nextflow_schema.json

{
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "$id": "https://raw.githubusercontent.com/nf-core/drop/master/nextflow_schema.json",
    "title": "nf-core/drop pipeline parameters",
    "description": "The detection of RNA Outliers Pipeline (DROP) is an integrative workflow to detect aberrant expression, aberrant splicing, and mono-allelic expression from raw sequencing files.",
    "type": "object",
    "$defs": {
        "global_parameters": {
            "title": "Global parameters",
            "type": "object",
            "fa_icon": "fas fa-cogs",
            "description": "Global parameters for the pipeline.",
            "required": ["input", "outdir", "genome"],
            "properties": {
                "input": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "pattern": "^\\S+\\.tsv$",
                    "description": "Path to the samplesheet file used by the pipeline. The file should be a TSV file. Equivalent to the `sampleAnnotation` parameter in the snakemake pipeline.",
                    "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. See [usage docs](https://nf-co.re/drop/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. Equivalent to the `root` parameter in the snakemake pipeline.",
                    "fa_icon": "fas fa-folder-open"
                },
                "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"
                },
                "project_title": {
                    "type": "string",
                    "description": "Title of the project to be displayed on the rendered HTML output"
                },
                "genome": {
                    "type": "string",
                    "description": "Equivalent to the `genomeAssembly` parameter in the snakemake pipeline. Either hg19/hs37d5 or hg38/GRCh38, depending on the genome assembly used for mapping",
                    "enum": ["hg19", "hs37d5 ", "hg38", "GRCh38"],
                    "fa_icon": "fas fa-book"
                },
                "gene_annotation": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "mimetype": "text/plain",
                    "pattern": "^\\S+\\.(csv|tsv|json|yml|yaml)$",
                    "description": "Path to GTF gene annotations file. Equivalent to the `geneAnnotation` parameter in the snakemake pipeline, with the difference that a file depicting the kev-value pairs is expected here instead.",
                    "help_text": "See [example](https://github.com/nf-core/drop/blob/dev/assets/gene_annotation.yaml)",
                    "fa_icon": "far fa-file-code"
                },
                "hpo_file": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "mimetype": "text/plain",
                    "pattern": "^\\S+\\.tsv(\\.gz)?$",
                    "description": "Full path of the file containing HPO terms. If missing, it reads it from our webserver. Refer to [files-to-download](https://gagneurlab-drop.readthedocs.io/en/latest/prepare.html?highlight=drop_group#files-to-download). Equivalent to the `hpoFile` parameter in the snakemake pipeline.",
                    "fa_icon": "far fa-file-code"
                },
                "random_seed": {
                    "type": ["boolean", "integer"],
                    "description": "Specify a random seed for reproducibility"
                }
            }
        },
        "export_counts": {
            "title": "Export counts options",
            "type": "object",
            "fa_icon": "fas fa-file-export",
            "description": "Export counts options.",
            "properties": {
                "ec_gene_annotations": {
                    "type": "string",
                    "description": "A comma-separated list of gene annotations to export."
                },
                "ec_exclude_groups": {
                    "type": "string",
                    "description": "A comma-separated list of aberrant expression and aberrant splicing groups whose counts should not be exported. If empty, all groups are exported."
                }
            }
        },
        "aberrant_expression": {
            "title": "Aberrant expression options",
            "type": "object",
            "fa_icon": "fas fa-file-export",
            "description": "Aberrant expression options.",
            "properties": {
                "ae_skip": {
                    "type": "boolean",
                    "description": "Skip aberrant expression analysis.",
                    "fa_icon": "fas fa-file-export"
                },
                "ae_groups": {
                    "type": "string",
                    "description": "A comma-separated list of aberrant expression groups to run. If empty, all groups are run."
