-
Notifications
You must be signed in to change notification settings - Fork 3
/
modules.json
286 lines (286 loc) · 13.4 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
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
{
"name": "plant-food-research-open/assemblyqc",
"homePage": "https://github.com/plant-food-research-open/assemblyqc",
"repos": {
"https://github.com/GallVp/nxf-components.git": {
"modules": {
"gallvp": {
"busco/busco": {
"branch": "main",
"git_sha": "cc6ea1f3e96e8264d2cc99afed31bcf3b0bb03ca",
"installed_by": ["fasta_gxf_busco_plot"]
},
"busco/generateplot": {
"branch": "main",
"git_sha": "cc6ea1f3e96e8264d2cc99afed31bcf3b0bb03ca",
"installed_by": ["fasta_gxf_busco_plot"]
},
"bwa/index": {
"branch": "main",
"git_sha": "cc6ea1f3e96e8264d2cc99afed31bcf3b0bb03ca",
"installed_by": ["fastq_bwa_mem_samblaster"]
},
"bwa/mem": {
"branch": "main",
"git_sha": "a203a6035aed3f9b345ee380f5d497ca98504d98",
"installed_by": ["fastq_bwa_mem_samblaster"]
},
"cat/cat": {
"branch": "main",
"git_sha": "cc6ea1f3e96e8264d2cc99afed31bcf3b0bb03ca",
"installed_by": ["fasta_ltrretriever_lai"]
},
"custom/relabelfasta": {
"branch": "main",
"git_sha": "a203a6035aed3f9b345ee380f5d497ca98504d98",
"installed_by": ["modules"]
},
"custom/restoregffids": {
"branch": "main",
"git_sha": "a203a6035aed3f9b345ee380f5d497ca98504d98",
"installed_by": ["fasta_ltrretriever_lai"]
},
"custom/shortenfastaids": {
"branch": "main",
"git_sha": "a203a6035aed3f9b345ee380f5d497ca98504d98",
"installed_by": ["fasta_ltrretriever_lai"]
},
"gffread": {
"branch": "main",
"git_sha": "cc6ea1f3e96e8264d2cc99afed31bcf3b0bb03ca",
"installed_by": ["fasta_gxf_busco_plot"]
},
"gt/gff3": {
"branch": "main",
"git_sha": "cc6ea1f3e96e8264d2cc99afed31bcf3b0bb03ca",
"installed_by": ["gff3_gt_gff3_gff3validator_stat"]
},
"gt/gff3validator": {
"branch": "main",
"git_sha": "cc6ea1f3e96e8264d2cc99afed31bcf3b0bb03ca",
"installed_by": ["gff3_gt_gff3_gff3validator_stat"]
},
"gt/stat": {
"branch": "main",
"git_sha": "cc6ea1f3e96e8264d2cc99afed31bcf3b0bb03ca",
"installed_by": ["gff3_gt_gff3_gff3validator_stat"]
},
"ltrfinder": {
"branch": "main",
"git_sha": "cc6ea1f3e96e8264d2cc99afed31bcf3b0bb03ca",
"installed_by": ["fasta_ltrretriever_lai"]
},
"ltrharvest": {
"branch": "main",
"git_sha": "cc6ea1f3e96e8264d2cc99afed31bcf3b0bb03ca",
"installed_by": ["fasta_ltrretriever_lai"]
},
"ltrretriever/lai": {
"branch": "main",
"git_sha": "cc6ea1f3e96e8264d2cc99afed31bcf3b0bb03ca",
"installed_by": ["fasta_ltrretriever_lai"]
},
"ltrretriever/ltrretriever": {
"branch": "main",
"git_sha": "cc6ea1f3e96e8264d2cc99afed31bcf3b0bb03ca",
"installed_by": ["fasta_ltrretriever_lai"]
},
"plotsr": {
"branch": "main",
"git_sha": "a203a6035aed3f9b345ee380f5d497ca98504d98",
"installed_by": ["modules"]
},
"samblaster": {
"branch": "main",
"git_sha": "cc6ea1f3e96e8264d2cc99afed31bcf3b0bb03ca",
"installed_by": ["fastq_bwa_mem_samblaster"]
},
"samtools/faidx": {
"branch": "main",
"git_sha": "cc6ea1f3e96e8264d2cc99afed31bcf3b0bb03ca",
"installed_by": ["gff3_gt_gff3_gff3validator_stat"]
},
"seqkit/seq": {
"branch": "main",
"git_sha": "cc6ea1f3e96e8264d2cc99afed31bcf3b0bb03ca",
"installed_by": ["fasta_ltrretriever_lai"]
},
"syri": {
"branch": "main",
"git_sha": "a203a6035aed3f9b345ee380f5d497ca98504d98",
"installed_by": ["modules"]
}
}
},
"subworkflows": {
"gallvp": {
"fasta_gxf_busco_plot": {
"branch": "main",
"git_sha": "7bf6fbca23edc94490ffa6709f52b2f71c6fb130",
"installed_by": ["subworkflows"]
},
"fasta_ltrretriever_lai": {
