nextflow_schema.json

{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/sanger-tol/genomenote/master/nextflow_schema.json",
    "title": "sanger-tol/genomenote pipeline parameters",
    "description": "Creating standarised genome assembly publications",
    "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", "assembly", "biosample_wgs", "binsize", "kmer_size", "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://pipelines.tol.sanger.ac.uk/genomenote/usage#samplesheet-input).",
                    "fa_icon": "fas fa-file-csv"
                },
                "binsize": {
                    "type": "integer",
                    "default": 1000,
                    "description": "Bin size in base pairs for cooler cload"
                },
                "kmer_size": {
                    "type": "integer",
                    "default": 31,
                    "description": "Size for Fastk to create the k-mer library"
                },
                "assembly": {
                    "type": "string",
                    "description": "The Genbank assembly accession for the assembly, for example: GCA_922984935.2."
                },
                "biosample_wgs": {
                    "type": "string",
                    "description": "The biosample accesion(s) linked to the WGS samples in the experiment, for example: SAMEA7520803."
                },
                "biosample_rna": {
                    "type": "string",
                    "description": "The biosample accesion(s) linked to the RNA samples in the experiment, for example: SAMEA7521081."
                },
                "biosample_hic": {
                    "type": "string",
                    "description": "The biosample accesion(s) linked to the Hi-C samples in the experiment, for example: SAMEA7520846."
                },
                "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",
                    "default": "results"
                },
                "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"
                },
                "cool_order": {
                    "type": "string",
                    "format": "file-path",
                    "mimetype": "text/csv",
                    "description": "Path to a file that contains the sequence names in the order you want to represent them on the contact-map.",
                    "help_text": "If not specified, the pipeline will use the sequences in the same order they are listed by the NCI, which follows the karyotype.",
                    "fa_icon": "fas fa-file-lines"
                },
                "write_to_portal": {
                    "type": "boolean",
                    "description": "Flag to control if results are written to genome notes portal database .",
                    "default": false,
                    "fa_icon": "fas far fa-file-code",
                    "hidden": true
                },
                "genome_notes_api": {
                    "type": "string",
                    "description": "URL for Genome Notes Portal API .",
                    "fa_icon": "far fa-file-code"
                },
                "note_template": {
                    "type": "string",
                    "format": "file-path",
                    "description": "The path to a genome note template file.",
                    "help_text": "Set this parameter if you have a genome note template file that you wish to populate. Templates may be docx or xml files",
                    "fa_icon": "fas fa-folder-open"
                },
                "upload_higlass_data": {
                    "type": "boolean",
                    "description": "flag to control if Higlass server should be updated to add new files",
                    "default": false,
                    "fa_icon": "fas far fa-file-code",
                    "hidden": true
                },
                "higlass_url": {
                    "type": "string",
                    "description": "URL for the Higlass server",
                    "hidden": true
                },
                "higlass_upload_directory": {
                    "type": "string",
                    "format": "directory-path",
                    "description": "The ingress directory for the kubernetes cluster running the HiGlass server.",
                    "fa_icon": "fas fa-folder-open",
                    "hidden": true
                },
                "higlass_data_project_dir": {
                    "type": "string",
                    "format": "directory-path",
                    "description": "Subdirectory struture to use for organising HiGlass data, suggested format is <project_name>/<taxon_group> e.g. '/asg/algae'",
                    "fa_icon": "fas fa-folder-open",
                    "hidden": true
                },
                "higlass_kubeconfig": {
                    "type": "string",
                    "format": "file-path",
                    "description": "The path to the kubeconfig  for the kubernetes cluster running the HiGlass server.",
                    "fa_icon": "fas fa-folder-open",
                    "hidden": true
                },
                "higlass_deployment_name": {
                    "type": "string",
                    "description": "Name of the kubernetes deployment for the HiGlass server.",
