nextflow_schema.json

{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://github.com/JAlvarezJarreta/movelib-workflow/main/nextflow_schema.json",
    "title": "MEvoLib pipeline parameters",
    "type": "object",
    "definitions": {
        "fetch_options": {
            "title": "Sequence fetching options",
            "type": "object",
            "properties": {
                "query": {
                    "type": "string",
                    "description": "NCBI Entrez query."
                },
                "species": {
                    "type": "string",
                    "description": "Species to fetch sequences for."
                },
                "seq_type": {
                    "type": "string",
                    "description": "Sequence type."
                },
                "refseq": {
                    "type": "boolean",
                    "description": "Fetch only reference sequences.",
                    "default": false
                },
                "max_seqs": {
                    "type": "integer",
                    "minimum": 1,
                    "description": "Maximum number of sequences to fetch"
                }
            }
        },
        "cluster_options": {
            "title": "Clustering options",
            "type": "object",
            "properties": {
                "cluster_tool": {
                    "type": "string",
                    "description": "Clustering tool.",
                    "enum": ["genes"]
                }
            }
        },
        "align_options": {
            "title": "Multiple sequence alignment (MSA) options",
            "type": "object",
            "properties": {
                "align_tool": {
                    "type": "string",
                    "description": "MSA tool.",
                    "enum": ["mafft", "clustalo", "muscle"]
                },
                "align_args": {
                    "type": "string",
                    "description": "Arguments (or keyword) to use for the MSA tool.",
                    "default": "default"
                },
                "align_out_format": {
                    "type": "string",
                    "description": "Output MSA file format.",
                    "enum": [
                        "fasta", "clustal", "maf", "mauve", "nexus", "phylip", "phylip-sequential",
                        "phylip-relaxed", "stockholm"
                    ],
                    "default": "fasta"
                }
            }
        },
        "inference_options": {
            "title": "Phylogenetic inference options",
            "type": "object",
            "properties": {
                "inference_tool": {
                    "type": "string",
                    "description": "Phylogenetic inference tool.",
                    "enum": ["fasttree", "raxml"]
                },
                "inference_args": {
                    "type": "string",
                    "description": "Arguments (or keyword) to use for the phylogenetic inference tool.",
                    "default": "default"
                },
                "inference_out_format": {
                    "type": "string",
                    "description": "Output phylogeny file format.",
                    "enum": ["newick", "nexus", "nexml", "phyloxml"],
                    "default": "newick"
                },
                "inference_bootstraps": {
                    "type": "integer",
                    "minimum": 1,
                    "description": "Inference bootstraps",
                    "default": 200
                }
            }
        },
        "generic_options": {
            "title": "Generic options",
            "type": "object",
            "description": "Less common options for the pipeline, typically set in a config file.",
            "properties": {
                "help": {
                    "type": ["string", "boolean"],
                    "description": "Display help text.",
                    "hidden": true
                },
                "input_file": {
                    "type": "string",
                    "format": "file-path",
                    "description": "Input file path."
                },
                "input_format": {
                    "type": "string",
                    "description": "Input file format.",
                    "enum": [
                        "embl", "fasta", "fastq", "fastq-illumina", "fastq-sanger", "fastq-solexa", "gb",
                        "genbank"
                    ]
                },
                "output_dir": {
                    "type": "string",
                    "format": "directory-path",
                    "description": "Output directory."
                },
                "validate_params": {
                    "type": "boolean",
                    "description": "Boolean whether to validate parameters against the schema at runtime",
                    "default": true,
                    "hidden": true
                },
                "validationShowHiddenParams": {
                    "type": "boolean",
                    "description": "Show all params when using `--help`",
                    "hidden": true
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/fetch_options"
        },
        {
            "$ref": "#/definitions/align_options"
        },
        {
            "$ref": "#/definitions/inference_options"
        },
        {
            "$ref": "#/definitions/generic_options"
        }
    ]
}