nextflow_schema.json

{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/nf-core/bigbacter/master/nextflow_schema.json",
    "title": "nf-core/bigbacter pipeline parameters",
    "description": "Bacterial genomic surviellance pipeline",
    "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": [
                "outdir",
                "db"
            ],
            "properties": {
                "input": {
                    "type": "string",
                    "format": "file-path",
                    "mimetype": "text/csv",
                    "pattern": "^\\S+\\.csv$",
                    "schema": "assets/schema_input.json",
                    "description": "Path to comma-separated file containing information about the samples in the experiment.",
                    "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/bigbacter/usage#samplesheet-input).",
                    "fa_icon": "fas fa-file-csv"
                },
                "ncbi": {
                    "type": "string",
                    "description": "Path to comma-separated file containing information for samples that should be pulled from NCBI.",
                    "pattern": "^\\S+\\.csv$",
                    "format": "file-path"
                },
                "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"
                },
                "db": {
                    "type": "string",
                    "description": "Path to the BigBacter database.",
                    "fa_icon": "fas fa-folder-open"
                },
                "push": {
                    "type": "boolean",
                    "fa_icon": "fas fa-file-export",
                    "description": "Push files to database (Default: false). It is recommended that you check all outputs before pushing files to your BigBacter database. If results are deemed acceptable, the run can be resumed with this option set to 'true'. This avoids adding abnormal samples that may impact future analyses."
                }
            }
        },
        "qc_reads_assembly": {
            "title": "QC: Reads & Assembly",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "read_qc": {
                    "type": "boolean",
                    "fa_icon": "fas fa-chart-pie",
                    "description": "Whether read QC should be performed.",
                    "default": true
                },
                "assembly_qc": {
                    "type": "boolean",
                    "default": true,
                    "fa_icon": "fas fa-chart-pie",
                    "description": "Whether assembly QC should be performed."
                },
                "min_contig_len": {
                    "type": "integer",
                    "default": 300,
                    "fa_icon": "fas fa-chart-pie",
                    "description": "Minimum contig length retained in assembly."
                }
            }
        },
        "qc_variant_calling": {
            "title": "QC: Variant Calling",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "min_genfrac": {
                    "type": "integer",
                    "default": 90,
                    "description": "Percent of the reference covered by a sample for it to be included in the core SNP analysis (default: 90)",
                    "fa_icon": "fas fa-chart-pie"
                },
                "max_het": {
                    "type": "integer",
                    "default": 1,
                    "description": "Percentage of heterozygous sites allowed for a sample to be included in the core SNP analysis (default: 1)",
                    "fa_icon": "fas fa-chart-pie"
                },
                "max_lowcov": {
                    "type": "integer",
                    "default": 5,
                    "description": "Percentage of low coverage sites allowed for a sample to be included in the core SNP analysis (default: 5)",
                    "fa_icon": "fas fa-chart-pie"
                },
                "max_depth": {
                    "type": "integer",
                    "default": 100,
                    "fa_icon": "fas fa-chart-pie",
                    "description": "Maximum read depth per sample. This is used by Snippy to randomly subsample reads."
                }
            }
        },
        "tree_options": {
            "title": "Tree options",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "max_ml": {
                    "type": "integer",
                    "default": 100,
                    "description": "Maximum number of samples in a cluster for IQTREE to be run. This is to avoid extremely long analyses due to large trees. If the number of samples in a cluster exceeds this amount, Rapidnj will be used instead.",
                    "fa_icon": "fas fa-tree"
                },
                "min_tree": {
                    "type": "integer",
                    "default": 2,
                    "fa_icon": "fas fa-tree",
                    "description": "Minimum number of samples in a cluster for a tree to be generated (sans reference). Must be greater than 2."
                }
            }
        },
        "reporting_options": {
            "title": "Reporting options",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "strong_link_cutoff": {
                    "type": "integer",
                    "default": 10,
                    "description": "SNP distance threshold used to classify strong genomic linkages (default: 10)",
                    "fa_icon": "fas fa-link"
                },
                "inter_link_cutoff": {
                    "type": "integer",
                    "default": 50,
                    "description": "SNP distance threshold used to classify intermediate genomic linkages (default: 50)",
                    "fa_icon": "fas fa-link"
                }
            }
        },
        "other_options_caution": {
            "title": "Other options (caution)",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "resolve_merged": {
                    "type": "boolean",
                    "fa_icon": "fas fa-object-group",
                    "description": "Option to resolve merged PopPUNK clusters. WARNING: Failure to resolve merged clusters may lead to missed genetic relationships.",
                    "default": true
                },
                "run_id": {
                    "fa_icon": "fas fa-skull-crossbones",
                    "description": "Run ID. This will bypass the epoch timestamp. Only change if you know what you are doing."
                }
            },
            "fa_icon": "fas fa-terminal"
        },
        "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"
                }
            }
        },
        "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": {
                "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"
                },
                "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})$"
                },
                "help": {
                    "type": "boolean",
                    "description": "Display help text.",
                    "fa_icon": "fas fa-question-circle",
                    "hidden": true
                },
                "version": {
                    "type": "boolean",
                    "description": "Display version and exit.",
                    "fa_icon": "fas fa-question-circle",
                    "hidden": true
                },
                "publish_dir_mode": {
                    "type": "string",
                    "default": "copy",
                    "description": "Method used to save pipeline results to output directory.",
                    "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
                    "fa_icon": "fas fa-copy",
                    "enum": [
                        "symlink",
                        "rellink",
                        "link",
                        "copy",
                        "copyNoFollow",
                        "move"
                    ],
                    "hidden": true
                },
                "email_on_fail": {
                    "type": "string",
                    "description": "Email address for completion summary, only when pipeline fails.",
                    "fa_icon": "fas fa-exclamation-triangle",
                    "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$",
                    "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$",
                    "default": "25.MB",
                    "fa_icon": "fas fa-file-upload",
                    "hidden": true
                },
                "monochrome_logs": {
                    "type": "boolean",
                    "description": "Do not use coloured log outputs.",
                    "fa_icon": "fas fa-palette",
                    "hidden": true
                },
                "hook_url": {
                    "type": "string",
                    "description": "Incoming hook URL for messaging service",
                    "fa_icon": "fas fa-people-group",
                    "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.",
                    "hidden": true
                },
                "multiqc_config": {
                    "type": "string",
                    "description": "Custom config file to supply to MultiQC.",
                    "fa_icon": "fas fa-cog",
                    "hidden": true
                },
                "multiqc_logo": {
                    "type": "string",
                    "description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file",
                    "fa_icon": "fas fa-image",
                    "hidden": true
                },
                "multiqc_methods_description": {
                    "type": "string",
                    "description": "Custom MultiQC yaml file containing HTML including a methods description.",
                    "fa_icon": "fas fa-cog"
                },
                "tracedir": {
                    "type": "string",
                    "description": "Directory to keep pipeline Nextflow logs and reports.",
                    "default": "${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."
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/input_output_options"
        },
        {
            "$ref": "#/definitions/qc_reads_assembly"
        },
        {
            "$ref": "#/definitions/qc_variant_calling"
        },
        {
            "$ref": "#/definitions/tree_options"
        },
        {
            "$ref": "#/definitions/reporting_options"
        },
        {
            "$ref": "#/definitions/other_options_caution"
        },
        {
            "$ref": "#/definitions/institutional_config_options"
        },
        {
            "$ref": "#/definitions/max_job_request_options"
        },
        {
            "$ref": "#/definitions/generic_options"
        }
    ],
    "properties": {
        "schema_ignore_params": {
            "type": "string",
            "default": "genomes"
        }
    }
}