-
Notifications
You must be signed in to change notification settings - Fork 7
/
Copy pathnextflow_schema.json
308 lines (308 loc) · 11 KB
/
nextflow_schema.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
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
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
{
"$schema": "http://json-schema.org/draft-07/schema",
"$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json",
"title": "GPS Pipeline Parameters",
"description": "",
"type": "object",
"definitions": {
"input_output": {
"title": "Input / Output",
"type": "object",
"description": "",
"default": "",
"properties": {
"reads": {
"type": "string",
"description": "Path to the input directory that contains the reads to be processed.",
"format": "directory-path"
},
"output": {
"type": "string",
"description": "Path to the output directory that save the results.",
"format": "directory-path"
},
"db": {
"type": "string",
"description": "Path to the directory saving databases used by the pipeline",
"format": "directory-path"
},
"singularity_cachedir": {
"type": "string",
"description": "(Only required when Singularity is used) Path to the directory where Singularity images should be saved to.",
"format": "directory-path"
},
"assembly_publish": {
"type": "string",
"description": "Method used by Nextflow to publish the generated assemblies.",
"hidden": true,
"enum": [
"link",
"symlink",
"copy"
]
}
},
"required": [
"reads",
"output",
"db",
"assembly_publish"
]
},
"qc_parameters": {
"title": "QC Parameters",
"type": "object",
"description": "",
"default": "",
"properties": {
"spneumo_percentage": {
"type": "number",
"description": "Minimum S. pneumoniae percentage in reads to pass Taxonomy QC.",
"hidden": true,
"minimum": 0,
"maximum": 100
},
"non_strep_percentage": {
"type": "number",
"hidden": true,
"description": "Maximum non-Streptococcus genus percentage in reads to pass Taxonomy QC.",
"minimum": 0,
"maximum": 100
},
"ref_coverage": {
"type": "number",
"description": "Minimum reference coverage percentage by the reads to pass Mapping QC.",
"hidden": true,
"minimum": 0,
"maximum": 100
},
"het_snp_site": {
"type": "integer",
"description": "Maximum non-cluster heterozygous SNP (Het-SNP) site count to pass Mapping QC.",
"hidden": true,
"minimum": 0
},
"contigs": {
"type": "integer",
"hidden": true,
"description": "Maximum contig count in assembly to pass Assembly QC.",
"minimum": 0
},
"length_low": {
"type": "integer",
"hidden": true,
"description": "Minimum assembly length to pass Assembly QC.",
"minimum": 0
},
"length_high": {
"type": "integer",
"hidden": true,
"description": "Maximum assembly length to pass Assembly QC.",
"minimum": 0
},
"depth": {
"type": "number",
"hidden": true,
"description": "Minimum sequencing depth to pass Assembly QC.",
"minimum": 0
}
},
"required": [
"spneumo_percentage",
"non_strep_percentage",
"ref_coverage",
"het_snp_site",
"contigs",
"length_low",
"length_high",
"depth"
]
},
"assembly": {
"title": "Assembly",
"type": "object",
"description": "",
"default": "",
"properties": {
"assembler": {
"type": "string",
"hidden": true,
"description": "Using which SPAdes-based assembler to assemble the reads.",
"enum": [
"shovill",
"unicycler"
]
},
"assembler_thread": {
"type": "integer",
"description": "Number of threads used by the assembler. 0 means all available.",
"hidden": true
},
"min_contig_length": {
"type": "integer",
"description": "Minimum legnth of contig to be included in the assembly.",
"hidden": true,
"minimum": 0
}
},
"required": [
"assembler",
"min_contig_length",
"assembler_thread"
]
},
"mapping": {
"title": "Mapping",
"type": "object",
"description": "",
"default": "",
"properties": {
"ref_genome": {
"type": "string",
"hidden": true,
"description": "Path to the reference genome for mapping.",
"pattern": ".+\\.(fa|fasta)$",
"format": "file-path",
"mimetype": "text/x-fasta"
}
},
"required": [
"ref_genome"
]
},
"taxonomy": {
"title": "Taxonomy",
"type": "object",
"description": "",
"default": "",
"properties": {
"kraken2_db_remote": {
"type": "string",
"hidden": true,
"description": "URL to a Kraken2 database.",
"pattern": "^(https?:\\/\\/)?(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)\\.(tar\\.gz|tgz)$"
},
"kraken2_memory_mapping": {
"type": "boolean",
"hidden": true,
"description": "Using the memory mapping option of Kraken2 or not."
}
},
"required": [
"kraken2_db_remote",
"kraken2_memory_mapping"
]
},
"serotype": {
"title": "Serotype",
"type": "object",
"description": "",
"default": "",
"properties": {
"seroba_db_remote": {
"type": "string",
"hidden": true,
"description": "URL to a SeroBA release.",
"pattern": "^(https?:\\/\\/)?(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)\\.(tar\\.gz|tgz)$"
},
"seroba_kmer": {
"type": "integer",
"hidden": true,
"description": "Kmer size for creating the KMC database of SeroBA.",
"minimum": 0
}
},
"required": [
"seroba_db_remote",
"seroba_kmer"
]
},
"lineage": {
"title": "Lineage",
"type": "object",
"description": "",
"default": "",
"properties": {
"poppunk_db_remote": {
"type": "string",
"hidden": true,
"description": "URL to a PopPUNK database.",
"pattern": "^(https?:\\/\\/)?(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)\\.(tar\\.gz|tgz)$"
},
"poppunk_ext_remote": {
"type": "string",
"hidden": true,
"description": "URL to a PopPUNK external clusters file.",
"pattern": "^(https?:\\/\\/)?(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)\\.csv$"
}
},
"required": [
"poppunk_db_remote",
"poppunk_ext_remote"
]
},
"other_amr": {
"title": "Other AMR",
"type": "object",
"description": "",
"default": "",
"properties": {
"ariba_ref": {
"type": "string",
"hidden": true,
"description": "Path to the reference sequences for ARIBA.",
"pattern": ".+\\.(fa|fasta)$",
"format": "file-path",
"mimetype": "text/x-fasta"
},
"ariba_metadata": {
"type": "string",
"hidden": true,
"description": "Path to the metadata file for ARIBA.",
"pattern": "/.+\\.tsv$",
"format": "file-path",
"mimetype": "text/tab-separated-values"
},
"resistance_to_mic": {
"type": "string",
"hidden": true,
"description": "Path to the resistance phenotypes to MIC (minimum inhibitory concentration) lookup table.",
"pattern": "/.+\\.tsv$",
"format": "file-path",
"mimetype": "text/tab-separated-values"
}
},
"required": [
"ariba_ref",
"ariba_metadata",
"resistance_to_mic"
]
}
},
"allOf": [
{
"$ref": "#/definitions/input_output"
},
{
"$ref": "#/definitions/qc_parameters"
},
{
"$ref": "#/definitions/assembly"
},
{
"$ref": "#/definitions/mapping"
},
{
"$ref": "#/definitions/taxonomy"
},
{
"$ref": "#/definitions/serotype"
},
{
"$ref": "#/definitions/lineage"
},
{
"$ref": "#/definitions/other_amr"
}
]
}