{
  "params": {
    "// SYNTHEA PARAMETERS": {},
    "n_pat": {
      "type": "integer",
      "description": "Number of patients to generate (must be >= 2)",
      "default": 2,
      "required": true,
      "pipeline_io": "parameter",
      "var_name": "params.n_pat",
      "examples": [2, 10, 100],
      "pattern": "^[0-9]+$",
      "validation": {
        "min": 2
      },
      "notes": "Minimum of 2 patients required (one male, one female)"
    },
    "percent_male": {
      "type": "number",
      "description": "Percentage of male patients (between 0-1)",
      "default": 0.5,
      "required": true,
      "pipeline_io": "parameter",
      "var_name": "params.percent_male",
      "examples": [0.0, 0.5, 1.0],
      "pattern": "^0(\\.\\d+)?|1(\\.0)?$",
      "validation": {
        "min": 0.0,
        "max": 1.0
      },
      "notes": "Value must be between 0 and 1 inclusive"
    },
    "imputed_store": {
      "type": "folder",
      "description": "Path to imputed UKBB data",
      "default": "/mnt/Avatar/imputed/ukbb/imputed",
      "required": true,
      "pipeline_io": "input",
      "var_name": "params.imputed_store",
      "examples": [
        "/mnt/Avatar/imputed/ukbb/imputed",
        "/rosalind/ukbb/imputed"
      ],
      "pattern": ".*",
      "validation": {},
      "notes": "Directory containing imputed UKBB data"
    },
    "pheno_store": {
      "type": "file",
      "description": "Path to phenotype data file",
      "default": "/mnt/Avatar/dd/synthea/metadata/ukbb_phenotypes_filtered.csv",
      "required": true,
      "pipeline_io": "input",
      "var_name": "params.pheno_store",
      "examples": [
        "/mnt/Avatar/dd/synthea/metadata/ukbb_phenotypes_filtered.csv"
      ],
      "pattern": ".*\\.csv$",
      "validation": {},
      "notes": "CSV file containing filtered UKBB phenotype data"
    },
    "disease": {
      "type": "string",
      "description": "Disease or condition to simulate",
      "default": "schizophrenia",
      "required": true,
      "pipeline_io": "parameter",
      "var_name": "params.disease",
      "examples": [
        "schizophrenia",
        "healthy",
        "leukaemia",
        "Purpura and other haemorrhagic conditions"
      ],
      "pattern": ".*",
      "enum": [
        "schizophrenia",
        "healthy",
        "leukaemia",
        "Purpura and other haemorrhagic conditions"
      ],
      "validation": {},
      "notes": "Use 'healthy' for healthy individuals or specify a disease condition"
    },
    "healthy_dir": {
      "type": "folder",
      "description": "Path to healthy patient data directory",
      "default": "/Workspace/next/registry/pipelines/digital_patient",
      "required": true,
      "pipeline_io": "input",
      "var_name": "params.healthy_dir",
      "examples": [
        "/Workspace/next/registry/pipelines/digital_patient",
        "/mnt/Avatar/digital_patient"
      ],
      "pattern": ".*",
      "validation": {},
      "notes": "Directory containing data for healthy patient generation"
    },
    "outdir": {
      "type": "folder",
      "description": "Output directory for results",
      "default": "/mnt/omic-next-apis/wes/digital_patients",
      "required": true,
      "pipeline_io": "output",
      "var_name": "params.outdir",
      "examples": [
        "/mnt/OmicNAS/dd/digital_patient",
        "/path/to/custom/output"
      ],
      "pattern": ".*",
      "validation": {},
      "notes": "Directory where all pipeline results will be stored"
    },
    "// BORZOI PARAMETERS": {},
    "container_borzoi": {
      "type": "string",
      "description": "Borzoi container image",
      "default": "borzoi:latest",
      "required": true,
      "pipeline_io": "parameter",
      "var_name": "params.container_borzoi",
      "examples": [
        "borzoi:latest",
        "borzoi:v1.0"
      ],
      "pattern": ".*",
      "validation": {},
      "notes": "Docker container image for Borzoi module"
    },
    "containerOptions": {
      "type": "string",
      "description": "Container runtime options",
      "default": "--gpus all --rm -v /mnt:/mnt",
      "required": false,
      "pipeline_io": "parameter",
      "var_name": "params.containerOptions",
      "examples": [
        "--gpus all --rm -v /mnt:/mnt",
        "--rm -v /data:/data"
      ],
      "pattern": ".*",
      "validation": {},
      "notes": "Docker container runtime options for GPU usage and volume mounts"
    },
    "project_name": {
      "type": "string",
      "description": "Project identifier",
      "default": "test",
      "required": true,
      "pipeline_io": "parameter",
      "var_name": "params.project_name",
      "examples": [
        "test",
        "production",
        "schizophrenia_study"
      ],
      "pattern": ".*",
      "validation": {},
      "notes": "Identifier for the digital patient project"
    },
    "mane": {
      "type": "file",
      "description": "Path to MANE reference file",
      "default": "/Workspace/next/registry/pipelines/digital_patient/MANE.GRCh38.v1.3.update.tsv",
      "required": true,
      "pipeline_io": "input",
      "var_name": "params.mane",
      "examples": [
