nextflow_schema.json

{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/IndexReferenceFasta-nf/master/nextflow_schema.json",
    "title": "IndexReferenceFasta-nf pipeline parameters",
    "description": "Pipeline for producing reference genome index files for WGS analysis",
    "type": "object",
    "definitions": {
        "options": {
            "title": "Options",
            "type": "object",
            "fa_icon": "fas fa-file-import",
            "description": "Options for running the workflow.",
            "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
            "properties": {
                "ref": {
                    "type": "string",
                    "default": "null",
                    "description": "Path to reference fasta",
                    "fa_icon": "fas fa-dna"
                },
                "bwa": {
                    "type": "boolean",
                    "description": "Generate bwa index files",
                    "fa_icon": "far fa-file-alt"
                },
                "gatk": {
                    "type": "boolean",
                    "description": "Generate gatk index files",
                    "fa_icon": "far fa-file-alt"
                },
                "samtools": {
                    "type": "boolean",
                    "default": true,
                    "description": "Generate samtools index files",
                    "fa_icon": "far fa-file-alt"
                },
                "help": {
                    "type": "boolean",
                    "description": "Display help text",
                    "fa_icon": "fas fa-question-circle",
                    "hidden": true
                },
                "whoami": {
                    "type": "string",
                    "default": "false",
                    "description": "User name for Pawsey and NCI runs",
                    "fa_icon": "fas fa-user-circle"
                },
                "pbs_account": {
                    "type": "string",
                    "default": "false",
                    "description": "Project name on NCI Gadi HPC",
                    "fa_icon": "fas fa-plug"
                },
                "slurm_account": {
                    "type": "string",
                    "default": "false",
                    "description": "Project name on Pawsey Setonix HPC",
                    "fa_icon": "fas fa-plug"
                }
            },
            "required": ["ref"]
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/options"
        }
    ]
}