Chai-1 uses FASTA format
  • stabiliNNator accepts both PDB and mmCIF
  • Output B-factors are in 0-1 range (not standard 0-100 crystallographic B-factors)

Adding New Workflows

  1. Create CWL file in cwl/workflows/
  2. Run cwltool --validate to check syntax
  3. Add to README Available Workflows table
  4. Update Repository Structure section
  5. Run ./tests/test_pipeline.sh --quick to verify

Related Repositories

  • CEPI infrastructure: /Users/me/Development/CEPI
  • Individual app containers in CEPI docker/ directory
  • GitHub org: https://github.com/CEPI-dxkb