nextflow_schema.json

{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/Sage-Bionetworks/genie-bpc-pipeline/develop/nextflow_schema.json",
    "title": "Sage-Bionetworks/genie-bpc-pipeline parameters",
    "description": "Nextflow pipeline for GENIE BPC processing",
    "type": "object",
    "definitions": {
        "parameters": {
            "title": "Input options",
            "type": "object",
            "fa_icon": "fas fa-terminal",
            "description": "Define GENIE BPC pipeline parameters.",
            "properties": {
                "cohort": {
                    "type": "string",
                    "default": "NSCLC",
                    "description": "Name of the cohort to process through GENIE BPC.",
                    "enum": [
                        "BLADDER",
                        "BrCa",
                        "CRC",
                        "NSCLC",
                        "PANC",
                        "Prostate",
                        "CRC2",
                        "NSCLC2",
                        "MELANOMA",
                        "OVARIAN",
                        "ESOPHAGO",
                        "RENAL"
                    ]
                },
                "comment": {
                    "type": "string",
                    "description": "Description for this cohort run of the BPC pipeline",
                    "default": "NSCLC public release update"
                },
                "production": {
                    "type": "boolean",
                    "description": "Uploads to production project or not (staging project).",
                    "default": false,
                    "enum": [
                        true,
                        false
                    ]
                },
                "step": {
                    "type": "string",
                    "default": "update_potential_phi_fields_table",
                    "description": "Available BPC steps",
                    "enum": [
                        "update_potential_phi_fields_table",
                        "merge_and_uncode_rca_uploads",
                        "update_data_table",
                        "genie_bpc_pipeline"
                    ]
                },
                "use_grs": {
                    "type": "boolean",
                    "description": "Whether to use grs as primary mapping (dd as secondary) or not (using dd only).",
                    "default": false,
                    "enum": [
                        true,
                        false
                    ]
                },
                "references_docker":{
                    "type": "string",
                    "description": "Name of docker to use in processes in scripts/references"
                },
                "uploads_docker":{
                    "type": "string",
                    "description": "Name of docker to use in processes in scripts/uploads"
                },
                "table_updates_docker":{
                    "type": "string",
                    "description": "Name of docker to use in processes in scripts/table_updates" 
                },
                "schema_ignore_params": {
                    "type": "string",
                    "description": "Put parameters to ignore for validation here separated by comma",
                    "default": ""
                },
                "help": {
                    "type": "boolean",
                    "description": "Display input options and descriptions",
                    "default": false
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/parameters"
        }
    ]
}