nextflow_schema.json

{
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "$id": "https://raw.githubusercontent.com/sanger-tol/genomeassembly/master/nextflow_schema.json",
    "title": "sanger-tol/genomeassembly pipeline parameters",
    "description": "A bioinformatics best-practice analysis pipeline for genome assembly from PacBio CCS and HiC reads",
    "type": "object",
    "$defs": {
        "input_output_options": {
            "title": "Input/output options",
            "type": "object",
            "fa_icon": "fas fa-terminal",
            "description": "Define where the pipeline should find input data and save output data.",
            "required": ["genomic_data", "assembly_specs"],
            "properties": {
                "genomic_data": {
                    "type": "string",
                    "description": "Input YAML specifying the location of all genomic data for assembly. See the documentation for a full specification.",
                    "format": "file-path",
                    "schema": "assets/schema_genomic.json"
                },
                "assembly_specs": {
                    "type": "string",
                    "description": "YAML file specifying the parameters for a set of assemblies, including datasets and arguments. See the documentation for a full specification.",
                    "format": "file-path",
                    "schema": "assets/schema_assembly.json"
                },
                "outdir": {
                    "type": "string",
                    "format": "directory-path",
                    "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
                    "fa_icon": "fas fa-folder-open"
                },
                "email": {
                    "type": "string",
                    "description": "Email address for completion summary.",
                    "fa_icon": "fas fa-envelope",
                    "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
                    "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
                }
            }
        },
        "input_preparation_options": {
            "title": "Input preparation options",
            "type": "object",
            "description": "Options to control input preparation prior to starting assembly.",
            "default": "",
            "properties": {
                "kmer_size": {
                    "type": "integer",
                    "default": 31,
                    "description": "Kmer size to use for all kmer-based subroutines in the Kmer profiling subworkflow. This parameter is overridden by the provided kmer size for a given input read set if a FastK database is provided."
                },
                "genomescope_args": {
                    "type": "string",
                    "description": "Optional command-line arguments to pass to genomescope2."
                },
                "save_fastk_databases": {
                    "type": "boolean",
                    "description": "Save the FastK databases generated by the pipeline to the output directory."
                }
            },
            "fa_icon": "fas fa-signal"
        },
        "purging_options": {
            "title": "Purging options",
            "type": "object",
            "description": "Options to contol the purging of duplicated haplotigs from an assembly.",
            "default": "",
            "properties": {
                "purging_reads_chunk_size": {
                    "type": "integer",
                    "default": 500000,
                    "description": "How many reads to map in a single chunk when mapping reads to the primary assembly during purging."
                },
                "ont_minimap2_map_mode": {
                    "type": "string",
                    "default": "map-ont",
                    "description": "Which minimap2 mapping mode to use when mapping ONT? See https://lh3.github.io/minimap2/minimap2.html for a full list."
                }
            },
            "required": ["purging_reads_chunk_size", "ont_minimap2_map_mode"]
        },
        "polishing_options": {
            "title": "Polishing options",
            "type": "object",
            "description": "Options to control polishing an assembly.",
            "default": "",
            "properties": {
                "polishing_longranger_container_path": {
                    "type": "string",
                    "description": "Path to a container with longranger to use for the longranger processes. Required for polishing to run."
                },
                "polishing_n_chunks_bed": {
                    "type": "integer",
                    "default": 100,
                    "description": "Number of chunks to split assembly into for polishing."
                }
            }
        },
        "hi_c_mapping_and_scaffolding_options": {
            "title": "Hi-C mapping and scaffolding options",
            "type": "object",
            "description": "Options to control the mapping of Hi-C reads and scaffolding of an assembly.",
            "default": "",
            "properties": {
                "hic_aligner": {
                    "type": "string",
                    "default": "bwamem2",
                    "enum": ["bwamem2", "minimap2"],
                    "description": "Which aligner to use to align Hi-C reads to the reference"
                },
                "hic_mapping_cram_chunk_size": {
                    "type": "integer",
                    "default": 10000,
                    "description": "Number of CRAM slices to include per CRAM file per mapping chunk. Lower values mean more Hi-C mapping jobs are spawned, but each should have a lower run time."
                },
                "hic_mapping_minq": {
                    "type": "integer",
                    "default": 10,
                    "description": "Minimum MapQ score for a Hi-C read to be retained for scaffolding."
                },
                "scaffolding_cool_bin_size": {
                    "type": "integer",
                    "default": 1000,
                    "description": "Bin size to use when building cooler contact maps."
                }
            }
        },
        "assembly_qc_options": {
            "title": "Assembly QC options",
            "type": "object",
            "description": "Parameters to configure the assembly QC steps that run for each assembly generated.",
            "default": "",
            "properties": {
                "busco_lineage_directory": {
                    "type": "string",
                    "description": "Path to a local directory containing pre-downloade BUSCO lineages.",
                    "help_text": "Lineage datasets can be downloaded using `busco --download`.",
                    "format": "directory-path"
                }
            }
        },
        "organelle_assembly_options": {
            "title": "Organelle assembly options",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "mitohifi_min_ref_len": {
                    "type": "integer",
                    "default": 15000,
                    "description": "The minimum size of a reference organellar genome to use in reference-based organelle assembly with Mitohifi"
                }
            },
            "required": ["mitohifi_min_ref_len"]
        },
        "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"
                }
            }
        },
        "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": {
                "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
                },
                "monochrome_logs": {
                    "type": "boolean",
                    "description": "Do not use coloured log outputs.",
                    "fa_icon": "fas fa-palette",
                    "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
                },
                "pipelines_testdata_base_path": {
                    "type": "string",
                    "fa_icon": "far fa-check-circle",
                    "description": "Base URL or local path to location of pipeline test dataset files",
                    "default": "https://raw.githubusercontent.com/nf-core/test-datasets/",
                    "hidden": true
                },
                "trace_report_suffix": {
                    "type": "string",
                    "fa_icon": "far calendar",
                    "description": "Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.",
                    "hidden": true
                },
                "help": {
                    "type": ["boolean", "string"],
                    "description": "Display the help message."
                },
                "help_full": {
                    "type": "boolean",
                    "description": "Display the full detailed help message."
                },
                "show_hidden": {
                    "type": "boolean",
                    "description": "Display hidden parameters in the help message (only works when --help or --help_full are provided)."
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/$defs/input_output_options"
        },
        {
            "$ref": "#/$defs/input_preparation_options"
        },
        {
            "$ref": "#/$defs/purging_options"
        },
        {
            "$ref": "#/$defs/polishing_options"
        },
        {
            "$ref": "#/$defs/hi_c_mapping_and_scaffolding_options"
        },
        {
            "$ref": "#/$defs/assembly_qc_options"
        },
        {
            "$ref": "#/$defs/organelle_assembly_options"
        },
        {
            "$ref": "#/$defs/institutional_config_options"
        },
        {
            "$ref": "#/$defs/generic_options"
        }
    ]
}