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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/PacB-flow/master/nextflow_schema.json",
"title": "PacB-flow pipeline parameters",
"description": "PacBio pipeline for genome assembly, polishing and cleanup",
"type": "object",
"definitions": {
"institutional_config_options": {
"title": "Institutional config options",
"type": "object",
"fa_icon": "fas fa-university",
"description": "Parameters used to describe centralised config profiles. These should not be edited.",
"help_text": "The centralised nf-core configuration profiles use a handful of pipeline parameters to describe themselves. This information is then printed to the Nextflow log when you run a pipeline. You should not need to change these values when you run a pipeline.",
"properties": {
"custom_config_base": {
"type": "string",
"description": "Base directory for Institutional configs.",
"default": ".",
"hidden": true,
"help_text": "If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.",
"fa_icon": "fas fa-users-cog"
}
}
},
"generic_options": {
"title": "Generic options",
"type": "object",
"fa_icon": "fas fa-file-import",
"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
}
}
},
"abyss_stats": {
"title": "Abyss stats",
"type": "object",
"description": "",
"default": "",
"properties": {
"ng50": {
"type": "boolean",
"description": "Run abyss-fac as NG50",
"default": false
},
"abyss_gensize": {
"type": "integer",
"default": 42000000,
"description": "Genome size in bp to use for NG50"
}
}
},
"ntlink": {
"title": "ntLink",
"type": "object",
"description": "",
"default": "",
"properties": {
"ntlink_run": {
"type": "boolean",
"description": "Run ntLink in pipleine",
"default": false
},
"ntlink_w": {
"type": "integer",
"default": 100,
"description": "W value for ntLink (see tool manual)"
},
"ntlink_k": {
"type": "integer",
"default": 32,
"description": "K value for ntLink (see tool manual)"
},
"ntlink_z": {
"type": "integer",
"default": 1000,
"description": "Z value for ntLink (see tool manual)"
},
"ntlink_rounds": {
"type": "integer",
"default": 3,
"description": "Number of iterations, scaffolding and gap filling"
}
}
},
"ntjoin": {
"title": "ntJoin",
"type": "object",
"description": "",
"default": "",
"properties": {
"ntjoin_ref": {
"type": "string",
"description": "Path to reference genome to use for scaffolding"
},
"ntjoin_ref_weights": {
"type": "integer",
"default": 2,
"description": "Weight score for reference genome"
},
"ntjoin_k": {
"type": "integer",
"default": 32,
"description": "K value for ntjoin (see tool manual)"
},
"ntjoin_w": {
"type": "integer",
"default": 1000,
"description": "W value for ntjoin (see tool manual)"
},
"ntjoin_no_cut": {
"type": "boolean",
"description": "No cut on reference genome, maintains integrity of input genome"
}
}
},
"mitochondrion_screening": {
"title": "Mitochondrion screening",
"type": "object",
"description": "",
"default": "",
"properties": {
"mito_dw": {
"type": "string",
"default": "https://ftp.ncbi.nlm.nih.gov/refseq/release/mitochondrion/",
"description": "Path to ncbi all mitochondrion genomes"
},
"mito_species": {
"type": "string",
"description": "Path to user speciefied mitos (non in use)"
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/institutional_config_options"
},
{
"$ref": "#/definitions/generic_options"
},
{
"$ref": "#/definitions/abyss_stats"
},
{
"$ref": "#/definitions/ntlink"
},
{
"$ref": "#/definitions/ntjoin"
},
{
"$ref": "#/definitions/mitochondrion_screening"
}
],
"properties": {
"manifest": {
"type": "string",
"description": "Path to manifest file"
},
"genome_size": {
"type": "string",
"default": "42m",
"description": "Genome size for CANU assembler"
},
"outputdir": {
"type": "string",
"description": "Name of output directory",
"default": "results"
}
},
"required": [
"manifest"
]
}