nextflow_schema.json

{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/MTBseq-nf/master/nextflow_schema.json",
    "title": "MTBseq-nf pipeline parameters",
    "description": "MTBSeq packaged as a Nextflow Workflow for usability and sensible defaults",
    "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.",
            "properties": {
                "reads": {
                    "type": "string"
                },
                "genomeIds": {
                    "type": "string"
                },
                "outdir": {
                    "type": "string",
                    "default": "results",
                    "fa_icon": "fas fa-folder-open"
                },
                "run_type": {
                    "type": "string"
                },
                "library_name": {
                    "type": "string",
                    "default": "illumina"
                },
                "local_location": {
                    "type": "string"
                },
                "gatk38_jar": {
                    "type": "string"
                }
            },
            "required": [
                "gatk38_jar"
            ]
        },
        "reference_genome_options": {
            "title": "Reference genome options",
            "type": "object",
            "fa_icon": "fas fa-dna",
            "properties": {
                "mtb_reference_fasta": {
                    "type": "string"
                }
            }
        },
        "generic_options": {
            "title": "Generic options",
            "type": "object",
            "fa_icon": "fas fa-file-import",
            "help_text": "These options are common to all MTBseq processes.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
            "properties": {
                "project_name": {
                    "type": "string",
                    "default": "prj"
                },
                "analysis_mode": {
                    "type": "string",
                    "default": "parallel"
                },
                "cohort_tsv": {
                    "type": "string",
                    "default": "samplesheet.tsv"
                },
                "ncbi_api_key": {
                    "type": "string"
                },
                "user": {
                    "type": "string",
                    "default": "alice"
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/input_output_options"
        },
        {
            "$ref": "#/definitions/reference_genome_options"
        },
        {
            "$ref": "#/definitions/generic_options"
        }
    ]
}