nextflow_schema.json

{
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "$id": "https://raw.githubusercontent.com/CCBR/TOOL_NAME//nextflow_schema.json",
    "title": "CCBR/TOOL_NAME pipeline parameters",
    "description": "TODO one-line description of TOOL_NAME goes here",
    "type": "object",
    "$defs": {
        "input_output_options": {
            "title": "Input/output options",
            "type": "object",
            "fa_icon": "fas fa-terminal",
            "description": "Define where the pipeline should find input data and save output data.",
            "required": [
                "input"
            ],
            "properties": {
                "input": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "mimetype": "text/csv",
                    "pattern": "^\\S+\\.csv$",
                    "description": "Path to comma-separated file containing information about the samples in the experiment.",
                    "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row.",
                    "fa_icon": "fas fa-file-csv"
                },
                "genome": {
                    "type": "string",
                    "description": "Reference genome (e.g. hg38, mm10). This can be a genome in conf/genomes.config, or see 'Custom genome options' to build a custom reference from a fasta & gtf file."
                },
                "outputDir": {
                    "type": "string",
                    "default": "results",
                    "fa_icon": "fas fa-folder",
                    "hidden": true
                },
                "tracedir": {
                    "type": "string",
                    "default": "${outputDir}/pipeline_info",
                    "fa_icon": "fas fa-folder",
                    "hidden": true
                },
                "publish_dir_mode": {
                    "type": "string",
                    "default": "link",
                    "enum": [
                        "link",
                        "copy",
                        "move",
                        "copyNoFollow",
                        "rellink",
                        "symlink"
                    ],
                    "description": "How to publish files to the results directory. This parameter sets Nextflow's workflow.output.mode configuration option."
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/$defs/input_output_options"
        }
    ]
}