/
params.json
62 lines (62 loc) · 2.47 KB
/
params.json
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{
"$schema": "http://json-schema.org/draft-07/schema",
"$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/gtdbtk/classifywf/params.json",
"title": "GTDB Classify Module",
"description": "Identify marker genes and assign taxonomic classifications",
"type": "object",
"definitions": {
"gtdb_classifywf_parameters": {
"title": "GTDB Classify Parameters",
"type": "object",
"description": "",
"default": "",
"fa_icon": "fas fa-exclamation-circle",
"properties": {
"min_af": {
"type": "number",
"default": 0.65,
"description": "Minimum alignment fraction to consider closest genome",
"fa_icon": "fas fa-expand-arrows-alt"
},
"min_perc_aa": {
"type": "integer",
"default": 10,
"description": "Filter genomes with an insufficient percentage of AA in the MSA",
"fa_icon": "fas fa-expand-arrows-alt"
},
"gtdb_tmp": {
"type": "boolean",
"default": "/tmp",
"description": "Specify alternative directory for temporary files",
"fa_icon": "fas fa-expand-arrows-alt",
"hidden": true
},
"gtdb_use_scratch": {
"type": "boolean",
"default": false,
"description": "Reduce pplacer memory usage by writing to --gtdb_tmp location (slower)",
"fa_icon": "fas fa-expand-arrows-alt",
"hidden": true
},
"gtdb_debug": {
"type": "boolean",
"default": false,
"description": "Create intermediate files for debugging purposes",
"fa_icon": "fas fa-expand-arrows-alt",
"hidden": true
},
"force_gtdb": {
"type": "boolean",
"default": false,
"description": "Continue processing if an error occurs on a single genome",
"fa_icon": "fas fa-expand-arrows-alt"
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/gtdb_classifywf_parameters"
}
]
}