nextflow_schema.json

{
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "$id": "https://raw.githubusercontent.com/nf-core/variantprioritization/master/nextflow_schema.json",
    "title": "nf-core/variantprioritization pipeline parameters",
    "description": "pipeline for the functional annotation and translation of somatic SNVs/InDels and copy number abberations for precision cancer medicine",
    "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": "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. See [usage docs](https://nf-co.re/variantprioritization/usage#samplesheet-input).",
                    "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"
                },
                "email": {
                    "type": "string",
                    "description": "Email address for completion summary.",
                    "fa_icon": "fas fa-envelope",
                    "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
                    "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
                },
                "multiqc_title": {
                    "type": "string",
                    "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
                    "fa_icon": "fas fa-file-signature"
                }
            }
        },
        "reference_options": {
            "title": "Reference options",
            "type": "object",
            "fa_icon": "fas fa-dna",
            "description": "Reference genome related files and options required for the workflow.",
            "properties": {
                "genome": {
                    "type": "string",
                    "description": "Name of iGenomes reference.",
                    "fa_icon": "fas fa-book",
                    "help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details."
                },
                "igenomes_ignore": {
                    "type": "boolean",
                    "description": "Do not load the iGenomes reference config.",
                    "fa_icon": "fas fa-ban",
                    "hidden": true,
                    "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`."
                },
                "igenomes_base": {
                    "type": "string",
                    "format": "directory-path",
                    "description": "The base path to the igenomes reference files",
                    "fa_icon": "fas fa-ban",
                    "hidden": true,
                    "default": "s3://ngi-igenomes/igenomes/"
                },
                "pcgr_bundleversion": {
                    "type": "integer",
                    "default": 20250314,
                    "description": "PCGR/CPSR reference data bundle version.",
                    "help_text": "Version tag for the downloadable PCGR reference bundle. Keep this aligned with the PCGR container/software version for compatibility."
                },
                "pcgr_database_dir": {
                    "type": "string",
                    "description": "Path to PCGR database. Set `pcgr_download` to `false` when using this."
                },
                "pcgr_download": {
                    "type": "boolean",
                    "description": "Download PCGR reference database from the PCGR site. Set to `false` if you want to use a local path.",
                    "default": true
                },
                "vep_cache": {
                    "type": "string",
                    "fa_icon": "fas fa-cloud-download-alt",
                    "default": "s3://annotation-cache/vep_cache/",
                    "description": "Path to VEP cache.",
                    "help_text": "Path to VEP cache which should contain the relevant species, genome and build directories at the path `${vep_species}/${vep_genome}_${vep_cache_version}`."
                },
                "vep_cache_version": {
                    "type": "integer",
                    "fa_icon": "fas fa-tag",
                    "default": 113,
                    "description": "VEP cache version.",
                    "help_text": "Alternative cache version can be used to specify the correct Ensembl Genomes version number as these differ from the concurrent Ensembl/VEP version numbers."
                },
                "vep_species": {
                    "type": "string",
                    "fa_icon": "fas fa-microscope",
                    "description": "VEP species. Defaults to `homo_sapiens`.",
                    "default": "homo_sapiens",
                    "hidden": true
                }
            }
        },
        "cpsr_options": {
            "title": "CPSR options",
            "type": "object",
            "description": "Configuration options for germline cancer predisposition reporting (CPSR).",
            "default": "",
            "properties": {
                "panel_id": {
                    "type": "string",
                    "default": "0",
                    "description": "Comma-separated CPSR virtual panel identifier(s).",
                    "help_text": "Maps to CPSR `--panel_id`. Use `0` for the exploratory panel, or a comma-separated list (e.g. `1,10,44`).",
                    "pattern": "^\\d+(,\\d+)*$"
                },
                "custom_list": {
                    "type": "string",
                    "description": "Path to custom gene list file (single-column Ensembl gene identifiers).",
                    "help_text": "Alternative to predefined panels (`--custom_list`)"
                },
                "custom_list_name": {
                    "type": "string",
                    "description": "Display name for custom panel/list.",
                    "help_text": "Maps to CPSR `--custom_list_name`."
                },
                "diagnostic_grade_only": {
                    "type": "boolean",
                    "description": "For PanelApp panels (1-44), include GREEN-status genes only."
                },
                "secondary_findings": {
                    "type": "boolean",
                    "description": "Include variants in ACMG secondary findings gene list (v3.2)."
                },
                "pgx_findings": {
                    "type": "boolean",
                    "description": "Report overlap with pharmacogenomic toxicity variants (CPIC/PgX)."