                },
                "ae_min_ids": {
                    "type": "integer",
                    "description": "A positive number indicating the minimum number of samples that a group needs in order to be analyzed. We recommend at least 50.",
                    "default": 1,
                    "minimum": 1,
                    "fa_icon": "fas fa-file-export"
                },
                "ae_fpkm_cutoff": {
                    "type": "integer",
                    "description": "A positive number indicating the minimum FPKM value for a gene to be considered expressed.",
                    "default": 1,
                    "minimum": 0,
                    "fa_icon": "fas fa-file-export"
                },
                "ae_implementation": {
                    "type": "string",
                    "description": "Methods to remove sample covariation in OUTRIDER.",
                    "enum": ["autoencoder", "pca", "peer"],
                    "default": "autoencoder",
                    "fa_icon": "fas fa-file-export"
                },
                "ae_padj_cutoff": {
                    "type": "number",
                    "description": "A number between (0, 1] indicating the maximum FDR an event can have in order to be considered an outlier.",
                    "default": 0.05,
                    "minimum": 0,
                    "maximum": 1,
                    "fa_icon": "fas fa-file-export"
                },
                "ae_z_score_cutoff": {
                    "type": "number",
                    "description": "A non-negative number. Z scores (in absolute value) greater than this cutoff are considered as outliers.",
                    "default": 0.0,
                    "minimum": 0,
                    "fa_icon": "fas fa-file-export"
                },
                "ae_max_tested_dimension_proportion": {
                    "type": "integer",
                    "description": "An integer that controls the maximum value that the encoding dimension can take.",
                    "minimum": 1,
                    "default": 3
                },
                "ae_yield_size": {
                    "type": "integer",
                    "description": "An integer that sets the batch size for counting reads within a bam file. If memory issues persist lower the yieldSize.",
                    "minimum": 1,
                    "default": 2000000
                },
                "ae_genes_to_test": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "schema": "assets/schema_genes_to_test.json",
                    "pattern": "^\\S+\\.(yaml|yml)$",
                    "description": "Full path to a yaml file specifying lists of candidate genes per sample to test during FDR correction. See the documentation for details on the structure of this file.",
                    "help_text": "In addition to returning transcriptome-wide results, DROP provides the option to limit the FDR correction to user-provided genes of interest. See more [details](https://gagneurlab-drop.readthedocs.io/en/latest/prepare.html?highlight=hpo#limiting-fdr-correction-to-subsets-of-genes-of-interest)"
                },
                "ae_use_grid_search_to_obtain_q": {
                    "type": "boolean",
                    "description": "If true, the optimal latent space dimension for the autoencoder will be determined by grid search. If false, OHT will be performed..",
                    "fa_icon": "fas fa-file-export"
                }
            }
        },
        "aberrant_splicing": {
            "title": "Aberrant splicing options",
            "type": "object",
            "fa_icon": "fas fa-file-export",
            "description": "Aberrant splicing options.",
            "properties": {
                "as_skip": {
                    "type": "boolean",
                    "description": "Skip aberrant splicing analysis.",
                    "fa_icon": "fas fa-file-export"
                },
                "as_groups": {
                    "type": "string",
                    "description": "A comma-separated list of aberrant splicing groups to run. If empty, all groups are run."
                },
                "as_min_ids": {
                    "type": "integer",
                    "description": "A positive number indicating the minimum number of samples that a group needs in order to be analyzed. We recommend at least 50.",
                    "default": 1,
                    "minimum": 1,
                    "fa_icon": "fas fa-file-export"
                },
                "as_recount": {
                    "type": "boolean",
                    "description": "If true, it forces samples to be recounted.",
                    "fa_icon": "fas fa-file-export"
                },
                "as_long_read": {
                    "type": "boolean",
                    "description": "Set to true only if counting Nanopore or PacBio long reads.",
                    "fa_icon": "fas fa-file-export"
                },
                "as_keep_non_standard_chrs": {
                    "type": "boolean",
                    "description": "Set to true if non standard chromosomes are to be kept for further analysis.",
                    "fa_icon": "fas fa-file-export"
                },
                "as_skip_filter": {
                    "type": "boolean",
                    "description": "If true, no filter is applied. We recommend filtering.",
                    "fa_icon": "fas fa-file-export"
                },
                "as_min_expression_in_one_sample": {
                    "type": "integer",
                    "description": "The minimal read count in at least one sample required for an intron to pass the filter.",
                    "default": 20,
                    "minimum": 1,
                    "fa_icon": "fas fa-file-export"
                },
                "as_quantile_min_expression": {
                    "type": "integer",
                    "description": "The minimum total read count (N) an intron needs to have at the specified quantile across samples to pass the filter. See --as_quantile_for_filtering.",
                    "default": 10,
