nextflow_schema.json

{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/nf-core/raredisease/master/nextflow_schema.json",
    "title": "nf-core/raredisease pipeline parameters",
    "description": "call and score variants from WGS/WES of rare disease patients",
    "type": "object",
    "definitions": {
        "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",
                    "mimetype": "text/csv",
                    "pattern": "^\\S+\\.csv$",
                    "schema": "assets/schema_input.json",
                    "description": "Path to comma-separated file containing information about the samples in the experiment.",
                    "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/raredisease/usage#samplesheet-input).",
                    "fa_icon": "fas fa-file-csv"
                },
                "outdir": {
                    "type": "string",
                    "format": "directory-path",
                    "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
                    "fa_icon": "fas fa-folder-open"
                },
                "email": {
                    "type": "string",
                    "description": "Email address for completion summary.",
                    "fa_icon": "fas fa-envelope",
                    "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
                    "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
                },
                "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_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": {
                "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."
                },
                "fasta": {
                    "type": "string",
                    "format": "file-path",
                    "mimetype": "text/plain",
                    "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
                    "description": "Path to FASTA genome file.",
                    "help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.",
                    "fa_icon": "far fa-file-code"
                },
                "fasta_fai": {
                    "type": "string",
                    "format": "file-path",
                    "help_text": "If none provided, will be generated automatically from the FASTA reference",
                    "description": "Path to FASTA genome index file.",
                    "fa_icon": "far fa-file-code",
                    "hidden": true
                },
                "igenomes_base": {
                    "type": "string",
                    "format": "directory-path",
                    "description": "Directory / URL base for iGenomes references.",
                    "default": "s3://ngi-igenomes/igenomes",
                    "fa_icon": "fas fa-cloud-download-alt",
                    "hidden": true
                },
                "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`."
                },
                "bwamem2_index": {
                    "type": "string",
                    "format": "directory-path",
                    "description": "Directory for pre-built bwamem2 index.",
                    "help_text": "If none provided, will be generated automatically from the FASTA reference.",
                    "fa_icon": "fas fa-folder-open",
                    "hidden": true
                },
                "gnomad": {
                    "type": "string",
                    "format": "path",
                    "fa_icon": "fas fa-bezier-curve",
                    "description": "Path to directory for gnomad vcf.",
                    "help_text": "Path to the gnomad annotations vcf file. If you don't provide one, gnomad annotations will not be used."
                },
                "gnomad_af": {
                    "type": "string",
                    "format": "path",
                    "fa_icon": "fas fa-file",
                    "description": "Path to the gnomad tab file with allele frequencies.",
                    "help_text": "Path to the gnomad tab file with CHR/START/REF,ALT/AF. Can be generated from the gnomad annotations vcf."
                },
                "gnomad_af_tbi": {
                    "type": "string",
                    "format": "path",
                    "fa_icon": "fas fa-file",
                    "description": "Path to the index file for the gnomad tab file with allele frequencies.",
                    "help_text": "Path to the index of gnomad tab file with CHR/START/REF,ALT/AF"
                },
                "intervals_mt": {
                    "type": "string",
                    "format": "path",
                    "fa_icon": "fas fa-file",
                    "description": "Path to the interval list of the non control mitochondral region.",
                    "help_text": "Path to the interval list of the non control mitochondral regions for Mutect2"
                },
                "known_dbsnp": {
                    "type": "string",
                    "format": "path",
                    "fa_icon": "fas fa-chart-bar",
                    "description": "Path to known dbSNP file.",
                    "hidden": true
                },
                "known_dbsnp_tbi": {
                    "type": "string",
                    "format": "path",
                    "fa_icon": "fas fa-chart-bar",
                    "description": "Path to known dbSNP file index.",
                    "hidden": true
                },
                "known_indels": {
                    "type": "string",
                    "format": "path",
                    "fa_icon": "fas fa-chart-bar",
