nextflow_schema.json

{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/Sage-Bionetworks-Workflows/nf-genie/master/nextflow_schema.json",
    "title": "Sage-Bionetworks-Workflows/nf-genie pipeline parameters",
    "description": "Nextflow pipeline for main GENIE processing",
    "type": "object",
    "definitions": {
        "parameters": {
            "title": "Input options",
            "type": "object",
            "fa_icon": "fas fa-terminal",
            "description": "Define GENIE pipeline parameters.",
            "properties": {
                "process_type": {
                    "type": "string",
                    "default": "only_validate",
                    "description": "Available processing functions",
                    "enum": [
                        "only_validate",
                        "main_process",
                        "maf_process",
                        "consortium_release",
                        "public_release",
                        "consortium_release_step_only",
                        "public_release_step_only"
                    ]
                },
                "center": {
                    "type": "string",
                    "description": "Pick a center to process or validate. Defaults to ALL which means all centers. This value should be ALL if you pick consortium release or public release.",
                    "default": "ALL"
                },
                "create_new_maf_db": {
                    "type": "boolean",
                    "description": "Create a new maf Synapse Table. Toggle this for every consortium release."
                },
                "release": {
                    "type": "string",
                    "description": "Release name (specify TEST.consortium/TEST.public to test consortium and public releases). E.g: 13.1-consortium",
                    "default": "TEST.consortium",
                    "pattern": "\\d+[.]\\d+-(consortium|public)$|TEST.public|TEST.consortium|STAGING.consortium|STAGING.public"
                },
                "main_pipeline_docker":{
                    "type": "string",
                    "description": "Docker used in main processes - validate_data, process_main, process_maf, create_consortium_release, create_public_release, create_consortium_release_only, and create_public_release_only"
                },
                "main_release_utils_docker":{
                    "type": "string",
                    "description": "Docker used in check_for_retractions and load_to_bpc processes"
                },
                "find_maf_artifacts_docker":{
                    "type": "string",
                    "description": "Docker used in find_maf_artifiacts process"
                },
                "create_data_guide_docker":{
                    "type": "string",
                    "description": "Docker used in create_data_guide process"
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/parameters"
        }
    ]
}