103 lines
3.7 KiB
JSON
103 lines
3.7 KiB
JSON
{
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"$schema": "http://json-schema.org/draft-07/schema",
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"$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json",
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"title": ". pipeline parameters",
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"description": "",
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"type": "object",
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"definitions": {
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"basic_input_output_options": {
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"title": "Basic Input/Output Options",
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"type": "object",
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"fa_icon": "fas fa-terminal",
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"description": "Define where the pipeline should find input data and save output data.",
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"properties": {
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"out_dir": {
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"type": "string",
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"default": "output",
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"description": "Directory for output of all user-facing files."
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},
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"fastq": {
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"type": "string",
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"description": "Directory containing fastq input files. May contain fastq files directly or directories name barcodeXX relating to independent samples."
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},
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"samples": {
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"type": "string",
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"description": "CSV file with columns named `barcode` and `sample_name`. (or simply a sample name for non-multiplexed data)"
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},
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"sanitize_fastq": {
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"type": "boolean",
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"description": "Use additional heuristics to identify barcodes from file paths.",
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"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)."
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}
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},
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"required": [
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"fastq"
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]
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},
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"meta_data": {
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"title": "Meta Data",
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"type": "object",
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"description": "",
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"default": "",
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"properties": {
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"report_name": {
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"type": "string",
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"default": "report",
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"description": "Output report filename suffix."
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}
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}
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},
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"generic_options": {
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"title": "Generic options",
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"type": "object",
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"fa_icon": "far fa-question-circle",
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"description": "Less common options for the pipeline, typically set in a config file.",
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"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`.",
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"properties": {
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"help": {
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"type": "boolean",
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"description": "Display help text.",
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"fa_icon": "fas fa-question-circle",
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"hidden": true
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}
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}
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}
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},
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"allOf": [
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{
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"$ref": "#/definitions/basic_input_output_options"
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},
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{
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"$ref": "#/definitions/meta_data"
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},
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{
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"$ref": "#/definitions/generic_options"
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}
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],
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"properties": {
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"aws_image_prefix": {
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"type": "string",
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"hidden": true
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},
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"aws_queue": {
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"type": "string",
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"hidden": true
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},
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"wfversion": {
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"type": "string",
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"default": "v0.3.3",
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"hidden": true
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},
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"monochrome_logs": {
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"type": "boolean"
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},
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"validate_params": {
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"type": "boolean",
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"default": true
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},
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"show_hidden_params": {
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"type": "boolean"
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}
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}
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}
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