                    "description": "Path to known indels file.",
                    "hidden": true
                },
                "known_mills": {
                    "type": "string",
                    "format": "path",
                    "fa_icon": "fas fa-chart-bar",
                    "description": "Path to known Mills file.",
                    "hidden": true
                },
                "ml_model": {
                    "type": "string",
                    "format": "path",
                    "fa_icon": "fas fa-chart-bar",
                    "description": "Path to sentieon machine learning model file.",
                    "hidden": true
                },
                "reduced_penetrance": {
                    "type": "string",
                    "format": "path",
                    "fa_icon": "fas fa-chart-bar",
                    "description": "File with gene ids that have reduced penetrance. For use with genmod",
                    "hidden": true
                },
                "score_config_snv": {
                    "type": "string",
                    "format": "path",
                    "fa_icon": "fas fa-chart-bar",
                    "description": "SNV rank model config file for genmod.",
                    "hidden": true
                },
                "score_config_sv": {
                    "type": "string",
                    "format": "path",
                    "fa_icon": "fas fa-chart-bar",
                    "description": "SV rank model config file for genmod.",
                    "hidden": true
                },
                "vep_filters": {
                    "type": "string",
                    "format": "path",
                    "fa_icon": "fas fa-chart-bar",
                    "description": "File containing HGNC_IDs of interest on separate lines.",
                    "hidden": true
                },
                "target_bed": {
                    "type": "string",
                    "format": "path",
                    "fa_icon": "fas fa-bezier-curve",
                    "description": "Path to directory for target bed file.",
                    "help_text": "If you would like to limit your analysis to specific regions of the genome, you can pass those regions in a bed file using this option",
                    "hidden": true
                },
                "sentieonbwa_index": {
                    "type": "string",
                    "format": "directory-path",
                    "default": null,
                    "description": "Directory for pre-built sentieon index.",
                    "help_text": "If none provided, will be generated automatically from the FASTA reference.",
                    "fa_icon": "fas fa-folder-open",
                    "hidden": true
                },
                "svdb_query_dbs": {
                    "type": "string",
                    "format": "file-path",
                    "description": "Databases used for structural variant annotation.",
                    "fa_icon": "far fa-file-code",
                    "help_text": "Path to comma-separated file containing information about the databases used for structural variant annotation."
                },
                "variant_catalog": {
                    "type": "string",
                    "format": "file-path",
                    "description": "Path to variant catalog file",
                    "help_text": "Used with ExpansionHunter and if no catalogue is passed, then a default will be used.",
                    "fa_icon": "far fa-file-code",
                    "hidden": true
                },
                "vcfanno_resources": {
                    "type": "string",
                    "description": "Directory path or tar.gz archive that holds resources defined within the vcfanno toml file.",
                    "help_text": "If no directory path is passed, default configurations will be used according to genome build within the context of the pipeline.",
                    "fa_icon": "fas fa-folder-open",
                    "hidden": true
                },
                "vcfanno_toml": {
                    "type": "string",
                    "description": "Path to the vcfanno toml file.",
                    "help_text": "If no toml is passed, default configurations will be used according to genome build within the context of the pipeline.",
                    "fa_icon": "fas fa-file-csv",
                    "hidden": true
                },
                "vep_cache": {
                    "type": "string",
                    "description": "Path to vep's cache directory.",
                    "help_text": "If no directory path is passed, vcf files will not be annotated by vep.",
                    "fa_icon": "fas fa-folder-open"
                },
                "save_reference": {
                    "type": "boolean",
                    "description": "If generated by the pipeline save the required indices/references in the results directory.",
                    "help_text": "The saved references can be used for future pipeline runs, reducing processing times.",
                    "fa_icon": "fas fa-save"
                },
                "local_genomes": {
                    "type": "string",
                    "format": "directory-path",
                    "fa_icon": "fas fa-map-marker-alt",
                    "description": "Local directory base for genome references that map to the config.",
                    "help_text": "This folder is a flat structure with file names that map to the config."