                    "hidden": true
                },
                "higlass_namespace": {
                    "type": "string",
                    "description": "The name for the namespace used in the Kubernetes cluster running the HiGlass server.",
                    "hidden": true
                },
                "annotation_set": {
                    "type": "string",
                    "format": "file-path",
                    "mimetype": "text/plain",
                    "pattern": "^(?:[\\w/]+/)?\\S+\\.gff3?(?:\\.gz)?$",
                    "description": "Path to annotation file :gff.",
                    "help_text": "You will need to specify the path to the annotation file as eith gff or gff.gz.",
                    "fa_icon": "fas fa-file-code"
                }
            }
        },

        "databases": {
            "title": "Databases",
            "type": "object",
            "description": "Define where the pipeline should find databases.",
            "default": "",
            "properties": {
                "lineage_db": {
                    "type": "string",
                    "format": "directory-path",
                    "description": "Local directory where clade-specific BUSCO lineage datasets are stored.",
                    "fa_icon": "fas fa-folder-open"
                },
                "lineage_tax_ids": {
                    "type": "string",
                    "format": "file-path",
                    "description": "Local file that holds a mapping between BUSCO lineages and taxon IDs.",
                    "help_text": "Initialised from https://busco-data.ezlab.org/v5/data/placement_files/mapping_taxids-busco_dataset_name.eukaryota_odb10.2019-12-16.txt.tar.gz",
                    "fa_icon": "fas fa-file-code"
                }
            },
            "fa_icon": "fas fa-database"
        },
        "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": {
                "fasta": {
                    "type": "string",
                    "format": "file-path",
                    "mimetype": "text/plain",
                    "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
                    "description": "Path to FASTA genome file.",
                    "fa_icon": "far fa-file-code"
                }
            },
            "required": ["fasta"]
        },
        "execution": {
            "title": "Execution",
            "type": "object",
            "description": "Control the execution of the pipeline.",
            "default": "",
            "properties": {
                "use_work_dir_as_temp": {
                    "type": "boolean",
                    "description": "Set to true to make tools (e.g. sort, FastK, MerquryFK) use the work directory for their temporary files, rather than the system default.",
                    "fa_icon": "fas fa-arrow-circle-down",
                    "hidden": true
                }
            },
            "fa_icon": "fas fa-running"
        },
        "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": {
                "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$",
                    "default": "25.MB",
                    "fa_icon": "fas fa-file-upload",
                    "hidden": true
                },
                "monochrome_logs": {
                    "type": "boolean",
                    "description": "Do not use coloured log outputs.",
                    "fa_icon": "fas fa-palette",
                    "hidden": true
                },
                "hook_url": {
                    "type": "string",
                    "description": "Incoming hook URL for messaging service",
                    "fa_icon": "fas fa-people-group",
                    "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.",
                    "hidden": true
                },
                "multiqc_config": {
                    "type": "string",
                    "description": "Custom config file to supply to MultiQC.",
                    "fa_icon": "fas fa-cog",
                    "hidden": true
                },
                "multiqc_logo": {
                    "type": "string",
                    "description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file",
                    "fa_icon": "fas fa-image",
                    "hidden": true
                },
                "multiqc_methods_description": {
                    "type": "string",
                    "description": "Custom MultiQC yaml file containing HTML including a methods description.",
                    "fa_icon": "fas fa-cog",
                    "hidden": true
                },
                "tracedir": {
                    "type": "string",
                    "description": "Directory to keep pipeline Nextflow logs and reports.",
                    "default": "${params.outdir}/pipeline_info/genomenote",
                    "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/databases"
        },
        {
            "$ref": "#/definitions/reference_genome_options"
        },
        {
            "$ref": "#/definitions/execution"
        },
        {
            "$ref": "#/definitions/institutional_config_options"
        },
        {
            "$ref": "#/definitions/max_job_request_options"
        },
        {
            "$ref": "#/definitions/generic_options"
        }
    ]
}