{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/nf-core/epitopeprediction/master/nextflow_schema.json",
    "title": "nf-core/epitopeprediction pipeline parameters",
    "description": "A fully reproducible and state of the art epitope prediction 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": ["input", "outdir"],
            "properties": {
                "input": {
                    "type": "string",
                    "format": "file-path",
                    "mimetype": "text/csv",
                    "pattern": "^\\S+\\.csv$",
                    "schema": "assets/schema_input.json",
                    "description": "Path to comma-separated file containing information about the samples in the experiment.",
                    "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/epitopeprediction/usage#samplesheet-input).",
                    "fa_icon": "fas fa-file-csv"
                },
                "outdir": {
                    "type": "string",
                    "format": "directory-path",
                    "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
                    "fa_icon": "fas fa-folder-open"
                },
                "email": {
                    "type": "string",
                    "description": "Email address for completion summary.",
                    "fa_icon": "fas fa-envelope",
                    "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
                    "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
                },
                "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_options": {
            "title": "Reference options",
            "type": "object",
            "description": "Options for the genome and proteome reference.",
            "fa_icon": "fas fa-stream",
            "properties": {
                "genome_version": {
                    "type": "string",
                    "default": "GRCh37",
                    "help_text": "This defines against which human reference genome the pipeline performs the analysis including the incorporation of genetic variants e.g..",
                    "enum": ["GRCh37", "GRCh38"],
                    "description": "Specifies  the human reference genome version."
                },
                "proteome": {
                    "type": "string",
                    "help_text": "Specifies the reference proteome files that are used for self-filtering. Should be either a folder of FASTA files or a single FASTA file containing the reference proteome(s).",
                    "description": "Specifies the reference proteome."
                }
            }
        },
        "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`."
                }
            }
        },
        "peptide_prediction_options": {
            "title": "Peptide prediction options",
            "type": "object",
            "description": "Options for the peptide prediction step.",
            "fa_icon": "far fa-chart-bar",
            "properties": {
                "filter_self": {
                    "type": "boolean",
                    "description": "Filter against human proteome.",
                    "help_text": "Specifies that peptides should be filtered against the specified human proteome references."
                },
                "max_peptide_length": {
                    "type": "integer",
                    "default": 11,
                    "description": "Specifies the maximum peptide length.",
                    "help_text": "Specifies the maximum peptide length (not applied when `--peptides` is specified). Default: MHC class I: 11 aa, MHC class II: 16 aa"
                },
                "min_peptide_length": {
                    "type": "integer",
                    "default": 8,
                    "description": "Specifies the minimum peptide length.",
                    "help_text": "Specifies the minimum peptide length (not applied when `--peptides` is specified). Default: MCH class I: 8 aa, MHC class II: 15 aa"
                },
                "max_peptide_length_class2": {
                    "type": "integer",
                    "default": 16,
                    "description": "Specifies the maximum peptide length for MHC class II peptides."
                },
                "min_peptide_length_class2": {
                    "type": "integer",
                    "default": 15,
                    "description": "Specifies the minimum peptide length for MHC class II peptides."
                },
                "tools": {
                    "type": "string",
                    "default": "syfpeithi",
                    "help_text": "Specifies the tool(s) to use. Multiple tools can be combined in a list separated by comma.\nAvailable are: `syfpeithi`, `mhcflurry`, `mhcnuggets-class-1`, `mhcnuggets-class-2`,`netmhcpan-4.0`,`netmhcpan-4.1`,`netmhc-4.0`,`netmhciipan-4.1`.",
                    "description": "Specifies the prediction tool(s) to use."
                },
                "tool_thresholds": {
                    "type": "string",
                    "description": "Specifies tool-specific binder thresholds in a JSON file. This can be used to override the given default binder threshold values.",
                    "help_text": "Default thresholds to determine whether a peptide is considered as a binder are the following: `syfpeithi` > 50, `mhcflurry` <=500, `mhcnuggets-class-1` <= 500, `mhcnuggets-class-2` <= 500, `netmhc` <= 2, `netmhcpan` <= 2, `netmhcii` <= 5, `netmhciipan` <= 5. Note that the default threshold for NetMHC tools is based on the rank metric. The remaining predictors thresholds are based on affinities. Thresholds can be customized in a JSON file: `tool-name:value`"
                },
                "use_affinity_thresholds": {
                    "type": "boolean",
                    "description": "Specifies the affinity metric instead of the rank metric used for determining whether a peptide is considered as a binder.",
                    "help_text": "Switches the prediction metric of netMHC tools from rank to affinity. Default: `netmhc` <= 500, `netmhcpan` <= 500, `netmhcii` <= 500, `netmhciipan` <= 500."
