nextflow_schema.json

{
  "$schema": "http://json-schema.org/draft-07/schema",
  "title": "/Volumes/falmeida1TB/Git_Repos/bacannot pipeline parameters",
  "description": "",
  "type": "object",
  "definitions": {
    "download_databases_options": {
      "title": "Download databases options",
      "type": "object",
      "description": "",
      "default": "",
      "properties": {
        "get_dbs": {
          "type": "boolean",
          "description": "Download and build all the required databases on the fly (get today's version)"
        },
        "force_update": {
          "type": "boolean",
          "description": "Should we overwriting existing databases if any?"
        },
        "get_zenodo_db": {
          "type": "boolean",
          "description": "Download latest pre-built databases from Zenodo?"
        }
      }
    },
    "input_output_options": {
      "title": "Input/output options",
      "type": "object",
      "fa_icon": "fas fa-terminal",
      "description": "Set input and output parameters",
      "properties": {
        "input": {
          "type": "string",
          "description": "Path to input samplesheet"
        },
        "enable_deduplication": {
          "type": "boolean",
          "description": "Execute deduplication on reads before assembly."
        },
        "output": {
          "type": "string",
          "description": "Path for output directory",
          "default": "results"
        },
        "bacannot_db": {
          "type": "string",
          "description": "Path for root directory containing required bacannot databases"
        },
        "bakta_db": {
          "type": "string",
          "help_text": "If this parameter is set, the pipeline will perform starting annotation with Bakta instead of Prokka.",
          "description": "Path for pre-built bakta database"
        }
      }
    },
    "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",
          "default": 16,
          "description": "Maximum number of cpus a single module can use."
        },
        "max_memory": {
          "type": "string",
          "default": "20.GB",
          "description": "Maximum memory a single module can use."
        },
        "max_time": {
          "type": "string",
          "default": "40.h",
          "description": "Maximum time a module can run."
        }
      }
    },
    "prokka_optional_parameters": {
      "title": "Prokka optional parameters",
      "type": "object",
      "description": "Sets parameters specific for prokka",
      "default": "",
      "properties": {
        "prokka_use_pgap": {
          "type": "boolean",
          "description": "Include comprehensive PGAP hmm database in prokka annotation instead of TIGRFAM. Although comprehensive it increases runtime."
        },
        "prokka_kingdom": {
          "type": "string",
          "description": "Prokka annotation mode. Prokka defaults are for Bacteria.",
          "help_text": "Select which prokka annotation mode to run.",
          "enum": ["Archaea", "Bacteria", "Mitochondria", "Viruses"]
        },
        "prokka_genetic_code": {
          "type": "number",
          "description": "Translation table code. Prokka defaults are for Bacteria."
        },
        "prokka_use_rnammer": {
          "type": "boolean",
          "description": "Use rnammer instead of Barrnap?"
        }
      },
      "fa_icon": "fas fa-cog"
    },
    "resfinder_optional_process": {
      "title": "Resfinder optional process",
      "type": "object",
      "description": "Set default resfinder species panel to use",
      "default": "",
      "properties": {
        "resfinder_species": {
          "type": "string",
          "description": "Select the resfinder species panel to use",
          "help_text": "If blank, resfinder will not be executed. Sets a default value for all samples in the samplesheet. If a sample has another value set inside the samplesheet, the pipeline will use for that specific sample the value inside the samplesheet. Users must check Resfinder website to know the panels. If your species is not available in resfinder species panels you may set it to \"Other\"."
        }
      },
      "fa_icon": "fas fa-cog"
    },
    "sourmash_optional_parameters": {
      "title": "Sourmash optional parameters",
      "type": "object",
      "description": "Set parameters for sourmash analysis",
      "default": "",
      "properties": {
        "sourmash_kmer": {
          "type": "integer",
          "default": 31,
          "help_text": "Select which kmer size to run sourmash with. Options are: 21, 31 and 51.\nThe bigger the value, the more stringent the results are.",
          "enum": [21, 31, 51],
          "description": "Kmer size to run sourmash analysis"
        },
        "sourmash_scale": {
          "type": "integer",
          "default": 1000,
          "description": "Scale to run sourmash analysis",
          "help_text": "The scale define the size of the generated hashes. For example, scale=1000 in a 5MB genome will generate 5000 hashes. 1000 as scale is generally recommended by the tool's developers."
