nextflow_schema.json

{
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "$id": "https://raw.githubusercontent.com/nf-core/tres/main/nextflow_schema.json",
    "title": "nf-core/tres pipeline parameters",
    "description": "Repo-owned Nextflow DSL2 implementation of the TrES core RNA and DNA workflows",
    "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.",
            "properties": {
                "input": {
                    "type": "string",
                    "format": "file-path",
                    "mimetype": "text/yaml",
                    "description": "Reserved nf-core schema placeholder. TrESFlow uses --samplesheet as the supported public input contract.",
                    "hidden": true
                },
                "samplesheet": {
                    "type": "string",
                    "format": "file-path",
                    "mimetype": "text/yaml",
                    "description": "Hierarchical YAML samplesheet describing runtime, references, biological groups, and modality-specific FASTQ inputs."
                },
                "outdir": {
                    "type": "string",
                    "format": "directory-path",
                    "description": "Output directory for published pipeline results and pipeline_info artifacts.",
                    "fa_icon": "fas fa-folder-open"
                }
            }
        },
        "execution_options": {
            "title": "Execution options",
            "type": "object",
            "description": "Pipeline execution options. Runtime environment and references are configured in the YAML samplesheet.",
            "properties": {
                "core_scripts_dir": {
                    "type": "string",
                    "description": "Directory containing the vendored TrES core runtime scripts used by the local wrapper modules."
                },
                "max_cpus": {
                    "type": "integer",
                    "description": "Maximum local CPU budget used to derive per-process scheduler reservations in the bundled local profiles.",
                    "default": 64
                },
                "cleanup_work": {
                    "type": "boolean",
                    "description": "Enable Nextflow cleanup of successful task work directories after a successful run. This reduces retained work/ storage and makes --resume unreliable for cleaned tasks.",
                    "default": true
                },
                "tagging_cpus": {
                    "type": "integer",
                    "description": "Default local CPU reservation for barcode-tagging processes. The value is capped by --max_cpus.",
                    "default": 4
                },
                "tagging_memory": {
                    "type": "string",
                    "description": "Default local memory reservation for barcode-tagging processes.",
                    "default": "32 GB"
                },
                "helper_cpus": {
                    "type": "integer",
                    "description": "Default local CPU reservation for trim, split, filtered-BAM, and duplicate-filter helper processes. The value is capped by --max_cpus.",
                    "default": 4
                },
                "rna_starsolo_cpus": {
                    "type": "integer",
                    "description": "Default local CPU reservation for RNA_STARSOLO_ALIGN. The value is capped by --max_cpus.",
                    "default": 16
                },
                "dna_align_cpus": {
                    "type": "integer",
                    "description": "Default local CPU reservation for ALIGN_DNA and its bwa-mem2/samtools wrapper. The value is capped by --max_cpus.",
                    "default": 16
                },
                "coverage_cpus": {
                    "type": "integer",
                    "description": "Default local CPU reservation for RNA_COVERAGE and BAM_COVERAGE_DNA. The value is capped by --max_cpus.",
                    "default": 8
                },
                "publish_dir_mode": {
                    "type": "string",
                    "description": "PublishDir mode applied by the lightweight modules.config layer.",
                    "default": "copy"
                },
                "config_profile_name": {
                    "type": "string",
                    "description": "Optional human-readable active profile name used in reporting."
                },
                "config_profile_description": {
                    "type": "string",
                    "description": "Optional human-readable active profile description used in reporting."
                },
                "custom_config_version": {
                    "type": "string",
                    "description": "Version selector for remote nf-core/configs loading.",
                    "default": "master"
                },
                "custom_config_base": {
                    "type": "string",
                    "description": "Base URL used to load remote nf-core/configs institutional profiles.",
                    "default": "https://raw.githubusercontent.com/nf-core/configs/master"
                }
            }
        },
        "advanced_options": {
            "title": "Advanced options",
            "type": "object",
            "description": "Internal advanced defaults kept out of the main public YAML input contract.",
            "properties": {
                "barcode_defaults": {
                    "type": "string",
                    "description": "Internal barcode parsing defaults used by the samplesheet parser and local wrapper modules."
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/$defs/input_output_options"
        },
        {
            "$ref": "#/$defs/execution_options"
        },
        {
            "$ref": "#/$defs/advanced_options"
        }
    ]
}