        "/Workspace/next/registry/pipelines/digital_patient/MANE.GRCh38.v1.3.update.tsv"
      ],
      "pattern": ".*\\.tsv$",
      "validation": {},
      "notes": "MANE transcripts reference file in TSV format"
    },
    "// VCF2PROT PARAMETERS": {},
    "container_vcf2prot": {
      "type": "string",
      "description": "VCF2PROT container image",
      "default": "vcf2prot:latest",
      "required": true,
      "pipeline_io": "parameter",
      "var_name": "params.container_vcf2prot",
      "examples": [
        "vcf2prot:latest",
        "vcf2prot:v1.0"
      ],
      "pattern": ".*",
      "validation": {},
      "notes": "Docker container image for VCF2PROT module"
    },
    "// RNA2PROTEINEXPRESSION PARAMETERS": {},
    "container_rna2protexpression": {
      "type": "string",
      "description": "RNA2PROTEINEXPRESSION container image",
      "default": "rna2protexpression:latest",
      "required": true,
      "pipeline_io": "parameter",
      "var_name": "params.container_rna2protexpression",
      "examples": [
        "rna2protexpression:latest",
        "rna2protexpression:v1.0"
      ],
      "pattern": ".*",
      "validation": {},
      "notes": "Docker container image for RNA2PROTEINEXPRESSION module"
    },
    "containerOptions_rna2protexpression": {
      "type": "string",
      "description": "Container options for RNA2PROTEINEXPRESSION",
      "default": "--gpus all --rm -v /mnt:/mnt -v /dbs:/dbs",
      "required": false,
      "pipeline_io": "parameter",
      "var_name": "params.containerOptions_rna2protexpression",
      "examples": [
        "--gpus all --rm -v /mnt:/mnt -v /dbs:/dbs"
      ],
      "pattern": ".*",
      "validation": {},
      "notes": "Docker container runtime options for RNA2PROTEINEXPRESSION with GPU and database volume mounts"
    },
    "// CORTO PARAMETERS": {},
    "container_corto": {
      "type": "string",
      "description": "CORTO container image",
      "default": "corto:latest",
      "required": true,
      "pipeline_io": "parameter",
      "var_name": "params.container_corto",
      "examples": [
        "corto:latest",
        "corto:v1.0"
      ],
      "pattern": ".*",
      "validation": {},
      "notes": "Docker container image for CORTO module"
    },
    "regulon": {
      "type": "file",
      "description": "Path to regulon RDA file",
      "default": "/Workspace/next/registry/pipelines/digital_patient/regulon.rda",
      "required": true,
      "pipeline_io": "input",
      "var_name": "params.regulon",
      "examples": [
        "/Workspace/next/registry/pipelines/digital_patient/regulon.rda"
      ],
      "pattern": ".*\\.rda$",
      "validation": {},
      "notes": "Regulon data file in RDA format for CORTO module"
    },
    "// CIBERSORT PARAMETERS": {},
    "cibersortx_username": {
      "type": "string",
      "description": "CIBERSORTx username for authentication",
      "default": "gabriel.richman.2009@anderson.ucla.edu",
      "required": true,
      "pipeline_io": "parameter",
      "var_name": "params.cibersortx_username",
      "examples": [
        "gabriel.richman.2009@anderson.ucla.edu"
      ],
      "pattern": "^[a-zA-Z0-9._%+-]+@[a-zA-Z0-9.-]+\\.[a-zA-Z]{2,}$",
      "validation": {},
      "notes": "Username (email) for CIBERSORTx authentication"
    },
    "cibersortx_token": {
      "type": "string",
      "description": "CIBERSORTx authentication token",
      "default": "b5b39e563fb947df4cfd4843d40fdb99",
      "required": true,
      "pipeline_io": "parameter",
      "var_name": "params.cibersortx_token",
      "examples": [
        "b5b39e563fb947df4cfd4843d40fdb99"
      ],
      "pattern": "^[a-f0-9]{32}$",
      "validation": {},
      "notes": "Authentication token for CIBERSORTx API access"
    },
    "container_ecotyper": {
      "type": "string",
      "description": "ECOTyper container image",
      "default": "ecotyper:latest",
      "required": true,
      "pipeline_io": "parameter",
      "var_name": "params.container_ecotyper",
      "examples": [
        "ecotyper:latest",
        "ecotyper:v1.0"
      ],
      "pattern": ".*",
      "validation": {},
      "notes": "Docker container image for ECOTyper module"
    },
    "signature_matrix": {
      "type": "file",
      "description": "Path to signature matrix file",
      "default": "/Workspace/next/registry/pipelines/digital_patient/LM22_sourceGEP_ensg.txt",
      "required": true,
      "pipeline_io": "input",
      "var_name": "params.signature_matrix",
      "examples": [
        "/Workspace/next/registry/pipelines/digital_patient/LM22_sourceGEP_ensg.txt"
      ],
      "pattern": ".*\\.txt$",
      "validation": {},
      "notes": "Signature matrix file for CIBERSORTx analysis"
    },
    "ecotyper_outdir": {
      "type": "folder",
      "description": "Output directory for ECOTyper results",
      "default": "/mnt/omic-next-apis/wes/digital-patients/ecotyper",
      "required": true,
      "pipeline_io": "output",
      "var_name": "params.ecotyper_outdir",
      "examples": [
        "/mnt/OmicNAS/olamide/ecotyper/results/ecotyper"
      ],
      "pattern": ".*",
      "validation": {},
      "notes": "Directory where ECOTyper results will be stored"
    }
  }
}