                },
                "gwas_findings": {
                    "type": "boolean",
                    "description": "Report overlap with low/moderate-risk GWAS cancer variants."
                },
                "pop_gnomad": {
                    "type": "string",
                    "default": "nfe",
                    "enum": ["afr", "amr", "eas", "sas", "asj", "nfe", "fin", "global"],
                    "description": "gnomAD population source used for ACMG frequency assessment."
                },
                "maf_upper_threshold": {
                    "type": "number",
                    "default": 0.9,
                    "description": "Upper gnomAD global MAF threshold for variants included in report."
                },
                "classify_all": {
                    "type": "boolean",
                    "description": "Also provide CPSR TIER classifications for variants with existing ClinVar classifications."
                },
                "clinvar_report_noncancer": {
                    "type": "boolean",
                    "description": "Include ClinVar variants linked to non-cancer phenotypes/conditions."
                },
                "ignore_noncoding": {
                    "type": "boolean",
                    "description": "Ignore non-coding (non protein-altering) variants in CPSR report."
                },
                "vep_gencode_basic": {
                    "type": "boolean",
                    "description": "Consider basic GENCODE transcript set only with Variant Effect Predictor (VEP) (option '--gencode_basic' in VEP)."
                }
            }
        },
        "pcgr_options": {
            "title": "PCGR options",
            "type": "object",
            "description": "Configuration options for somatic interpretation and reporting with PCGR.",
            "default": "",
            "properties": {
                "vcf2maf": {
                    "type": "boolean",
                    "description": "Generate a MAF file for the input VCF using vcf2maf."
                },
                "assay": {
                    "type": "string",
                    "enum": ["WGS", "WES", "TARGETED"],
                    "description": "Type of DNA sequencing assay performed for input data.",
                    "help_text": "PCGR option `--assay` (default in PCGR: WES)."
                },
                "tumor_site": {
                    "type": "integer",
                    "default": 0,
                    "description": "Primary tumor type/site code used for site-specific interpretation.",
                    "help_text": "PCGR `--tumor_site` supports codes 0-30, where 0 means any tumor type."
                },
                "tumor_ploidy": {
                    "type": "string",
                    "description": "Estimated tumor ploidy."
                },
                "cna_analysis": {
                    "type": "boolean",
                    "description": "Enable copy-number alteration (CNA) analysis and reporting."
                },
                "cna_overlap_pct": {
                    "type": "integer",
                    "default": 50,
                    "description": "Mean percent overlap between CNA segment and gene transcripts for reporting gains/losses."
                },
                "tumor_dp_tag": {
                    "type": "string",
                    "description": "VCF INFO tag for tumor sequencing depth.",
                    "help_text": "Maps to PCGR `--tumor_dp_tag`."
                },
                "tumor_af_tag": {
                    "type": "string",
                    "description": "VCF INFO tag for tumor variant allelic fraction.",
                    "help_text": "Maps to PCGR `--tumor_af_tag`."
                },
                "control_dp_tag": {
                    "type": "string",
                    "description": "VCF INFO tag for control/normal sequencing depth.",
                    "help_text": "Maps to PCGR `--control_dp_tag`."
                },
                "control_af_tag": {
                    "type": "string",
                    "description": "VCF INFO tag for control/normal variant allelic fraction.",
                    "help_text": "Maps to PCGR `--control_af_tag`."
                },
                "call_conf_tag": {
                    "type": "string",
                    "description": "VCF INFO tag for somatic call confidence.",
                    "help_text": "Maps to PCGR `--call_conf_tag`."
                },
                "tumor_purity": {
                    "description": "Estimated tumor purity.",
                    "minimum": 0,
                    "maximum": 1
                },
                "effective_target_size_mb": {
                    "type": "integer",
                    "default": 34,
                    "description": "Effective target size in Mb for TMB calculation."
                },
                "input_cpsr": {
                    "type": "string",
                    "description": "Path to CPSR-classified germline calls file.",
                    "help_text": "Maps to PCGR `--input_cpsr`."
                },
                "input_cpsr_yaml": {
                    "type": "string",
                    "description": "Path to CPSR YAML configuration file.",
                    "help_text": "Maps to PCGR `--input_cpsr_yaml`."
                },
                "estimate_tmb": {
                    "type": "boolean",
                    "description": "Estimate tumor mutational burden (TMB)."
                },
                "estimate_msi": {
                    "type": "boolean",
                    "description": "Predict microsatellite instability (MSI) status."
