nextflow_schema.json

{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com//master/nextflow_schema.json",
    "title": " pipeline parameters",
    "description": "",
    "type": "object",
    "definitions": {
        "essential_parameters": {
            "title": "Essential Parameters",
            "type": "object",
            "description": "These parameters are required for BioModStack and are used by every mode.",
            "default": "",
            "properties": {
                "rfd_mode": {
                    "type": "string",
                    "description": "Pipeline mode. Choose from 'binder_denovo', 'binder_foldcond', 'binder_motifscaff', 'binder_partialdiff', 'monomer_denovo', 'monomer_foldcond', 'monomer_motifscaff', or 'monomer_partialdiff'."
                },
                "rfd_num_designs": {
                    "type": "integer",
                    "default": 8,
                    "description": "Number of designs to generate using RFdiffusion."
                },
                "seqs_per_design": {
                    "type": "integer",
                    "default": 8,
                    "description": "Number of sequences to generate per RFdiffusion design."
                },
                "out_dir": {
                    "type": "string",
                    "default": "${projectDir}/bms_results",
                    "description": "Output directory for results.",
                    "format": "directory-path"
                }
            },
            "required": [
                "rfd_mode",
                "rfd_num_designs",
                "seqs_per_design",
                "out_dir"
            ]
        },
        "mode_specific_parameters": {
            "title": "Mode-Specific Parameters",
            "type": "object",
            "description": "These parameters are used for some of the BioModStack modes.",
            "default": "",
            "properties": {
                "rfd_contigs": {
                    "type": "string",
                    "description": "Contigs specification. See examples in documentation. e.g. '[A17-145/0 50-100]'.",
                    "pattern": "^\\[[A-Z0-9\\-\\/ \\[\\]]+\\]$"
                },
                "rfd_input_pdb": {
                    "type": "string",
                    "pattern": ".*\\.pdb$",
                    "format": "file-path",
                    "description": "Path to an input PDB file. e.g. 'target.pdb'"
                },
                "rfd_hotspots": {
                    "type": "string",
                    "description": "Specifies hotspot residues for binding. e.g. '[A56,A115,A123]'",
                    "pattern": "^\\[[A-Z]\\d+(,[A-Z]\\d+)*\\]$"
                },
                "rfd_scaffold_dir": {
                    "type": "string",
                    "format": "directory-path",
                    "description": "Path to directory containing scaffold files. e.g. 'binderscaffolds/scaffolds_assorted'"
                },
                "rfd_target_adj": {
                    "type": "string",
                    "description": "Block adjacency file for scaffold-guided target. e.g. 'target_adj.pt'",
                    "format": "file-path",
                    "pattern": "^.*adj\\.pt$"
                },
                "rfd_target_ss": {
                    "type": "string",
                    "description": "Secondary structure file for scaffold-guided target. e.g. 'target_ss.pt'",
                    "pattern": "^.*ss\\.pt$"
                },
                "rfd_mask_loops": {
                    "type": "boolean",
                    "default": true,
                    "description": "Whether to ignore loop regions when applying secondary structure constraints from scaffolds (default=true). Recommended to set to false for binder design as the scaffold sets have enough diversity"
                },
                "rfd_inpaint_seq": {
                    "type": "string",
                    "description": "Residues that will have their sequence masked when diffusing. e.g. '[A17-19/A143-145]'",
                    "pattern": "^\\[([A-Z]?\\d+(?:-\\d+)?(?:\\/\\d+)?)(?:\\/([A-Z]?\\d+(?:-\\d+)?(?:\\/\\d+)?))*\\]$"
                },
                "rfd_length": {
                    "type": "string",
                    "description": "Length of diffused chain when performing motif scaffolding e.g. 100-120",
                    "pattern": "^\\d+-\\d+$"
                },
                "rfd_partial_diffusion_timesteps": {
                    "type": "integer",
                    "description": "Number of timesteps for partial diffusion. e.g. 20"
                }
            }
        },
        "workflow_advanced_parameters": {
            "title": "Mode-Specific Parameters",
            "type": "object",
            "description": "These parameters are used for some of the BioModStack modes.",
            "default": "",
            "properties": {
                "seq_method": {
                    "type": "string",
                    "default": "mpnn",
