-
Notifications
You must be signed in to change notification settings - Fork 1
/
modules.json
246 lines (246 loc) · 11.1 KB
/
modules.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
{
"name": "plant-food-research-open/genepal",
"homePage": "https://github.com/plant-food-research-open/genepal",
"repos": {
"https://github.com/GallVp/nxf-components.git": {
"modules": {
"gallvp": {
"agat/spaddintrons": {
"branch": "main",
"git_sha": "a8939d36280e7d9037c7cf164eeede19e46546a4",
"installed_by": ["gxf_fasta_agat_spaddintrons_spextractsequences"]
},
"agat/spextractsequences": {
"branch": "main",
"git_sha": "a8939d36280e7d9037c7cf164eeede19e46546a4",
"installed_by": ["gxf_fasta_agat_spaddintrons_spextractsequences"]
},
"braker3": {
"branch": "main",
"git_sha": "a8939d36280e7d9037c7cf164eeede19e46546a4",
"installed_by": ["modules"]
},
"busco/busco": {
"branch": "main",
"git_sha": "92d59e5f578a2929b75f7588985b9bf451f4c370",
"installed_by": ["fasta_gxf_busco_plot"]
},
"busco/generateplot": {
"branch": "main",
"git_sha": "ae9714c21ede9199a3118e3c20b65484aa73e232",
"installed_by": ["fasta_gxf_busco_plot"]
},
"custom/restoregffids": {
"branch": "main",
"git_sha": "a8939d36280e7d9037c7cf164eeede19e46546a4",
"installed_by": ["fasta_edta_lai"]
},
"custom/rmouttogff3": {
"branch": "main",
"git_sha": "cf6e6dee79b29313ed6cda962908056a15f8c531",
"installed_by": ["modules"]
},
"custom/shortenfastaids": {
"branch": "main",
"git_sha": "a8939d36280e7d9037c7cf164eeede19e46546a4",
"installed_by": ["fasta_edta_lai"]
},
"edta/edta": {
"branch": "main",
"git_sha": "a8939d36280e7d9037c7cf164eeede19e46546a4",
"installed_by": ["fasta_edta_lai"]
},
"gffread": {
"branch": "main",
"git_sha": "ae9714c21ede9199a3118e3c20b65484aa73e232",
"installed_by": ["fasta_gxf_busco_plot"]
},
"ltrretriever/lai": {
"branch": "main",
"git_sha": "ae9714c21ede9199a3118e3c20b65484aa73e232",
"installed_by": ["fasta_edta_lai"]
},
"repeatmasker/repeatmasker": {
"branch": "main",
"git_sha": "a8939d36280e7d9037c7cf164eeede19e46546a4",
"installed_by": ["modules"]
}
}
},
"subworkflows": {
"gallvp": {
"fasta_edta_lai": {
"branch": "main",
"git_sha": "7bf6fbca23edc94490ffa6709f52b2f71c6fb130",
"installed_by": ["subworkflows"]
},
"fasta_gxf_busco_plot": {
"branch": "main",
"git_sha": "7bf6fbca23edc94490ffa6709f52b2f71c6fb130",
"installed_by": ["subworkflows"]
},
"gxf_fasta_agat_spaddintrons_spextractsequences": {
"branch": "main",
"git_sha": "7bf6fbca23edc94490ffa6709f52b2f71c6fb130",
"installed_by": ["subworkflows"]
}
}
}
},
"https://github.com/nf-core/modules.git": {
"modules": {
"nf-core": {
"agat/convertspgff2gtf": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"agat/convertspgxf2gxf": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"agat/spfilterfeaturefromkilllist": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"agat/spmergeannotations": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"cat/cat": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"cat/fastq": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"eggnogmapper": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"fastavalidator": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"fastp": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["fastq_fastqc_umitools_fastp"]
},
"fastqc": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["fastq_fastqc_umitools_fastp", "modules"]
},
"gffcompare": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"gffread": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"gt/gff3": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"gunzip": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"liftoff": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"orthofinder": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"repeatmodeler/builddatabase": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"repeatmodeler/repeatmodeler": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"samtools/cat": {
"branch": "master",
"git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
"installed_by": ["modules"]
},
"seqkit/rmdup": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"sortmerna": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"star/align": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"star/genomegenerate": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"tsebra": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"umitools/extract": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["fastq_fastqc_umitools_fastp"]
}
}
},
"subworkflows": {
"nf-core": {
"fastq_fastqc_umitools_fastp": {
"branch": "master",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"installed_by": ["subworkflows"]
},
"utils_nextflow_pipeline": {
"branch": "master",
"git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352",
"installed_by": ["subworkflows"]
},
"utils_nfcore_pipeline": {
"branch": "master",
"git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab",
"installed_by": ["subworkflows"]
},
"utils_nfvalidation_plugin": {
"branch": "master",
"git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
"installed_by": ["subworkflows"]
}
}
}
}
}
}