{
    "params": {
        "protein_fasta": {
            "type": "file",
            "description": "Path to protein FASTA file for structure prediction",
            "default": "s3://omic/eureka/rosettafold-all-atom/input/protein.fasta",
            "required": true,
            "pipeline_io": "input",
            "var_name": "params.protein_fasta",
            "examples": [
                "s3://omic/eureka/rosettafold-all-atom/input/protein.fasta"
            ],
            "pattern": ".*\\.(fasta|fa)$",
            "enum": [],
            "validation": {},
            "notes": "FASTA file containing protein sequence(s). Required for all prediction modes."
        },
        "na_fasta": {
            "type": "file",
            "description": "Path to nucleic acid FASTA file (DNA or RNA)",
            "default": "",
            "required": false,
            "pipeline_io": "input",
            "var_name": "params.na_fasta",
            "examples": [
                "s3://omic/eureka/rosettafold-all-atom/input/dna_strand.fasta"
            ],
            "pattern": ".*\\.(fasta|fa)$",
            "enum": [],
            "validation": {},
            "notes": "Optional. For protein-nucleic acid complex prediction."
        },
        "na_type": {
            "type": "string",
            "description": "Type of nucleic acid input",
            "default": "dna",
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.na_type",
            "examples": [
                "dna",
                "rna"
            ],
            "pattern": "^(dna|rna)$",
            "enum": ["dna", "rna"],
            "validation": {},
            "notes": "Specify whether the nucleic acid is DNA or RNA."
        },
        "sm_file": {
            "type": "file",
            "description": "Path to small molecule file (SDF format)",
            "default": "",
            "required": false,
            "pipeline_io": "input",
            "var_name": "params.sm_file",
            "examples": [
                "s3://omic/eureka/rosettafold-all-atom/input/ligand.sdf"
            ],
            "pattern": ".*\\.sdf$",
            "enum": [],
            "validation": {},
            "notes": "Optional. For protein-small molecule complex prediction."
        },
        "sm_type": {
            "type": "string",
            "description": "Type of small molecule input",
            "default": "sdf",
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.sm_type",
            "examples": [
                "sdf",
                "smiles"
            ],
            "pattern": "^(sdf|smiles)$",
            "enum": ["sdf", "smiles"],
            "validation": {},
            "notes": "Format of small molecule input. SDF recommended for covalent modifications."
        },
        "covale_inputs": {
            "type": "string",
            "description": "Covalent bond specifications for modified proteins",
            "default": "",
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.covale_inputs",
            "examples": [
                "[((\"A\", \"74\", \"ND2\"), (\"B\", \"1\"), (\"CW\", \"null\"))]"
            ],
            "pattern": ".*",
            "enum": [],
            "validation": {},
            "notes": "Format: [((chain, residue, atom), (sm_chain, atom_idx), (chirality1, chirality2))]"
        },
        "outdir": {
            "type": "folder",
            "description": "Directory for RFAA prediction results",
            "default": "s3://omic/eureka/rosettafold-all-atom/output",
            "required": true,
            "pipeline_io": "output",
            "var_name": "params.outdir",
            "examples": [
                "s3://omic/eureka/rosettafold-all-atom/output"
            ],
            "pattern": ".*",
            "enum": [],
            "validation": {},
            "notes": "Output directory for PDB structures and confidence metrics."
        },
        "job_name": {
            "type": "string",
            "description": "Name for the prediction job",
            "default": "rfaa_prediction",
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.job_name",
            "examples": [
                "rfaa_prediction",
                "my_protein"
            ],
            "pattern": "^[a-zA-Z0-9_-]+$",
            "enum": [],
            "validation": {},
            "notes": "Used to name output files."
        },
        "max_cycle": {
            "type": "integer",
            "description": "Number of inference cycles for structure refinement",
            "default": 4,
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.max_cycle",
            "examples": [
                4,
                10
            ],
            "enum": [],
            "validation": {},
            "notes": "Default is 4. Increase to 10 for difficult cases."
        },
        "db_uniref30": {
            "type": "folder",
            "description": "Path to UniRef30_2020_06 database directory",
            "default": "/mnt/databases/UniRef30_2020_06",
            "required": true,
            "pipeline_io": "input",
            "var_name": "params.db_uniref30",
            "examples": [
                "/mnt/databases/UniRef30_2020_06"
            ],
            "pattern": ".*",
            "enum": [],
            "validation": {},
            "notes": "Required for MSA generation. ~46GB."
        },
        "db_bfd": {
            "type": "folder",
            "description": "Path to BFD database directory",
            "default": "/mnt/databases/bfd",
            "required": true,
            "pipeline_io": "input",
            "var_name": "params.db_bfd",
            "examples": [
                "/mnt/databases/bfd"
            ],
            "pattern": ".*",
            "enum": [],
            "validation": {},
            "notes": "Required for MSA generation. ~272GB."
        },
        "db_pdb100": {
            "type": "folder",
            "description": "Path to pdb100_2021Mar03 template database",
            "default": "/mnt/databases/pdb100_2021Mar03",
            "required": true,
            "pipeline_io": "input",
            "var_name": "params.db_pdb100",
            "examples": [
                "/mnt/databases/pdb100_2021Mar03"
            ],
            "pattern": ".*",
            "enum": [],
            "validation": {},
            "notes": "Required for template search. ~81GB."
        },
        "weights": {
            "type": "file",
            "description": "Path to RFAA model weights file",
            "default": "/mnt/databases/RFAA_paper_weights.pt",
            "required": true,
            "pipeline_io": "input",
            "var_name": "params.weights",
            "examples": [
                "/mnt/databases/RFAA_paper_weights.pt"
            ],
            "pattern": ".*\\.pt$",
            "enum": [],
            "validation": {},
            "notes": "Download from: http://files.ipd.uw.edu/pub/RF-All-Atom/weights/RFAA_paper_weights.pt"
        }
    }
}