/
params.json
100 lines (100 loc) · 4.1 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/checkm/lineagewf/params.json",
"title": "CheckM Module",
"description": "A module to assess the assembly quality of your samples",
"type": "object",
"definitions": {
"checkm_parameters": {
"title": "CheckM Parameters",
"type": "object",
"description": "",
"default": "",
"properties": {
"checkm_unique": {
"type": "integer",
"description": "Minimum number of unique phylogenetic markers required to use lineage-specific marker set.",
"default": 10,
"fa_icon": "fas fa-angle-double-down"
},
"checkm_multi": {
"type": "integer",
"description": "Maximum number of multi-copy phylogenetic markers before defaulting to domain-level marker set.",
"default": 10,
"fa_icon": "fas fa-angle-double-up"
},
"aai_strain": {
"type": "number",
"description": "AAI threshold used to identify strain heterogeneity",
"default": 0.9,
"fa_icon": "fas fa-hashtag"
},
"checkm_length": {
"type": "number",
"description": "Percent overlap between target and query",
"default": 0.7,
"fa_icon": "fas fa-hashtag"
},
"full_tree": {
"type": "boolean",
"description": "Use the full tree (requires ~40GB of memory) for determining lineage of each bin.",
"fa_icon": "fas fa-tree",
"hidden": true
},
"skip_pseudogene_correction": {
"type": "boolean",
"description": "Skip identification and filtering of pseudogene",
"fa_icon": "fas fa-fast-forward",
"hidden": true
},
"ignore_thresholds": {
"type": "boolean",
"description": "Ignore model-specific score thresholds",
"fa_icon": "fas fa-eye-slash",
"hidden": true
},
"checkm_ali": {
"type": "boolean",
"description": "Generate HMMER alignment file for each bin",
"fa_icon": "fas fa-hard-hat",
"hidden": true
},
"checkm_nt": {
"type": "boolean",
"description": "Generate nucleotide gene sequences for each bin",
"fa_icon": "fas fa-hard-hat",
"hidden": true
},
"force_domain": {
"type": "boolean",
"description": "Use domain-level sets for all bins",
"fa_icon": "fas fa-hammer",
"hidden": true
},
"no_refinement": {
"type": "boolean",
"description": "Do not perform lineage-specific marker set refinement",
"fa_icon": "fas fa-fast-forward",
"hidden": true
},
"individual_markers": {
"type": "boolean",
"description": "Treat marker as independent",
"fa_icon": "fas fa-check",
"hidden": true
},
"skip_adj_correction": {
"type": "boolean",
"description": "Do not exclude adjacent marker genes when estimating contamination",
"fa_icon": "fas fa-fast-forward",
"hidden": true
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/checkm_parameters"
}
]
}