nf-aggregate/nextflow_schema.json at main · seqeralabs/nf-aggregate · GitHub

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{
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "$id": "https://raw.githubusercontent.com/seqeralabs/nf-aggregate/main/nextflow_schema.json",
    "title": "seqeralabs/nf-aggregate pipeline parameters",
    "description": "Pipeline to aggregate pertinent metrics across pipeline runs on the Seqera Platform",
    "type": "object",
    "$defs": {
        "input_output_options": {
            "title": "Input/output options",
            "type": "object",
            "fa_icon": "fas fa-terminal",
            "description": "Define where the pipeline should find input data and save output data.",
            "required": ["input", "outdir"],
            "properties": {
                "input": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "schema": "assets/schema_input.json",
                    "mimetype": "text/csv",
                    "pattern": "^\\S+\\.csv$",
                    "description": "File containing Seqera Platform run identifiers one per line.",
                    "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"
                },
                "outdir": {
                    "type": "string",
                    "format": "directory-path",
                    "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
                    "fa_icon": "fas fa-folder-open",
                    "default": "results"
                }
            }
        },
        "pipeline_options": {
            "title": "Pipeline-specific options",
            "type": "object",
            "fa_icon": "fas fa-terminal",
            "description": "Generic options for the pipeline.",
            "help_text": "Core options that should be reviewed before pipeline execution.",
            "properties": {
                "seqera_api_endpoint": {
                    "type": "string",
                    "default": "https://api.cloud.seqera.io",
                    "description": "Seqera Platform API endpoint URL.",
                    "fa_icon": "fas fa-question-circle"
                },
                "java_truststore_path": {
                    "type": "string",
                    "description": "Path to custom cacerts Java truststore used by Seqera Platform.",
                    "fa_icon": "fas fa-key"
                },
                "java_truststore_password": {
                    "type": "string",
                    "description": "Password for custom cacerts Java truststore used by Seqera Platform.",
                    "fa_icon": "fas fa-key"
                },
                "generate_benchmark_report": {
                    "type": "boolean",
                    "default": false,
                    "fa_icon": "fas fa-tachometer-alt",
                    "description": "Compile a benchmarking report for Seqera Platform runs."
                },
                "benchmark_aws_cur_report": {
                    "type": "string",
                    "fa_icon": "fas fa-dollar-sign",
                    "description": "AWS CUR report from data exports.",
                    "pattern": "^\\S+\\.parquet",
                    "format": "file-path"
                },
                "include_failed_runs": {
                    "type": "boolean",
                    "default": false,
                    "fa_icon": "fas fa-exclamation-triangle",
                    "description": "Include workflow-level failed runs in downstream benchmark sections and charts. Cancelled workflows remain excluded."
                },
                "benchmark_aws_cur_label_map": {
                    "type": "string",
                    "fa_icon": "fas fa-tags",
                    "description": "Optional YAML file mapping logical benchmark cost labels to one or more CUR resource tag aliases.",
                    "pattern": "^\\S+\\.(ya?ml)$",
                    "format": "file-path"
                }
            },
            "required": ["seqera_api_endpoint"]
        },
        "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": {
                "version": {
                    "type": "boolean",
                    "description": "Display version and exit.",
                    "fa_icon": "fas fa-question-circle",
                    "hidden": true
                },
                "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"]
                },
                "monochrome_logs": {
                    "type": "boolean",
                    "description": "Do not use coloured log outputs.",
                    "fa_icon": "fas fa-palette",
                    "hidden": true
                },
                "validate_params": {
                    "type": "boolean",
                    "description": "Boolean whether to validate parameters against the schema at runtime",
                    "default": true,
                    "fa_icon": "fas fa-check-square",
                    "hidden": true
                },
                "trace_report_suffix": {
                    "type": "string",
                    "fa_icon": "far calendar",
                    "description": "Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.",
                    "hidden": true
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/$defs/input_output_options"
        },
        {
            "$ref": "#/$defs/pipeline_options"
        },
        {
            "$ref": "#/$defs/generic_options"
        }
    ]
}