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": {
        "generic_options": {
            "title": "Generic options",
            "type": "object",
            "fa_icon": "fas fa-file-import",
            "description": "Less common options for the pipeline, typically set in a config file.",
            "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": {
                "publish_dir_mode": {
                    "type": "string",
                    "default": "copy",
                    "description": "Method used to save pipeline results to output directory.",
                    "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
                    "fa_icon": "fas fa-copy",
                    "enum": [
                        "symlink",
                        "rellink",
                        "link",
                        "copy",
                        "copyNoFollow",
                        "move"
                    ],
                    "hidden": true
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/generic_options"
        }
    ],
    "properties": {
        "samplesheet": {
            "type": "string",
            "default": "None"
        },
        "enable_conda": {
            "type": "boolean",
            "description": "use conda (not supported)"
        },
        "min_contig_length": {
            "type": "string",
            "default": "5000",
            "description": "Minimum contig length to keep"
        },
        "reference_proteins": {
            "type": "string",
            "default": "'/dss/dsslegfs01/pn73so/pn73so-dss-0000/becker_common/reference_genomes/Arabidopsis/Col-CEN/Col-CEN_v1.2_proteins.fasta'",
            "description": "Reference proteins for miniprot"
        },
        "out": {
            "type": "string",
            "default": "./results",
            "description": "Directory for outputs"
        },
        "porechop": {
            "type": "boolean",
            "description": "Run porechop"
        },
        "exclude_pattern": {
            "type": "string",
            "description": "Pattern to exclude for HRP",
            "default": "ATMG"
        },
        "nevm": {
            "type": "string",
            "hidden": true,
            "description": "not used",
            "default": "10"
        }
    },
    "required": [
        "samplesheet"
    ]
}