{
    "params": {
        "TPM": {
            "type": "file",
            "description": "Path to TPM (Transcripts Per Million) CSV file",
            "default": "/data/olamide/corto/corto_metabolite_prediction/20002_1289_female_patient_0_TPM.csv",
            "required": true,
            "pipeline_io": "input",
            "var_name": "params.TPM",
            "examples": [
                "/data/olamide/corto/corto_metabolite_prediction/20002_1289_female_patient_0_TPM.csv",
                "/path/to/your/sample_TPM.csv"
            ],
            "pattern": ".*\\.csv$",
            "enum": [],
            "validation": {},
            "notes": "A CSV file containing TPM values with ENSG IDs as rows and samples as columns"
        },
        "regulon": {
            "type": "file",
            "description": "Path to regulon RDA file",
            "default": "/data/olamide/corto/corto_metabolite_prediction/regulon.rda",
            "required": true,
            "pipeline_io": "input",
            "var_name": "params.regulon",
            "examples": [
                "/data/olamide/corto/corto_metabolite_prediction/regulon.rda",
                "/path/to/your/custom_regulon.rda"
            ],
            "pattern": ".*\\.rda$",
            "enum": [],
            "validation": {},
            "notes": "An R data file containing regulon information for the CORTO analysis"
        },
        "outdir": {
            "type": "folder",
            "description": "Directory for CORTO analysis results",
            "default": "/mnt/OmicNAS/private/old/gabe/corto/outputs",
            "required": true,
            "pipeline_io": "output",
            "var_name": "params.outdir",
            "examples": [
                "/mnt/OmicNAS/private/old/gabe/corto/outputs",
                "/path/to/custom/output"
            ],
            "pattern": ".*",
            "enum": [],
            "validation": {},
            "notes": "Directory where metabolome prediction results will be stored"
        },
        "project_name": {
            "type": "string",
            "description": "Project name for output directory organization",
            "default": "test",
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.project_name",
            "examples": [
                "test",
                "patient_analysis",
                "metabolite_prediction_run1"
            ],
            "pattern": "^[A-Za-z0-9_-]+$",
            "enum": [],
            "validation": {},
            "notes": "Name used to create a subdirectory within the output directory"
        },
        "container_corto": {
            "type": "string",
            "description": "Docker container for CORTO",
            "default": "corto:latest",
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.container_corto",
            "examples": [
                "corto:latest",
                "yourregistry/corto:v1.0"
            ],
            "pattern": ".*",
            "enum": [],
            "validation": {},
            "notes": "Docker container image to use for the CORTO analysis"
        },
        "containerOptions": {
            "type": "string",
            "description": "Docker container 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 /custom/path:/mnt"
            ],
            "pattern": ".*",
            "enum": [],
            "validation": {},
            "notes": "Options to pass to the Docker container runtime"
        }
    }
}