{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/nf-core/bactmap/master/nextflow_schema.json",
    "title": "nf-core/bactmap pipeline parameters",
    "description": "A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences",
    "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"
            ],
            "properties": {
                "input": {
                    "type": "string",
                    "fa_icon": "fas fa-file",
                    "description": "Path to a sample sheet describing paths to input fastq files"
                },
                "outdir": {
                    "type": "string",
                    "description": "The output directory where the results will be saved.",
                    "default": "./results",
                    "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})$"
                }
            }
        },
        "compulsory_parameters": {
            "title": "Compulsory parameters",
            "type": "object",
            "description": "",
            "default": "",
            "fa_icon": "fas fa-exclamation-circle",
            "properties": {
                "reference": {
                    "type": "string",
                    "fa_icon": "fas fa-file",
                    "description": "Path to a fasta file of the reference sequence"
                }
            },
            "required": [
                "reference"
            ]
        },
        "optional_pipeline_steps": {
            "title": "Optional pipeline steps",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "trim": {
                    "type": "boolean",
                    "default": true,
                    "description": "Trim reads",
                    "fa_icon": "fas fa-cut"
                },
                "save_trimmed_fail": {
                    "type": "boolean",
                    "description": "Saved failed read files after trimminng",
                    "fa_icon": "fas fa-cut"
                },
                "adapter_file": {
                    "type": "string",
                    "default": "${baseDir}/assets/adapters.fas",
                    "fa_icon": "fas fa-cut",
                    "description": "path to file containing adapters in fasta format"
                },
                "subsampling_off": {
                    "type": "boolean",
                    "description": "Turn off subsampling",
                    "fa_icon": "fas fa-angle-double-down"
                },
                "subsampling_depth_cutoff": {
                    "type": "integer",
                    "default": 100,
                    "description": "Desired coverage depth when subsampling",
                    "fa_icon": "fas fa-angle-double-down"
                },
                "genome_size": {
                    "type": "string",
                    "description": "Specify genome size for subsampling rather than estimation using mash sketch",
                    "fa_icon": "fas fa-arrows-alt-h"
                },
                "remove_recombination": {
                    "type": "boolean",
                    "description": "Remove recombination using gubbins",
                    "fa_icon": "fas fa-exchange-alt"
                },
                "non_GATC_threshold": {
                    "type": "number",
                    "default": 0.5,
                    "fa_icon": "fas fa-percent",
                    "description": "Maximum non GATC bases (i.e - and N) to allow in pseudogenome sequences"
                },
                "rapidnj": {
                    "type": "boolean",
                    "description": "Build a tree using the RapidNJ neighbour-joining algorithm",
                    "fa_icon": "fas fa-tree"
                },
                "fasttree": {
                    "type": "boolean",
                    "description": "Build a tree using the FastTree approximate ML algorithm",
                    "fa_icon": "fas fa-tree"
                },
                "iqtree": {
                    "type": "boolean",
                    "description": "Build a tree using the IQ-TREE ML algorithm",
                    "fa_icon": "fas fa-tree"
                },
                "raxmlng": {
                    "type": "boolean",
                    "description": "Build a tree using the RAxML-NG ML algorithm",
                    "fa_icon": "fas fa-tree"
                }
            },
            "fa_icon": "fas fa-project-diagram"
        },
        "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.",
                    "hidden": true,
                    "fa_icon": "fas fa-question-circle"
                },
                "publish_dir_mode": {
                    "type": "string",
                    "default": "copy",
                    "hidden": true,
                    "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"
                    ]
                },
                "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})$",
                    "hidden": true,
                    "help_text": "This works exactly as with `--email`, except emails are only sent if the workflow is not successful."
                },
                "plaintext_email": {
                    "type": "boolean",
                    "description": "Send plain-text email instead of HTML.",
                    "fa_icon": "fas fa-remove-format",
                    "hidden": true,
                    "help_text": "Set to receive plain-text e-mails instead of HTML formatted."