        }
      }
    },
    "select_unselect_tasks_to_be_run": {
      "title": "Select/unselect tasks to be run",
      "type": "object",
      "description": "Select the tasks you want to SKIP",
      "default": "",
      "help_text": "When true, the specific task will be skipped (not executed)",
      "properties": {
        "skip_antismash": {
          "type": "boolean",
          "description": "Skip (do not run) antismash?",
          "help_text": "If true, the process will be skipped!",
          "hidden": true
        },
        "skip_circos": {
          "type": "boolean",
          "description": "Skip (do not run) circos?",
          "help_text": "If true, the process will be skipped!",
          "hidden": true
        },
        "skip_plasmid_search": {
          "type": "boolean",
          "description": "Skip (do not run) plasmidfinder?",
          "help_text": "If true, the process will be skipped!",
          "hidden": true
        },
        "skip_virulence_search": {
          "type": "boolean",
          "description": "Skip (do not run) virulence factors annotation?",
          "help_text": "If true, the process will be skipped!",
          "hidden": true
        },
        "skip_resistance_search": {
          "type": "boolean",
          "description": "Skip (do not run) resistance genes annotation?",
          "help_text": "If true, the process will be skipped!",
          "hidden": true
        },
        "skip_iceberg_search": {
          "type": "boolean",
          "description": "Skip (do not run) ICEs annotation?",
          "help_text": "If true, the process will be skipped!",
          "hidden": true
        },
        "skip_integron_finder": {
          "type": "boolean",
          "description": "Skip (do not run) integron finder?",
          "help_text": "If true, the process will be skipped!",
          "hidden": true
        },
        "skip_prophage_search": {
          "type": "boolean",
          "description": "Skip (do not run) prophage annotation?",
          "help_text": "If true, the process will be skipped!",
          "hidden": true
        },
        "skip_kofamscan": {
          "type": "boolean",
          "description": "Skip (do not run) KO annotation?",
          "help_text": "If true, the process will be skipped!",
          "hidden": true
        },
        "skip_sourmash": {
          "type": "boolean",
          "description": "Skip (do not run) sourmash tool?",
          "help_text": "If true, the process will be skipped!",
          "hidden": true
        }
      },
      "fa_icon": "fas fa-tasks"
    },
    "configure_thresholds_of_annotation_tasks": {
      "title": "Configure thresholds of annotation tasks",
      "type": "object",
      "description": "Set the minimum thresholds for annotation",
      "default": "",
      "properties": {
        "plasmids_minid": {
          "type": "number",
          "description": "Identity threshold for plasmid annotation",
          "default": 90,
          "minimum": 0,
          "maximum": 100,
          "help_text": "Must be between 0 and 100",
          "hidden": true
        },
        "plasmids_mincov": {
          "type": "number",
          "description": "overage threshold for plasmid annotation",
          "default": 60,
          "minimum": 0,
          "maximum": 100,
          "help_text": "Must be between 0 and 100",
          "hidden": true
        },
        "blast_virulence_minid": {
          "type": "number",
          "description": "Identity threshold for virulence factors annotation",
          "default": 90,
          "minimum": 0,
          "maximum": 100,
          "help_text": "Must be between 0 and 100",
          "hidden": true
        },
        "blast_virulence_mincov": {
          "type": "number",
          "description": "overage threshold for virulence factors annotation",
          "default": 90,
          "minimum": 0,
          "maximum": 100,
          "help_text": "Must be between 0 and 100",
          "hidden": true
        },
        "blast_resistance_minid": {
          "type": "number",
          "description": "Identity threshold for resistance genes annotation",
          "default": 90,
          "minimum": 0,
          "maximum": 100,
          "help_text": "Must be between 0 and 100",
          "hidden": true
        },
        "blast_resistance_mincov": {
          "type": "number",
          "description": "overage threshold for resistance genes annotation",
          "default": 90,
          "minimum": 0,
          "maximum": 100,
          "help_text": "Must be between 0 and 100",
          "hidden": true
        },
        "blast_MGEs_minid": {
          "type": "number",
          "description": "Identity threshold for ICEs and prophages annotation",
          "default": 85,
          "minimum": 0,
          "maximum": 100,
          "help_text": "Must be between 0 and 100",
