nextflow_schema.json

{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json",
    "title": ". pipeline parameters",
    "description": "",
    "type": "object",
    "definitions": {
        "input_output_options": {
            "title": "Input/output options",
            "type": "object",
            "fa_icon": "fas fa-terminal",
            "description": "Define where the pipeline should find input data and save output data.",
            "required": [
                "outdir",
                "inputdir"
            ],
            "properties": {
                "outdir": {
                    "type": "string",
                    "format": "directory-path",
                    "description": "The directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
                    "fa_icon": "fas fa-folder-open"
                },
                "inputdir": {
                    "type": "string",
                    "default": "/vast/scratch/users/iskander.j/nf-alphafold/example/af_test232",
                    "description": "The directory where fasta files to be folded reside"
                }
            }
        },
        "model_parameters": {
            "title": "Model Parameters",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "model_indices": {
                    "type": "string",
                    "default": "0",
                    "description": "Model indices coma-separated list. Values can be any combination of number between 0,4 example: 0,1 or 0,2,3 or 0,1,2,3,4 or 1"
                },
               
                "model_to_relax": {
                    "type": "string",
                    "default": "best",
                    "description": "Values can be (all|best|none)"
                },
                "max_template_date": {
                    "type": "string"
                },
                "num_predictions": {
                    "type": "integer",
                    "default": 2
                },
                "database_preset": {
                    "type": "string",
                    "default": "full_dbs"
                }
            },
            "required": [
                "model_indices",
                "model_to_relax",
                "max_template_date",
                "num_predictions",
                "database_preset"
            ]
        },
        "extra_parameters": {
            "title": "Extra Parameters, NOT YET IMPLEMENTED",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "pdb_seqres_db_path": {
                    "type": "string",
                    "hidden": true
                },
                "custom_templates_path": {
                    "type": "string",
                    "hidden": true
                },
                "AF_UNIREF30_DB": {
                    "type": "string",
                    "hidden": true
                },
                "AF_PDB70_DB": {
                    "type": "string",
                    "hidden": true
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/input_output_options"
        },
        {
            "$ref": "#/definitions/model_parameters"
        },
        {
            "$ref": "#/definitions/extra_parameters"
        }
    ]
}