                    "description": "Sequence design method. Choose from 'mpnn' (ProteinMPNN Fast-Relax) or 'fampnn' (Full-Atom MPNN).",
                    "enum": [
                        "mpnn",
                        "fampnn"
                    ]
                },
                "pred_method": {
                    "type": "string",
                    "default": "af2",
                    "description": "Structure prediction method. Choose from 'af2' (AlphaFold2 Initial-Guess) or 'boltz' (Boltz-2).",
                    "enum": [
                        "af2",
                        "boltz"
                    ]
                },
                "zip_pdbs": {
                    "type": "boolean",
                    "description": "Whether to compress output final designs in a tar.gz archive. If false, results will be output as uncompressed PDB files.",
                    "default": true,
                    "hidden": true
                },
                "run_rfd_only": {
                    "type": "boolean",
                    "description": "Whether to run RFdiffusion only and skip downstream stages (i.e. sequence design, prediction, and analysis)",
                    "hidden": true
                },
                "skip_rfd": {
                    "type": "boolean",
                    "description": "Skip RFdiffusion and run Sequence Design, Structure Prediction, and Analysis only. Must provide 'skip_input_dir' directory below containing PDB and JSON files with metadata. Binder design PDBs must have binder as chain A and target as chain B.",
                    "hidden": true
                },
                "skip_rfd_seq": {
                    "type": "boolean",
                    "description": "Skip RFdiffusion and run Sequence Design, Structure Prediction, and Analysis only. Must provide 'skip_input_dir' directory below containing PDB and JSON files with metadata. Binder design PDBs must have binder as chain A and target as chain B.",
                    "hidden": true
                },
                "skip_rfd_seq_pred": {
                    "type": "boolean",
                    "description": "Skip RFdiffusion and run Sequence Design, Structure Prediction, and Analysis only. Must provide 'skip_input_dir' directory below containing PDB and JSON files with metadata. Binder design PDBs must have binder as chain A and target as chain B.",
                    "hidden": true
                },
                "skip_input_dir": {
                    "type": "string",
                    "description": "Path to input files when skipping stages e.g. './rfd_results'",
                    "format": "directory-path",
                    "hidden": true
                },
                "run_maturation": {
                    "type": "boolean",
                    "default": false,
                    "description": "Enable PPIFlow maturation after FAMPNN.",
                    "hidden": true
                },
                "maturation_designs_per_job": {
                    "type": "integer",
                    "default": 4,
                    "description": "Number of designs per PPIFlow child job.",
                    "hidden": true
                },
                "maturation_anchor_threshold": {
                    "type": "number",
                    "default": -5.0,
                    "description": "Anchor residue energy threshold (REU).",
                    "hidden": true
                },
                "maturation_anchor_distance_cutoff": {
                    "type": "number",
                    "default": 12.0,
                    "description": "Distance cutoff (A) for binder-target interface pair energies.",
                    "hidden": true
                },
                "maturation_min_improvement": {
                    "type": "number",
                    "default": -1.0,
                    "description": "Minimum delta interface score required to pass.",
                    "hidden": true
                },
                "maturation_filter_percentile": {
                    "type": "number",
                    "default": 0,
                    "description": "Optional percentile threshold for maturation filtering.",
                    "hidden": true
                },
                "maturation_design_mode": {
                    "type": "string",
                    "default": "inherit",
                    "description": "Design mode for maturation redesign constraints. Use 'inherit' to follow antibody_design_mode.",
                    "hidden": true
                },
                "maturation_repack_enabled": {
                    "type": "boolean",
                    "description": "Run selected side-chain repacking independently of partial flow."
                },
                "maturation_anchors_enabled": {
                    "type": "boolean",
                    "description": "Run selected anchor analysis independently of partial flow."
                },
                "maturation_flow_enabled": {
                    "type": "boolean",
                    "description": "Run partial flow only when selected."