"branch": "main",
"git_sha": "8ec55a2c8e4ce3af070393768f6c2c57f5c34076",
"installed_by": ["subworkflows"]
},
"fastq_bwa_mem_samblaster": {
"branch": "main",
"git_sha": "775762619b57101ca800269b6ecda0b915fb9913",
"installed_by": ["subworkflows"]
},
"gff3_gt_gff3_gff3validator_stat": {
"branch": "main",
"git_sha": "58c5f9e695b9e03d43e4c59d9339af7c93f0acbe",
"installed_by": ["subworkflows"]
}
}
}
},
"https://github.com/nf-core/modules.git": {
"modules": {
"nf-core": {
"custom/sratoolsncbisettings": {
"branch": "master",
"git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
},
"fastavalidator": {
"branch": "master",
"git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["modules"]
},
"fastp": {
"branch": "master",
"git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["fastq_fastqc_umitools_fastp"]
},
"fastqc": {
"branch": "master",
"git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["fastq_fastqc_umitools_fastp"]
},
"fcs/fcsadaptor": {
"branch": "master",
"git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["modules"]
},
"gunzip": {
"branch": "master",
"git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["modules"]
},
"merqury/hapmers": {
"branch": "master",
"git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["modules"]
},
"merqury/merqury": {
"branch": "master",
"git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["modules"]
},
"meryl/count": {
"branch": "master",
"git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["modules"]
},
"meryl/unionsum": {
"branch": "master",
"git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["modules"]
},
"minimap2/align": {
"branch": "master",
"git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["modules"]
},
"seqkit/rmdup": {
"branch": "master",
"git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["modules"]
},
"seqkit/seq": {
"branch": "master",
"git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["fasta_explore_search_plot_tidk", "fasta_ltrretriever_lai"]
},
"seqkit/sort": {
"branch": "master",
"git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["fasta_explore_search_plot_tidk"]
},
"sratools/fasterqdump": {
"branch": "master",
"git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["fastq_download_prefetch_fasterqdump_sratools", "modules"]
},
"sratools/prefetch": {
"branch": "master",
"git_sha": "368e6c90b91adbd171e7c0a1c85a700b86a915af",
"installed_by": ["fastq_download_prefetch_fasterqdump_sratools", "modules"]
},
"tidk/explore": {
"branch": "master",
"git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["fasta_explore_search_plot_tidk"]
},
"tidk/plot": {
"branch": "master",
"git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["fasta_explore_search_plot_tidk"]
},
"tidk/search": {
"branch": "master",
"git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["fasta_explore_search_plot_tidk"]
},
"umitools/extract": {
"branch": "master",
"git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["fastq_fastqc_umitools_fastp"]
},
"untar": {
"branch": "master",
"git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["modules"]
}
}
},
"subworkflows": {
"nf-core": {
"fasta_explore_search_plot_tidk": {
"branch": "master",
"git_sha": "ab80a04707104a4baf39341581dfbced5da05479",
"installed_by": ["subworkflows"]
},
"fastq_download_prefetch_fasterqdump_sratools": {
"branch": "master",
"git_sha": "1fc29f92e439d5631fdf34b8ac4687297d70f5ec",
"installed_by": ["subworkflows"]
},
"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"]
}
}
}
}
}
}