                    "minimum": 1,
                    "fa_icon": "fas fa-file-export"
                },
                "as_min_delta_psi": {
                    "type": "number",
                    "description": "The minimal variation (in delta psi) required for an intron to pass the filter.",
                    "default": 0.05,
                    "minimum": 0,
                    "maximum": 1,
                    "fa_icon": "fas fa-file-export"
                },
                "as_implementation": {
                    "type": "string",
                    "description": "Methods to remove sample covariation in FRASER.",
                    "enum": ["PCA", "PCA-BB-Decoder"],
                    "default": "PCA",
                    "fa_icon": "fas fa-file-export"
                },
                "as_fraser_version": {
                    "type": "string",
                    "description": "Version of FRASER to use.",
                    "enume": ["FRASER", "FRASER2"],
                    "default": "FRASER2",
                    "fa_icon": "fas fa-file-export"
                },
                "as_delta_psi_cutoff": {
                    "type": "number",
                    "description": "A non-negative number. Delta psi values greater than this cutoff are considered as outliers. Recommand 0.3 for FRASER, 0.1 for FRASER2.",
                    "default": 0.3,
                    "minimum": 0,
                    "maximum": 1,
                    "fa_icon": "fas fa-file-export"
                },
                "as_quantile_for_filtering": {
                    "type": "number",
                    "description": "Defines at which percentile the as_quantile_min_expression filter is applied. Recommand 0.95 for FRASER, 0.75 for FRASER2.",
                    "help_text": "A value of 0.95 means that at least 5% of the samples need to have a total read count N >= as_quantile_min_expression to pass the filter.",
                    "default": 0.75,
                    "minimum": 0,
                    "maximum": 1,
                    "fa_icon": "fas fa-file-export"
                },
                "as_padj_cutoff": {
                    "type": "number",
                    "description": "Same as in aberrant expression.",
                    "default": 0.1,
                    "minimum": 0,
                    "maximum": 1,
                    "fa_icon": "fas fa-file-export"
                },
                "as_max_tested_dimension_proportion": {
                    "type": "integer",
                    "description": "An integer that controls the maximum value that the encoding dimension can take.",
                    "minimum": 1,
                    "default": 6
                },
                "as_genes_to_test": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "schema": "assets/schema_genes_to_test.json",
                    "pattern": "^\\S+\\.(yaml|yml)$",
                    "description": "Full path to a yaml file specifying lists of candidate genes per sample to test during FDR correction. See the documentation for details on the structure of this file."
                },
                "as_use_grid_search_to_obtain_q": {
                    "type": "boolean",
                    "description": "If true, the optimal latent space dimension for the autoencoder will be determined by grid search. If false, OHT will be performed.."
                }
            }
        },
        "mono_allelic_expression": {
            "title": "Mono-allelic expression options",
            "type": "object",
            "fa_icon": "fas fa-file-export",
            "description": "Mono-allelic expression options.",
            "properties": {
                "mae_skip": {
                    "type": "boolean",
                    "description": "Skip mono-allelic expression analysis.",
                    "fa_icon": "fas fa-file-export"
                },
                "mae_groups": {
                    "type": "string",
                    "description": "A comma-separated list of mono-allelic expression groups to run. If empty, all groups are run."
                },
                "ucsc_fasta": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "mimetype": "text/plain",
                    "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
                    "description": "Path to UCSC FASTA genome file. Equivalent to the `ucsc` option in the `genome` parameter in the snakemake pipeline.",
                    "fa_icon": "far fa-file-code"
                },
                "ucsc_fai": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "mimetype": "text/plain",
                    "pattern": "^\\S+\\.fai$",
                    "description": "Path to UCSC FASTA index file.",
                    "fa_icon": "far fa-file-code"
                },
                "ucsc_dict": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "mimetype": "text/plain",
                    "pattern": "^\\S+\\.dict$",
                    "description": "Path to UCSC sequence dictionary file. . If not provided, the pipeline will try to create it from the FASTA file.",
                    "fa_icon": "far fa-file-code"
                },
                "ncbi_fasta": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "mimetype": "text/plain",
                    "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
                    "description": "Path to NCBI FASTA genome file. Equivalent to the `ncbi` option in the `genome` parameter in the snakemake pipeline.",
                    "fa_icon": "far fa-file-code"
                },
                "ncbi_fai": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "mimetype": "text/plain",
                    "pattern": "^\\S+\\.fai$",
                    "description": "Path to NCBI FASTA index file.",
                    "fa_icon": "far fa-file-code"
                },
                "ncbi_dict": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "mimetype": "text/plain",
                    "pattern": "^\\S+\\.dict$",
                    "description": "Path to NCBI sequence dictionary file. If not provided, the pipeline will try to create it from the FASTA file.",
                    "fa_icon": "far fa-file-code"