                },
                "maturation_redesign_enabled": {
                    "type": "boolean",
                    "default": true,
                    "description": "Run FAMPNN redesign after partial flow.",
                    "hidden": true
                },
                "maturation_redesign_top_n": {
                    "type": "integer",
                    "default": 0,
                    "description": "Redesign only the top N partial-flow designs (0 = all).",
                    "hidden": true
                },
                "maturation_redesign_temp": {
                    "type": "number",
                    "default": 0.1,
                    "description": "FAMPNN temperature for maturation redesign.",
                    "hidden": true
                },
                "maturation_redesign_steps": {
                    "type": "integer",
                    "default": 100,
                    "description": "FAMPNN denoising steps for maturation redesign.",
                    "hidden": true
                },
                "ppiflow_start_t": {
                    "type": "number",
                    "default": 0.5,
                    "description": "Partial flow start t for PPIFlow.",
                    "hidden": true
                },
                "ppiflow_samples_per_target": {
                    "type": "integer",
                    "default": 3,
                    "description": "Samples per target for PPIFlow partial flow.",
                    "hidden": true
                },
                "ppiflow_retry_limit": {
                    "type": "integer",
                    "default": 10,
                    "description": "Retry limit for PPIFlow sampling.",
                    "hidden": true
                },
                "ppiflow_rotamer_enrichment_enabled": {
                    "type": "boolean",
                    "default": true,
                    "description": "Run Rosetta-style interface rotamer enrichment before anchor selection.",
                    "hidden": true
                },
                "ppiflow_require_anchors": {
                    "type": "boolean",
                    "default": true,
                    "description": "Fail PPIFlow maturation when no anchor residues pass the strict energy threshold.",
                    "hidden": true
                },
                "ppiflow_rotamer_shell_cutoff": {
                    "type": "number",
                    "default": 20.0,
                    "description": "Shell distance (A) for local interface relax/repack before anchor selection.",
                    "hidden": true
                },
                "ppiflow_config": {
                    "type": "string",
                    "default": "/app/ppiflow/configs/inference_nanobody.yaml",
                    "description": "PPIFlow config path inside container.",
                    "hidden": true
                },
                "ppiflow_checkpoint": {
                    "type": "string",
                    "default": "antibody",
                    "description": "PPIFlow checkpoint name (without extension).",
                    "hidden": true
                },
                "ppiflow_checkpoint_path": {
                    "type": "string",
                    "description": "Explicit PPIFlow checkpoint path.",
                    "hidden": true
                },
                "ppiflow_weights_dir": {
                    "type": "string",
                    "default": "BMS_WEIGHTS/ppiflow",
                    "description": "Host directory with PPIFlow weights (BMS_WEIGHTS/ppiflow).",
                    "hidden": true
                },
                "ppiflow_heavy_chain": {
                    "type": "string",
                    "description": "Override heavy chain ID for PPIFlow.",
                    "hidden": true
                },
                "ppiflow_light_chain": {
                    "type": "string",
                    "description": "Override light chain ID for PPIFlow.",
                    "hidden": true
                },
                "ppiflow_antigen_chain": {
                    "type": "string",
                    "description": "Override antigen chain ID for PPIFlow.",
                    "hidden": true
                },
                "run_anarcii_post": {
                    "type": "boolean",
                    "default": false,
                    "description": "Run ANARCII CDR annotation after the pipeline completes.",
                    "hidden": true
                },
                "anarcii_include_children": {
                    "type": "boolean",
                    "default": true,
                    "description": "Include child jobs when annotating CDRs.",
                    "hidden": true
                }
            }
        },
        "rfdiffusion_advanced_parameters": {
            "title": "RFdiffusion Advanced Parameters",
            "type": "object",
            "description": "Advanced parameters to control the behaviour of RFdiffusion.",
            "default": "",
            "help_text": "",
            "properties": {
                "rfd_ckpt_override": {
                    "type": "string",
                    "description": "Override the diffusion model checkpoint used by RFdiffusion. Choose from: 'active_site', 'base', 'base_epoch8', 'complex_base', 'complex_beta', 'complex_fold_base', 'inpaint_seq', 'inpaint_seq_fold'. RFdiffusion will automatically select a checkpoint. Not recommended to override except for 'binder_denovo' mode i.e. 'complex_beta'",
                    "enum": [
                        "active_site",
                        "base",
                        "base_epoch8",
                        "complex_base",
