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nextflow_schema.json
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nextflow_schema.json
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{
"$schema": "http://json-schema.org/draft-07/schema",
"$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json",
"title": "epi2me-labs/wf-template",
"description": "Nextflow workflow template repository.",
"url": "https://github.com/epi2me-labs/wf-template",
"type": "object",
"definitions": {
"basic_input_output_options": {
"title": "Basic Input/Output Options",
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Define where the pipeline should find input data and save output data.",
"properties": {
"out_dir": {
"type": "string",
"default": "output",
"description": "Directory for output of all user-facing files."
},
"fastq": {
"type": "string",
"format": "path",
"description": "A fastq file or directory containing fastq input files or directories of input files.",
"help_text": "If directories named \\\"barcode*\\\" are found under the `--fastq` directory the data is assumed to be multiplex and each barcode directory will be processed independently. If `.fastq(.gz)` files are found under the `--fastq` directory the sample is assumed to not be multiplexed. In this second case `--samples` should be a simple name rather than a CSV file."
},
"sample": {
"type": "string",
"description": "A sample name for non-multiplexed data. Permissible if passing a file or directory of .fastq(.gz)."
},
"sample_sheet": {
"type": "string",
"description": "CSV file with columns named `barcode`, `sample_name` and `type`. Permissible if passing a directory containing barcodeXX sub-directories."
},
"assembly": {
"type": "boolean",
"description": "Perform assembly with flye.",
"default": true
},
"medaka_options": {
"type": "string",
"description": "Pass through options to medaka."
},
"reference": {
"type": "string",
"description": "The reference genome to use for mapping.",
"enum": [
"MN648051.1",
"MT903344.1",
"ON568298.1",
"ON563414.1"
]
},
"threads": {
"type": "number",
"description": "Number of threads to use.",
"default": 4
},
"sanitize_fastq": {
"type": "boolean",
"description": "Use additional heuristics to identify barcodes from file paths.",
"help_text": "Enabling this option will group together files into samples by the presence of strings of the form `barcodeXXX` present in filenames, rather than simply files grouped into directories (as output by MinKNOW and the Guppy basecaller)."
}
},
"required": [
"fastq"
]
},
"meta_data": {
"title": "Meta Data",
"type": "object",
"description": "",
"default": "",
"properties": {
"report_name": {
"type": "string",
"default": "report",
"description": "Output report filename suffix."
},
"disable_ping": {
"type": "boolean",
"default": "false",
"description": "Enable to prevent sending a workflow ping."
}
}
},
"generic_options": {
"title": "Generic options",
"type": "object",
"fa_icon": "far fa-question-circle",
"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
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/basic_input_output_options"
},
{
"$ref": "#/definitions/meta_data"
},
{
"$ref": "#/definitions/generic_options"
}
],
"properties": {
"process_label": {
"type": "string",
"description": "The main process label for template processes to use by default",
"hidden": true,
"default": "wf-mpx"
},
"aws_image_prefix": {
"type": "string",
"hidden": true
},
"aws_queue": {
"type": "string",
"hidden": true
},
"wfversion": {
"type": "string",
"default": "v0.0.2",
"hidden": true
},
"monochrome_logs": {
"type": "boolean"
},
"validate_params": {
"type": "boolean",
"default": true
},
"show_hidden_params": {
"type": "boolean"
}
},
"docs": {
"intro": "## Introduction\n\nThis workflow provides a simple way to analyse Monkeypox sequencing data; taking raw Oxford Nanopore Technologies reads and creating a draft consensus and assembly. No trimming of sequences is carried out so be vigilant when using targeted data.\n",
"links": "## Useful links\n\n* [nextflow](https://www.nextflow.io/)\n* [docker](https://www.docker.com/products/docker-desktop)\n* [conda](https://docs.conda.io/en/latest/miniconda.html)\n"
}
}