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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": ". pipeline parameters",
"description": "",
"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",
"description": "Directory containing fastq input files. May contain fastq files directly or directories name barcodeXX relating to independent samples."
},
"samples": {
"type": "string",
"description": "CSV file with columns named `barcode`, `sample_id`, and `type`, where type can be `test_sample` or `no_template_control`. (or simply a sample name for non-multiplexed data)"
},
"genotype_variants": {
"type": "string",
"description": "Report genotyping information for scheme's known variants of interest, optionally provide file path as argument."
},
"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"
]
},
"primer_scheme_selection": {
"title": "Primer Scheme Selection",
"type": "object",
"fa_icon": "fas fa-code",
"description": "Reference genome related files and options required for the workflow.",
"properties": {
"scheme_name": {
"type": "string",
"default": "SARS-CoV-2",
"description": "Scheme name.",
"enum": [
"SARS-CoV-2",
"spike-seq"
]
},
"scheme_version": {
"type": "string",
"default": "V3",
"description": "Scheme version.",
"enum": [
"V1",
"V2",
"V3",
"V4",
"V4.1",
"V1200"
]
}
}
},
"meta_data": {
"title": "Meta Data",
"type": "object",
"description": "",
"default": "",
"properties": {
"report_name": {
"type": "string",
"default": "report",
"description": "Output report filename suffix."
},
"lab_id": {
"type": "string",
"description": "Laboratory identifier, used in reporting."
},
"testkit": {
"type": "string",
"description": "Test kit identifier, used in reporting."
}
}
},
"advanced_options": {
"title": "Advanced options",
"type": "object",
"description": "Data filtering and algorithm options",
"default": "",
"properties": {
"min_len": {
"type": "number",
"description": "Minimum read length (default: set by scheme)."
},
"max_len": {
"type": "number",
"description": "Maximum read length (default: set by scheme)."
},
"max_softclip_length": {
"type": "integer",
"description": "Remove reads with alignments showing large softclipping"
},
"medaka_model": {
"type": "string",
"default": "r941_prom_variant_g360",
"description": "Medaka model name.",
"enum": [
"r103_fast_variant_g507",
"r103_hac_variant_g507",
"r103_prom_variant_g3210",
"r103_sup_variant_g507",
"r941_min_fast_variant_g507",
"r941_min_hac_variant_g507",
"r941_min_sup_variant_g507",
"r941_prom_fast_variant_g507",
"r941_prom_hac_variant_g507",
"r941_prom_sup_variant_g507",
"r941_prom_variant_g303",
"r941_prom_variant_g322",
"r941_prom_variant_g360"
],
"help_text": "The correct medaka model to use is determined by the Guppy basecaller version, see [Medaka Models](https://github.com/nanoporetech/medaka#models) for more information."
}
},
"fa_icon": "fas fa-cogs"
},
"reporting_options": {
"title": "Reporting Options",
"type": "object",
"description": "Options controlling report outputs",
"default": "",
"properties": {
"report_depth": {
"type": "integer",
"default": 100,
"description": "Min. depth for percentage coverage. (e.g. 89% genome covered at > `report_depth`)",
"minimum": 0,
"maximum": 100
},
"report_clade": {
"type": "boolean",
"default": true,
"description": "Show results of Nextclade analysis in report."
},
"report_coverage": {
"type": "boolean",
"default": true,
"description": "Show genome coverage traces in report."
},
"report_lineage": {
"type": "boolean",
"default": true,
"description": "Show results of Pangolin analysis in report."
},
"report_variant_summary": {
"type": "boolean",
"default": true,
"description": "Show / hide variant information in report."
},
"report_detailed": {
"type": "boolean",
"default": false,
"description": "Show / hide some extra plots for detailed batch analysis."
}
},
"fa_icon": "fas fa-address-card",
"help_text": ""
},
"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/primer_scheme_selection"
},
{
"$ref": "#/definitions/meta_data"
},
{
"$ref": "#/definitions/advanced_options"
},
{
"$ref": "#/definitions/reporting_options"
},
{
"$ref": "#/definitions/generic_options"
}
],
"properties": {
"aws_image_prefix": {
"type": "string",
"hidden": true
},
"aws_queue": {
"type": "string",
"hidden": true
},
"wfversion": {
"type": "string",
"default": "v0.3.9",
"hidden": true
},
"pangolin_version": {
"type": "string",
"default": "3.1.16-0.3.9",
"hidden": true
},
"_min_len": {
"type": "string",
"hidden": true
},
"_max_len": {
"type": "string",
"hidden": true
},
"_max_softclip_length": {
"type": "string",
"hidden": true
},
"full_scheme_name": {
"type": "string",
"hidden": true
},
"monochrome_logs": {
"type": "boolean"
},
"validate_params": {
"type": "boolean",
"default": true
},
"show_hidden_params": {
"type": "boolean"
}
}
}