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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": "genomiqueens/wf-toulligqc",
"description": "Nextflow workflow template repository.",
"demo_url": "https://github.com/GenomiqueENS/wf-toulligqc/raw/main/demo_data/wf-toulligqc-demo.tar.gz",
"aws_demo_url": "https://github.com/GenomiqueENS/wf-toulligqc/raw/main/demo_data/demo.nextflow.config",
"url": "https://github.com/GenomiqueENS/wf-toulligqc",
"type": "object",
"definitions": {
"input": {
"title": "Input Options",
"type": "object",
"fa_icon": "fas fa-arrow-right",
"description": "Parameters for finding and handling input data for analysis.",
"properties": {
"input_files": {
"type": "string",
"description": "Note that fastq/ bam only QC will result in some missing data and will significantly increase the running time",
"enum": [
"sequencing_summary only",
"sequencing_summary + telemetry_source",
"telemetry_source + fast5",
"fastq/ bam only"
],
"default": "sequencing_summary only"
}
},
"required": [
"input_files"
]
},
"samples": {
"title": "Sample Options",
"type": "object",
"fa_icon": "fas fa-vials",
"description": "Parameters that relate to input files for QC.",
"properties": {
"sequencing_summary_source": {
"type": "string",
"format": "file-path",
"description": "Basecaller sequencing summary source, can be compressed with gzip (.gz) or bzip2 (.bz2)",
"help_text": "",
"demo_data": "demo_data/sequencing_summary.txt"
},
"telemetry_source": {
"type": "string",
"format": "file-path",
"description": "Basecaller telemetry file source, can be compressed with gzip (.gz) or bzip2 (.bz2)",
"help_text": "",
"demo_data": "demo_data/sequencing_telemetry.js"
},
"fast5_source": {
"type": "string",
"format": "file-path",
"description": "Fast5 file source",
"help_text": "Necessary if no telemetry file"
},
"fastq_source": {
"type": "string",
"format": "file-path",
"description": "FASTQ file source",
"help_text": "Necessary if no sequencing summary file"
},
"bam_source": {
"type": "string",
"format": "file-path",
"description": "BAM file source",
"help_text": "Necessary if no sequencing summary file"
}
},
"anyOf": [
{
"required": [
"sequencing_summary_source"
]
},
{
"required": [
"telemetry_source"
]
},
{
"required": [
"fast5_source"
]
},
{
"required": [
"fastq_source"
]
},
{
"required": [
"bam_source"
]
}
]
},
"barcoding": {
"title": "Barcoding Options",
"type": "object",
"fa_icon": "fas fa-arrow-left",
"description": "Parameters for barcoded samples ",
"properties": {
"barcoding": {
"type": "boolean",
"default": false,
"description": "Option for barcode usage."
},
"barcodes": {
"type": "string",
"description": "Coma separated barcode list (e.g. BC05,RB09,NB01,barcode10)"
},
"barcoding_summary_pass": {
"type": "string",
"format": "file-path",
"description": "Basecaller barcoding summary source of passed reads, can be compressed with gzip (.gz) or bzip2 (.bz2).",
"help_text": ""
},
"barcoding_summary_fail": {
"type": "string",
"format": "file-path",
"description": "Basecaller barcoding summary source of failed reads, can be compressed with gzip (.gz) or bzip2 (.bz2)",
"help_text": ""
}
}
},
"output": {
"title": "Output Options",
"type": "object",
"fa_icon": "fas fa-arrow-left",
"description": "Parameters for saving and naming workflow outputs.",
"properties": {
"out_dir": {
"type": "string",
"default": "output",
"format": "directory-path",
"description": "Directory for output of all workflow results."
}
}
},
"advanced_options": {
"title": "Advanced Options",
"type": "object",
"description": "Advanced options for configuring processes inside the workflow.",
"help_text": "These advanced options do not need to be changed for typical use, but allow fine tuning of workflows for users who want more control over the workflow.",
"properties": {
"report_name": {
"type": "string",
"description": "report_name.",
"help_text": "."
},
"disable_ping": {
"type": "boolean",
"default": false,
"description": "Enable to prevent sending a workflow ping."
},
"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
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/input"
},
{
"$ref": "#/definitions/samples"
},
{
"$ref": "#/definitions/output"
},
{
"$ref": "#/definitions/advanced_options"
}
],
"properties": {
"process_label": {
"type": "string",
"description": "The main process label for template processes to use by default",
"hidden": true,
"default": "wf-template"
},
"aws_image_prefix": {
"type": "string",
"hidden": true
},
"aws_queue": {
"type": "string",
"hidden": true
},
"monochrome_logs": {
"type": "boolean"
},
"validate_params": {
"type": "boolean",
"default": true
},
"show_hidden_params": {
"type": "boolean"
}
},
"docs": {
"intro": "## Introduction\n\nThis section of documentation typically contains an overview of the workflow in terms of motivation\nand bioinformatics methods, listing any key tools or algorithms employed, whilst also describing its\nrange of use-cases and what a suitable input dataset should look like.\n\n",
"links": "## Useful links\n\n* [nextflow](https://www.nextflow.io/)\n* [docker](https://www.docker.com/products/docker-desktop)\n* [singularity](https://docs.sylabs.io/guides/latest/user-guide/)\n"
}
}