                },
                "estimate_signatures": {
                    "type": "boolean",
                    "description": "Estimate mutational signature contributions by re-fitting."
                },
                "tmb_display": {
                    "type": "string",
                    "default": "coding_and_silent",
                    "description": "TMB measure to show in report.",
                    "help_text": "Allowed PCGR values: coding_and_silent, coding_non_silent, missense_only.",
                    "enum": ["coding_and_silent", "coding_non_silent", "missense_only"]
                },
                "tmb_dp_min": {
                    "type": "integer",
                    "description": "Minimum tumor depth required for inclusion in TMB calculation when depth tag is available."
                },
                "tmb_af_min": {
                    "type": "number",
                    "description": "Minimum tumor allelic fraction required for inclusion in TMB calculation when AF tag is available."
                },
                "tmb_ad_min": {
                    "type": "integer",
                    "description": "Minimum tumor allelic depth (ALT-supporting reads) required for TMB calculation when depth+AF tags are available."
                },
                "min_mutations_signatures": {
                    "type": "integer",
                    "default": 200,
                    "description": "Minimum number of SNVs required for mutational signature re-fitting."
                },
                "all_reference_signatures": {
                    "type": "boolean",
                    "description": "Use all reference SBS signatures during signature re-fitting."
                },
                "include_artefact_signatures": {
                    "type": "boolean",
                    "description": "Include sequencing artefact signatures during fitting."
                },
                "prevalence_reference_signatures": {
                    "type": "number",
                    "default": 0.1,
                    "description": "Minimum tumor-type prevalence (%) of reference signatures to include in re-fitting."
                },
                "tumor_dp_min": {
                    "type": "integer",
                    "default": 0,
                    "description": "Minimum tumor depth for variant inclusion when tumor depth tag is provided."
                },
                "tumor_ad_min": {
                    "type": "integer",
                    "description": "Minimum tumor allelic depth (ALT-supporting reads) for variant inclusion when tumor depth+AF tags are provided."
                },
                "tumor_af_min": {
                    "type": "integer",
                    "default": 0,
                    "description": "Minimum tumor allelic fraction for variant inclusion when tumor AF tag is provided."
                },
                "control_dp_min": {
                    "type": "integer",
                    "default": 0,
                    "description": "Minimum control/normal depth for variant inclusion when control depth tag is provided."
                },
                "control_ad_max": {
                    "type": "integer",
                    "description": "Maximum control/normal allelic depth (ALT-supporting reads) allowed when control depth+AF tags are provided."
                },
                "control_af_max": {
                    "type": "integer",
                    "default": 1,
                    "description": "Maximum control/normal allelic fraction allowed when control AF tag is provided."
                },
                "no_html": {
                    "type": "boolean",
                    "description": "Do not generate PCGR HTML report."
                }
            }
        },
        "pcgr_tumoronly_options": {
            "title": "PCGR tumor-only options",
            "type": "object",
            "description": "Additional filtering options for tumor-only somatic interpretation.",
            "default": "",
            "properties": {
                "tumor_only": {
                    "type": "boolean",
                    "description": "Run in tumor-only mode (no matched normal sample)."
                },
                "pon_vcf": {
                    "type": "string",
                    "description": "Path to panel-of-normals (PoN) VCF used to suppress recurrent artefacts."
                },
                "exclude_pon": {
                    "type": "boolean",
                    "description": "Exclude variants overlapping panel-of-normals calls."
                },
                "exclude_likely_hom_germline": {
                    "type": "boolean",
                    "description": "Exclude variants likely to represent homozygous germline events."
                },
                "exclude_likely_het_germline": {
                    "type": "boolean",
                    "description": "Exclude variants likely to represent heterozygous germline events."
                },
                "exclude_dbsnp_nonsomatic": {
                    "type": "boolean",
                    "description": "Exclude variants with dbSNP support for non-somatic origin."
                },
                "exclude_nonexonic": {
                    "type": "boolean",
                    "description": "Exclude non-exonic variants in tumor-only filtering."
                },
                "maf_gnomad_nfe": {
                    "type": "number",
                    "default": 0.002,
                    "description": "Maximum gnomAD NFE population AF tolerated in tumor-only filtering."
                },
                "maf_gnomad_fin": {
                    "type": "number",
                    "default": 0.002,
                    "description": "Maximum gnomAD FIN population AF tolerated in tumor-only filtering."
