-
Notifications
You must be signed in to change notification settings - Fork 5
/
config.schema.yml
177 lines (164 loc) · 2.96 KB
/
config.schema.yml
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
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
$schema: "http://json-schema.org/draft-06/schema#"
description: snakemake configuration file
type: object
properties:
poppipe_location:
type: string
poppunk_rfile:
type: string
poppunk_clusters:
type: string
poppunk_h5:
type: string
transmission_metadata:
type: string
default: ""
min_cluster_size:
type: integer
minimum: 3
ska:
type: object
properties:
fastq_qual:
type: integer
minimum: 0
maximum: 100
default: 20
fastq_cov:
type: integer
minimum: 0
maximum: 2000
default: 4
kmer:
type: integer
minimum: 7
maximum: 63
default: 21
single_strand:
type: boolean
default: false
freq_filter:
type: number
minimum: 0.0
maximum: 1.0
default: 0.9
iqtree:
type: object
properties:
enabled:
type: boolean
mode:
type: string
pattern: "^(fast|full)$"
model:
type: string
required:
- enabled
- mode
- model
gubbins:
type: object
properties:
prefix:
type: string
tree_builder:
type: string
min_snps:
type: integer
default: 3
min_window_size:
type: integer
default: 100
max_window_size:
type: integer
default: 10000
iterations:
type: integer
default: 10
required:
- prefix
- tree_builder
- min_snps
- min_window_size
- max_window_size
- iterations
transphylo:
type: object
properties:
w_shape:
type: number
default: 10
w_scale:
type: number
default: 0.1
mcmcIterations:
type: integer
default: 1000
startNeg:
type: number
default: 0.1
startOff_r:
type: number
default: 1
startOff_p:
type: number
default: 0.5
startPi:
type: number
default: 0.5
optiStart:
type: number
default: 2
dateT:
type: number
default: 0
fastbaps:
type: object
properties:
levels:
type: integer
minimum: 1
required:
- levels
mandrake:
type: object
properties:
perplexity:
type: number
minimum: 5
maximum: 100
knn:
type: integer
minimum: 2
maxIter:
type: integer
minimum: 10000
default: 100000
required:
- perplexity
- knn
microreact:
type: object
properties:
name:
type: string
website:
type: string
email:
type: string
api_token:
type: string
required:
- name
- website
- email
- api_token
required:
- poppipe_location
- poppunk_rfile
- poppunk_clusters
- poppunk_h5
- iqtree
- fastbaps
- mandrake
- microreact