/
params.json
140 lines (140 loc) · 5.38 KB
/
params.json
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
{
"$schema": "http://json-schema.org/draft-07/schema",
"$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/bakta/params.json",
"title": "Bakta Module",
"description": "A module for rapidly annotating baterial genomes",
"type": "object",
"definitions": {
"bakta_parameters": {
"title": "Bakta Parameters",
"type": "object",
"description": "",
"default": "",
"fa_icon": "fas fa-exclamation-circle",
"properties": {
"proteins": {
"type": "string",
"description": "FASTA file of trusted proteins to first annotate from",
"fa_icon": "fas fa-file-alt",
"hidden": true
},
"prodigal_tf": {
"type": "string",
"description": "Training file to use for Prodigal",
"fa_icon": "fas fa-file-alt",
"hidden": true
},
"replicons": {
"type": "string",
"description": "Replicon information table (tsv/csv)",
"fa_icon": "fas fa-file-alt",
"hidden": true
},
"min_contig_length": {
"type": "integer",
"description": "Minimum contig size to annotate",
"default": 1,
"fa_icon": "fas fa-hashtag",
"hidden": true
},
"keep_contig_headers": {
"type": "boolean",
"description": "Keep original contig headers",
"default": false,
"fa_icon": "fas fa-italic",
"hidden": true
},
"compliant": {
"type": "boolean",
"description": "Force Genbank/ENA/DDJB compliance",
"default": false,
"fa_icon": "fas fa-italic",
"hidden": true
},
"skip_trna": {
"type": "boolean",
"description": "Skip tRNA detection & annotation",
"default": false,
"fa_icon": "fas fa-italic",
"hidden": true
},
"skip_tmrna": {
"type": "boolean",
"description": "Skip tmRNA detection & annotation",
"default": false,
"fa_icon": "fas fa-italic",
"hidden": true
},
"skip_rrna": {
"type": "boolean",
"description": "Skip rRNA detection & annotation",
"default": false,
"fa_icon": "fas fa-italic",
"hidden": true
},
"skip_ncrna": {
"type": "boolean",
"description": "Skip ncRNA detection & annotation",
"default": false,
"fa_icon": "fas fa-italic",
"hidden": true
},
"skip_ncrna_region": {
"type": "boolean",
"description": "Skip ncRNA region detection & annotation",
"default": false,
"fa_icon": "fas fa-italic",
"hidden": true
},
"skip_crispr": {
"type": "boolean",
"description": "Skip CRISPR array detection & annotation",
"default": false,
"fa_icon": "fas fa-italic",
"hidden": true
},
"skip_cds": {
"type": "boolean",
"description": "Skip CDS detection & annotation",
"default": false,
"fa_icon": "fas fa-italic",
"hidden": true
},
"skip_sorf": {
"type": "boolean",
"description": "Skip sORF detection & annotation",
"default": false,
"fa_icon": "fas fa-italic",
"hidden": true
},
"skip_gap": {
"type": "boolean",
"description": "Skip gap detection & annotation",
"default": false,
"fa_icon": "fas fa-italic",
"hidden": true
},
"skip_ori": {
"type": "boolean",
"description": "Skip oriC/oriT detection & annotation",
"default": false,
"fa_icon": "fas fa-italic",
"hidden": true
},
"bakta_opts": {
"type": "string",
"description": "Extra Backa options in quotes. Example: '--gram +'",
"help": "Useful if you would like to fine tune your Bakta analysis.",
"default": "",
"fa_icon": "fas fa-italic",
"hidden": true
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/bakta_parameters"
}
]
}