                },
                "mae_gatk_header_check": {
                    "type": "boolean",
                    "description": "If true (recommended), it emits the header warnings of a VCF file when performing the allelic counts",
                    "fa_icon": "fas fa-file-export"
                },
                "mae_padj_cutoff": {
                    "type": "number",
                    "description": "Same as in aberrant expression.",
                    "default": 0.05,
                    "minimum": 0,
                    "maximum": 1,
                    "fa_icon": "fas fa-file-export"
                },
                "mae_allelic_ratio_cutoff": {
                    "type": "number",
                    "description": "A number between [0.5, 1) indicating the maximum allelic ratio allele1/(allele1+allele2) for the test to be significant.",
                    "default": 0.8,
                    "minimum": 0.5,
                    "maximum": 1,
                    "fa_icon": "fas fa-file-export"
                },
                "mae_add_af": {
                    "type": "boolean",
                    "description": "Add the allele frequencies from gnomAD",
                    "fa_icon": "fas fa-file-export"
                },
                "mae_max_af": {
                    "type": "number",
                    "description": "Maximum allele frequency (of the minor allele) cut-off. Variants with AF equal or below this number are considered rare.",
                    "default": 0.001,
                    "minimum": 0,
                    "maximum": 1,
                    "fa_icon": "fas fa-file-export"
                },
                "mae_max_var_freq_cohort": {
                    "type": "number",
                    "description": "Maximum variant frequency among the cohort.",
                    "default": 0.05,
                    "minimum": 0,
                    "maximum": 1,
                    "fa_icon": "fas fa-file-export"
                },
                "mae_qc_vcf": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "mimetype": "text/plain",
                    "pattern": "^\\S+\\.vcf\\.gz$",
                    "description": "Full path to the vcf file used for VCF-BAM matching. Refer to [files-to-download](https://gagneurlab-drop.readthedocs.io/en/latest/prepare.html?highlight=drop_group#files-to-download).",
                    "fa_icon": "far fa-file-code"
                },
                "mae_qc_vcf_tbi": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "mimetype": "text/plain",
                    "pattern": "^\\S+\\.tbi$",
                    "description": "Full path to the index of the vcf file used for VCF-BAM matching. Refer to [files-to-download](https://gagneurlab-drop.readthedocs.io/en/latest/prepare.html?highlight=drop_group#files-to-download)",
                    "fa_icon": "far fa-file-code"
                },
                "mae_qc_groups": {
                    "type": "string",
                    "description": "Same as 'groups', but for the VCF-BAM matching"
                },
                "mae_dna_rna_match_cutoff": {
                    "type": "number",
                    "description": "fraction (0-1) used to seperate 'matching' samples and 'non-matching' samples comparing the DNA and RNA data during QC.",
                    "default": 0.05,
                    "minimum": 0,
                    "maximum": 1,
                    "fa_icon": "fas fa-file-export"
                }
            }
        },
        "reference_genome_options": {
            "title": "Reference genome options",
            "type": "object",
            "fa_icon": "fas fa-dna",
            "description": "Reference genome related files and options required for the workflow.",
            "properties": {
                "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/"
                }
            }
        },
        "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": {
                "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})$"
                },
                "version": {
                    "type": "boolean",
                    "description": "Display version and exit.",
                    "fa_icon": "fas fa-question-circle",
                    "hidden": true
                },
                "publish_dir_mode": {
                    "type": "string",
                    "default": "copy",
                    "description": "Method used to save pipeline results to output directory.",
                    "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
                    "fa_icon": "fas fa-copy",
                    "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
                    "hidden": true
                },
                "email_on_fail": {
                    "type": "string",
                    "description": "Email address for completion summary, only when pipeline fails.",
                    "fa_icon": "fas fa-exclamation-triangle",
                    "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$",
                    "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/refs/heads/drop/data/",
                    "hidden": true
                },
                "modules_testdata_base_path": {
                    "type": "string",
                    "fa_icon": "far fa-check-circle",
                    "description": "Base URL or local path to location of module test dataset files",
                    "default": "https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/",
                    "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": "#/$defs/global_parameters"
        },
        {
            "$ref": "#/$defs/export_counts"
        },
        {
            "$ref": "#/$defs/aberrant_expression"
        },
        {
            "$ref": "#/$defs/aberrant_splicing"
        },
        {
            "$ref": "#/$defs/mono_allelic_expression"
        },
        {
            "$ref": "#/$defs/reference_genome_options"
        },
        {
            "$ref": "#/$defs/institutional_config_options"
        },
        {
            "$ref": "#/$defs/generic_options"
        }
    ]
}