                },
                "gens_interval_list": {
                    "type": "string",
                    "format": "file-path",
                    "default": null,
                    "fa_icon": "fas fa-bezier-curve",
                    "description": "Path to interval list for Gens.",
                    "help_text": "This file contains the binning intervals used for CollectReadCounts.",
                    "hidden": true
                },
                "gens_pon": {
                    "type": "string",
                    "format": "file-path",
                    "default": null,
                    "fa_icon": "far fa-file-code",
                    "description": "Path to panel of normals for Gens.",
                    "help_text": "The panel used to run DenoiseReadCounts.",
                    "hidden": true
                },
                "gens_gnomad_pos": {
                    "type": "string",
                    "format": "file-path",
                    "default": null,
                    "fa_icon": "far fa-bezier-curve",
                    "description": "Path to a list of common SNP locations for Gens.",
                    "help_text": "Locations of gnomad SNPs with a high enough BAF.",
                    "hidden": true
                }
            }
        },
        "analysis_options": {
            "title": "Analysis options",
            "type": "object",
            "fa_icon": "fas fa-user-cog",
            "description": "Options used to steer the direction of the pipeline.",
            "properties": {
                "analysis_type": {
                    "type": "string",
                    "default": "wgs",
                    "description": "Specifies which analysis type for the pipeline- either 'wgs','wes','mito'. This changes resources consumed and tools used.",
                    "fa_icon": "fas fa-book",
                    "enum": ["wgs", "wes", "mito"]
                },
                "annotate_snv_switch": {
                    "type": "boolean",
                    "default": true,
                    "description": "Specifies whether or not to run annotate SNV subworkflow.",
                    "fa_icon": "fas fa-book"
                },
                "annotate_sv_switch": {
                    "type": "boolean",
                    "default": false,
                    "description": "Specifies whether or not to run annotate structural variant subworkflow.",
                    "fa_icon": "fas fa-book"
                },
                "gens_switch": {
                    "type": "boolean",
                    "default": false,
                    "description": "Specifies whether or not to run gens preprocessing subworkflow.",
                    "fa_icon": "fas fa-book"
                }
            }
        },
        "alignment_options": {
            "title": "Alignment options",
            "type": "object",
            "fa_icon": "fas fa-map-signs",
            "description": "Options to adjust parameters and filtering criteria for read alignments.",
            "properties": {
                "aligner": {
                    "type": "string",
                    "default": "bwamem2",
                    "description": "Specifies the alignment algorithm to use - available options are 'bwamem2' and 'sentieon'.",
                    "fa_icon": "fas fa-map-signs",
                    "enum": ["bwamem2", "sentieon"]
                },
                "rmdup": {
                    "type": "boolean",
                    "default": false,
                    "description": "Specifies whether duplicates reads should be removed prior to variant calling.",
                    "fa_icon": "fas fa-map-signs",
                    "hidden": true
                }
            }
        },
        "variant_calling_options": {
            "title": "Variant calling options",
            "type": "object",
            "fa_icon": "fas fa-map-signs",
            "description": "Options to adjust parameters and filtering criteria for variant calling.",
            "properties": {
                "call_interval": {
                    "type": "string",
                    "format": "path",
                    "fa_icon": "fas fa-chart-bar",
                    "description": "Interval in the reference that will be used in the software",
                    "hidden": true
                },
                "pcrfree": {
                    "type": "boolean",
                    "default": true,
                    "description": "indicates whether the sample is PCR Free or not. Set to true for PCR Free samples.",
                    "fa_icon": "fas fa-map-signs"
                },
                "variant_type": {
                    "type": "string",
                    "default": "snp",
                    "description": "Specifies the variant types for sentieon variant caller.",
                    "fa_icon": "fas fa-map-signs",
                    "enum": ["snp", "indel", "snp,indel"]
                },
                "variant_caller": {
                    "type": "string",
                    "default": "deepvariant",
                    "description": "Specifies the variant caller to use - available options are 'deepvariant' and 'sentieon'.",
                    "fa_icon": "fas fa-map-signs",
                    "enum": ["deepvariant", "sentieon"]
                }
            }
        },
        "sv_caller_options": {
            "title": "Structural variant calling options",
            "type": "object",
            "fa_icon": "fas fa-map-signs",
            "description": "Options to adjust parameters and filtering criteria for structural variant callers.",
            "properties": {
                "cnvpytor_chr": {
                    "type": "string",
                    "default": null,
                    "description": "Chromosome names must be specified the same way as they are described in the sam/bam/cram header, e.g., chrX or X. One can specify multiple chromosomes separated by space.",
                    "fa_icon": "fas fa-map-signs"
                },
                "cnvpytor_binsizes": {
                    "type": "string",
                    "default": "1000",
                    "description": "List of binsizes separated by space e.g. '1000 10000' and '1000'",
