nextflow_schema.json

{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/nf-core/mpxvassembly/master/nextflow_schema.json",
    "title": "nf-core/mpxvassembly pipeline parameters",
    "description": "A workflow for filtering, trimming, and QC of mpx samples. From raw fastq to consensus and de-novo based as",
    "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": [
                "outdir",
                "fasta",
                "gff",
                "kraken_db",
                "workflow"
            ],
            "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/mpxvassembly/usage#samplesheet-input).",
                    "fa_icon": "fas fa-file-csv"
                },
                "indir": {
                    "type": "string",
                    "format": "directory-path",
                    "description": "An input directory where the samples are located.  Use if you want the pipeline to create your samplesheet. You have to use absolute paths to storage on Cloud infrastructure.",
                    "fa_icon": "fas fa-folder-open"
                },
                "sra": {
                    "type": "boolean",
                    "format": "boolean",
                    "description": "True/False if using SRA accessions",
                    "fa_icon": "fas fa-folder-open"
                },
                "sra_ids": {
                    "type": "string",
                    "format": "file-path",
                    "schema": "assets/schema_input.json",
                    "description": "Path to file with simple list of SRA Accessions",
                    "help_text": "Create a file with a list of SRA Accessions",
                    "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"
                },
                "paired": {
                    "type": "boolean",
                    "description": "True if reads are paired-end, false if reads are single.",
                    "fa_icon": "fas fa-down-left-and-up-right-to-center"
                },
                "project_name": {
                    "type": "string",
                    "description": "A name for the run (will be the prefix of samplesheet.csv).",
                    "fa_icon": "fas fa-file-signature"
                },
                "file_levels": {
                    "type": "string",
                    "pattern": "top|nested",
                    "description": "Whether fq files are in directory top level, nested one level under, or both.",
                    "fa_icon": "fas fa-file-signature"
                },
                "workflow": {
                    "type": "string",
                    "description": "Choose from: read_filter, ref_based, denovo, full.",
                    "fa_icon": "fas fa-map"
                },
                "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_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.",
                    "help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.",
                    "fa_icon": "far fa-file-code"
                }
            }
        },
        "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
                },
                "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$",
                    "default": "25.MB",
                    "fa_icon": "fas fa-file-upload",
                    "hidden": true
                },
                "monochrome_logs": {
                    "type": "boolean",
                    "description": "Do not use coloured log outputs.",
                    "fa_icon": "fas fa-palette",
                    "hidden": true
                },
                "multiqc_config": {
                    "type": "string",
                    "description": "Custom config file to supply to MultiQC.",
                    "fa_icon": "fas fa-cog",
                    "hidden": true
                },
                "tracedir": {
                    "type": "string",
                    "description": "Directory to keep pipeline Nextflow logs and reports.",
                    "default": "${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."
                },
                "enable_conda": {
                    "type": "boolean",
                    "description": "Run this workflow with Conda. You can also use '-profile conda' instead of providing this parameter.",
                    "hidden": true,
                    "fa_icon": "fas fa-bacon"
                },
                "workflow": {
                    "type": "string",
                    "description": "Define which entrypoint you wish to run in the workflow, options include filter_reads,ref_based,denovo, and full",
                    "hidden": true,
                    "fa_icon": "fas fa-bacon"
                },
                "gff": {
                    "type": "string",
                    "default": null
                },
                "filter": {
                    "type": "boolean",
                    "default": null,
                    "help_text": "true/false for whether or not to filter variants from IVAR Variant to coordinates specified by the coords parameter."
                },
                "kraken_db": {
                    "type": "string",
                    "default": null,
                    "help_text": "By default, this parameter uses a DB that includes one MPOX Clade IIb sample and human (GRCh38), if you would like to specify an alternative db, you also need to also modify the kraken2_tax_ids parameter so that it points to a file with your desired NCBI Tax IDs (https://www.ncbi.nlm.nih.gov/taxonomy) for filtering at the seqtk step"
                },
                "kraken2_tax_ids": {
                    "type": "string",
                    "default": null,
                    "help_text": "By default, this parameter filters NCBI Tax IDs (https://www.ncbi.nlm.nih.gov/taxonomy) for all Refseq genomes within the Orthopox Genus, as well as MPOX. If you supply a different Kraken DB than the one set by default, make sure this file contains the Tax IDs you would like to retain."

                },
                "altQ_cutoff": {
                    "type": "integer",
                    "default": null,
                    "help_text": "Quality score threshold of alternative allele for a SNP to be retained during variant filtering"
                },
                "altDP_cutoff": {
                    "type": "integer",
                    "default": null,
                    "help_text": "Sequencing depth threshold of alternative allele for a SNP to be retained during variant filtering"

                },
                "DP_cutoff": {
                    "type": "integer",
                    "default": null,
                    "help_text": "Sequencing depth threshold of reference allele for a SNP to be retained during variant filtering"

                },
                "af_cutoff": {
                    "type": "number",
                    "default": null,
                    "help_text": "Allele frequency threshold of reference allele for a SNP to be retained during variant filtering. Should be decimal like 0.05 for 5%"

                },
                "fai": {
                    "type": "string",
                    "default": null
                },
                "coords": {
                    "type": "string",
                    "default": null,
                    "help_text": "List of four strings such as 1111,2222,3333,4444 representing coordinates in the genome used for filtering. Currently the pipeline conducts SNP filtering based on two regions, given by Region1 Start, Region1 End, Region2 Start, Region2 End."

                },
                "locus1_name": {
                    "type": "string",
                    "default": null,
                    "help_text": "Name of your first locus used for variant filtering. Can be left blank if not running ref_based or full entrypoints"

                },
                "locus2_name": {
                    "type": "string",
                    "default": null,
                    "help_text": "Name of your second locus used for variant filtering. Can be left blank if not running ref_based or full entrypoints"

                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/input_output_options"
        },
        {
            "$ref": "#/definitions/reference_genome_options"
        },
        {
            "$ref": "#/definitions/institutional_config_options"
        },
        {
            "$ref": "#/definitions/max_job_request_options"
        },
        {
            "$ref": "#/definitions/generic_options"
        }
    ]
}