          "hidden": true
        },
        "blast_MGEs_mincov": {
          "type": "number",
          "description": "overage threshold for ICEs and prophages annotation",
          "default": 85,
          "minimum": 0,
          "maximum": 100,
          "help_text": "Must be between 0 and 100",
          "hidden": true
        }
      },
      "fa_icon": "fas fa-cogs"
    },
    "user_custom_database": {
      "title": "User custom database",
      "type": "object",
      "description": "Set up a custom database for analysis",
      "default": "",
      "fa_icon": "fas fa-cog",
      "properties": {
        "custom_db": {
          "type": "string",
          "description": "Path to the nucleotide FASTA",
          "help_text": "Path to the (properly formatted) nucleotide or protein FASTA file containing the user's custom database for annotation.\nMultiple FASTAs can be provided separated by comma. E.g. db1.fasta,db2.fasta,etc.\n\nCheck out the required header format at: https://bacannot.readthedocs.io/en/latest/custom-db",
          "hidden": true
        },
        "ncbi_proteins": {
          "type": "string",
          "description": "Path to file with NCBI protein IDs",
          "hidden": true
        },
        "blast_custom_minid": {
          "type": "number",
          "description": "Min. identity % for the annotation using user's custom database",
          "default": 65,
          "minimum": 0,
          "maximum": 100,
          "hidden": true
        },
        "blast_custom_mincov": {
          "type": "number",
          "description": "Min. gene/subject coverage % for the annotation using user's custom database",
          "default": 65,
          "minimum": 0,
          "maximum": 100,
          "hidden": true
        }
      }
    },
    "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"
        },
        "get_config": {
          "type": "boolean",
          "description": "Download template config for parameters",
          "fa_icon": "fas fa-question-circle"
        },
        "get_docker_config": {
          "type": "boolean",
          "description": "Download template docker config for containers.",
          "fa_icon": "fas fa-question-circle"
        },
        "get_singularity_config": {
          "type": "boolean",
          "description": "Download template singularity config for containers.",
          "fa_icon": "fas fa-question-circle"
        },
        "get_samplesheet": {
          "type": "boolean",
          "fa_icon": "fas fa-question-circle",
          "description": "Download template samplesheet"
        },
        "bedtools_merge_distance": {
          "type": "number",
          "help_text": "Number of minimum overlapping base pairs required for merging\nNegative values, such as -20, means the number of required overlapping bases for merging.\nPositive values, such as 5, means the maximum distance accepted between features for merging.\nBy default (if Blank), this process is not executed. For execution the user needs to provide a value",
          "description": "Minimum overlapping base pairs required for merging"
        },
        "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."
        },
        "unicycler_version": {
          "type": "string",
          "description": "Select quay.io image tag for tool",
          "default": "0.5.0--py310h6cc9453_3"
        },
        "flye_version": {
          "type": "string",
          "description": "Select quay.io image tag for tool",
          "default": "2.9--py39h6935b12_1",
          "hidden": true,
          "help_text": "Select a different version of tool based on the bioconda containers tag."
        },
        "bakta_version": {
          "type": "string",
          "description": "Select quay.io image tag for tool",
          "default": "1.7.0--pyhdfd78af_1",
          "hidden": true,
          "help_text": "Select a different version of tool based on the bioconda containers tag."
        }
      }
    },
    "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"
        }
      }
    }
  },
  "allOf": [
    {
      "$ref": "#/definitions/download_databases_options"
    },
    {
      "$ref": "#/definitions/input_output_options"
    },
    {
      "$ref": "#/definitions/max_job_request_options"
    },
    {
      "$ref": "#/definitions/prokka_optional_parameters"
    },
    {
      "$ref": "#/definitions/resfinder_optional_process"
    },
    {
      "$ref": "#/definitions/sourmash_optional_parameters"
    },
    {
      "$ref": "#/definitions/select_unselect_tasks_to_be_run"
    },
    {
      "$ref": "#/definitions/configure_thresholds_of_annotation_tasks"
    },
    {
      "$ref": "#/definitions/user_custom_database"
    },
    {
      "$ref": "#/definitions/generic_options"
    },
    {
      "$ref": "#/definitions/institutional_config_options"
    }
  ]
}