                        "complex_beta",
                        "complex_fold_base",
                        "inpaint_seq",
                        "inpaint_seq_fold"
                    ],
                    "hidden": true
                },
                "rfd_noise_scale": {
                    "type": "number",
                    "description": "Scale of noise for RFdiffusion translations (C-alpha) and rotations (frames). 1 (default) is recommended for monomer modes to increase diversity. 0-0.5 is recommended for binder modes to increase success rates.",
                    "minimum": 0,
                    "maximum": 1,
                    "hidden": true
                },
                "rfd_extra_config": {
                    "type": "string",
                    "description": "Additional configuration parameters to pass to RFdiffusion. e.g. 'contigmap.inpaint_str=[B165-178]'",
                    "hidden": true
                }
            }
        },
        "proteinmpnn_fastrelax_parameters": {
            "title": "ProteinMPNN-FastRelax Parameters",
            "type": "object",
            "description": "Advanced parameters to control the behaviour of ProteinMPNN-FastRelax. Used for binder design modes only.",
            "default": "",
            "properties": {
                "mpnn_omitAAs": {
                    "type": "string",
                    "default": "CX",
                    "pattern": "^[A-Za-z]*$",
                    "description": "A string of all residue types (one letter case-insensitive) to avoid for design. Default: CX",
                    "hidden": true
                },
                "mpnn_temperature": {
                    "type": "number",
                    "default": 0.1,
                    "description": "Temperature for sequence sampling. Higher values increase sequence diversity.",
                    "hidden": true
                },
                "mpnn_checkpoint_type": {
                    "type": "string",
                    "default": "soluble",
                    "enum": [
                        "vanilla",
                        "soluble"
                    ],
                    "description": "Checkpoint type to use for ProteinMPNN. Choose from 'vanilla' or 'soluble' (default = 'soluble').",
                    "hidden": true
                },
                "mpnn_checkpoint_model": {
                    "type": "string",
                    "default": "v_48_020",
                    "description": "Checkpoint model to use for ProteinMPNN. Indicates noise level used during training for backbone atoms.  Choose from 'v_48_002','v_48_010,'v_48_020','v_48_030'. (default = 'v_48_020', noised with 0.20Å Gaussian noise)",
                    "enum": [
                        "v_48_002",
                        "v_48_010",
                        "v_48_020",
                        "v_48_030"
                    ],
                    "hidden": true
                },
                "mpnn_backbone_noise": {
                    "type": "number",
                    "default": 0,
                    "description": "Standard deviation of Gaussian noise to add to backbone atoms. 0 = no change to backbone, 0.1-0.3 = allows mild perturbation of backbone.",
                    "hidden": true
                },
                "mpnn_relax_max_cycles": {
                    "type": "integer",
                    "default": 0,
                    "description": "Maximum number of fast relax cycles to run on each sequence. Set to zero to disable.",
                    "hidden": true
                },
                "mpnn_relax_seqs_per_cycle": {
                    "type": "integer",
                    "default": 1,
                    "description": "Number of sequences to generate between relaxation steps. The sequence with the best score will be kept.",
                    "hidden": true
                },
                "mpnn_relax_output": {
                    "type": "boolean",
                    "description": "Whether to run a relaxation cycle before saving output.",
                    "hidden": true
                },
                "mpnn_relax_convergence_rmsd": {
                    "type": "number",
                    "default": 0.2,
                    "description": "Design is considered converged if the C-alpha RMSD (Å) between cycles is <= this threshold.",
                    "hidden": true
                },
                "mpnn_relax_convergence_score": {
                    "type": "number",
                    "default": 0.1,
                    "description": "Design is considered converged if the improvement in score between cycles is <= this threshold.",
                    "hidden": true
                },
                "mpnn_relax_convergence_max_cycles": {
                    "type": "integer",
                    "default": 1,
                    "description": "Design is considered converged if it meets both convergence criteria for n consecutive cycles.",
                    "hidden": true
                },
                "mpnn_extra_config": {
                    "type": "string",
                    "description": "Additional configuration parameters to pass to ProteinMPNN-FastRelax that are not externalised in Nextflow. e.g. '-protein_features=\"full\"'",
                    "hidden": true
                }
            }
        },
        "full_atom_mpnn_parameters": {
            "title": "Full-Atom MPNN Parameters",
            "type": "object",
            "description": "Advanced parameters to control the behaviour of Full-Atom MPNN",
            "default": "",
            "properties": {
                "fampnn_fix_target_sidechains": {
                    "type": "boolean",
                    "default": false,