                },
                "monochrome_logs": {
                    "type": "boolean",
                    "description": "Do not use coloured log outputs.",
                    "fa_icon": "fas fa-palette",
                    "hidden": true,
                    "help_text": "Set to disable colourful command line output and live life in monochrome."
                },
                "tracedir": {
                    "type": "string",
                    "description": "Directory to keep pipeline Nextflow logs and reports.",
                    "default": "${params.outdir}/pipeline_info",
                    "fa_icon": "fas fa-cogs",
                    "hidden": true
                },
                "singularity_pull_docker_container": {
                    "type": "boolean",
                    "description": "Instead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead.",
                    "fa_icon": "fab fa-docker",
                    "hidden": true
                },
                "max_multiqc_email_size": {
                    "type": "string",
                    "default": "25.MB",
                    "fa_icon": "fas fa-envelope",
                    "description": "NOT USED: File size limit when attaching MultiQC reports to summary emails.",
                    "hidden": true
                },
                "skip_multiqc": {
                    "type": "boolean",
                    "fa_icon": "fas fa-fast-forward",
                    "description": "NOT USED: Skip MultiQC",
                    "hidden": true
                },
                "multiqc_config": {
                    "type": "string",
                    "description": "Custom config file to supply to MultiQC.",
                    "fa_icon": "fas fa-cog",
                    "hidden": true
                },
                "multiqc_title": {
                    "type": "string",
                    "hidden": true,
                    "fa_icon": "fas fa-signature",
                    "description": "Custom title for the MultiQC report."
                },
                "enable_conda": {
                    "type": "boolean",
                    "fa_icon": "fas fa-laptop-code",
                    "description": "enable conda rather than use containers"
                },
                "validate_params": {
                    "type": "boolean",
                    "default": true,
                    "fa_icon": "fas fa-tasks",
                    "description": "Boolean whether to validate parameters against the schema at runtime"
                },
                "show_hidden_params": {
                    "type": "boolean",
                    "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.",
                    "description": "Show all params when using `--help`",
                    "fa_icon": "fas fa-eye-slash"
                }
            }
        },
        "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": 4,
                    "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": "16.GB",
                    "fa_icon": "fas fa-memory",
                    "pattern": "^[\\d\\.]+\\s*.(K|M|G|T)?B$",
                    "hidden": true,
                    "help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`"
                },
                "max_time": {
                    "type": "string",
                    "description": "Maximum amount of time that can be requested for any single job.",
                    "default": "240.h",
                    "fa_icon": "far fa-clock",
                    "pattern": "^[\\d\\.]+\\.*(s|m|h|d)$",
                    "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'`"
                }
            }
        },
        "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",
                    "help_text": "Provide git commit id for custom Institutional configs hosted at `nf-core/configs`. This was implemented for reproducibility purposes. Default: `master`.\n\n```bash\n## Download and use config file with following git commit id\n--custom_config_version d52db660777c4bf36546ddb188ec530c3ada1b96\n```"
                },
                "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 the `custom_config_base` option. For example:\n\n```bash\n## Download and unzip the config files\ncd /path/to/my/configs\nwget https://github.com/nf-core/configs/archive/master.zip\nunzip master.zip\n\n## Run the pipeline\ncd /path/to/my/data\nnextflow run /path/to/pipeline/ --custom_config_base /path/to/my/configs/configs-master/\n```\n\n> Note that the nf-core/tools helper package has a `download` command to download all required pipeline files + singularity containers + institutional configs in one go for you, to make this process easier.",
                    "fa_icon": "fas fa-users-cog"
                },
                "hostnames": {
                    "type": "string",
                    "description": "Institutional configs hostname.",
                    "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": [
        {
            "$ref": "#/definitions/input_output_options"
        },
        {
            "$ref": "#/definitions/compulsory_parameters"
        },
        {
            "$ref": "#/definitions/optional_pipeline_steps"
        },
        {
            "$ref": "#/definitions/generic_options"
        },
        {
            "$ref": "#/definitions/max_job_request_options"
        },
        {
            "$ref": "#/definitions/institutional_config_options"
        }
    ]
}