                },
                "wild_type": {
                    "type": "boolean",
                    "help_text": "Specifies whether wild-type sequences of mutated peptides should be predicted as well.",
                    "description": "Specifies whether wild-type sequences should be predicted."
                },
                "fasta_output": {
                    "type": "boolean",
                    "description": "Specifies that sequences of proteins, affected by provided variants, will be written to a FASTA file.",
                    "help_text": "Specifies that sequences of proteins that are affected by the provided genomic variants are written to a `FASTA` file. The resulting `FASTA` file will contain the wild-type and mutated protein sequences."
                },
                "show_supported_models": {
                    "type": "boolean",
                    "description": "Writes out supported prediction models.",
                    "help_text": "Writes out supported models. Does not run any predictions."
                }
            }
        },
        "run_optimisation": {
            "title": "Run optimisation",
            "type": "object",
            "description": "Options for optimising the pipeline run execution.",
            "fa_icon": "fas fa-history",
            "properties": {
                "split_by_variants": {
                    "type": "boolean",
                    "description": "Split VCF file into multiple files by number of variants."
                },
                "split_by_variants_size": {
                    "type": "integer",
                    "default": 0,
                    "description": "Number of variants that should be written into one file. Default: number of variants divided by ten"
                },
                "split_by_variants_distance": {
                    "type": "integer",
                    "default": 110000,
                    "description": "Number of nucleotides between previous and current variant across split.",
                    "help_text": "This can be used to avoid that variants end up in separate splits that fall onto the same transcript and therefore potentially contribute to the same mutated protein. "
                },
                "peptides_split_maxchunks": {
                    "type": "integer",
                    "default": 100,
                    "help_text": "Used in combination with `--peptides` or `--proteins`. Maximum number of peptide chunks that will be created for parallelisation.",
                    "description": "Specifies the maximum number of peptide chunks."
                },
                "peptides_split_minchunksize": {
                    "type": "integer",
                    "default": 5000,
                    "help_text": "Used in combination with `--peptides` or `--proteins`: minimum number of peptides that should be written into one chunk.",
                    "description": "Specifies the minimum number of peptides that should be written into one chunk."
                }
            }
        },
        "external_software": {
            "title": "External software",
            "type": "object",
            "description": "External MHC binding prediction software that is not shipped with the pipeline.",
            "default": null,
            "properties": {
                "external_tools_meta": {
                    "type": "string",
                    "default": "${projectDir}/assets/external_tools_meta.json",
                    "description": "Specifies the path to the JSON file with meta information on external prediction tools."
                },
                "netmhc_system": {
                    "type": "string",
                    "default": "linux",
                    "description": "Specifies the operating system in use (Linux or Darwin). This is only necessary if conda is used."
                },
                "netmhcpan_path": {
                    "type": "string",
                    "default": "None",
                    "description": "To use the 'netmhcpan' tool, specify the path to the original software tarball for NetMHCpan 4.0 here."
                },
                "netmhc_path": {
                    "type": "string",
                    "default": "None",
                    "description": "To use the 'netmhc' tool, specify the path to the original software tarball for NetMHC 4.0 here."
                },
                "netmhciipan_path": {
                    "type": "string",
                    "default": "None",
                    "description": "To use the 'netmhciipan' tool, specify the path to the original software tarball for NetMHCIIpan 3.1 here."
                },
                "netmhcii_path": {
                    "type": "string",
                    "default": "None",
                    "description": "To use the 'netmhcii' tool, specify the path to the original software tarball for NetMHCII 2.2 here."
                }
            }
        },
        "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"
                },
                "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": {
                "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/reference_options"
        },
        {
            "$ref": "#/definitions/reference_genome_options"
        },
        {
            "$ref": "#/definitions/peptide_prediction_options"
        },
        {
            "$ref": "#/definitions/run_optimisation"
        },
        {
            "$ref": "#/definitions/external_software"
        },
        {
            "$ref": "#/definitions/institutional_config_options"
        },
        {
            "$ref": "#/definitions/max_job_request_options"
        },
        {
            "$ref": "#/definitions/generic_options"
        }
    ]
}