                    "description": "Fix target side-chain positions when performing binder sequence design (default: false)",
                    "hidden": true
                },
                "fampnn_constraint_mode": {
                    "type": "string",
                    "default": "generic",
                    "description": "Constraint mode for FAMPNN. 'generic' uses no fixed residues; 'antibody' applies CDR-aware constraints.",
                    "enum": [
                        "generic",
                        "antibody"
                    ],
                    "hidden": true
                },
                "fampnn_psce_threshold": {
                    "type": "number",
                    "default": 0.3,
                    "description": "Only keep sidechains below this PSCE threshold during design; null to keep all.",
                    "hidden": true
                },
                "fampnn_temperature": {
                    "type": "number",
                    "default": 0.1,
                    "description": "Temperature for sequence sampling. Higher values increase sequence diversity.",
                    "hidden": true
                },
                "fampnn_mutation_top_n": {
                    "type": "integer",
                    "default": 25,
                    "description": "Top FA-MPNN seq_probs-derived model-favored single-substitution log-odds deltas to report per sampled design.",
                    "hidden": true
                },
                "fampnn_mutation_min_log_odds_delta": {
                    "type": "number",
                    "default": 0.0,
                    "description": "Minimum log(P_alt)-log(P_sampled) delta for reporting FA-MPNN model-favored single substitutions.",
                    "hidden": true
                },
                "fampnn_exclude_cys": {
                    "type": "boolean",
                    "default": true,
                    "description": "Exclude cysteine residues from sequence design.",
                    "hidden": true
                },
                "fampnn_extra_config": {
                    "type": "string",
                    "description": "Additional configuration parameters to pass to Full-Atom MPNN that are not externalised in Nextflow. e.g. 'timestep_schedule.num_steps=100 seq_only=true'",
                    "hidden": true
                }
            }
        },
        "prediction_advanced_parameters": {
            "title": "Structure Prediction Advanced Parameters",
            "type": "object",
            "description": "Parameters for AlphaFold2 Initial-Guess and Boltz-2",
            "default": "",
            "properties": {
                "uncropped_target_pdb": {
                    "type": "string",
                    "description": "Path to uncropped target PDB file to use in structure prediction e.g. 'benchmarkdata/5o45_pd-l1_uncropped.pdb'",
                    "hidden": true,
                    "format": "file-path",
                    "pattern": "\\.pdb$"
                },
                "af2_initial_guess": {
                    "type": "boolean",
                    "default": true,
                    "description": "Use an initial-guess of the target chain(s) when performing binder structure prediction. When false, AF2 will not use an initial guess. Default = true",
                    "hidden": true
                },
                "af2_extra_config": {
                    "type": "string",
                    "hidden": true,
                    "description": "Additional configuration parameters to pass to AlphaFold2 Initial-Guess that are not externalised in Nextflow. e.g. '-recycle 3'"
                },
                "boltz_recycling_steps": {
                    "type": "integer",
                    "default": 3,
                    "description": "The number of recycling steps to use for prediction.",
                    "minimum": 1,
                    "hidden": true
                },
                "boltz_diffusion_samples": {
                    "type": "integer",
                    "default": 1,
                    "description": "The number of diffusion samples to use for prediction.",
                    "minimum": 1,
                    "hidden": true
                },
                "boltz_sampling_steps": {
                    "type": "integer",
                    "default": 200,
                    "description": "The number of sampling steps to use for prediction.",
                    "minimum": 1,
                    "hidden": true
                },
                "boltz_use_potentials": {
                    "type": "boolean",
                    "default": false,
                    "description": "Use physics-based potentials during inference to improve physical plausibility of predictions (also known as Boltz-2x). Increases prediction time. Default = false",
                    "hidden": true
                },
                "boltz_extra_config": {
                    "type": "string",
                    "hidden": true,
                    "description": "Additional configuration parameters to pass to Boltz-2 that are not externalised in Nextflow. e.g. '--msa_pairing_strategy complete'"
                }
            }
        },
        "filtering_parameters": {
            "title": "Filtering Parameters",
            "type": "object",
            "description": "Metrics are calculated on the binder chain only in binder design modes, otherwise all chains are used in calculations.",
            "default": "",
            "properties": {
                "rfd_min_helices": {
                    "type": "integer",
                    "description": "Minimum number of alpha-helices required. e.g. 3",
                    "hidden": true
                },
