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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/Zymo-Research/aladdin-bisulfitebolt/main/nextflow_schema.json",
"title": "Zymo-Research/aladdin-bisulfitebolt pipeline parameters",
"description": "Bisulfitebolt analysis pipeline, part of the Aladdin Bioinformatics Platform pipeline catalog.",
"type": "object",
"custom_request": true,
"custom_request_instruction": "Please provide as much detail as possible for your request. For example, a request for a reference genome should include links to the genome and its annotations.",
"definitions": {
"input_output_options": {
"title": "Input/output options",
"type": "object",
"description": "Define where the pipeline should find input data and save output data",
"properties": {
"design": {
"type": "string",
"description": "Path to a design CSV file with sample & group labels, and paths to reads files",
"hidden": true
},
"outdir": {
"type": "string",
"description": "The output directory where the results will be saved",
"default": "./results",
"hidden": true
},
"project": {
"type": "string",
"description": "The file name of multiqc report",
"hidden": true
}
},
"required": [
"design"
]
},
"reference_genome_options": {
"title": "Reference genome options",
"type": "object",
"description": "Options for the reference genome indices used to align reads",
"default": "",
"properties": {
"genome": {
"type": "string",
"description": "Reference genome used to align reads.",
"enum": ["hg38",
"mm10"]
}
},
"required": [
"genome"
]
},
"read_trimming_options": {
"title": "Read trimming options",
"type": "object",
"description": "Options to adjust read trimming criteria",
"properties": {
"adapter_first_read": {
"type": "string",
"description": "Sequence of an adapter ligated to the 3' end (paired data: of the first read). The adapter and subsequent bases are trimmed.",
"advanced": true,
"default": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCA"
},
"adapter_second_read": {
"type": "string",
"description": "3' adapter to be removed from second read in a pair",
"advanced": true,
"default": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT"
},
"minimum_length": {
"type": "integer",
"description": "Discard reads shorter than this.",
"advanced": true,
"minimum": 1,
"default": 1
},
"cores": {
"type": "integer",
"description": "Number of CPU cores to use. Use 0 to auto-detect. Default: 7",
"hidden": true,
"minimum": 1,
"maximum": 8,
"default": 7
}
},
"required": [
"adapter_first_read",
"adapter_second_read"
]
},
"callmethylation_options": {
"title": "Callmethylation options",
"type": "object",
"description": "Options to adjust parameters to call methylation",
"default": "",
"properties": {
"base_quality": {
"type": "integer",
"description": "minimum base quality",
"advanced": true,
"default": 10
},
"alignment_quality": {
"type": "integer",
"description": "minimum alignment quality",
"advanced": true,
"minimum": 10,
"default": 20
},
"max_read_depth": {
"type": "integer",
"description": "max read depth to call methylation",
"advanced": true,
"minimum": 100,
"default": 8000
},
"minimum_read_depth": {
"type": "integer",
"description": "minimum read depth required to report methylation site",
"advanced": true,
"minimum": 10,
"default": 10
}
}
},
"max_job_request_options": {
"title": "Max job request options",
"type": "object",
"description": "Set the top limit for requested resources for any single job",
"default": "",
"help_text": "",
"properties": {
"max_time": {
"type": "string",
"description": "Maximum amount of time that can be requested for any single job",
"hidden": true,
"default": "48.h"
},
"max_memory": {
"type": "string",
"description": "Maximum number of CPUs that can be requested for any single job",
"hidden": true,
"default": "32.GB"
},
"max_cpus": {
"type": "integer",
"description": "Maximum number of CPUs that can be requested for any single job",
"hidden": true,
"minimum": 1,
"default": 8
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/input_output_options"
},
{
"$ref": "#/definitions/reference_genome_options"
},
{
"$ref": "#/definitions/read_trimming_options"
},
{
"$ref": "#/definitions/callmethylation_options"
},
{
"$ref": "#/definitions/max_job_request_options"
}
]
}