                },
                "maf_gnomad_asj": {
                    "type": "number",
                    "default": 0.002,
                    "description": "Maximum gnomAD ASJ population AF tolerated in tumor-only filtering."
                },
                "maf_gnomad_oth": {
                    "type": "number",
                    "default": 0.002,
                    "description": "Maximum gnomAD OTH population AF tolerated in tumor-only filtering."
                },
                "maf_gnomad_amr": {
                    "type": "number",
                    "default": 0.002,
                    "description": "Maximum gnomAD AMR population AF tolerated in tumor-only filtering."
                },
                "maf_gnomad_afr": {
                    "type": "number",
                    "default": 0.002,
                    "description": "Maximum gnomAD AFR population AF tolerated in tumor-only filtering."
                },
                "maf_gnomad_eas": {
                    "type": "number",
                    "default": 0.002,
                    "description": "Maximum gnomAD EAS population AF tolerated in tumor-only filtering."
                },
                "maf_gnomad_sas": {
                    "type": "number",
                    "default": 0.002,
                    "description": "Maximum gnomAD SAS population AF tolerated in tumor-only filtering."
                },
                "maf_gnomad_global": {
                    "type": "number",
                    "default": 0.002,
                    "description": "Maximum global gnomAD AF tolerated in tumor-only filtering."
                }
            }
        },
        "variantfiltering_options": {
            "title": "Variant filtering options",
            "type": "object",
            "description": "Custom expressions for caller-specific hard filtering.",
            "default": "",
            "properties": {
                "filter_haplotypecaller": {
                    "type": "string",
                    "default": "-i\\'FORMAT/DP>10\\",
                    "description": "Filtering expression for HaplotypeCaller VCF records."
                },
                "filter_deepvariant": {
                    "type": "string",
                    "default": "-i\\'FORMAT/DP>10\\",
                    "description": "Filtering expression for DeepVariant VCF records."
                },
                "filter_strelka_variants": {
                    "type": "string",
                    "default": "-i\\'FORMAT/DP>10\\",
                    "description": "Filtering expression for combined Strelka variant records."
                },
                "filter_freebayes_germline": {
                    "type": "string",
                    "default": "-i\\'FORMAT/DP>10\\",
                    "description": "Filtering expression for FreeBayes germline VCF records."
                },
                "filter_mutect2": {
                    "type": "string",
                    "default": "-i\\'FORMAT/DP>10\\",
                    "description": "Filtering expression for Mutect2 VCF records."
                },
                "filter_freebayes_somatic": {
                    "type": "string",
                    "default": "-i\\'FORMAT/DP>10\\",
                    "description": "Filtering expression for FreeBayes somatic VCF records."
                },
                "filter_strelka_indels": {
                    "type": "string",
                    "default": "-i\\'FORMAT/DP>10\\",
                    "description": "Filtering expression for Strelka INDEL records."
                },
                "filter_strelka_snvs": {
                    "type": "string",
                    "default": "-i\\'FORMAT/DP>10\\",
                    "description": "Filtering expression for Strelka SNV records."
                }
            }
        },
        "vep_params_options": {
            "title": "VEP options",
            "type": "object",
            "description": "Runtime and annotation behavior options for Ensembl VEP.",
            "properties": {
                "vep_n_forks": {
                    "type": "integer",
                    "default": 4,
                    "description": "Number of parallel VEP forks.",
                    "help_text": "Higher values can improve throughput but increase CPU and memory usage."
                },
                "vep_buffer_size": {
                    "type": "integer",
                    "default": 500,
                    "description": "Number of variants buffered per VEP processing block."
                },
                "vep_gencode_all": {
                    "type": "boolean",
                    "default": true,
                    "description": "Use full GENCODE transcript set during annotation."
                },
                "vep_pick_order": {
                    "type": "string",
                    "default": "mane_select,mane_plus_clinical,canonical,biotype,ccds,rank,tsl,appris,length",
                    "description": "Priority order used by VEP when selecting a single representative consequence."
                },
                "vep_no_intergenic": {
                    "type": "boolean",
                    "description": "Skip annotation of intergenic variants."