                "rfd_max_helices": {
                    "type": "integer",
                    "description": "Maximum number of alpha-helices allowed. e.g. 6",
                    "hidden": true
                },
                "rfd_min_strands": {
                    "type": "integer",
                    "description": "Minimum number of beta-strands required. e.g. 2",
                    "hidden": true
                },
                "rfd_max_strands": {
                    "type": "integer",
                    "description": "Maximum number of beta-strands allowed. e.g. 6",
                    "hidden": true
                },
                "rfd_min_ss": {
                    "type": "integer",
                    "description": "Minimum number of secondary structure elements (α-helices + β-strands). e.g. 4",
                    "hidden": true
                },
                "rfd_max_ss": {
                    "type": "integer",
                    "description": "Maximum number of secondary structure elements (α-helices + β-strands). e.g. 8",
                    "hidden": true
                },
                "rfd_min_rog": {
                    "type": "number",
                    "description": "Minimum radius of gyration (Å). e.g. 10",
                    "hidden": true
                },
                "rfd_max_rog": {
                    "type": "number",
                    "description": "Maximum radius of gyration (Å). e.g. 20",
                    "hidden": true
                },
                "mpnn_max_score": {
                    "type": "number",
                    "description": "Maximum MPNN score (negative log likelihood). A lower score means ProteinMPNN is more confident in the sequence.",
                    "hidden": true
                },
                "fampnn_max_psce": {
                    "type": "number",
                    "description": "Max PSCE score for designed side-chains. A lower score means FAMPNN is more confident in the sequence.",
                    "hidden": true
                },
                "af2_max_pae_interaction": {
                    "type": "number",
                    "description": "Max predicted aligned error for interactions e.g. 10",
                    "hidden": true
                },
                "af2_max_pae_overall": {
                    "type": "number",
                    "description": "Max predicted aligned error for all chains e.g. 10",
                    "hidden": true
                },
                "af2_max_pae_binder": {
                    "type": "number",
                    "description": "Max predicted aligned error for binder e.g. 5",
                    "hidden": true
                },
                "af2_max_pae_target": {
                    "type": "number",
                    "description": "Max predicted aligned error for target e.g. 5",
                    "hidden": true
                },
                "af2_min_plddt_overall": {
                    "type": "number",
                    "description": "Min average pLDDT score for target and binder chains e.g. 90",
                    "hidden": true
                },
                "af2_min_plddt_binder": {
                    "type": "number",
                    "description": "Min pLDDT score required for binder e.g. 85",
                    "hidden": true
                },
                "af2_min_plddt_target": {
                    "type": "number",
                    "description": "Min pLDDT score required for target e.g 90",
                    "hidden": true
                },
                "af2_max_rmsd_overall": {
                    "type": "number",
                    "description": "Max RMSD when all chains are aligned e.g. 2",
                    "hidden": true
                },
                "af2_max_rmsd_binder_bndaln": {
                    "type": "number",
                    "description": "Max binder RMSD when binder chains are aligned e.g. 1",
                    "hidden": true
                },
                "af2_max_rmsd_binder_tgtaln": {
                    "type": "number",
                    "description": "Max binder RMSD when target chains are aligned e.g. 2",
                    "hidden": true
                },
                "af2_max_rmsd_target": {
                    "type": "number",
                    "description": "Max target RMSD when target chains are aligned e.g. 2",
                    "hidden": true
                },
                "boltz_max_overall_rmsd": {
                    "type": "number",
                    "description": "Max RMSD between all chains of Boltz-2 prediction and input design. e.g. 2",
                    "hidden": true
                },
                "boltz_max_binder_rmsd": {
                    "type": "number",
                    "description": "Max RMSD between binder chains of Boltz-2 prediction and input design. e.g. 1",
                    "hidden": true
                },
                "boltz_max_target_rmsd": {
                    "type": "number",
                    "description": "Max RMSD between target chains of Boltz-2 prediction and input design. e.g. 1",
                    "hidden": true
                },
                "boltz_min_conf_score": {
                    "type": "number",
                    "description": "Minimum confidence score e.g. 0.85",
                    "hidden": true
                },
                "boltz_min_ptm": {
                    "type": "number",
                    "description": "Minimum predicted TM-score e.g. 0.7",
                    "hidden": true
                },
                "boltz_min_ptm_interface": {
                    "type": "number",
