nextflow_schema.json

{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/Zymo-Research/aladdin-miqScore16S/main/nextflow_schema.json",
    "title": "Zymo-Research/aladdin-miqScore16S pipeline parameters",
    "description": "Nextflow pipeline for calculating MIQ scores, part of the Aladdin Bioinformatics Platform pipeline catalog",
    "single_sample": true,
    "compatible_clouds": ["awsbatch", "zymohpc"],
    "type": "object",
    "definitions": {
        "input_output_options": {
            "title": "Input/output options",
            "type": "object",
            "description": "Define where the pipeline should find input data and save output data",
            "properties": {
                "design": {
                    "type": "string",
                    "description": "Path to a design CSV file with sample & group labels, and paths to reads files",
                    "hidden": true
                },
                "outdir": {
                    "type": "string",
                    "description": "The output directory where the results will be saved",
                    "default": "./results",
                    "hidden": true
                }
            },
            "required": ["design"]
        },
        "amplicon_options": {
            "title": "Amplicon and primer options",
            "type": "object",
            "description": "Options about primer and amplicon lengths",
            "properties": {
                "forward_primer_length": {
                    "type": "integer",
                    "description": "Length of the forward primer, excluding the adapter. For example, the forward primer sequence in the Zymo Quick 16S Plus Kit (V3-V4) is CCTACGGGDGGCWGCAG, whihc is 17 bp long.",
                    "minimum": 0,
                    "maximum": 30,
                    "default": 17
                },
                "reverse_primer_length": {
                    "type": "integer",
                    "description": "Length of the reverse primer, excluding the adapter. For example, the reverse primer sequence in the Zymo Quick 16S Plus Kit (V3-V4) is GACTACNVGGGTMTCTAATCC, which is 24 bp long.",
                    "minimum": 0,
                    "maximum": 30,
                    "default": 24
                },
                "amplicon_length": {
                    "type": "integer",
                    "description": "The maximum expected length of the amplicon, including the primers.",
                    "minimum": 1,
                    "maximum": 1000,
                    "default": 510
                }
            },
            "required": ["forward_primer_length", "reverse_primer_length", "amplicon_length"]
        },
        "max_job_request_options": {
            "title": "Max job request options",
            "type": "object",
            "description": "Set the top limit for requested resources for any single job",
            "properties": {
                "max_cpus": {
                    "type": "integer",
                    "description": "Maximum number of CPUs that can be requested for any single job",
                    "hidden": true,
                    "minimum": 1,
                    "default": 8
                },
                "max_memory": {
                    "type": "string",
                    "description": "Maximum amount of memory that can be requested for any single job",
                    "hidden": true,
                    "default": "60.GB"
                },
                "max_time": {
                    "type": "string",
                    "description": "Maximum amount of time that can be requested for any single job",
                    "hidden": true,
                    "default": "2.h"
                }
            }
        },
        "generic_options": {
            "title": "Generic options",
            "type": "object",
            "description": "Less common options for the pipeline, typically set in a config file",
            "properties": {
                "downsample_num": {
                    "type": "integer",
                    "description": "Number of read pairs to downsample to. If input has fewer reads than this, downsampling will not happen. Set to 0 to turn this off.",
                    "minimum": 0,
                    "default": 100000
                },
                "name": {
                    "type": "string",
                    "description": "Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic",
                    "hidden": true
                },
                "help": {
                    "type": "boolean",
                    "description": "Whether to display the help message",
                    "hidden": true,
                    "default": false
                },
                "tracedir": {
                    "type": "string",
                    "description": "Path to save trace file",
                    "hidden": true,
                    "default": "${params.outdir}/pipeline_info"
                },
                "awsqueue": {
                    "type": "string",
                    "description": "AWS Batch queue to submit jobs to",
                    "hidden": true
                },
                "awsregion": {
                    "type": "string",
                    "description": "AWS region",
                    "hidden": true,
                    "default": "us-east-1"
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/input_output_options"
        },
        {
            "$ref": "#/definitions/amplicon_options"
        },
        {
            "$ref": "#/definitions/max_job_request_options"
        },
        {
            "$ref": "#/definitions/generic_options"
        }
    ]
}