                }
            }
        },
        "institutional_config_options": {
            "title": "Institutional config options",
            "type": "object",
            "fa_icon": "fas fa-university",
            "description": "Parameters used to describe centralised config profiles. These should not be edited.",
            "help_text": "The centralised nf-core configuration profiles use a handful of pipeline parameters to describe themselves. This information is then printed to the Nextflow log when you run a pipeline. You should not need to change these values when you run a pipeline.",
            "properties": {
                "custom_config_version": {
                    "type": "string",
                    "description": "Git commit id for Institutional configs.",
                    "default": "master",
                    "hidden": true,
                    "fa_icon": "fas fa-users-cog"
                },
                "custom_config_base": {
                    "type": "string",
                    "description": "Base directory for Institutional configs.",
                    "default": "https://raw.githubusercontent.com/nf-core/configs/master",
                    "hidden": true,
                    "help_text": "If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.",
                    "fa_icon": "fas fa-users-cog"
                },
                "config_profile_name": {
                    "type": "string",
                    "description": "Institutional config name.",
                    "hidden": true,
                    "fa_icon": "fas fa-users-cog"
                },
                "config_profile_description": {
                    "type": "string",
                    "description": "Institutional config description.",
                    "hidden": true,
                    "fa_icon": "fas fa-users-cog"
                },
                "config_profile_contact": {
                    "type": "string",
                    "description": "Institutional config contact information.",
                    "hidden": true,
                    "fa_icon": "fas fa-users-cog"
                },
                "config_profile_url": {
                    "type": "string",
                    "description": "Institutional config URL link.",
                    "hidden": true,
                    "fa_icon": "fas fa-users-cog"
                }
            }
        },
        "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"],
                    "hidden": true
                },
                "email_on_fail": {
                    "type": "string",
                    "description": "Email address for completion summary, only when pipeline fails.",
                    "fa_icon": "fas fa-exclamation-triangle",
                    "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$",
                    "help_text": "An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.",
                    "hidden": true
                },
                "plaintext_email": {
                    "type": "boolean",
                    "description": "Send plain-text email instead of HTML.",
                    "fa_icon": "fas fa-remove-format",
                    "hidden": true
                },
                "max_multiqc_email_size": {
                    "type": "string",
                    "description": "File size limit when attaching MultiQC reports to summary emails.",
                    "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
                    "default": "25.MB",
                    "fa_icon": "fas fa-file-upload",
                    "hidden": true
                },
                "monochrome_logs": {
                    "type": "boolean",
                    "description": "Do not use coloured log outputs.",
                    "fa_icon": "fas fa-palette",
                    "hidden": true
                },
                "hook_url": {
                    "type": "string",
                    "description": "Incoming hook URL for messaging service",
                    "fa_icon": "fas fa-people-group",
                    "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.",
                    "hidden": true
                },
                "multiqc_config": {
                    "type": "string",
                    "format": "file-path",
                    "description": "Custom config file to supply to MultiQC.",
                    "fa_icon": "fas fa-cog",
                    "hidden": true
                },
                "multiqc_logo": {
                    "type": "string",
                    "description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file",
                    "fa_icon": "fas fa-image",
                    "hidden": true
                },
                "multiqc_methods_description": {
                    "type": "string",
                    "description": "Custom MultiQC yaml file containing HTML including a methods description.",
                    "fa_icon": "fas fa-cog"
                },
                "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
                },
                "pipelines_testdata_base_path": {
                    "type": "string",
                    "fa_icon": "far fa-check-circle",
                    "description": "Base URL or local path to location of pipeline test dataset files",
                    "default": "https://raw.githubusercontent.com/nf-core/test-datasets/",
                    "hidden": true
                },
                "modules_testdata_base_path": {
                    "type": "string",
                    "fa_icon": "far fa-check-circle",
                    "description": "Base URL or local path to location of pipeline test dataset files",
                    "default": "https://raw.githubusercontent.com/nf-core/test-datasets/",
                    "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
                },
                "help": {
                    "type": ["boolean", "string"],
                    "description": "Display the help message."
                },
                "help_full": {
                    "type": "boolean",
                    "description": "Display the full detailed help message."
                },
                "show_hidden": {
                    "type": "boolean",
                    "description": "Display hidden parameters in the help message (only works when --help or --help_full are provided)."
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/$defs/input_output_options"
        },
        {
            "$ref": "#/$defs/reference_options"
        },
        {
            "$ref": "#/$defs/cpsr_options"
        },
        {
            "$ref": "#/$defs/pcgr_options"
        },
        {
            "$ref": "#/$defs/pcgr_tumoronly_options"
        },
        {
            "$ref": "#/$defs/variantfiltering_options"
        },
        {
            "$ref": "#/$defs/vep_params_options"
        },
        {
            "$ref": "#/$defs/institutional_config_options"
        },
        {
            "$ref": "#/$defs/generic_options"
        }
    ]
}