                    "description": "Minimum predicted TM-score of binder-target interface e.g. 0.65",
                    "hidden": true
                },
                "boltz_min_plddt": {
                    "type": "number",
                    "description": "Minimum pLDDT score e.g. 0.85",
                    "hidden": true
                },
                "boltz_min_plddt_interface": {
                    "type": "number",
                    "description": "Minimum pLDDT score of the binder-target interface e.g. 0.8",
                    "hidden": true
                },
                "boltz_max_pde": {
                    "type": "number",
                    "description": "Maximum predicted distance error e.g. 10",
                    "hidden": true
                },
                "boltz_max_pde_interface": {
                    "type": "number",
                    "description": "Maximum predicted distance error for the binder-target interface e.g 12",
                    "hidden": true
                }
            }
        },
        "cluster_parameters": {
            "title": "Cluster Parameters",
            "type": "object",
            "description": "The cluster parameters may need adjusting depending on your HPC setup and available hardware. You must ensure that the paths to the containers and models for RFdiffusion, AlphaFold2 and Boltz-2 are valid and contain the expected files.",
            "default": "",
            "properties": {
                "container_dir": {
                    "type": "string",
                    "format": "directory-path",
                    "description": "Path to pipeline containers directory.",
                    "hidden": true
                },
                "rfd_models": {
                    "type": "string",
                    "format": "directory-path",
                    "description": "Path to the RFdiffusion model checkpoints.",
                    "hidden": true
                },
                "af2_models": {
                    "type": "string",
                    "format": "directory-path",
                    "description": "Path to the AlphaFold2 databases.",
                    "hidden": true
                },
                "boltz_models": {
                    "type": "string",
                    "format": "directory-path",
                    "description": "Path to the Boltz-2 models.",
                    "hidden": true
                },
                "gpu_model": {
                    "type": "string",
                    "default": "A30",
                    "description": "GPU model to request, e.g., 'A30'.",
                    "hidden": true
                },
                "gpu_queue": {
                    "type": "string",
                    "description": "GPU queue name or partition (if applicable, e.g. 'gpuq')",
                    "hidden": true
                },
                "gpus": {
                    "type": "integer",
                    "default": 4,
                    "description": "Number of GPUs to request.",
                    "hidden": true
                },
                "cpus": {
                    "type": "integer",
                    "default": 24,
                    "description": "Number of CPUs requested for CPU-only jobs",
                    "hidden": true
                },
                "cpus_per_gpu": {
                    "type": "integer",
                    "default": 8,
                    "description": "Number of CPUs requested per GPU",
                    "hidden": true
                },
                "memory_gpu": {
                    "type": "string",
                    "default": "24GB",
                    "description": "Memory requested for GPU jobs",
                    "hidden": true
                },
                "memory_cpu": {
                    "type": "string",
                    "default": "24GB",
                    "description": "Memory requested for CPU-only jobs",
                    "hidden": true
                }
            }
        },
        "protenix_parameters": {
            "title": "Protenix Parameters",
            "type": "object",
            "description": "Protenix parameters, including the MSA inputs the controller hands to the pipeline. Fold-CP runs through the same Protenix parameter surface, and these names are read at config time, so they must be declared here or Nextflow rejects the run before it starts.",
            "default": "",
            "properties": {
                "protenix_container_path": {
                    "type": "string",
                    "default": null,
                    "description": "Reviewed Protenix container image used for remote execution.",
                    "hidden": true
                },
                "protenix_weights": {
                    "type": "string",
                    "default": null,
                    "description": "Root directory holding the Protenix/Fold-CP weight set.",
                    "hidden": true
                },
                "protenix_use_msa": {
                    "type": "boolean",
                    "default": true,
                    "description": "Whether Protenix consumes an MSA. When false the MSA lanes are skipped.",
                    "hidden": true
                },
                "protenix_msa_backend": {
                    "type": "string",
                    "default": "auto",
                    "enum": ["auto", "local", "colabfold_api", "neurosnap_api", "neurosnap"],
                    "description": "MSA backend Protenix uses when it consumes an MSA.",
                    "hidden": true
                },
                "protenix_prepared_msa_dir": {
                    "type": "string",
                    "default": null,