                    "fa_icon": "fas fa-map-signs"
                }
            }
        },
        "annotation_options": {
            "title": "Annotation options",
            "type": "object",
            "fa_icon": "fas fa-user-cog",
            "description": "Options used to facilitate the annotation of the variants.",
            "properties": {
                "vep_cache_version": {
                    "type": "string",
                    "default": "104",
                    "description": "Specifies which analysis type for the pipeline- either 'wgs','wes','mito'. This changes resources consumed and tools used.",
                    "fa_icon": "fas fa-book",
                    "enum": ["104", "105"]
                }
            }
        },
        "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"
                },
                "local_config_path": {
                    "type": "string",
                    "description": "Path to local config",
                    "fa_icon": "fas fa-users-cog"
                }
            }
        },
        "max_job_request_options": {
            "title": "Max job request options",
            "type": "object",
            "fa_icon": "fab fa-acquisitions-incorporated",
            "description": "Set the top limit for requested resources for any single job.",
            "help_text": "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.",
            "properties": {
                "max_cpus": {
                    "type": "integer",
                    "description": "Maximum number of CPUs that can be requested for any single job.",
                    "default": 16,
                    "fa_icon": "fas fa-microchip",
                    "hidden": true,
                    "help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`"
                },
                "max_memory": {
                    "type": "string",
                    "description": "Maximum amount of memory that can be requested for any single job.",
                    "default": "128.GB",
                    "fa_icon": "fas fa-memory",
                    "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
                    "hidden": true,
                    "help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`"
                },
                "max_time": {
                    "type": "string",
                    "description": "Maximum amount of time that can be requested for any single job.",
                    "default": "240.h",
                    "fa_icon": "far fa-clock",
                    "pattern": "^(\\d+\\.?\\s*(s|m|h|day)\\s*)+$",
                    "hidden": true,
                    "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`"
                }
            }
        },
        "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": {
                "help": {
                    "type": "boolean",
                    "description": "Display help text.",
                    "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$",
                    "default": "25.MB",
                    "fa_icon": "fas fa-file-upload",
                    "hidden": true
                },
                "monochrome_logs": {
                    "type": "boolean",
                    "description": "Do not use coloured log outputs.",
                    "fa_icon": "fas fa-palette",
                    "hidden": true
                },
                "hook_url": {
                    "type": "string",
                    "description": "Incoming hook URL for messaging service",
                    "fa_icon": "fas fa-people-group",
                    "help_text": "Incoming hook URL for messaging service. Currently, only MS Teams is supported.",
                    "hidden": true
                },
                "multiqc_config": {
                    "type": "string",
                    "description": "Custom config file to supply to MultiQC.",
                    "fa_icon": "fas fa-cog",
                    "hidden": true
                },
                "multiqc_logo": {
                    "type": "string",
                    "description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file",
                    "fa_icon": "fas fa-image",
                    "hidden": true
                },
                "multiqc_methods_description": {
                    "type": "string",
                    "description": "Custom MultiQC yaml file containing HTML including a methods description.",
                    "fa_icon": "fas fa-cog"
                },
                "tracedir": {
                    "type": "string",
                    "description": "Directory to keep pipeline Nextflow logs and reports.",
                    "default": "${params.outdir}/pipeline_info",
                    "fa_icon": "fas fa-cogs",
                    "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
                },
                "show_hidden_params": {
                    "type": "boolean",
                    "fa_icon": "far fa-eye-slash",
                    "description": "Show all params when using `--help`",
                    "hidden": true,
                    "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
                },
                "enable_conda": {
                    "type": "boolean",
                    "description": "Run this workflow with Conda. You can also use '-profile conda' instead of providing this parameter.",
                    "hidden": true,
                    "fa_icon": "fas fa-bacon"
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/input_output_options"
        },
        {
            "$ref": "#/definitions/reference_genome_options"
        },
        {
            "$ref": "#/definitions/analysis_options"
        },
        {
            "$ref": "#/definitions/alignment_options"
        },
        {
            "$ref": "#/definitions/sv_caller_options"
        },
        {
            "$ref": "#/definitions/variant_calling_options"
        },
        {
            "$ref": "#/definitions/annotation_options"
        },
        {
            "$ref": "#/definitions/institutional_config_options"
        },
        {
            "$ref": "#/definitions/max_job_request_options"
        },
        {
            "$ref": "#/definitions/generic_options"
        }
    ]
}