                    "description": "Directory of prepared MSA inputs supplied by the controller for this run.",
                    "hidden": true
                }
            }
        },
        "bindcraft2_campaign_parameters": {
            "title": "BindCraft2 Native Campaign Handoff",
            "type": "object",
            "properties": {
                "bc2_compilation": {"type": "string", "description": "Job-owned pinned native compilation receipt", "hidden": true},
                "bc2_campaign_dir": {"type": "string", "description": "Job-owned campaign directory", "hidden": true},
                "bc2_gpu_ids": {"type": "string", "description": "Scheduler-assigned devices", "hidden": true}
            }
        },
        "ligandmpnn_interface_context_parameters": {
            "title": "Selected LigandMPNN Interface Context Inputs",
            "type": "object",
            "properties": {
                "interface_context_manifest": {"type": "string", "description": "Selected, materialized invocation manifest", "hidden": true}
            }
        },
        "blind_pose_parameters": {
            "title": "Selected Blind Pose Inputs",
            "type": "object",
            "properties": {
                "blind_pose_selection_manifest": {"type": "string"},
                "blind_pose_candidate_pdbs": {"type": "string"},
                "esmfold2_validation_variant": {"type": "string"},
                "esmfold2_validation_num_loops": {"type": "integer"},
                "esmfold2_validation_num_sampling_steps": {"type": "integer"},
                "esmfold2_validation_num_diffusion_samples": {"type": "integer"}
            }
        },
        "binder_generation_parameters": {
            "title": "Model-owned Initial Binder Generation",
            "type": "object",
            "properties": {
                "ppiflow_generation_request": {"type": "string", "format": "directory-path", "hidden": true, "description": "Owned PPIFlow request directory; preserves the model-native settings and source snapshots."},
                "caliby_request_dir": {"type": "string", "format": "directory-path", "hidden": true, "description": "Owned Caliby request directory with typed settings and retained structure snapshots."},
                "protonpottsmpnn_design_request": {"type": "string", "format": "file-path", "hidden": true, "description": "Owned ProtonPottsMPNN native request."},
                "protonpottsmpnn_design_input": {"type": "string", "format": "file-path", "hidden": true, "description": "Owned ProtonPottsMPNN source snapshot."},
                "protonpottsmpnn_device": {"type": "string", "hidden": true, "description": "System-owned native device: local CPU or allocated remote CUDA."},
                "protonpottsmpnn_container_path": {"type": "string", "format": "file-path", "hidden": true, "description": "Selected immutable ProtonPottsMPNN image, transported with the workflow."},
                "ligandmpnn_design_request": {"type": "string", "format": "file-path", "hidden": true, "description": "Owned ordinary LigandMPNN native request document."},
                "ligandmpnn_design_input": {"type": "string", "format": "file-path", "hidden": true, "description": "Owned LigandMPNN input complex snapshot."},
                "boltzgen_generation_mode": {"type": "string", "enum": ["protein_binder", "peptide_binder", "nanobody_binder"]},
                "boltzgen_target_chains": {"type": ["string", "null"]},
                "boltzgen_target_binding_positions": {"type": ["string", "null"]},
                "boltzgen_binder_sequence": {"type": ["string", "null"]},
                "boltzgen_scaffold_path": {"type": ["string", "null"]},
                "boltzgen_scaffold_chain": {"type": ["string", "null"]},
                "boltzgen_scaffold_design_ranges": {"type": ["string", "null"]}
            }
        },
        "scheduler_assignment_parameters": {
            "title": "Scheduler Assignment Parameters",
            "type": "object",
            "description": "Physical device identities the external scheduler assigns and the pipeline reads at config time. These are system-owned values, never operator scientific settings.",
            "default": "",
            "properties": {
                "frustrampnn_physical_gpu_id": {
                    "type": "string",
                    "default": null,
                    "description": "Scheduler-assigned physical GPU id for CanonicalFrustraMPNN. Required when the frustrampnn GPU lane is active.",
                    "hidden": true
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/essential_parameters"
        },
        {
            "$ref": "#/definitions/mode_specific_parameters"
        },
        {
            "$ref": "#/definitions/workflow_advanced_parameters"
        },
        {
            "$ref": "#/definitions/rfdiffusion_advanced_parameters"
        },
        {
            "$ref": "#/definitions/proteinmpnn_fastrelax_parameters"
        },
        {
            "$ref": "#/definitions/full_atom_mpnn_parameters"
        },
        {
            "$ref": "#/definitions/prediction_advanced_parameters"
        },
        {
            "$ref": "#/definitions/filtering_parameters"
        },
        {
            "$ref": "#/definitions/cluster_parameters"
        },
        {
            "$ref": "#/definitions/protenix_parameters"
        },
        {
            "$ref": "#/definitions/bindcraft2_campaign_parameters"
        },
        {
            "$ref": "#/definitions/ligandmpnn_interface_context_parameters"
        },
        {
            "$ref": "#/definitions/blind_pose_parameters"
        },
        {
            "$ref": "#/definitions/binder_generation_parameters"
        },
        {
            "$ref": "#/definitions/scheduler_assignment_parameters"
        }
    ]
}